[{"scopus_import":1,"article_processing_charge":"No","day":"09","page":"871 - 888","article_type":"original","citation":{"chicago":"Burton, Benjamin, Arnaud N de Mesmay, and Uli Wagner. “Finding Non-Orientable Surfaces in 3-Manifolds.” Discrete & Computational Geometry. Springer, 2017. https://doi.org/10.1007/s00454-017-9900-0.","short":"B. Burton, A.N. de Mesmay, U. Wagner, Discrete & Computational Geometry 58 (2017) 871–888.","mla":"Burton, Benjamin, et al. “Finding Non-Orientable Surfaces in 3-Manifolds.” Discrete & Computational Geometry, vol. 58, no. 4, Springer, 2017, pp. 871–88, doi:10.1007/s00454-017-9900-0.","apa":"Burton, B., de Mesmay, A. N., & Wagner, U. (2017). Finding non-orientable surfaces in 3-Manifolds. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-017-9900-0","ieee":"B. Burton, A. N. de Mesmay, and U. Wagner, “Finding non-orientable surfaces in 3-Manifolds,” Discrete & Computational Geometry, vol. 58, no. 4. Springer, pp. 871–888, 2017.","ista":"Burton B, de Mesmay AN, Wagner U. 2017. Finding non-orientable surfaces in 3-Manifolds. Discrete & Computational Geometry. 58(4), 871–888.","ama":"Burton B, de Mesmay AN, Wagner U. Finding non-orientable surfaces in 3-Manifolds. Discrete & Computational Geometry. 2017;58(4):871-888. doi:10.1007/s00454-017-9900-0"},"publication":"Discrete & Computational Geometry","date_published":"2017-06-09T00:00:00Z","type":"journal_article","issue":"4","abstract":[{"text":"We investigate the complexity of finding an embedded non-orientable surface of Euler genus g in a triangulated 3-manifold. This problem occurs both as a natural question in low-dimensional topology, and as a first non-trivial instance of embeddability of complexes into 3-manifolds. We prove that the problem is NP-hard, thus adding to the relatively few hardness results that are currently known in 3-manifold topology. In addition, we show that the problem lies in NP when the Euler genus g is odd, and we give an explicit algorithm in this case.","lang":"eng"}],"intvolume":" 58","title":"Finding non-orientable surfaces in 3-Manifolds","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"534","oa_version":"Preprint","publication_identifier":{"issn":["01795376"]},"month":"06","quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1602.07907","open_access":"1"}],"external_id":{"arxiv":["1602.07907"]},"language":[{"iso":"eng"}],"doi":"10.1007/s00454-017-9900-0","publist_id":"7283","publisher":"Springer","department":[{"_id":"UlWa"}],"publication_status":"published","year":"2017","volume":58,"date_updated":"2023-02-21T17:01:34Z","date_created":"2018-12-11T11:47:01Z","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"1379"}]},"author":[{"first_name":"Benjamin","last_name":"Burton","full_name":"Burton, Benjamin"},{"full_name":"De Mesmay, Arnaud N","last_name":"De Mesmay","first_name":"Arnaud N","id":"3DB2F25C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Wagner, Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568","first_name":"Uli","last_name":"Wagner"}]},{"has_accepted_license":"1","day":"20","citation":{"ista":"Kainrath S, Stadler M, Gschaider-Reichhart E, Distel M, Janovjak HL. 2017. Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen. Angewandte Chemie. 129(16), 4679–4682.","ieee":"S. Kainrath, M. Stadler, E. Gschaider-Reichhart, M. Distel, and H. L. Janovjak, “Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen,” Angewandte Chemie, vol. 129, no. 16. Wiley, pp. 4679–4682, 2017.","apa":"Kainrath, S., Stadler, M., Gschaider-Reichhart, E., Distel, M., & Janovjak, H. L. (2017). Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen. Angewandte Chemie. Wiley. https://doi.org/10.1002/ange.201611998","ama":"Kainrath S, Stadler M, Gschaider-Reichhart E, Distel M, Janovjak HL. Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen. Angewandte Chemie. 2017;129(16):4679-4682. doi:10.1002/ange.201611998","chicago":"Kainrath, Stephanie, Manuela Stadler, Eva Gschaider-Reichhart, Martin Distel, and Harald L Janovjak. “Grünlicht-Induzierte Rezeptorinaktivierung Durch Cobalamin-Bindende Domänen.” Angewandte Chemie. Wiley, 2017. https://doi.org/10.1002/ange.201611998.","mla":"Kainrath, Stephanie, et al. “Grünlicht-Induzierte Rezeptorinaktivierung Durch Cobalamin-Bindende Domänen.” Angewandte Chemie, vol. 129, no. 16, Wiley, 2017, pp. 4679–82, doi:10.1002/ange.201611998.","short":"S. Kainrath, M. Stadler, E. Gschaider-Reichhart, M. Distel, H.L. Janovjak, Angewandte Chemie 129 (2017) 4679–4682."},"publication":"Angewandte Chemie","page":"4679 - 4682","date_published":"2017-05-20T00:00:00Z","type":"journal_article","issue":"16","abstract":[{"text":"Optogenetik und Photopharmakologie ermöglichen präzise räumliche und zeitliche Kontrolle von Proteinwechselwirkung und -funktion in Zellen und Tieren. Optogenetische Methoden, die auf grünes Licht ansprechen und zum Trennen von Proteinkomplexen geeignet sind, sind nichtweitläufig verfügbar, würden jedoch mehrfarbige Experimente zur Beantwortung von biologischen Fragestellungen ermöglichen. Hier demonstrieren wir die Verwendung von Cobalamin(Vitamin B12)-bindenden Domänen von bakteriellen CarH-Transkriptionsfaktoren zur Grünlicht-induzierten Dissoziation von Rezeptoren. Fusioniert mit dem Fibroblasten-W achstumsfaktor-Rezeptor 1 führten diese im Dunkeln in kultivierten Zellen zu Signalaktivität durch Oligomerisierung, welche durch Beleuchten umgehend aufgehoben wurde. In Zebrafischembryonen, die einen derartigen Rezeptor exprimieren, ermöglichte grünes Licht die Kontrolle über abnormale Signalaktivität während der Embryonalentwicklung. ","lang":"ger"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"538","intvolume":" 129","title":"Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen","status":"public","ddc":["571"],"pubrep_id":"932","oa_version":"Published Version","file":[{"date_created":"2018-12-12T10:13:24Z","date_updated":"2020-07-14T12:46:39Z","checksum":"d66fee867e7cdbfa3fe276c2fb0778bb","file_id":"5007","relation":"main_file","creator":"system","file_size":1668557,"content_type":"application/pdf","file_name":"IST-2018-932-v1+1_Kainrath_et_al-2017-Angewandte_Chemie.pdf","access_level":"open_access"}],"month":"05","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"project":[{"name":"Microbial Ion Channels for Synthetic Neurobiology","call_identifier":"FP7","_id":"25548C20-B435-11E9-9278-68D0E5697425","grant_number":"303564"},{"grant_number":"W1232-B24","_id":"255A6082-B435-11E9-9278-68D0E5697425","name":"Molecular Drug Targets","call_identifier":"FWF"}],"quality_controlled":"1","doi":"10.1002/ange.201611998","language":[{"iso":"eng"}],"ec_funded":1,"publist_id":"7279","file_date_updated":"2020-07-14T12:46:39Z","license":"https://creativecommons.org/licenses/by/4.0/","year":"2017","department":[{"_id":"CaGu"},{"_id":"HaJa"}],"publisher":"Wiley","publication_status":"published","author":[{"first_name":"Stephanie","last_name":"Kainrath","id":"32CFBA64-F248-11E8-B48F-1D18A9856A87","full_name":"Kainrath, Stephanie"},{"full_name":"Stadler, Manuela","first_name":"Manuela","last_name":"Stadler"},{"full_name":"Gschaider-Reichhart, Eva","id":"3FEE232A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7218-7738","first_name":"Eva","last_name":"Gschaider-Reichhart"},{"full_name":"Distel, Martin","first_name":"Martin","last_name":"Distel"},{"full_name":"Janovjak, Harald L","first_name":"Harald L","last_name":"Janovjak","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315"}],"volume":129,"date_created":"2018-12-11T11:47:02Z","date_updated":"2021-01-12T08:01:33Z"},{"type":"journal_article","abstract":[{"text":"RNA-dependent RNA polymerases (RdRps) play a key role in the life cycle of RNA viruses and impact their immunobiology. The arenavirus lymphocytic choriomeningitis virus (LCMV) strain Clone 13 provides a benchmark model for studying chronic infection. A major genetic determinant for its ability to persist maps to a single amino acid exchange in the viral L protein, which exhibits RdRp activity, yet its functional consequences remain elusive. To unravel the L protein interactions with the host proteome, we engineered infectious L protein-tagged LCMV virions by reverse genetics. A subsequent mass-spectrometric analysis of L protein pulldowns from infected human cells revealed a comprehensive network of interacting host proteins. The obtained LCMV L protein interactome was bioinformatically integrated with known host protein interactors of RdRps from other RNA viruses, emphasizing interconnected modules of human proteins. Functional characterization of selected interactors highlighted proviral (DDX3X) as well as antiviral (NKRF, TRIM21) host factors. To corroborate these findings, we infected Trim21-/-mice with LCMV and found impaired virus control in chronic infection. These results provide insights into the complex interactions of the arenavirus LCMV and other viral RdRps with the host proteome and contribute to a better molecular understanding of how chronic viruses interact with their host.","lang":"eng"}],"issue":"12","status":"public","title":"Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein","ddc":["576","616"],"intvolume":" 13","_id":"540","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"checksum":"1aa20f19a1e90664fadce6e7d5284fdc","date_created":"2018-12-12T10:12:26Z","date_updated":"2020-07-14T12:46:44Z","relation":"main_file","file_id":"4944","file_size":4106772,"content_type":"application/pdf","creator":"system","access_level":"open_access","file_name":"IST-2018-931-v1+1_journal.ppat.1006758.pdf"}],"oa_version":"Published Version","pubrep_id":"931","scopus_import":1,"day":"01","has_accepted_license":"1","publication":"PLoS Pathogens","citation":{"ieee":"K. Khamina et al., “Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein,” PLoS Pathogens, vol. 13, no. 12. Public Library of Science, 2017.","apa":"Khamina, K., Lercher, A., Caldera, M., Schliehe, C., Vilagos, B., Sahin, M., … Bergthaler, A. (2017). Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein. PLoS Pathogens. Public Library of Science. https://doi.org/10.1371/journal.ppat.1006758","ista":"Khamina K, Lercher A, Caldera M, Schliehe C, Vilagos B, Sahin M, Kosack L, Bhattacharya A, Májek P, Stukalov A, Sacco R, James L, Pinschewer D, Bennett K, Menche J, Bergthaler A. 2017. Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein. PLoS Pathogens. 13(12), e1006758.","ama":"Khamina K, Lercher A, Caldera M, et al. Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein. PLoS Pathogens. 2017;13(12). doi:10.1371/journal.ppat.1006758","chicago":"Khamina, Kseniya, Alexander Lercher, Michael Caldera, Christopher Schliehe, Bojan Vilagos, Mehmet Sahin, Lindsay Kosack, et al. “Characterization of Host Proteins Interacting with the Lymphocytic Choriomeningitis Virus L Protein.” PLoS Pathogens. Public Library of Science, 2017. https://doi.org/10.1371/journal.ppat.1006758.","short":"K. Khamina, A. Lercher, M. Caldera, C. Schliehe, B. Vilagos, M. Sahin, L. Kosack, A. Bhattacharya, P. Májek, A. Stukalov, R. Sacco, L. James, D. Pinschewer, K. Bennett, J. Menche, A. Bergthaler, PLoS Pathogens 13 (2017).","mla":"Khamina, Kseniya, et al. “Characterization of Host Proteins Interacting with the Lymphocytic Choriomeningitis Virus L Protein.” PLoS Pathogens, vol. 13, no. 12, e1006758, Public Library of Science, 2017, doi:10.1371/journal.ppat.1006758."},"date_published":"2017-12-01T00:00:00Z","article_number":"e1006758","file_date_updated":"2020-07-14T12:46:44Z","publist_id":"7276","publication_status":"published","publisher":"Public Library of Science","department":[{"_id":"GaNo"}],"year":"2017","date_created":"2018-12-11T11:47:03Z","date_updated":"2021-01-12T08:01:48Z","volume":13,"author":[{"full_name":"Khamina, Kseniya","last_name":"Khamina","first_name":"Kseniya"},{"first_name":"Alexander","last_name":"Lercher","full_name":"Lercher, Alexander"},{"last_name":"Caldera","first_name":"Michael","full_name":"Caldera, Michael"},{"full_name":"Schliehe, Christopher","last_name":"Schliehe","first_name":"Christopher"},{"first_name":"Bojan","last_name":"Vilagos","full_name":"Vilagos, Bojan"},{"first_name":"Mehmet","last_name":"Sahin","full_name":"Sahin, Mehmet"},{"first_name":"Lindsay","last_name":"Kosack","full_name":"Kosack, Lindsay"},{"last_name":"Bhattacharya","first_name":"Anannya","full_name":"Bhattacharya, Anannya"},{"full_name":"Májek, Peter","last_name":"Májek","first_name":"Peter"},{"full_name":"Stukalov, Alexey","last_name":"Stukalov","first_name":"Alexey"},{"full_name":"Sacco, Roberto","first_name":"Roberto","last_name":"Sacco","id":"42C9F57E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Leo","last_name":"James","full_name":"James, Leo"},{"last_name":"Pinschewer","first_name":"Daniel","full_name":"Pinschewer, Daniel"},{"last_name":"Bennett","first_name":"Keiryn","full_name":"Bennett, Keiryn"},{"full_name":"Menche, Jörg","last_name":"Menche","first_name":"Jörg"},{"full_name":"Bergthaler, Andreas","first_name":"Andreas","last_name":"Bergthaler"}],"month":"12","publication_identifier":{"issn":["15537366"]},"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1371/journal.ppat.1006758"},{"month":"07","publication_identifier":{"issn":["18605974"]},"tmp":{"short":"CC BY-ND (4.0)","image":"/image/cc_by_nd.png","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode"},"oa":1,"quality_controlled":"1","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"grant_number":"701309","_id":"2590DB08-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Atomic-Resolution Structures of Mitochondrial Respiratory Chain Supercomplexes (H2020)"}],"doi":"10.23638/LMCS-13(2:15)2017","language":[{"iso":"eng"}],"article_number":"15","file_date_updated":"2020-07-14T12:46:33Z","ec_funded":1,"publist_id":"7355","license":"https://creativecommons.org/licenses/by-nd/4.0/","year":"2017","publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"International Federation of Computational Logic","author":[{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Křetínská","first_name":"Zuzana","full_name":"Křetínská, Zuzana"},{"first_name":"Jan","last_name":"Kretinsky","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8122-2881","full_name":"Kretinsky, Jan"}],"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"1657"},{"status":"public","relation":"earlier_version","id":"5429"},{"relation":"earlier_version","status":"public","id":"5435"}]},"date_updated":"2023-02-23T12:26:16Z","date_created":"2018-12-11T11:46:38Z","volume":13,"scopus_import":1,"day":"03","has_accepted_license":"1","publication":"Logical Methods in Computer Science","citation":{"apa":"Chatterjee, K., Křetínská, Z., & Kretinsky, J. (2017). Unifying two views on multiple mean-payoff objectives in Markov decision processes. Logical Methods in Computer Science. International Federation of Computational Logic. https://doi.org/10.23638/LMCS-13(2:15)2017","ieee":"K. Chatterjee, Z. Křetínská, and J. Kretinsky, “Unifying two views on multiple mean-payoff objectives in Markov decision processes,” Logical Methods in Computer Science, vol. 13, no. 2. International Federation of Computational Logic, 2017.","ista":"Chatterjee K, Křetínská Z, Kretinsky J. 2017. Unifying two views on multiple mean-payoff objectives in Markov decision processes. Logical Methods in Computer Science. 13(2), 15.","ama":"Chatterjee K, Křetínská Z, Kretinsky J. Unifying two views on multiple mean-payoff objectives in Markov decision processes. Logical Methods in Computer Science. 2017;13(2). doi:10.23638/LMCS-13(2:15)2017","chicago":"Chatterjee, Krishnendu, Zuzana Křetínská, and Jan Kretinsky. “Unifying Two Views on Multiple Mean-Payoff Objectives in Markov Decision Processes.” Logical Methods in Computer Science. International Federation of Computational Logic, 2017. https://doi.org/10.23638/LMCS-13(2:15)2017.","short":"K. Chatterjee, Z. Křetínská, J. Kretinsky, Logical Methods in Computer Science 13 (2017).","mla":"Chatterjee, Krishnendu, et al. “Unifying Two Views on Multiple Mean-Payoff Objectives in Markov Decision Processes.” Logical Methods in Computer Science, vol. 13, no. 2, 15, International Federation of Computational Logic, 2017, doi:10.23638/LMCS-13(2:15)2017."},"date_published":"2017-07-03T00:00:00Z","type":"journal_article","abstract":[{"text":"We consider Markov decision processes (MDPs) with multiple limit-average (or mean-payoff) objectives. There exist two different views: (i) the expectation semantics, where the goal is to optimize the expected mean-payoff objective, and (ii) the satisfaction semantics, where the goal is to maximize the probability of runs such that the mean-payoff value stays above a given vector. We consider optimization with respect to both objectives at once, thus unifying the existing semantics. Precisely, the goal is to optimize the expectation while ensuring the satisfaction constraint. Our problem captures the notion of optimization with respect to strategies that are risk-averse (i.e., ensure certain probabilistic guarantee). Our main results are as follows: First, we present algorithms for the decision problems which are always polynomial in the size of the MDP. We also show that an approximation of the Pareto-curve can be computed in time polynomial in the size of the MDP, and the approximation factor, but exponential in the number of dimensions. Second, we present a complete characterization of the strategy complexity (in terms of memory bounds and randomization) required to solve our problem. ","lang":"eng"}],"issue":"2","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"466","title":"Unifying two views on multiple mean-payoff objectives in Markov decision processes","ddc":["004"],"status":"public","intvolume":" 13","pubrep_id":"957","file":[{"access_level":"open_access","file_name":"IST-2018-957-v1+1_2017_Chatterjee_Unifying_two.pdf","creator":"system","file_size":511832,"content_type":"application/pdf","file_id":"5354","relation":"main_file","checksum":"bfa405385ec6229ad5ead89ab5751639","date_updated":"2020-07-14T12:46:33Z","date_created":"2018-12-12T10:18:32Z"}],"oa_version":"Published Version"},{"oa_version":"Preprint","_id":"467","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Nested weighted automata","status":"public","intvolume":" 18","abstract":[{"lang":"eng","text":"Recently there has been a significant effort to handle quantitative properties in formal verification and synthesis. While weighted automata over finite and infinite words provide a natural and flexible framework to express quantitative properties, perhaps surprisingly, some basic system properties such as average response time cannot be expressed using weighted automata or in any other known decidable formalism. In this work, we introduce nested weighted automata as a natural extension of weighted automata, which makes it possible to express important quantitative properties such as average response time. In nested weighted automata, a master automaton spins off and collects results from weighted slave automata, each of which computes a quantity along a finite portion of an infinite word. Nested weighted automata can be viewed as the quantitative analogue of monitor automata, which are used in runtime verification. We establish an almost-complete decidability picture for the basic decision problems about nested weighted automata and illustrate their applicability in several domains. In particular, nested weighted automata can be used to decide average response time properties."}],"issue":"4","type":"journal_article","date_published":"2017-12-01T00:00:00Z","publication":"ACM Transactions on Computational Logic (TOCL)","citation":{"ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, “Nested weighted automata,” ACM Transactions on Computational Logic (TOCL), vol. 18, no. 4. ACM, 2017.","apa":"Chatterjee, K., Henzinger, T. A., & Otop, J. (2017). Nested weighted automata. ACM Transactions on Computational Logic (TOCL). ACM. https://doi.org/10.1145/3152769","ista":"Chatterjee K, Henzinger TA, Otop J. 2017. Nested weighted automata. ACM Transactions on Computational Logic (TOCL). 18(4), 31.","ama":"Chatterjee K, Henzinger TA, Otop J. Nested weighted automata. ACM Transactions on Computational Logic (TOCL). 2017;18(4). doi:10.1145/3152769","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Nested Weighted Automata.” ACM Transactions on Computational Logic (TOCL). ACM, 2017. https://doi.org/10.1145/3152769.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, ACM Transactions on Computational Logic (TOCL) 18 (2017).","mla":"Chatterjee, Krishnendu, et al. “Nested Weighted Automata.” ACM Transactions on Computational Logic (TOCL), vol. 18, no. 4, 31, ACM, 2017, doi:10.1145/3152769."},"day":"01","scopus_import":1,"author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"},{"first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Otop","full_name":"Otop, Jan"}],"related_material":{"record":[{"id":"1656","relation":"earlier_version","status":"public"},{"id":"5415","status":"public","relation":"earlier_version"},{"id":"5436","status":"public","relation":"earlier_version"}]},"date_updated":"2023-02-23T12:26:19Z","date_created":"2018-12-11T11:46:38Z","volume":18,"year":"2017","publication_status":"published","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publisher":"ACM","ec_funded":1,"publist_id":"7354","article_number":"31","doi":"10.1145/3152769","language":[{"iso":"eng"}],"oa":1,"external_id":{"arxiv":["1606.03598"]},"main_file_link":[{"url":"https://arxiv.org/abs/1606.03598","open_access":"1"}],"quality_controlled":"1","project":[{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"},{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"month":"12","publication_identifier":{"issn":["15293785"]}},{"publication_status":"published","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publisher":"International Federation of Computational Logic","year":"2017","date_updated":"2023-02-23T12:26:25Z","date_created":"2018-12-11T11:46:37Z","volume":13,"author":[{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A"},{"first_name":"Rasmus","last_name":"Ibsen-Jensen","id":"3B699956-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4783-0389","full_name":"Ibsen-Jensen, Rasmus"},{"last_name":"Otop","first_name":"Jan","full_name":"Otop, Jan"}],"related_material":{"record":[{"id":"1610","status":"public","relation":"earlier_version"},{"relation":"earlier_version","status":"public","id":"5438"}]},"file_date_updated":"2020-07-14T12:46:33Z","publist_id":"7356","ec_funded":1,"quality_controlled":"1","project":[{"name":"Moderne Concurrency Paradigms","call_identifier":"FWF","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"name":"The Wittgenstein 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13","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"465","file":[{"creator":"system","content_type":"application/pdf","file_size":279071,"file_name":"IST-2015-321-v1+1_main.pdf","access_level":"open_access","date_created":"2018-12-12T10:14:37Z","date_updated":"2020-07-14T12:46:33Z","checksum":"08041379ba408d40664f449eb5907a8f","file_id":"5090","relation":"main_file"},{"creator":"system","content_type":"application/pdf","file_size":279071,"file_name":"IST-2018-955-v1+1_2017_Chatterjee_Edit_distance.pdf","access_level":"open_access","date_created":"2018-12-12T10:14:38Z","date_updated":"2020-07-14T12:46:33Z","checksum":"08041379ba408d40664f449eb5907a8f","file_id":"5091","relation":"main_file"}],"oa_version":"Published Version","pubrep_id":"955","type":"journal_article","abstract":[{"text":"The edit distance between two words w 1 , w 2 is the minimal number of word operations (letter insertions, deletions, and substitutions) necessary to transform w 1 to w 2 . The edit distance generalizes to languages L 1 , L 2 , where the edit distance from L 1 to L 2 is the minimal number k such that for every word from L 1 there exists a word in L 2 with edit distance at most k . We study the edit distance computation problem between pushdown automata and their subclasses. The problem of computing edit distance to a pushdown automaton is undecidable, and in practice, the interesting question is to compute the edit distance from a pushdown automaton (the implementation, a standard model for programs with recursion) to a regular language (the specification). In this work, we present a complete picture of decidability and complexity for the following problems: (1) deciding whether, for a given threshold k , the edit distance from a pushdown automaton to a finite automaton is at most k , and (2) deciding whether the edit distance from a pushdown automaton to a finite automaton is finite. ","lang":"eng"}],"issue":"3","publication":"Logical Methods in Computer Science","citation":{"ama":"Chatterjee K, Henzinger TA, Ibsen-Jensen R, Otop J. Edit distance for pushdown automata. Logical Methods in Computer Science. 2017;13(3). doi:10.23638/LMCS-13(3:23)2017","ieee":"K. Chatterjee, T. A. Henzinger, R. Ibsen-Jensen, and J. Otop, “Edit distance for pushdown automata,” Logical Methods in Computer Science, vol. 13, no. 3. International Federation of Computational Logic, 2017.","apa":"Chatterjee, K., Henzinger, T. A., Ibsen-Jensen, R., & Otop, J. (2017). Edit distance for pushdown automata. Logical Methods in Computer Science. International Federation of Computational Logic. https://doi.org/10.23638/LMCS-13(3:23)2017","ista":"Chatterjee K, Henzinger TA, Ibsen-Jensen R, Otop J. 2017. Edit distance for pushdown automata. Logical Methods in Computer Science. 13(3).","short":"K. Chatterjee, T.A. Henzinger, R. Ibsen-Jensen, J. Otop, Logical Methods in Computer Science 13 (2017).","mla":"Chatterjee, Krishnendu, et al. “Edit Distance for Pushdown Automata.” Logical Methods in Computer Science, vol. 13, no. 3, International Federation of Computational Logic, 2017, doi:10.23638/LMCS-13(3:23)2017.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, Rasmus Ibsen-Jensen, and Jan Otop. “Edit Distance for Pushdown Automata.” Logical Methods in Computer Science. International Federation of Computational Logic, 2017. https://doi.org/10.23638/LMCS-13(3:23)2017."},"date_published":"2017-09-13T00:00:00Z","scopus_import":1,"day":"13","has_accepted_license":"1"},{"scopus_import":1,"day":"06","has_accepted_license":"1","article_processing_charge":"No","publication":"Scientific Reports","citation":{"mla":"Pavlogiannis, Andreas, et al. “Amplification on Undirected Population Structures: Comets Beat Stars.” Scientific Reports, vol. 7, no. 1, 82, Nature Publishing Group, 2017, doi:10.1038/s41598-017-00107-w.","short":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M. Nowak, Scientific Reports 7 (2017).","chicago":"Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. “Amplification on Undirected Population Structures: Comets Beat Stars.” Scientific Reports. Nature Publishing Group, 2017. https://doi.org/10.1038/s41598-017-00107-w.","ama":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. Amplification on undirected population structures: Comets beat stars. Scientific Reports. 2017;7(1). doi:10.1038/s41598-017-00107-w","ista":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. 2017. Amplification on undirected population structures: Comets beat stars. Scientific Reports. 7(1), 82.","apa":"Pavlogiannis, A., Tkadlec, J., Chatterjee, K., & Nowak, M. (2017). Amplification on undirected population structures: Comets beat stars. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/s41598-017-00107-w","ieee":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. Nowak, “Amplification on undirected population structures: Comets beat stars,” Scientific Reports, vol. 7, no. 1. Nature Publishing Group, 2017."},"date_published":"2017-03-06T00:00:00Z","type":"journal_article","abstract":[{"text":"The fixation probability is the probability that a new mutant introduced in a homogeneous population eventually takes over the entire population. The fixation probability is a fundamental quantity of natural selection, and known to depend on the population structure. Amplifiers of natural selection are population structures which increase the fixation probability of advantageous mutants, as compared to the baseline case of well-mixed populations. In this work we focus on symmetric population structures represented as undirected graphs. In the regime of undirected graphs, the strongest amplifier known has been the Star graph, and the existence of undirected graphs with stronger amplification properties has remained open for over a decade. In this work we present the Comet and Comet-swarm families of undirected graphs. We show that for a range of fitness values of the mutants, the Comet and Cometswarm graphs have fixation probability strictly larger than the fixation probability of the Star graph, for fixed population size and at the limit of large populations, respectively. ","lang":"eng"}],"issue":"1","status":"public","title":"Amplification on undirected population structures: Comets beat stars","ddc":["004"],"intvolume":" 7","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"512","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"IST-2018-938-v1+1_2017_Pavlogiannis_Amplification_on.pdf","creator":"system","file_size":1536783,"content_type":"application/pdf","file_id":"5357","relation":"main_file","checksum":"7d05cbdd914e194a019c0f91fb64e9a8","date_updated":"2020-07-14T12:46:36Z","date_created":"2018-12-12T10:18:35Z"}],"pubrep_id":"938","month":"03","publication_identifier":{"issn":["20452322"]},"quality_controlled":"1","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"doi":"10.1038/s41598-017-00107-w","article_number":"82","file_date_updated":"2020-07-14T12:46:36Z","ec_funded":1,"publist_id":"7307","publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"Nature Publishing Group","year":"2017","date_updated":"2023-02-23T12:26:57Z","date_created":"2018-12-11T11:46:53Z","volume":7,"author":[{"id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722","first_name":"Andreas","last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas"},{"orcid":"0000-0002-1097-9684","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","last_name":"Tkadlec","first_name":"Josef","full_name":"Tkadlec, Josef"},{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"}],"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"5449"}]}},{"external_id":{"arxiv":["1910.00241"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"}],"quality_controlled":"1","doi":"10.1145/3158118","conference":{"name":"POPL: Programming Languages","end_date":"2018-01-13","location":"Los Angeles, CA, United States","start_date":"2018-01-07"},"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2475-1421"]},"month":"12","acknowledgement":"The research was partly supported by Austrian Science Fund (FWF) Grant No P23499-N23, FWF NFN Grant No S11407-N23 (RiSE/SHiNE), and ERC Start grant (279307: Graph Games).\r\n","year":"2017","publisher":"Association for Computing Machinery","department":[{"_id":"KrCh"}],"publication_status":"published","related_material":{"record":[{"id":"5455","status":"public","relation":"earlier_version"}]},"author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"first_name":"Bhavya","last_name":"Choudhary","full_name":"Choudhary, Bhavya"},{"orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis","first_name":"Andreas","full_name":"Pavlogiannis, Andreas"}],"volume":2,"date_created":"2021-12-05T23:01:48Z","date_updated":"2023-02-23T12:27:13Z","article_number":"30","ec_funded":1,"file_date_updated":"2021-12-07T08:06:28Z","citation":{"short":"K. Chatterjee, B. Choudhary, A. Pavlogiannis, Proceedings of the ACM on Programming Languages 2 (2017).","mla":"Chatterjee, Krishnendu, et al. “Optimal Dyck Reachability for Data-Dependence and Alias Analysis.” Proceedings of the ACM on Programming Languages, vol. 2, no. POPL, 30, Association for Computing Machinery, 2017, doi:10.1145/3158118.","chicago":"Chatterjee, Krishnendu, Bhavya Choudhary, and Andreas Pavlogiannis. “Optimal Dyck Reachability for Data-Dependence and Alias Analysis.” Proceedings of the ACM on Programming Languages. Association for Computing Machinery, 2017. https://doi.org/10.1145/3158118.","ama":"Chatterjee K, Choudhary B, Pavlogiannis A. Optimal Dyck reachability for data-dependence and Alias analysis. Proceedings of the ACM on Programming Languages. 2017;2(POPL). doi:10.1145/3158118","ieee":"K. Chatterjee, B. Choudhary, and A. Pavlogiannis, “Optimal Dyck reachability for data-dependence and Alias analysis,” Proceedings of the ACM on Programming Languages, vol. 2, no. POPL. Association for Computing Machinery, 2017.","apa":"Chatterjee, K., Choudhary, B., & Pavlogiannis, A. (2017). Optimal Dyck reachability for data-dependence and Alias analysis. Proceedings of the ACM on Programming Languages. Los Angeles, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3158118","ista":"Chatterjee K, Choudhary B, Pavlogiannis A. 2017. Optimal Dyck reachability for data-dependence and Alias analysis. Proceedings of the ACM on Programming Languages. 2(POPL), 30."},"publication":"Proceedings of the ACM on Programming Languages","article_type":"original","date_published":"2017-12-27T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"27","_id":"10416","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","intvolume":" 2","ddc":["000"],"title":"Optimal Dyck reachability for data-dependence and Alias analysis","status":"public","file":[{"file_size":460188,"content_type":"application/pdf","creator":"cchlebak","access_level":"open_access","file_name":"2017_ACMProgLang_Chatterjee.pdf","checksum":"faa3f7b3fe8aab84b50ed805c26a0ee5","success":1,"date_updated":"2021-12-07T08:06:28Z","date_created":"2021-12-07T08:06:28Z","relation":"main_file","file_id":"10421"}],"oa_version":"Published Version","type":"journal_article","issue":"POPL","abstract":[{"text":"A fundamental algorithmic problem at the heart of static analysis is Dyck reachability. The input is a graph where the edges are labeled with different types of opening and closing parentheses, and the reachability information is computed via paths whose parentheses are properly matched. We present new results for Dyck reachability problems with applications to alias analysis and data-dependence analysis. Our main contributions, that include improved upper bounds as well as lower bounds that establish optimality guarantees, are as follows: First, we consider Dyck reachability on bidirected graphs, which is the standard way of performing field-sensitive points-to analysis. Given a bidirected graph with n nodes and m edges, we present: (i) an algorithm with worst-case running time O(m + n · α(n)), where α(n) is the inverse Ackermann function, improving the previously known O(n2) time bound; (ii) a matching lower bound that shows that our algorithm is optimal wrt to worst-case complexity; and (iii) an optimal average-case upper bound of O(m) time, improving the previously known O(m · logn) bound. Second, we consider the problem of context-sensitive data-dependence analysis, where the task is to obtain analysis summaries of library code in the presence of callbacks. Our algorithm preprocesses libraries in almost linear time, after which the contribution of the library in the complexity of the client analysis is only linear, and only wrt the number of call sites. Third, we prove that combinatorial algorithms for Dyck reachability on general graphs with truly sub-cubic bounds cannot be obtained without obtaining sub-cubic combinatorial algorithms for Boolean Matrix Multiplication, which is a long-standing open problem. Thus we establish that the existing combinatorial algorithms for Dyck reachability are (conditionally) optimal for general graphs. We also show that the same hardness holds for graphs of constant treewidth. Finally, we provide a prototype implementation of our algorithms for both alias analysis and data-dependence analysis. Our experimental evaluation demonstrates that the new algorithms significantly outperform all existing methods on the two problems, over real-world benchmarks.","lang":"eng"}]},{"_id":"5455","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","ddc":["000"],"title":"Optimal Dyck reachability for data-dependence and alias analysis","pubrep_id":"870","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"IST-2017-870-v1+1_main.pdf","creator":"system","file_size":960491,"content_type":"application/pdf","file_id":"5524","relation":"main_file","checksum":"177a84a46e3ac17e87b31534ad16a4c9","date_created":"2018-12-12T11:54:02Z","date_updated":"2020-07-14T12:46:59Z"}],"type":"technical_report","alternative_title":["IST Austria Technical Report"],"abstract":[{"lang":"eng","text":"A fundamental algorithmic problem at the heart of static analysis is Dyck reachability. The input is a graphwhere the edges are labeled with different types of opening and closing parentheses, and the reachabilityinformation is computed via paths whose parentheses are properly matched. We present new results for Dyckreachability problems with applications to alias analysis and data-dependence analysis. Our main contributions,that include improved upper bounds as well as lower bounds that establish optimality guarantees, are asfollows:First, we consider Dyck reachability on bidirected graphs, which is the standard way of performing field-sensitive points-to analysis. Given a bidirected graph withnnodes andmedges, we present: (i) an algorithmwith worst-case running timeO(m+n·α(n)), whereα(n)is the inverse Ackermann function, improving thepreviously knownO(n2)time bound; (ii) a matching lower bound that shows that our algorithm is optimalwrt to worst-case complexity; and (iii) an optimal average-case upper bound ofO(m)time, improving thepreviously knownO(m·logn)bound.Second, we consider the problem of context-sensitive data-dependence analysis, where the task is to obtainanalysis summaries of library code in the presence of callbacks. Our algorithm preprocesses libraries in almostlinear time, after which the contribution of the library in the complexity of the client analysis is only linear,and only wrt the number of call sites.Third, we prove that combinatorial algorithms for Dyck reachability on general graphs with truly sub-cubic bounds cannot be obtained without obtaining sub-cubic combinatorial algorithms for Boolean MatrixMultiplication, which is a long-standing open problem. Thus we establish that the existing combinatorialalgorithms for Dyck reachability are (conditionally) optimal for general graphs. We also show that the samehardness holds for graphs of constant treewidth.Finally, we provide a prototype implementation of our algorithms for both alias analysis and data-dependenceanalysis. Our experimental evaluation demonstrates that the new algorithms significantly outperform allexisting methods on the two problems, over real-world benchmarks."}],"citation":{"ama":"Chatterjee K, Choudhary B, Pavlogiannis A. Optimal Dyck Reachability for Data-Dependence and Alias Analysis. IST Austria; 2017. doi:10.15479/AT:IST-2017-870-v1-1","ista":"Chatterjee K, Choudhary B, Pavlogiannis A. 2017. Optimal Dyck reachability for data-dependence and alias analysis, IST Austria, 37p.","apa":"Chatterjee, K., Choudhary, B., & Pavlogiannis, A. (2017). Optimal Dyck reachability for data-dependence and alias analysis. IST Austria. https://doi.org/10.15479/AT:IST-2017-870-v1-1","ieee":"K. Chatterjee, B. Choudhary, and A. Pavlogiannis, Optimal Dyck reachability for data-dependence and alias analysis. IST Austria, 2017.","mla":"Chatterjee, Krishnendu, et al. Optimal Dyck Reachability for Data-Dependence and Alias Analysis. IST Austria, 2017, doi:10.15479/AT:IST-2017-870-v1-1.","short":"K. Chatterjee, B. Choudhary, A. Pavlogiannis, Optimal Dyck Reachability for Data-Dependence and Alias Analysis, IST Austria, 2017.","chicago":"Chatterjee, Krishnendu, Bhavya Choudhary, and Andreas Pavlogiannis. Optimal Dyck Reachability for Data-Dependence and Alias Analysis. IST Austria, 2017. https://doi.org/10.15479/AT:IST-2017-870-v1-1."},"page":"37","date_published":"2017-10-23T00:00:00Z","article_processing_charge":"No","has_accepted_license":"1","day":"23","year":"2017","department":[{"_id":"KrCh"}],"publisher":"IST Austria","publication_status":"published","related_material":{"record":[{"id":"10416","status":"public","relation":"later_version"}]},"author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"},{"last_name":"Choudhary","first_name":"Bhavya","full_name":"Choudhary, Bhavya"},{"id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722","first_name":"Andreas","last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas"}],"date_updated":"2023-02-21T15:54:10Z","date_created":"2018-12-12T11:39:26Z","file_date_updated":"2020-07-14T12:46:59Z","oa":1,"doi":"10.15479/AT:IST-2017-870-v1-1","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2664-1690"]},"month":"10"},{"publisher":"IST Austria","department":[{"_id":"E-Lib"}],"title":"Implementing the institutional data repository IST DataRep","status":"public","_id":"5450","year":"2017","file":[{"date_updated":"2020-07-14T12:46:59Z","date_created":"2018-12-12T11:53:22Z","checksum":"6321792dcfa82bf490f17615a9b22355","file_id":"5483","relation":"main_file","creator":"system","file_size":3460985,"content_type":"application/pdf","file_name":"IST-2017-724-v1+1_DataRep_Project_Report_2017.pdf","access_level":"open_access"}],"date_updated":"2020-07-14T23:05:03Z","date_created":"2018-12-12T11:39:24Z","pubrep_id":"724","author":[{"last_name":"Petritsch","first_name":"Barbara","orcid":"0000-0003-2724-4614","id":"406048EC-F248-11E8-B48F-1D18A9856A87","full_name":"Barbara Petritsch"}],"type":"report","extern":0,"abstract":[{"text":"In this report the implementation of the institutional data repository IST DataRep at IST Austria will be covered: Starting with the research phase when requirements for a repository were established, the procedure of choosing a repository-software and its customization based on the results of user-testings will be discussed. Followed by reflections on the marketing strategies in regard of impact, and at the end sharing some experiences of one year operating IST DataRep.","lang":"eng"}],"file_date_updated":"2020-07-14T12:46:59Z","oa":1,"main_file_link":[{"open_access":"1","url":"https://repository.ist.ac.at/id/eprint/724."}],"publication_date":"2017-06-26","citation":{"chicago":"Petritsch, Barbara. Implementing the Institutional Data Repository IST DataRep. IST Austria, 2017.","short":"B. Petritsch, Implementing the Institutional Data Repository IST DataRep, IST Austria, 2017.","mla":"Petritsch, Barbara. Implementing the Institutional Data Repository IST DataRep. IST Austria, 2017.","ieee":"B. Petritsch, Implementing the institutional data repository IST DataRep. IST Austria, 2017.","apa":"Petritsch, B. (2017). Implementing the institutional data repository IST DataRep. IST Austria.","ista":"Petritsch B. 2017. Implementing the institutional data repository IST DataRep, IST Austria,p.","ama":"Petritsch B. Implementing the Institutional Data Repository IST DataRep. IST Austria; 2017."},"date_published":"2017-06-26T00:00:00Z","month":"06","day":"26"},{"date_created":"2021-12-05T23:01:49Z","date_updated":"2023-02-23T12:27:16Z","volume":2,"author":[{"full_name":"Chalupa, Marek","last_name":"Chalupa","first_name":"Marek"},{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"full_name":"Pavlogiannis, Andreas","first_name":"Andreas","last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722"},{"last_name":"Sinha","first_name":"Nishant","full_name":"Sinha, Nishant"},{"last_name":"Vaidya","first_name":"Kapil","full_name":"Vaidya, Kapil"}],"related_material":{"record":[{"id":"5448","status":"public","relation":"earlier_version"},{"id":"5456","relation":"earlier_version","status":"public"}]},"publication_status":"published","publisher":"Association for Computing Machinery","department":[{"_id":"KrCh"}],"acknowledgement":"The research was partly supported by Austrian Science Fund (FWF) Grant No P23499- N23, FWF\r\nNFN Grant No S11407-N23 (RiSE/SHiNE), ERC Start grant (279307: Graph Games), and Czech\r\nScience Foundation grant GBP202/12/G061.","year":"2017","ec_funded":1,"article_number":"31","language":[{"iso":"eng"}],"conference":{"end_date":"2018-01-13","location":"Los Angeles, CA, United States","start_date":"2018-01-07","name":"POPL: Programming Languages"},"doi":"10.1145/3158119","quality_controlled":"1","project":[{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"}],"oa":1,"external_id":{"arxiv":["1610.01188"]},"main_file_link":[{"open_access":"1","url":"https://dl.acm.org/doi/10.1145/3158119"}],"month":"12","publication_identifier":{"eissn":["2475-1421"]},"oa_version":"Published Version","status":"public","title":"Data-centric dynamic partial order reduction","intvolume":" 2","_id":"10417","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","abstract":[{"text":"We present a new dynamic partial-order reduction method for stateless model checking of concurrent programs. A common approach for exploring program behaviors relies on enumerating the traces of the program, without storing the visited states (aka stateless exploration). As the number of distinct traces grows exponentially, dynamic partial-order reduction (DPOR) techniques have been successfully used to partition the space of traces into equivalence classes (Mazurkiewicz partitioning), with the goal of exploring only few representative traces from each class.\r\n\r\nWe introduce a new equivalence on traces under sequential consistency semantics, which we call the observation equivalence. Two traces are observationally equivalent if every read event observes the same write event in both traces. While the traditional Mazurkiewicz equivalence is control-centric, our new definition is data-centric. We show that our observation equivalence is coarser than the Mazurkiewicz equivalence, and in many cases even exponentially coarser. We devise a DPOR exploration of the trace space, called data-centric DPOR, based on the observation equivalence.","lang":"eng"}],"issue":"POPL","type":"journal_article","date_published":"2017-12-27T00:00:00Z","article_type":"original","publication":"Proceedings of the ACM on Programming Languages","citation":{"mla":"Chalupa, Marek, et al. “Data-Centric Dynamic Partial Order Reduction.” Proceedings of the ACM on Programming Languages, vol. 2, no. POPL, 31, Association for Computing Machinery, 2017, doi:10.1145/3158119.","short":"M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, K. Vaidya, Proceedings of the ACM on Programming Languages 2 (2017).","chicago":"Chalupa, Marek, Krishnendu Chatterjee, Andreas Pavlogiannis, Nishant Sinha, and Kapil Vaidya. “Data-Centric Dynamic Partial Order Reduction.” Proceedings of the ACM on Programming Languages. Association for Computing Machinery, 2017. https://doi.org/10.1145/3158119.","ama":"Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. Data-centric dynamic partial order reduction. Proceedings of the ACM on Programming Languages. 2017;2(POPL). doi:10.1145/3158119","ista":"Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. 2017. Data-centric dynamic partial order reduction. Proceedings of the ACM on Programming Languages. 2(POPL), 31.","apa":"Chalupa, M., Chatterjee, K., Pavlogiannis, A., Sinha, N., & Vaidya, K. (2017). Data-centric dynamic partial order reduction. Proceedings of the ACM on Programming Languages. Los Angeles, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3158119","ieee":"M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, and K. Vaidya, “Data-centric dynamic partial order reduction,” Proceedings of the ACM on Programming Languages, vol. 2, no. POPL. Association for Computing Machinery, 2017."},"day":"27","article_processing_charge":"No","scopus_import":"1"},{"doi":"10.15479/AT:IST-2017-872-v1-1","date_published":"2017-10-23T00:00:00Z","language":[{"iso":"eng"}],"oa":1,"citation":{"chicago":"Chalupa, Marek, Krishnendu Chatterjee, Andreas Pavlogiannis, Nishant Sinha, and Kapil Vaidya. Data-Centric Dynamic Partial Order Reduction. IST Austria, 2017. https://doi.org/10.15479/AT:IST-2017-872-v1-1.","mla":"Chalupa, Marek, et al. Data-Centric Dynamic Partial Order Reduction. IST Austria, 2017, doi:10.15479/AT:IST-2017-872-v1-1.","short":"M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, K. Vaidya, Data-Centric Dynamic Partial Order Reduction, IST Austria, 2017.","ista":"Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. 2017. Data-centric dynamic partial order reduction, IST Austria, 36p.","apa":"Chalupa, M., Chatterjee, K., Pavlogiannis, A., Sinha, N., & Vaidya, K. (2017). Data-centric dynamic partial order reduction. IST Austria. https://doi.org/10.15479/AT:IST-2017-872-v1-1","ieee":"M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, and K. Vaidya, Data-centric dynamic partial order reduction. IST Austria, 2017.","ama":"Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. Data-Centric Dynamic Partial Order Reduction. IST Austria; 2017. doi:10.15479/AT:IST-2017-872-v1-1"},"page":"36","has_accepted_license":"1","publication_identifier":{"issn":["2664-1690"]},"month":"10","day":"23","related_material":{"record":[{"id":"10417","relation":"later_version","status":"public"},{"id":"5448","status":"public","relation":"earlier_version"}]},"pubrep_id":"872","author":[{"last_name":"Chalupa","first_name":"Marek","full_name":"Chalupa, Marek"},{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"last_name":"Pavlogiannis","first_name":"Andreas","orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87","full_name":"Pavlogiannis, Andreas"},{"last_name":"Sinha","first_name":"Nishant","full_name":"Sinha, Nishant"},{"full_name":"Vaidya, Kapil","first_name":"Kapil","last_name":"Vaidya"}],"file":[{"creator":"system","content_type":"application/pdf","file_size":910347,"access_level":"open_access","file_name":"IST-2017-872-v1+1_main.pdf","checksum":"d2635c4cf013000f0a1b09e80f9e4ab7","date_updated":"2020-07-14T12:46:59Z","date_created":"2018-12-12T11:53:26Z","file_id":"5487","relation":"main_file"}],"oa_version":"Published Version","date_updated":"2023-02-23T12:26:54Z","date_created":"2018-12-12T11:39:26Z","_id":"5456","year":"2017","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"IST Austria","department":[{"_id":"KrCh"}],"status":"public","ddc":["000"],"publication_status":"published","title":"Data-centric dynamic partial order reduction","file_date_updated":"2020-07-14T12:46:59Z","abstract":[{"lang":"eng","text":"We present a new dynamic partial-order reduction method for stateless model checking of concurrent programs. A common approach for exploring program behaviors relies on enumerating the traces of the program, without storing the visited states (aka stateless exploration). As the number of distinct traces grows exponentially, dynamic partial-order reduction (DPOR) techniques have been successfully used to partition the space of traces into equivalence classes (Mazurkiewicz partitioning), with the goal of exploring only few representative traces from each class.\r\nWe introduce a new equivalence on traces under sequential consistency semantics, which we call the observation equivalence. Two traces are observationally equivalent if every read event observes the same write event in both traces. While the traditional Mazurkiewicz equivalence is control-centric, our new definition is data-centric. We show that our observation equivalence is coarser than the Mazurkiewicz equivalence, and in many cases even exponentially coarser. We devise a DPOR exploration of the trace space, called data-centric DPOR, based on the observation equivalence.\r\n1. For acyclic architectures, our algorithm is guaranteed to explore exactly one representative trace from each observation class, while spending polynomial time per class. Hence, our algorithm is optimal wrt the observation equivalence, and in several cases explores exponentially fewer traces than any enumerative method based on the Mazurkiewicz equivalence.\r\n2. For cyclic architectures, we consider an equivalence between traces which is finer than the observation equivalence; but coarser than the Mazurkiewicz equivalence, and in some cases is exponentially coarser. Our data-centric DPOR algorithm remains optimal under this trace equivalence. \r\nFinally, we perform a basic experimental comparison between the existing Mazurkiewicz-based DPOR and our data-centric DPOR on a set of academic benchmarks. Our results show a significant reduction in both running time and the number of explored equivalence classes."}],"type":"technical_report","alternative_title":["IST Austria Technical Report"]},{"citation":{"chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Martin Nowak. “Faster Monte Carlo Algorithms for Fixation Probability of the Moran Process on Undirected Graphs.” In Leibniz International Proceedings in Informatics, Vol. 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.MFCS.2017.61.","mla":"Chatterjee, Krishnendu, et al. “Faster Monte Carlo Algorithms for Fixation Probability of the Moran Process on Undirected Graphs.” Leibniz International Proceedings in Informatics, vol. 83, 61, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.MFCS.2017.61.","short":"K. Chatterjee, R. Ibsen-Jensen, M. Nowak, in:, Leibniz International Proceedings in Informatics, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","ista":"Chatterjee K, Ibsen-Jensen R, Nowak M. 2017. Faster Monte Carlo algorithms for fixation probability of the Moran process on undirected graphs. Leibniz International Proceedings in Informatics. MFCS: Mathematical Foundations of Computer Science (SG), LIPIcs, vol. 83, 61.","ieee":"K. Chatterjee, R. Ibsen-Jensen, and M. Nowak, “Faster Monte Carlo algorithms for fixation probability of the Moran process on undirected graphs,” in Leibniz International Proceedings in Informatics, Aalborg, Denmark, 2017, vol. 83.","apa":"Chatterjee, K., Ibsen-Jensen, R., & Nowak, M. (2017). Faster Monte Carlo algorithms for fixation probability of the Moran process on undirected graphs. In Leibniz International Proceedings in Informatics (Vol. 83). Aalborg, Denmark: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.MFCS.2017.61","ama":"Chatterjee K, Ibsen-Jensen R, Nowak M. Faster Monte Carlo algorithms for fixation probability of the Moran process on undirected graphs. In: Leibniz International Proceedings in Informatics. Vol 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.MFCS.2017.61"},"publication":"Leibniz International Proceedings in Informatics","date_published":"2017-11-01T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"01","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"551","intvolume":" 83","status":"public","title":"Faster Monte Carlo algorithms for fixation probability of the Moran process on undirected graphs","ddc":["004"],"pubrep_id":"924","oa_version":"Published Version","file":[{"date_created":"2018-12-12T10:18:04Z","date_updated":"2020-07-14T12:47:00Z","checksum":"2eed5224c0e4e259484a1d71acb8ba6a","relation":"main_file","file_id":"5322","file_size":535077,"content_type":"application/pdf","creator":"system","file_name":"IST-2018-924-v1+1_LIPIcs-MFCS-2017-61.pdf","access_level":"open_access"}],"type":"conference","alternative_title":["LIPIcs"],"abstract":[{"lang":"eng","text":"Evolutionary graph theory studies the evolutionary dynamics in a population structure given as a connected graph. Each node of the graph represents an individual of the population, and edges determine how offspring are placed. We consider the classical birth-death Moran process where there are two types of individuals, namely, the residents with fitness 1 and mutants with fitness r. The fitness indicates the reproductive strength. The evolutionary dynamics happens as follows: in the initial step, in a population of all resident individuals a mutant is introduced, and then at each step, an individual is chosen proportional to the fitness of its type to reproduce, and the offspring replaces a neighbor uniformly at random. The process stops when all individuals are either residents or mutants. The probability that all individuals in the end are mutants is called the fixation probability, which is a key factor in the rate of evolution. We consider the problem of approximating the fixation probability. The class of algorithms that is extremely relevant for approximation of the fixation probabilities is the Monte-Carlo simulation of the process. Previous results present a polynomial-time Monte-Carlo algorithm for undirected graphs when r is given in unary. First, we present a simple modification: instead of simulating each step, we discard ineffective steps, where no node changes type (i.e., either residents replace residents, or mutants replace mutants). Using the above simple modification and our result that the number of effective steps is concentrated around the expected number of effective steps, we present faster polynomial-time Monte-Carlo algorithms for undirected graphs. Our algorithms are always at least a factor O(n2/ log n) faster as compared to the previous algorithms, where n is the number of nodes, and is polynomial even if r is given in binary. We also present lower bounds showing that the upper bound on the expected number of effective steps we present is asymptotically tight for undirected graphs. "}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","doi":"10.4230/LIPIcs.MFCS.2017.61","conference":{"name":"MFCS: Mathematical Foundations of Computer Science (SG)","start_date":"2017-08-21","location":"Aalborg, Denmark","end_date":"2017-08-25"},"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-395977046-0"]},"month":"11","year":"2017","department":[{"_id":"KrCh"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication_status":"published","author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"id":"3B699956-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4783-0389","first_name":"Rasmus","last_name":"Ibsen-Jensen","full_name":"Ibsen-Jensen, Rasmus"},{"first_name":"Martin","last_name":"Nowak","full_name":"Nowak, Martin"}],"volume":83,"date_updated":"2021-01-12T08:02:34Z","date_created":"2018-12-11T11:47:08Z","article_number":"61","publist_id":"7263","file_date_updated":"2020-07-14T12:47:00Z"},{"doi":"10.4230/LIPIcs.MFCS.2017.39","conference":{"location":"Aalborg, Denmark","start_date":"2017-08-21","end_date":"2017-08-25","name":"MFCS: Mathematical Foundations of Computer Science (SG)"},"language":[{"iso":"eng"}],"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","short":"CC BY (3.0)","image":"/images/cc_by.png"},"project":[{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"}],"quality_controlled":"1","publication_identifier":{"isbn":["978-395977046-0"]},"month":"11","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"full_name":"Henzinger, Monika H","last_name":"Henzinger","first_name":"Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"full_name":"Svozil, Alexander","first_name":"Alexander","last_name":"Svozil"}],"volume":83,"date_updated":"2023-02-14T10:06:46Z","date_created":"2018-12-11T11:47:08Z","year":"2017","department":[{"_id":"KrCh"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication_status":"published","publist_id":"7262","ec_funded":1,"file_date_updated":"2020-07-14T12:47:00Z","license":"https://creativecommons.org/licenses/by/3.0/","article_number":"39","date_published":"2017-11-01T00:00:00Z","citation":{"ama":"Chatterjee K, Henzinger MH, Svozil A. Faster algorithms for mean-payoff parity games. In: Leibniz International Proceedings in Informatics. Vol 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.MFCS.2017.39","ista":"Chatterjee K, Henzinger MH, Svozil A. 2017. Faster algorithms for mean-payoff parity games. Leibniz International Proceedings in Informatics. MFCS: Mathematical Foundations of Computer Science (SG), LIPIcs, vol. 83, 39.","apa":"Chatterjee, K., Henzinger, M. H., & Svozil, A. (2017). Faster algorithms for mean-payoff parity games. In Leibniz International Proceedings in Informatics (Vol. 83). Aalborg, Denmark: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.MFCS.2017.39","ieee":"K. Chatterjee, M. H. Henzinger, and A. Svozil, “Faster algorithms for mean-payoff parity games,” in Leibniz International Proceedings in Informatics, Aalborg, Denmark, 2017, vol. 83.","mla":"Chatterjee, Krishnendu, et al. “Faster Algorithms for Mean-Payoff Parity Games.” Leibniz International Proceedings in Informatics, vol. 83, 39, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.MFCS.2017.39.","short":"K. Chatterjee, M.H. Henzinger, A. Svozil, in:, Leibniz International Proceedings in Informatics, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","chicago":"Chatterjee, Krishnendu, Monika H Henzinger, and Alexander Svozil. “Faster Algorithms for Mean-Payoff Parity Games.” In Leibniz International Proceedings in Informatics, Vol. 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.MFCS.2017.39."},"publication":"Leibniz International Proceedings in Informatics","has_accepted_license":"1","article_processing_charge":"No","day":"01","scopus_import":"1","pubrep_id":"923","file":[{"checksum":"c67f4866ddbfd555afef1f63ae9a8fc7","date_updated":"2020-07-14T12:47:00Z","date_created":"2018-12-12T10:16:57Z","file_id":"5248","relation":"main_file","creator":"system","file_size":610339,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2018-923-v1+1_LIPIcs-MFCS-2017-39.pdf"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"552","intvolume":" 83","title":"Faster algorithms for mean-payoff parity games","ddc":["004"],"status":"public","abstract":[{"text":"Graph games provide the foundation for modeling and synthesis of reactive processes. Such games are played over graphs where the vertices are controlled by two adversarial players. We consider graph games where the objective of the first player is the conjunction of a qualitative objective (specified as a parity condition) and a quantitative objective (specified as a meanpayoff condition). There are two variants of the problem, namely, the threshold problem where the quantitative goal is to ensure that the mean-payoff value is above a threshold, and the value problem where the quantitative goal is to ensure the optimal mean-payoff value; in both cases ensuring the qualitative parity objective. The previous best-known algorithms for game graphs with n vertices, m edges, parity objectives with d priorities, and maximal absolute reward value W for mean-payoff objectives, are as follows: O(nd+1 . m . w) for the threshold problem, and O(nd+2 · m · W) for the value problem. Our main contributions are faster algorithms, and the running times of our algorithms are as follows: O(nd-1 · m ·W) for the threshold problem, and O(nd · m · W · log(n · W)) for the value problem. For mean-payoff parity objectives with two priorities, our algorithms match the best-known bounds of the algorithms for mean-payoff games (without conjunction with parity objectives). Our results are relevant in synthesis of reactive systems with both functional requirement (given as a qualitative objective) and performance requirement (given as a quantitative objective).","lang":"eng"}],"type":"conference","alternative_title":["LIPIcs"]},{"scopus_import":1,"has_accepted_license":"1","day":"01","citation":{"chicago":"Chatterjee, Krishnendu, Kristofer Hansen, and Rasmus Ibsen-Jensen. “Strategy Complexity of Concurrent Safety Games.” In Leibniz International Proceedings in Informatics, Vol. 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.MFCS.2017.55.","mla":"Chatterjee, Krishnendu, et al. “Strategy Complexity of Concurrent Safety Games.” Leibniz International Proceedings in Informatics, vol. 83, 55, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.MFCS.2017.55.","short":"K. Chatterjee, K. Hansen, R. Ibsen-Jensen, in:, Leibniz International Proceedings in Informatics, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","ista":"Chatterjee K, Hansen K, Ibsen-Jensen R. 2017. Strategy complexity of concurrent safety games. Leibniz International Proceedings in Informatics. MFCS: Mathematical Foundations of Computer Science (SG), LIPIcs, vol. 83, 55.","apa":"Chatterjee, K., Hansen, K., & Ibsen-Jensen, R. (2017). Strategy complexity of concurrent safety games. In Leibniz International Proceedings in Informatics (Vol. 83). Aalborg, Denmark: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.MFCS.2017.55","ieee":"K. Chatterjee, K. Hansen, and R. Ibsen-Jensen, “Strategy complexity of concurrent safety games,” in Leibniz International Proceedings in Informatics, Aalborg, Denmark, 2017, vol. 83.","ama":"Chatterjee K, Hansen K, Ibsen-Jensen R. Strategy complexity of concurrent safety games. In: Leibniz International Proceedings in Informatics. Vol 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.MFCS.2017.55"},"publication":"Leibniz International Proceedings in Informatics","date_published":"2017-11-01T00:00:00Z","alternative_title":["LIPIcs"],"type":"conference","abstract":[{"lang":"eng","text":"We consider two player, zero-sum, finite-state concurrent reachability games, played for an infinite number of rounds, where in every round, each player simultaneously and independently of the other players chooses an action, whereafter the successor state is determined by a probability distribution given by the current state and the chosen actions. Player 1 wins iff a designated goal state is eventually visited. We are interested in the complexity of stationary strategies measured by their patience, which is defined as the inverse of the smallest non-zero probability employed. Our main results are as follows: We show that: (i) the optimal bound on the patience of optimal and -optimal strategies, for both players is doubly exponential; and (ii) even in games with a single non-absorbing state exponential (in the number of actions) patience is necessary. "}],"intvolume":" 83","status":"public","ddc":["004"],"title":"Strategy complexity of concurrent safety games","_id":"553","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","file":[{"date_created":"2018-12-12T10:09:29Z","date_updated":"2020-07-14T12:47:00Z","checksum":"7101facb56ade363205c695d72dbd173","relation":"main_file","file_id":"4753","file_size":549967,"content_type":"application/pdf","creator":"system","file_name":"IST-2018-922-v1+1_LIPIcs-MFCS-2017-55.pdf","access_level":"open_access"}],"oa_version":"Published Version","pubrep_id":"922","publication_identifier":{"isbn":["978-395977046-0"]},"month":"11","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"main_file_link":[{"url":"https://arxiv.org/abs/1506.02434","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.4230/LIPIcs.MFCS.2017.55","conference":{"name":"MFCS: Mathematical Foundations of Computer Science (SG)","location":"Aalborg, Denmark","start_date":"2017-08-21","end_date":"2017-08-25"},"article_number":"55","publist_id":"7261","file_date_updated":"2020-07-14T12:47:00Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"KrCh"}],"publication_status":"published","year":"2017","volume":83,"date_created":"2018-12-11T11:47:08Z","date_updated":"2021-01-12T08:02:35Z","author":[{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"full_name":"Hansen, Kristofer","first_name":"Kristofer","last_name":"Hansen"},{"last_name":"Ibsen-Jensen","first_name":"Rasmus","orcid":"0000-0003-4783-0389","id":"3B699956-F248-11E8-B48F-1D18A9856A87","full_name":"Ibsen-Jensen, Rasmus"}]},{"type":"journal_article","issue":"2207","abstract":[{"lang":"eng","text":"In a recent article (Jentzen et al. 2016 Commun. Math. Sci. 14, 1477–1500 (doi:10.4310/CMS.2016.v14. n6.a1)), it has been established that, for every arbitrarily slow convergence speed and every natural number d ? {4, 5, . . .}, there exist d-dimensional stochastic differential equations with infinitely often differentiable and globally bounded coefficients such that no approximation method based on finitely many observations of the driving Brownian motion can converge in absolute mean to the solution faster than the given speed of convergence. In this paper, we strengthen the above result by proving that this slow convergence phenomenon also arises in two (d = 2) and three (d = 3) space dimensions."}],"_id":"560","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 473","status":"public","title":"On stochastic differential equations with arbitrarily slow convergence rates for strong approximation in two space dimensions","oa_version":"Submitted Version","scopus_import":1,"day":"01","citation":{"ista":"Gerencser M, Jentzen A, Salimova D. 2017. On stochastic differential equations with arbitrarily slow convergence rates for strong approximation in two space dimensions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. 473(2207), 0104.","apa":"Gerencser, M., Jentzen, A., & Salimova, D. (2017). On stochastic differential equations with arbitrarily slow convergence rates for strong approximation in two space dimensions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. Royal Society of London. https://doi.org/10.1098/rspa.2017.0104","ieee":"M. Gerencser, A. Jentzen, and D. Salimova, “On stochastic differential equations with arbitrarily slow convergence rates for strong approximation in two space dimensions,” Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol. 473, no. 2207. Royal Society of London, 2017.","ama":"Gerencser M, Jentzen A, Salimova D. On stochastic differential equations with arbitrarily slow convergence rates for strong approximation in two space dimensions. 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Salimova, Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 473 (2017)."},"publication":"Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences","date_published":"2017-11-01T00:00:00Z","article_number":"0104","publist_id":"7256","ec_funded":1,"year":"2017","department":[{"_id":"JaMa"}],"publisher":"Royal Society of London","publication_status":"published","author":[{"last_name":"Gerencser","first_name":"Mate","id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87","full_name":"Gerencser, Mate"},{"first_name":"Arnulf","last_name":"Jentzen","full_name":"Jentzen, Arnulf"},{"last_name":"Salimova","first_name":"Diyora","full_name":"Salimova, Diyora"}],"volume":473,"date_created":"2018-12-11T11:47:11Z","date_updated":"2021-01-12T08:03:04Z","publication_identifier":{"issn":["13645021"]},"month":"11","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1702.03229"}],"oa":1,"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"quality_controlled":"1","doi":"10.1098/rspa.2017.0104","language":[{"iso":"eng"}]},{"publication_identifier":{"eisbn":["978-1-4704-4194-4"],"isbn":["9-781-4704-3648-3"]},"month":"01","project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804","call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems"}],"quality_controlled":"1","doi":"10.1090/cln/028","language":[{"iso":"eng"}],"ec_funded":1,"publist_id":"7247","year":"2017","publisher":"American Mathematical Society","department":[{"_id":"LaEr"}],"publication_status":"published","author":[{"orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","first_name":"László","full_name":"Erdös, László"},{"last_name":"Yau","first_name":"Horng","full_name":"Yau, Horng"}],"volume":28,"date_updated":"2022-05-24T06:57:28Z","date_created":"2018-12-11T11:47:13Z","series_title":"Courant Lecture Notes","article_processing_charge":"No","day":"01","citation":{"ista":"Erdös L, Yau H. 2017. A Dynamical Approach to Random Matrix Theory, American Mathematical Society, 226p.","ieee":"L. Erdös and H. Yau, A Dynamical Approach to Random Matrix Theory, vol. 28. American Mathematical Society, 2017.","apa":"Erdös, L., & Yau, H. (2017). A Dynamical Approach to Random Matrix Theory (Vol. 28). American Mathematical Society. https://doi.org/10.1090/cln/028","ama":"Erdös L, Yau H. A Dynamical Approach to Random Matrix Theory. Vol 28. American Mathematical Society; 2017. doi:10.1090/cln/028","chicago":"Erdös, László, and Horng Yau. A Dynamical Approach to Random Matrix Theory. Vol. 28. Courant Lecture Notes. American Mathematical Society, 2017. https://doi.org/10.1090/cln/028.","mla":"Erdös, László, and Horng Yau. A Dynamical Approach to Random Matrix Theory. Vol. 28, American Mathematical Society, 2017, doi:10.1090/cln/028.","short":"L. Erdös, H. Yau, A Dynamical Approach to Random Matrix Theory, American Mathematical Society, 2017."},"page":"226","date_published":"2017-01-01T00:00:00Z","type":"book","alternative_title":["Courant Lecture Notes"],"abstract":[{"text":"This book is a concise and self-contained introduction of recent techniques to prove local spectral universality for large random matrices. Random matrix theory is a fast expanding research area, and this book mainly focuses on the methods that the authors participated in developing over the past few years. Many other interesting topics are not included, and neither are several new developments within the framework of these methods. The authors have chosen instead to present key concepts that they believe are the core of these methods and should be relevant for future applications. They keep technicalities to a minimum to make the book accessible to graduate students. With this in mind, they include in this book the basic notions and tools for high-dimensional analysis, such as large deviation, entropy, Dirichlet form, and the logarithmic Sobolev inequality.\r\n","lang":"eng"}],"_id":"567","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 28","title":"A Dynamical Approach to Random Matrix Theory","status":"public","oa_version":"None"},{"language":[{"iso":"eng"}],"doi":"10.4310/HHA.2017.v19.n2.a16","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"},{"grant_number":"701309","_id":"2590DB08-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Atomic-Resolution Structures of Mitochondrial Respiratory Chain Supercomplexes (H2020)"}],"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1507.04310"}],"publication_identifier":{"issn":["15320073"]},"month":"01","volume":19,"date_created":"2018-12-11T11:47:14Z","date_updated":"2021-01-12T08:03:12Z","author":[{"full_name":"Franek, Peter","first_name":"Peter","last_name":"Franek","id":"473294AE-F248-11E8-B48F-1D18A9856A87"},{"id":"33E21118-F248-11E8-B48F-1D18A9856A87","last_name":"Krcál","first_name":"Marek","full_name":"Krcál, Marek"}],"publisher":"International Press","department":[{"_id":"UlWa"},{"_id":"HeEd"}],"publication_status":"published","year":"2017","publist_id":"7246","ec_funded":1,"date_published":"2017-01-01T00:00:00Z","page":"313 - 342","citation":{"ama":"Franek P, Krcál M. Persistence of zero sets. Homology, Homotopy and Applications. 2017;19(2):313-342. doi:10.4310/HHA.2017.v19.n2.a16","ista":"Franek P, Krcál M. 2017. Persistence of zero sets. Homology, Homotopy and Applications. 19(2), 313–342.","apa":"Franek, P., & Krcál, M. (2017). Persistence of zero sets. Homology, Homotopy and Applications. International Press. https://doi.org/10.4310/HHA.2017.v19.n2.a16","ieee":"P. Franek and M. Krcál, “Persistence of zero sets,” Homology, Homotopy and Applications, vol. 19, no. 2. International Press, pp. 313–342, 2017.","mla":"Franek, Peter, and Marek Krcál. “Persistence of Zero Sets.” Homology, Homotopy and Applications, vol. 19, no. 2, International Press, 2017, pp. 313–42, doi:10.4310/HHA.2017.v19.n2.a16.","short":"P. Franek, M. Krcál, Homology, Homotopy and Applications 19 (2017) 313–342.","chicago":"Franek, Peter, and Marek Krcál. “Persistence of Zero Sets.” Homology, Homotopy and Applications. International Press, 2017. https://doi.org/10.4310/HHA.2017.v19.n2.a16."},"publication":"Homology, Homotopy and Applications","day":"01","scopus_import":1,"oa_version":"Submitted Version","intvolume":" 19","status":"public","title":"Persistence of zero sets","_id":"568","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","issue":"2","abstract":[{"text":"We study robust properties of zero sets of continuous maps f: X → ℝn. Formally, we analyze the family Z< r(f) := (g-1(0): ||g - f|| < r) of all zero sets of all continuous maps g closer to f than r in the max-norm. All of these sets are outside A := (x: |f(x)| ≥ r) and we claim that Z< r(f) is fully determined by A and an element of a certain cohomotopy group which (by a recent result) is computable whenever the dimension of X is at most 2n - 3. By considering all r > 0 simultaneously, the pointed cohomotopy groups form a persistence module-a structure leading to persistence diagrams as in the case of persistent homology or well groups. Eventually, we get a descriptor of persistent robust properties of zero sets that has better descriptive power (Theorem A) and better computability status (Theorem B) than the established well diagrams. Moreover, if we endow every point of each zero set with gradients of the perturbation, the robust description of the zero sets by elements of cohomotopy groups is in some sense the best possible (Theorem C).","lang":"eng"}],"type":"journal_article"},{"publication_identifier":{"issn":["2050084X"]},"month":"11","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"},{"grant_number":"648440","_id":"2578D616-B435-11E9-9278-68D0E5697425","name":"Selective Barriers to Horizontal Gene Transfer","call_identifier":"H2020"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.7554/eLife.28921","article_number":"e28921","publist_id":"7244","ec_funded":1,"file_date_updated":"2020-07-14T12:47:10Z","department":[{"_id":"CaGu"},{"_id":"JoBo"},{"_id":"NiBa"}],"publisher":"eLife Sciences Publications","publication_status":"published","year":"2017","volume":6,"date_created":"2018-12-11T11:47:14Z","date_updated":"2021-01-12T08:03:15Z","author":[{"full_name":"Lagator, Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87","last_name":"Lagator","first_name":"Mato"},{"id":"35F0286E-F248-11E8-B48F-1D18A9856A87","last_name":"Sarikas","first_name":"Srdjan","full_name":"Sarikas, Srdjan"},{"full_name":"Acar, Hande","id":"2DDF136A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1986-9753","first_name":"Hande","last_name":"Acar"},{"orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","last_name":"Bollback","first_name":"Jonathan P","full_name":"Bollback, Jonathan P"},{"full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","first_name":"Calin C","last_name":"Guet"}],"scopus_import":1,"has_accepted_license":"1","day":"13","citation":{"ieee":"M. Lagator, S. Sarikas, H. Acar, J. P. Bollback, and C. C. Guet, “Regulatory network structure determines patterns of intermolecular epistasis,” eLife, vol. 6. eLife Sciences Publications, 2017.","apa":"Lagator, M., Sarikas, S., Acar, H., Bollback, J. P., & Guet, C. C. (2017). Regulatory network structure determines patterns of intermolecular epistasis. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.28921","ista":"Lagator M, Sarikas S, Acar H, Bollback JP, Guet CC. 2017. Regulatory network structure determines patterns of intermolecular epistasis. eLife. 6, e28921.","ama":"Lagator M, Sarikas S, Acar H, Bollback JP, Guet CC. Regulatory network structure determines patterns of intermolecular epistasis. eLife. 2017;6. doi:10.7554/eLife.28921","chicago":"Lagator, Mato, Srdjan Sarikas, Hande Acar, Jonathan P Bollback, and Calin C Guet. “Regulatory Network Structure Determines Patterns of Intermolecular Epistasis.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.28921.","short":"M. Lagator, S. Sarikas, H. Acar, J.P. Bollback, C.C. Guet, ELife 6 (2017).","mla":"Lagator, Mato, et al. “Regulatory Network Structure Determines Patterns of Intermolecular Epistasis.” ELife, vol. 6, e28921, eLife Sciences Publications, 2017, doi:10.7554/eLife.28921."},"publication":"eLife","date_published":"2017-11-13T00:00:00Z","type":"journal_article","abstract":[{"text":"Most phenotypes are determined by molecular systems composed of specifically interacting molecules. However, unlike for individual components, little is known about the distributions of mutational effects of molecular systems as a whole. We ask how the distribution of mutational effects of a transcriptional regulatory system differs from the distributions of its components, by first independently, and then simultaneously, mutating a transcription factor and the associated promoter it represses. We find that the system distribution exhibits increased phenotypic variation compared to individual component distributions - an effect arising from intermolecular epistasis between the transcription factor and its DNA-binding site. In large part, this epistasis can be qualitatively attributed to the structure of the transcriptional regulatory system and could therefore be a common feature in prokaryotes. Counter-intuitively, intermolecular epistasis can alleviate the constraints of individual components, thereby increasing phenotypic variation that selection could act on and facilitating adaptive evolution. ","lang":"eng"}],"intvolume":" 6","title":"Regulatory network structure determines patterns of intermolecular epistasis","ddc":["576"],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"570","oa_version":"Published Version","file":[{"checksum":"273ab17f33305e4eaafd911ff88e7c5b","date_updated":"2020-07-14T12:47:10Z","date_created":"2018-12-12T10:14:42Z","file_id":"5096","relation":"main_file","creator":"system","file_size":8453470,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2017-918-v1+1_elife-28921-figures-v3.pdf"},{"relation":"main_file","file_id":"5097","date_created":"2018-12-12T10:14:43Z","date_updated":"2020-07-14T12:47:10Z","checksum":"b433f90576c7be597cd43367946f8e7f","file_name":"IST-2017-918-v1+2_elife-28921-v3.pdf","access_level":"open_access","file_size":1953221,"content_type":"application/pdf","creator":"system"}],"pubrep_id":"918"},{"has_accepted_license":"1","day":"06","scopus_import":1,"date_published":"2017-11-06T00:00:00Z","citation":{"ista":"Spira F, Cuylen Haering S, Mehta S, Samwer M, Reversat A, Verma A, Oldenbourg R, Sixt MK, Gerlich D. 2017. Cytokinesis in vertebrate cells initiates by contraction of an equatorial actomyosin network composed of randomly oriented filaments. eLife. 6, e30867.","ieee":"F. Spira et al., “Cytokinesis in vertebrate cells initiates by contraction of an equatorial actomyosin network composed of randomly oriented filaments,” eLife, vol. 6. eLife Sciences Publications, 2017.","apa":"Spira, F., Cuylen Haering, S., Mehta, S., Samwer, M., Reversat, A., Verma, A., … Gerlich, D. (2017). Cytokinesis in vertebrate cells initiates by contraction of an equatorial actomyosin network composed of randomly oriented filaments. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.30867","ama":"Spira F, Cuylen Haering S, Mehta S, et al. Cytokinesis in vertebrate cells initiates by contraction of an equatorial actomyosin network composed of randomly oriented filaments. eLife. 2017;6. doi:10.7554/eLife.30867","chicago":"Spira, Felix, Sara Cuylen Haering, Shalin Mehta, Matthias Samwer, Anne Reversat, Amitabh Verma, Rudolf Oldenbourg, Michael K Sixt, and Daniel Gerlich. “Cytokinesis in Vertebrate Cells Initiates by Contraction of an Equatorial Actomyosin Network Composed of Randomly Oriented Filaments.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.30867.","mla":"Spira, Felix, et al. “Cytokinesis in Vertebrate Cells Initiates by Contraction of an Equatorial Actomyosin Network Composed of Randomly Oriented Filaments.” ELife, vol. 6, e30867, eLife Sciences Publications, 2017, doi:10.7554/eLife.30867.","short":"F. Spira, S. Cuylen Haering, S. Mehta, M. Samwer, A. Reversat, A. Verma, R. Oldenbourg, M.K. Sixt, D. Gerlich, ELife 6 (2017)."},"publication":"eLife","abstract":[{"lang":"eng","text":"The actomyosin ring generates force to ingress the cytokinetic cleavage furrow in animal cells, yet its filament organization and the mechanism of contractility is not well understood. We quantified actin filament order in human cells using fluorescence polarization microscopy and found that cleavage furrow ingression initiates by contraction of an equatorial actin network with randomly oriented filaments. The network subsequently gradually reoriented actin filaments along the cell equator. This strictly depended on myosin II activity, suggesting local network reorganization by mechanical forces. Cortical laser microsurgery revealed that during cytokinesis progression, mechanical tension increased substantially along the direction of the cell equator, while the network contracted laterally along the pole-to-pole axis without a detectable increase in tension. Our data suggest that an asymmetric increase in cortical tension promotes filament reorientation along the cytokinetic cleavage furrow, which might have implications for diverse other biological processes involving actomyosin rings."}],"type":"journal_article","file":[{"file_size":9666973,"content_type":"application/pdf","creator":"system","file_name":"IST-2017-919-v1+1_elife-30867-figures-v1.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:10Z","date_created":"2018-12-12T10:10:40Z","checksum":"ba09c1451153d39e4f4b7cee013e314c","relation":"main_file","file_id":"4829"},{"file_id":"4830","relation":"main_file","date_created":"2018-12-12T10:10:41Z","date_updated":"2020-07-14T12:47:10Z","checksum":"01eb51f1d6ad679947415a51c988e137","file_name":"IST-2017-919-v1+2_elife-30867-v1.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":5951246}],"oa_version":"Published Version","pubrep_id":"919","intvolume":" 6","title":"Cytokinesis 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Shalin"},{"full_name":"Samwer, Matthias","last_name":"Samwer","first_name":"Matthias"},{"last_name":"Reversat","first_name":"Anne","orcid":"0000-0003-0666-8928","id":"35B76592-F248-11E8-B48F-1D18A9856A87","full_name":"Reversat, Anne"},{"full_name":"Verma, Amitabh","first_name":"Amitabh","last_name":"Verma"},{"full_name":"Oldenbourg, Rudolf","first_name":"Rudolf","last_name":"Oldenbourg"},{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt"},{"last_name":"Gerlich","first_name":"Daniel","full_name":"Gerlich, Daniel"}],"department":[{"_id":"MiSi"}],"publisher":"eLife Sciences Publications","publication_status":"published","year":"2017"},{"publication_identifier":{"issn":["00928674"]},"month":"11","language":[{"iso":"eng"}],"doi":"10.1016/j.cell.2017.11.001","project":[{"grant_number":"747687","_id":"260AA4E2-B435-11E9-9278-68D0E5697425","name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells","call_identifier":"H2020"}],"quality_controlled":"1","ec_funded":1,"publist_id":"7243","volume":171,"date_updated":"2021-01-12T08:03:15Z","date_created":"2018-12-11T11:47:15Z","author":[{"first_name":"Florian R","last_name":"Gärtner","id":"397A88EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6120-3723","full_name":"Gärtner, Florian R"},{"full_name":"Ahmad, Zerkah","last_name":"Ahmad","first_name":"Zerkah"},{"full_name":"Rosenberger, Gerhild","first_name":"Gerhild","last_name":"Rosenberger"},{"full_name":"Fan, Shuxia","last_name":"Fan","first_name":"Shuxia"},{"full_name":"Nicolai, Leo","first_name":"Leo","last_name":"Nicolai"},{"first_name":"Benjamin","last_name":"Busch","full_name":"Busch, Benjamin"},{"last_name":"Yavuz","first_name":"Gökce","full_name":"Yavuz, Gökce"},{"first_name":"Manja","last_name":"Luckner","full_name":"Luckner, Manja"},{"full_name":"Ishikawa Ankerhold, Hellen","first_name":"Hellen","last_name":"Ishikawa Ankerhold"},{"last_name":"Hennel","first_name":"Roman","full_name":"Hennel, Roman"},{"last_name":"Benechet","first_name":"Alexandre","full_name":"Benechet, Alexandre"},{"full_name":"Lorenz, Michael","last_name":"Lorenz","first_name":"Michael"},{"full_name":"Chandraratne, Sue","last_name":"Chandraratne","first_name":"Sue"},{"last_name":"Schubert","first_name":"Irene","full_name":"Schubert, Irene"},{"full_name":"Helmer, Sebastian","last_name":"Helmer","first_name":"Sebastian"},{"last_name":"Striednig","first_name":"Bianca","full_name":"Striednig, Bianca"},{"full_name":"Stark, Konstantin","last_name":"Stark","first_name":"Konstantin"},{"full_name":"Janko, Marek","last_name":"Janko","first_name":"Marek"},{"full_name":"Böttcher, Ralph","first_name":"Ralph","last_name":"Böttcher"},{"first_name":"Admar","last_name":"Verschoor","full_name":"Verschoor, Admar"},{"first_name":"Catherine","last_name":"Leon","full_name":"Leon, Catherine"},{"first_name":"Christian","last_name":"Gachet","full_name":"Gachet, Christian"},{"full_name":"Gudermann, Thomas","last_name":"Gudermann","first_name":"Thomas"},{"full_name":"Mederos Y Schnitzler, Michael","last_name":"Mederos Y Schnitzler","first_name":"Michael"},{"full_name":"Pincus, Zachary","last_name":"Pincus","first_name":"Zachary"},{"full_name":"Iannacone, Matteo","first_name":"Matteo","last_name":"Iannacone"},{"first_name":"Rainer","last_name":"Haas","full_name":"Haas, Rainer"},{"full_name":"Wanner, Gerhard","first_name":"Gerhard","last_name":"Wanner"},{"first_name":"Kirsten","last_name":"Lauber","full_name":"Lauber, Kirsten"},{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K"},{"last_name":"Massberg","first_name":"Steffen","full_name":"Massberg, Steffen"}],"department":[{"_id":"MiSi"}],"publisher":"Cell Press","publication_status":"published","year":"2017","day":"30","scopus_import":1,"date_published":"2017-11-30T00:00:00Z","page":"1368 - 1382","citation":{"mla":"Gärtner, Florian R., et al. “Migrating Platelets Are Mechano Scavengers That Collect and Bundle Bacteria.” Cell Press, vol. 171, no. 6, Cell Press, 2017, pp. 1368–82, doi:10.1016/j.cell.2017.11.001.","short":"F.R. Gärtner, Z. Ahmad, G. Rosenberger, S. Fan, L. Nicolai, B. Busch, G. Yavuz, M. Luckner, H. Ishikawa Ankerhold, R. Hennel, A. Benechet, M. Lorenz, S. Chandraratne, I. Schubert, S. Helmer, B. Striednig, K. Stark, M. Janko, R. Böttcher, A. Verschoor, C. Leon, C. Gachet, T. Gudermann, M. Mederos Y Schnitzler, Z. Pincus, M. Iannacone, R. Haas, G. Wanner, K. Lauber, M.K. Sixt, S. Massberg, Cell Press 171 (2017) 1368–1382.","chicago":"Gärtner, Florian R, Zerkah Ahmad, Gerhild Rosenberger, Shuxia Fan, Leo Nicolai, Benjamin Busch, Gökce Yavuz, et al. “Migrating Platelets Are Mechano Scavengers That Collect and Bundle Bacteria.” Cell Press. Cell Press, 2017. https://doi.org/10.1016/j.cell.2017.11.001.","ama":"Gärtner FR, Ahmad Z, Rosenberger G, et al. Migrating platelets are mechano scavengers that collect and bundle bacteria. Cell Press. 2017;171(6):1368-1382. doi:10.1016/j.cell.2017.11.001","ista":"Gärtner FR, Ahmad Z, Rosenberger G, Fan S, Nicolai L, Busch B, Yavuz G, Luckner M, Ishikawa Ankerhold H, Hennel R, Benechet A, Lorenz M, Chandraratne S, Schubert I, Helmer S, Striednig B, Stark K, Janko M, Böttcher R, Verschoor A, Leon C, Gachet C, Gudermann T, Mederos Y Schnitzler M, Pincus Z, Iannacone M, Haas R, Wanner G, Lauber K, Sixt MK, Massberg S. 2017. Migrating platelets are mechano scavengers that collect and bundle bacteria. Cell Press. 171(6), 1368–1382.","apa":"Gärtner, F. R., Ahmad, Z., Rosenberger, G., Fan, S., Nicolai, L., Busch, B., … Massberg, S. (2017). Migrating platelets are mechano scavengers that collect and bundle bacteria. Cell Press. Cell Press. https://doi.org/10.1016/j.cell.2017.11.001","ieee":"F. R. Gärtner et al., “Migrating platelets are mechano scavengers that collect and bundle bacteria,” Cell Press, vol. 171, no. 6. Cell Press, pp. 1368–1382, 2017."},"publication":"Cell Press","issue":"6","abstract":[{"lang":"eng","text":"Blood platelets are critical for hemostasis and thrombosis and play diverse roles during immune responses. Despite these versatile tasks in mammalian biology, their skills on a cellular level are deemed limited, mainly consisting in rolling, adhesion, and aggregate formation. Here, we identify an unappreciated asset of platelets and show that adherent platelets use adhesion receptors to mechanically probe the adhesive substrate in their local microenvironment. When actomyosin-dependent traction forces overcome substrate resistance, platelets migrate and pile up the adhesive substrate together with any bound particulate material. They use this ability to act as cellular scavengers, scanning the vascular surface for potential invaders and collecting deposited bacteria. Microbe collection by migrating platelets boosts the activity of professional phagocytes, exacerbating inflammatory tissue injury in sepsis. This assigns platelets a central role in innate immune responses and identifies them as potential targets to dampen inflammatory tissue damage in clinical scenarios of severe systemic infection. In addition to their role in thrombosis and hemostasis, platelets can also migrate to sites of infection to help trap bacteria and clear the vascular surface."}],"type":"journal_article","oa_version":"None","intvolume":" 171","status":"public","title":"Migrating platelets are mechano scavengers that collect and bundle bacteria","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"571"},{"day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2017-12-01T00:00:00Z","publication":"International Journal of Molecular Sciences","citation":{"chicago":"Olatunji, Damilola, Danny Geelen, and Inge Verstraeten. “Control of Endogenous Auxin Levels in Plant Root Development.” International Journal of Molecular Sciences. MDPI, 2017. https://doi.org/10.3390/ijms18122587.","mla":"Olatunji, Damilola, et al. “Control of Endogenous Auxin Levels in Plant Root Development.” International Journal of Molecular Sciences, vol. 18, no. 12, 2587, MDPI, 2017, doi:10.3390/ijms18122587.","short":"D. Olatunji, D. Geelen, I. Verstraeten, International Journal of Molecular Sciences 18 (2017).","ista":"Olatunji D, Geelen D, Verstraeten I. 2017. Control of endogenous auxin levels in plant root development. International Journal of Molecular Sciences. 18(12), 2587.","apa":"Olatunji, D., Geelen, D., & Verstraeten, I. (2017). Control of endogenous auxin levels in plant root development. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms18122587","ieee":"D. Olatunji, D. Geelen, and I. Verstraeten, “Control of endogenous auxin levels in plant root development,” International Journal of Molecular Sciences, vol. 18, no. 12. MDPI, 2017.","ama":"Olatunji D, Geelen D, Verstraeten I. Control of endogenous auxin levels in plant root development. International Journal of Molecular Sciences. 2017;18(12). doi:10.3390/ijms18122587"},"abstract":[{"text":"In this review, we summarize the different biosynthesis-related pathways that contribute to the regulation of endogenous auxin in plants. We demonstrate that all known genes involved in auxin biosynthesis also have a role in root formation, from the initiation of a root meristem during embryogenesis to the generation of a functional root system with a primary root, secondary lateral root branches and adventitious roots. Furthermore, the versatile adaptation of root development in response to environmental challenges is mediated by both local and distant control of auxin biosynthesis. In conclusion, auxin homeostasis mediated by spatial and temporal regulation of auxin biosynthesis plays a central role in determining root architecture.","lang":"eng"}],"issue":"12","type":"journal_article","pubrep_id":"917","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"4718","checksum":"82d51f11e493f7eec02976d9a9a9805e","date_updated":"2020-07-14T12:47:10Z","date_created":"2018-12-12T10:08:55Z","access_level":"open_access","file_name":"IST-2017-917-v1+1_ijms-18-02587.pdf","file_size":920962,"content_type":"application/pdf","creator":"system"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"572","title":"Control of endogenous auxin levels in plant root development","status":"public","ddc":["580"],"intvolume":" 18","month":"12","doi":"10.3390/ijms18122587","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","file_date_updated":"2020-07-14T12:47:10Z","publist_id":"7242","article_number":"2587","author":[{"first_name":"Damilola","last_name":"Olatunji","full_name":"Olatunji, Damilola"},{"full_name":"Geelen, Danny","first_name":"Danny","last_name":"Geelen"},{"first_name":"Inge","last_name":"Verstraeten","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7241-2328","full_name":"Verstraeten, Inge"}],"date_created":"2018-12-11T11:47:15Z","date_updated":"2021-01-12T08:03:16Z","volume":18,"year":"2017","publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"MDPI"},{"place":"Cham","extern":"1","department":[{"_id":"HeEd"}],"publisher":"Springer Nature","publication_status":"published","year":"2017","volume":10256,"date_updated":"2022-01-28T07:48:24Z","date_created":"2019-01-08T20:42:56Z","author":[{"full_name":"Biswas, Ranita","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5372-7890","first_name":"Ranita","last_name":"Biswas"},{"first_name":"Partha","last_name":"Bhowmick","full_name":"Bhowmick, Partha"}],"publication_identifier":{"issn":["0302-9743","1611-3349"],"isbn":["978-3-319-59107-0","978-3-319-59108-7"]},"month":"05","quality_controlled":"1","language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-59108-7_8","conference":{"name":"IWCIA: International Workshop on Combinatorial Image Analysis","location":"Plovdiv, Bulgaria","start_date":"2017-06-19","end_date":"2017-06-21"},"alternative_title":["LNCS"],"type":"book_chapter","abstract":[{"text":"Different distance metrics produce Voronoi diagrams with different properties. It is a well-known that on the (real) 2D plane or even on any 3D plane, a Voronoi diagram (VD) based on the Euclidean distance metric produces convex Voronoi regions. In this paper, we first show that this metric produces a persistent VD on the 2D digital plane, as it comprises digitally convex Voronoi regions and hence correctly approximates the corresponding VD on the 2D real plane. Next, we show that on a 3D digital plane D, the Euclidean metric spanning over its voxel set does not guarantee a digital VD which is persistent with the real-space VD. As a solution, we introduce a novel concept of functional-plane-convexity, which is ensured by the Euclidean metric spanning over the pedal set of D. Necessary proofs and some visual result have been provided to adjudge the merit and usefulness of the proposed concept.","lang":"eng"}],"intvolume":" 10256","title":"Construction of persistent Voronoi diagram on 3D digital plane","status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"5803","oa_version":"None","article_processing_charge":"No","day":"17","page":"93-104","citation":{"chicago":"Biswas, Ranita, and Partha Bhowmick. “Construction of Persistent Voronoi Diagram on 3D Digital Plane.” In Combinatorial Image Analysis, 10256:93–104. Cham: Springer Nature, 2017. https://doi.org/10.1007/978-3-319-59108-7_8.","mla":"Biswas, Ranita, and Partha Bhowmick. “Construction of Persistent Voronoi Diagram on 3D Digital Plane.” Combinatorial Image Analysis, vol. 10256, Springer Nature, 2017, pp. 93–104, doi:10.1007/978-3-319-59108-7_8.","short":"R. Biswas, P. Bhowmick, in:, Combinatorial Image Analysis, Springer Nature, Cham, 2017, pp. 93–104.","ista":"Biswas R, Bhowmick P. 2017.Construction of persistent Voronoi diagram on 3D digital plane. In: Combinatorial image analysis. LNCS, vol. 10256, 93–104.","apa":"Biswas, R., & Bhowmick, P. (2017). Construction of persistent Voronoi diagram on 3D digital plane. In Combinatorial image analysis (Vol. 10256, pp. 93–104). Cham: Springer Nature. https://doi.org/10.1007/978-3-319-59108-7_8","ieee":"R. Biswas and P. Bhowmick, “Construction of persistent Voronoi diagram on 3D digital plane,” in Combinatorial image analysis, vol. 10256, Cham: Springer Nature, 2017, pp. 93–104.","ama":"Biswas R, Bhowmick P. Construction of persistent Voronoi diagram on 3D digital plane. In: Combinatorial Image Analysis. Vol 10256. Cham: Springer Nature; 2017:93-104. doi:10.1007/978-3-319-59108-7_8"},"publication":"Combinatorial image analysis","date_published":"2017-05-17T00:00:00Z"},{"_id":"313","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Experimental evidence for Wigner's tunneling time","ddc":["530"],"intvolume":" 999","oa_version":"Published Version","file":[{"file_id":"5871","relation":"main_file","date_updated":"2020-07-14T12:46:00Z","date_created":"2019-01-22T08:34:10Z","checksum":"6e70b525a84f6d5fb175c48e9f5cb59a","file_name":"2017_Physics_Camus.pdf","access_level":"open_access","creator":"dernst","file_size":949321,"content_type":"application/pdf"}],"type":"conference","alternative_title":["Journal of Physics: Conference Series"],"abstract":[{"lang":"eng","text":"Tunneling of a particle through a potential barrier remains one of the most remarkable quantum phenomena. Owing to advances in laser technology, electric fields comparable to those electrons experience in atoms are readily generated and open opportunities to dynamically investigate the process of electron tunneling through the potential barrier formed by the superposition of both laser and atomic fields. Attosecond-time and angstrom-space resolution of the strong laser-field technique allow to address fundamental questions related to tunneling, which are still open and debated: Which time is spent under the barrier and what momentum is picked up by the particle in the meantime? In this combined experimental and theoretical study we demonstrate that for strong-field ionization the leading quantum mechanical Wigner treatment for the time resolved description of tunneling is valid. We achieve a high sensitivity on the tunneling barrier and unambiguously isolate its effects by performing a differential study of two systems with almost identical tunneling geometry. Moreover, working with a low frequency laser, we essentially limit the non-adiabaticity of the process as a major source of uncertainty. The agreement between experiment and theory implies two substantial corrections with respect to the widely employed quasiclassical treatment: In addition to a non-vanishing longitudinal momentum along the laser field-direction we provide clear evidence for a non-zero tunneling time delay. This addresses also the fundamental question how the transition occurs from the tunnel barrier to free space classical evolution of the ejected electron."}],"issue":"1","citation":{"ama":"Camus N, Yakaboylu E, Fechner L, et al. Experimental evidence for Wigner’s tunneling time. In: Vol 999. American Physical Society; 2017. doi:10.1088/1742-6596/999/1/012004","apa":"Camus, N., Yakaboylu, E., Fechner, L., Klaiber, M., Laux, M., Mi, Y., … Moshammer, R. (2017). Experimental evidence for Wigner’s tunneling time (Vol. 999). Presented at the Annual International Laser Physics Workshop LPHYS, Kazan, Russian Federation: American Physical Society. https://doi.org/10.1088/1742-6596/999/1/012004","ieee":"N. Camus et al., “Experimental evidence for Wigner’s tunneling time,” presented at the Annual International Laser Physics Workshop LPHYS, Kazan, Russian Federation, 2017, vol. 999, no. 1.","ista":"Camus N, Yakaboylu E, Fechner L, Klaiber M, Laux M, Mi Y, Hatsagortsyan K, Pfeifer T, Keitel C, Moshammer R. 2017. Experimental evidence for Wigner’s tunneling time. Annual International Laser Physics Workshop LPHYS, Journal of Physics: Conference Series, vol. 999, 012004.","short":"N. Camus, E. Yakaboylu, L. Fechner, M. Klaiber, M. Laux, Y. Mi, K. Hatsagortsyan, T. Pfeifer, C. Keitel, R. Moshammer, in:, American Physical Society, 2017.","mla":"Camus, Nicolas, et al. Experimental Evidence for Wigner’s Tunneling Time. Vol. 999, no. 1, 012004, American Physical Society, 2017, doi:10.1088/1742-6596/999/1/012004.","chicago":"Camus, Nicolas, Enderalp Yakaboylu, Lutz Fechner, Michael Klaiber, Martin Laux, Yonghao Mi, Karen Hatsagortsyan, Thomas Pfeifer, Cristoph Keitel, and Robert Moshammer. “Experimental Evidence for Wigner’s Tunneling Time,” Vol. 999. American Physical Society, 2017. https://doi.org/10.1088/1742-6596/999/1/012004."},"date_published":"2017-07-14T00:00:00Z","scopus_import":1,"day":"14","has_accepted_license":"1","year":"2017","publication_status":"published","department":[{"_id":"MiLe"}],"publisher":"American Physical Society","author":[{"first_name":"Nicolas","last_name":"Camus","full_name":"Camus, Nicolas"},{"orcid":"0000-0001-5973-0874","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87","last_name":"Yakaboylu","first_name":"Enderalp","full_name":"Yakaboylu, Enderalp"},{"full_name":"Fechner, Lutz","first_name":"Lutz","last_name":"Fechner"},{"last_name":"Klaiber","first_name":"Michael","full_name":"Klaiber, Michael"},{"full_name":"Laux, Martin","first_name":"Martin","last_name":"Laux"},{"full_name":"Mi, Yonghao","first_name":"Yonghao","last_name":"Mi"},{"full_name":"Hatsagortsyan, Karen","first_name":"Karen","last_name":"Hatsagortsyan"},{"last_name":"Pfeifer","first_name":"Thomas","full_name":"Pfeifer, Thomas"},{"full_name":"Keitel, Cristoph","first_name":"Cristoph","last_name":"Keitel"},{"last_name":"Moshammer","first_name":"Robert","full_name":"Moshammer, Robert"}],"related_material":{"record":[{"status":"public","relation":"later_version","id":"6013"}]},"date_updated":"2023-02-23T12:36:07Z","date_created":"2018-12-11T11:45:46Z","volume":999,"article_number":"012004","file_date_updated":"2020-07-14T12:46:00Z","publist_id":"7552","external_id":{"arxiv":["1611.03701"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","conference":{"end_date":"2017-08-21","start_date":"2017-08-17","location":"Kazan, Russian Federation","name":"Annual International Laser Physics Workshop LPHYS"},"doi":"10.1088/1742-6596/999/1/012004","language":[{"iso":"eng"}],"month":"07","publication_identifier":{"issn":["17426588"]}},{"article_number":"023201","author":[{"full_name":"Camus, Nicolas","last_name":"Camus","first_name":"Nicolas"},{"full_name":"Yakaboylu, Enderalp","orcid":"0000-0001-5973-0874","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87","last_name":"Yakaboylu","first_name":"Enderalp"},{"full_name":"Fechner, Lutz","last_name":"Fechner","first_name":"Lutz"},{"first_name":"Michael","last_name":"Klaiber","full_name":"Klaiber, Michael"},{"full_name":"Laux, Martin","first_name":"Martin","last_name":"Laux"},{"full_name":"Mi, Yonghao","last_name":"Mi","first_name":"Yonghao"},{"full_name":"Hatsagortsyan, Karen Z.","last_name":"Hatsagortsyan","first_name":"Karen Z."},{"last_name":"Pfeifer","first_name":"Thomas","full_name":"Pfeifer, Thomas"},{"first_name":"Christoph H.","last_name":"Keitel","full_name":"Keitel, Christoph H."},{"first_name":"Robert","last_name":"Moshammer","full_name":"Moshammer, Robert"}],"related_material":{"record":[{"id":"313","relation":"earlier_version","status":"public"}]},"date_updated":"2023-02-23T11:13:36Z","date_created":"2019-02-14T15:24:13Z","volume":119,"year":"2017","publication_status":"published","department":[{"_id":"MiLe"}],"publisher":"American Physical Society","month":"07","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"doi":"10.1103/PhysRevLett.119.023201","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1611.03701","open_access":"1"}],"external_id":{"arxiv":["1611.03701"]},"oa":1,"quality_controlled":"1","abstract":[{"text":"The first hundred attoseconds of the electron dynamics during strong field tunneling ionization are investigated. We quantify theoretically how the electron’s classical trajectories in the continuum emerge from the tunneling process and test the results with those achieved in parallel from attoclock measurements. An especially high sensitivity on the tunneling barrier is accomplished here by comparing the momentum distributions of two atomic species of slightly deviating atomic potentials (argon and krypton) being ionized under absolutely identical conditions with near-infrared laser pulses (1300 nm). The agreement between experiment and theory provides clear evidence for a nonzero tunneling time delay and a nonvanishing longitudinal momentum of the electron at the “tunnel exit.”","lang":"eng"}],"issue":"2","type":"journal_article","oa_version":"Preprint","_id":"6013","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Experimental evidence for quantum tunneling time","intvolume":" 119","day":"14","scopus_import":1,"date_published":"2017-07-14T00:00:00Z","publication":"Physical Review Letters","citation":{"mla":"Camus, Nicolas, et al. “Experimental Evidence for Quantum Tunneling Time.” Physical Review Letters, vol. 119, no. 2, 023201, American Physical Society, 2017, doi:10.1103/PhysRevLett.119.023201.","short":"N. Camus, E. Yakaboylu, L. Fechner, M. Klaiber, M. Laux, Y. Mi, K.Z. Hatsagortsyan, T. Pfeifer, C.H. Keitel, R. Moshammer, Physical Review Letters 119 (2017).","chicago":"Camus, Nicolas, Enderalp Yakaboylu, Lutz Fechner, Michael Klaiber, Martin Laux, Yonghao Mi, Karen Z. Hatsagortsyan, Thomas Pfeifer, Christoph H. Keitel, and Robert Moshammer. “Experimental Evidence for Quantum Tunneling Time.” Physical Review Letters. American Physical Society, 2017. https://doi.org/10.1103/PhysRevLett.119.023201.","ama":"Camus N, Yakaboylu E, Fechner L, et al. Experimental evidence for quantum tunneling time. Physical Review Letters. 2017;119(2). doi:10.1103/PhysRevLett.119.023201","ista":"Camus N, Yakaboylu E, Fechner L, Klaiber M, Laux M, Mi Y, Hatsagortsyan KZ, Pfeifer T, Keitel CH, Moshammer R. 2017. Experimental evidence for quantum tunneling time. Physical Review Letters. 119(2), 023201.","ieee":"N. Camus et al., “Experimental evidence for quantum tunneling time,” Physical Review Letters, vol. 119, no. 2. American Physical Society, 2017.","apa":"Camus, N., Yakaboylu, E., Fechner, L., Klaiber, M., Laux, M., Mi, Y., … Moshammer, R. (2017). Experimental evidence for quantum tunneling time. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.119.023201"}},{"day":"05","scopus_import":1,"date_published":"2017-11-05T00:00:00Z","page":"56 - 81","citation":{"ama":"Brody J, Dziembowski S, Faust S, Pietrzak KZ. Position based cryptography and multiparty communication complexity. In: Kalai Y, Reyzin L, eds. Vol 10677. Springer; 2017:56-81. doi:10.1007/978-3-319-70500-2_3","ista":"Brody J, Dziembowski S, Faust S, Pietrzak KZ. 2017. Position based cryptography and multiparty communication complexity. TCC: Theory of Cryptography Conference, LNCS, vol. 10677, 56–81.","apa":"Brody, J., Dziembowski, S., Faust, S., & Pietrzak, K. Z. (2017). Position based cryptography and multiparty communication complexity. In Y. Kalai & L. Reyzin (Eds.) (Vol. 10677, pp. 56–81). Presented at the TCC: Theory of Cryptography Conference, Baltimore, MD, United States: Springer. https://doi.org/10.1007/978-3-319-70500-2_3","ieee":"J. Brody, S. Dziembowski, S. Faust, and K. Z. Pietrzak, “Position based cryptography and multiparty communication complexity,” presented at the TCC: Theory of Cryptography Conference, Baltimore, MD, United States, 2017, vol. 10677, pp. 56–81.","mla":"Brody, Joshua, et al. Position Based Cryptography and Multiparty Communication Complexity. Edited by Yael Kalai and Leonid Reyzin, vol. 10677, Springer, 2017, pp. 56–81, doi:10.1007/978-3-319-70500-2_3.","short":"J. Brody, S. Dziembowski, S. Faust, K.Z. Pietrzak, in:, Y. Kalai, L. Reyzin (Eds.), Springer, 2017, pp. 56–81.","chicago":"Brody, Joshua, Stefan Dziembowski, Sebastian Faust, and Krzysztof Z Pietrzak. “Position Based Cryptography and Multiparty Communication Complexity.” edited by Yael Kalai and Leonid Reyzin, 10677:56–81. Springer, 2017. https://doi.org/10.1007/978-3-319-70500-2_3."},"abstract":[{"lang":"eng","text":"Position based cryptography (PBC), proposed in the seminal work of Chandran, Goyal, Moriarty, and Ostrovsky (SIAM J. Computing, 2014), aims at constructing cryptographic schemes in which the identity of the user is his geographic position. Chandran et al. construct PBC schemes for secure positioning and position-based key agreement in the bounded-storage model (Maurer, J. Cryptology, 1992). Apart from bounded memory, their security proofs need a strong additional restriction on the power of the adversary: he cannot compute joint functions of his inputs. Removing this assumption is left as an open problem. We show that an answer to this question would resolve a long standing open problem in multiparty communication complexity: finding a function that is hard to compute with low communication complexity in the simultaneous message model, but easy to compute in the fully adaptive model. On a more positive side: we also show some implications in the other direction, i.e.: we prove that lower bounds on the communication complexity of certain multiparty problems imply existence of PBC primitives. Using this result we then show two attractive ways to “bypass” our hardness result: the first uses the random oracle model, the second weakens the locality requirement in the bounded-storage model to online computability. The random oracle construction is arguably one of the simplest proposed so far in this area. Our results indicate that constructing improved provably secure protocols for PBC requires a better understanding of multiparty communication complexity. This is yet another example where negative results in one area (in our case: lower bounds in multiparty communication complexity) can be used to construct secure cryptographic schemes."}],"alternative_title":["LNCS"],"type":"conference","oa_version":"Submitted Version","intvolume":" 10677","title":"Position based cryptography and multiparty communication complexity","status":"public","_id":"605","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"isbn":["978-331970499-9"]},"month":"11","language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-70500-2_3","conference":{"name":"TCC: Theory of Cryptography Conference","end_date":"2017-11-15","location":"Baltimore, MD, United States","start_date":"2017-11-12"},"project":[{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815","call_identifier":"H2020","name":"Teaching Old Crypto New Tricks"}],"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2016/536"}],"ec_funded":1,"publist_id":"7200","volume":10677,"date_created":"2018-12-11T11:47:27Z","date_updated":"2021-01-12T08:05:53Z","author":[{"full_name":"Brody, Joshua","last_name":"Brody","first_name":"Joshua"},{"full_name":"Dziembowski, Stefan","first_name":"Stefan","last_name":"Dziembowski"},{"last_name":"Faust","first_name":"Sebastian","full_name":"Faust, Sebastian"},{"full_name":"Pietrzak, Krzysztof Z","first_name":"Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654"}],"department":[{"_id":"KrPi"}],"editor":[{"full_name":"Kalai, Yael","last_name":"Kalai","first_name":"Yael"},{"full_name":"Reyzin, Leonid","last_name":"Reyzin","first_name":"Leonid"}],"publisher":"Springer","publication_status":"published","year":"2017"},{"intvolume":" 11","status":"public","title":"Molecular impurities interacting with a many-particle environment: From ultracold gases to helium nanodroplets","_id":"604","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","alternative_title":["Theoretical and Computational Chemistry Series"],"type":"book_chapter","abstract":[{"text":"In several settings of physics and chemistry one has to deal with molecules interacting with some kind of an external environment, be it a gas, a solution, or a crystal surface. Understanding molecular processes in the presence of such a many-particle bath is inherently challenging, and usually requires large-scale numerical computations. Here, we present an alternative approach to the problem, based on the notion of the angulon quasiparticle. We show that molecules rotating inside superfluid helium nanodroplets and Bose–Einstein condensates form angulons, and therefore can be described by straightforward solutions of a simple microscopic Hamiltonian. Casting the problem in the language of angulons allows us not only to greatly simplify it, but also to gain insights into the origins of the observed phenomena and to make predictions for future experimental studies.","lang":"eng"}],"page":"444 - 495","citation":{"chicago":"Lemeshko, Mikhail, and Richard Schmidt. “Molecular Impurities Interacting with a Many-Particle Environment: From Ultracold Gases to Helium Nanodroplets.” In Cold Chemistry: Molecular Scattering and Reactivity Near Absolute Zero , edited by Oliver Dulieu and Andreas Osterwalder, 11:444–95. Theoretical and Computational Chemistry Series. The Royal Society of Chemistry, 2017. https://doi.org/10.1039/9781782626800-00444.","mla":"Lemeshko, Mikhail, and Richard Schmidt. “Molecular Impurities Interacting with a Many-Particle Environment: From Ultracold Gases to Helium Nanodroplets.” Cold Chemistry: Molecular Scattering and Reactivity Near Absolute Zero , edited by Oliver Dulieu and Andreas Osterwalder, vol. 11, The Royal Society of Chemistry, 2017, pp. 444–95, doi:10.1039/9781782626800-00444.","short":"M. Lemeshko, R. Schmidt, in:, O. Dulieu, A. Osterwalder (Eds.), Cold Chemistry: Molecular Scattering and Reactivity Near Absolute Zero , The Royal Society of Chemistry, 2017, pp. 444–495.","ista":"Lemeshko M, Schmidt R. 2017.Molecular impurities interacting with a many-particle environment: From ultracold gases to helium nanodroplets. In: Cold Chemistry: Molecular Scattering and Reactivity Near Absolute Zero . Theoretical and Computational Chemistry Series, vol. 11, 444–495.","ieee":"M. Lemeshko and R. Schmidt, “Molecular impurities interacting with a many-particle environment: From ultracold gases to helium nanodroplets,” in Cold Chemistry: Molecular Scattering and Reactivity Near Absolute Zero , vol. 11, O. Dulieu and A. Osterwalder, Eds. The Royal Society of Chemistry, 2017, pp. 444–495.","apa":"Lemeshko, M., & Schmidt, R. (2017). Molecular impurities interacting with a many-particle environment: From ultracold gases to helium nanodroplets. In O. Dulieu & A. Osterwalder (Eds.), Cold Chemistry: Molecular Scattering and Reactivity Near Absolute Zero (Vol. 11, pp. 444–495). The Royal Society of Chemistry. https://doi.org/10.1039/9781782626800-00444","ama":"Lemeshko M, Schmidt R. Molecular impurities interacting with a many-particle environment: From ultracold gases to helium nanodroplets. In: Dulieu O, Osterwalder A, eds. Cold Chemistry: Molecular Scattering and Reactivity Near Absolute Zero . Vol 11. Theoretical and Computational Chemistry Series. The Royal Society of Chemistry; 2017:444-495. doi:10.1039/9781782626800-00444"},"publication":"Cold Chemistry: Molecular Scattering and Reactivity Near Absolute Zero ","date_published":"2017-12-14T00:00:00Z","series_title":"Theoretical and Computational Chemistry Series","scopus_import":1,"day":"14","editor":[{"last_name":"Dulieu","first_name":"Oliver","full_name":"Dulieu, Oliver"},{"first_name":"Andreas","last_name":"Osterwalder","full_name":"Osterwalder, Andreas"}],"publisher":"The Royal Society of Chemistry","department":[{"_id":"MiLe"}],"publication_status":"published","year":"2017","volume":11,"date_created":"2018-12-11T11:47:27Z","date_updated":"2021-01-12T08:05:50Z","author":[{"full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","first_name":"Mikhail"},{"last_name":"Schmidt","first_name":"Richard","full_name":"Schmidt, Richard"}],"publist_id":"7201","quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1703.06753","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1039/9781782626800-00444","publication_identifier":{"issn":["20413181"]},"month":"12"},{"scopus_import":1,"day":"05","citation":{"ama":"Alwen JF, Tackmann B. Moderately hard functions: Definition, instantiations, and applications. In: Kalai Y, Reyzin L, eds. Vol 10677. Springer; 2017:493-526. doi:10.1007/978-3-319-70500-2_17","ista":"Alwen JF, Tackmann B. 2017. Moderately hard functions: Definition, instantiations, and applications. TCC: Theory of Cryptography, LNCS, vol. 10677, 493–526.","apa":"Alwen, J. F., & Tackmann, B. (2017). Moderately hard functions: Definition, instantiations, and applications. In Y. Kalai & L. Reyzin (Eds.) (Vol. 10677, pp. 493–526). Presented at the TCC: Theory of Cryptography, Baltimore, MD, United States: Springer. https://doi.org/10.1007/978-3-319-70500-2_17","ieee":"J. F. Alwen and B. Tackmann, “Moderately hard functions: Definition, instantiations, and applications,” presented at the TCC: Theory of Cryptography, Baltimore, MD, United States, 2017, vol. 10677, pp. 493–526.","mla":"Alwen, Joel F., and Björn Tackmann. Moderately Hard Functions: Definition, Instantiations, and Applications. Edited by Yael Kalai and Leonid Reyzin, vol. 10677, Springer, 2017, pp. 493–526, doi:10.1007/978-3-319-70500-2_17.","short":"J.F. Alwen, B. Tackmann, in:, Y. Kalai, L. Reyzin (Eds.), Springer, 2017, pp. 493–526.","chicago":"Alwen, Joel F, and Björn Tackmann. “Moderately Hard Functions: Definition, Instantiations, and Applications.” edited by Yael Kalai and Leonid Reyzin, 10677:493–526. Springer, 2017. https://doi.org/10.1007/978-3-319-70500-2_17."},"page":"493 - 526","date_published":"2017-11-05T00:00:00Z","type":"conference","alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"Several cryptographic schemes and applications are based on functions that are both reasonably efficient to compute and moderately hard to invert, including client puzzles for Denial-of-Service protection, password protection via salted hashes, or recent proof-of-work blockchain systems. Despite their wide use, a definition of this concept has not yet been distilled and formalized explicitly. Instead, either the applications are proven directly based on the assumptions underlying the function, or some property of the function is proven, but the security of the application is argued only informally. The goal of this work is to provide a (universal) definition that decouples the efforts of designing new moderately hard functions and of building protocols based on them, serving as an interface between the two. On a technical level, beyond the mentioned definitions, we instantiate the model for four different notions of hardness. We extend the work of Alwen and Serbinenko (STOC 2015) by providing a general tool for proving security for the first notion of memory-hard functions that allows for provably secure applications. The tool allows us to recover all of the graph-theoretic techniques developed for proving security under the older, non-composable, notion of security used by Alwen and Serbinenko. As an application of our definition of moderately hard functions, we prove the security of two different schemes for proofs of effort (PoE). We also formalize and instantiate the concept of a non-interactive proof of effort (niPoE), in which the proof is not bound to a particular communication context but rather any bit-string chosen by the prover."}],"_id":"609","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 10677","title":"Moderately hard functions: Definition, instantiations, and applications","status":"public","oa_version":"Submitted Version","publication_identifier":{"isbn":["978-331970499-9"]},"month":"11","oa":1,"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2017/945"}],"quality_controlled":"1","doi":"10.1007/978-3-319-70500-2_17","conference":{"end_date":"2017-11-15","start_date":"2017-11-12","location":"Baltimore, MD, United States","name":"TCC: Theory of Cryptography"},"language":[{"iso":"eng"}],"publist_id":"7196","year":"2017","publisher":"Springer","department":[{"_id":"KrPi"}],"editor":[{"last_name":"Kalai","first_name":"Yael","full_name":"Kalai, Yael"},{"last_name":"Reyzin","first_name":"Leonid","full_name":"Reyzin, Leonid"}],"publication_status":"published","author":[{"full_name":"Alwen, Joel F","last_name":"Alwen","first_name":"Joel F","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tackmann, Björn","first_name":"Björn","last_name":"Tackmann"}],"volume":10677,"date_updated":"2021-01-12T08:06:04Z","date_created":"2018-12-11T11:47:28Z"},{"doi":"10.1007/s11856-017-1607-7","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1610.09063","open_access":"1"}],"oa":1,"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"quality_controlled":"1","month":"10","related_material":{"record":[{"id":"1511","status":"public","relation":"earlier_version"}]},"author":[{"last_name":"Goaoc","first_name":"Xavier","full_name":"Goaoc, Xavier"},{"id":"32BF9DAA-F248-11E8-B48F-1D18A9856A87","first_name":"Isaac","last_name":"Mabillard","full_name":"Mabillard, Isaac"},{"first_name":"Pavel","last_name":"Paták","full_name":"Paták, Pavel"},{"last_name":"Patakova","first_name":"Zuzana","orcid":"0000-0002-3975-1683","id":"48B57058-F248-11E8-B48F-1D18A9856A87","full_name":"Patakova, Zuzana"},{"last_name":"Tancer","first_name":"Martin","orcid":"0000-0002-1191-6714","id":"38AC689C-F248-11E8-B48F-1D18A9856A87","full_name":"Tancer, Martin"},{"full_name":"Wagner, Uli","first_name":"Uli","last_name":"Wagner","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568"}],"volume":222,"date_updated":"2023-02-23T10:02:13Z","date_created":"2018-12-11T11:47:29Z","year":"2017","acknowledgement":"The work by Z. P. was partially supported by the Israel Science Foundation grant ISF-768/12. The work by Z. P. and M. T. was partially supported by the project CE-ITI (GACR P202/12/G061) of the Czech Science Foundation and by the ERC Advanced Grant No. 267165. Part of the research work of M.T. was conducted at IST Austria, supported by an IST Fellowship. The research of P. P. was supported by the ERC Advanced grant no. 320924. The work by I. M. and U. W. was supported by the Swiss National Science Foundation (grants SNSF-200020-138230 and SNSF-PP00P2-138948). The collaboration between U. W. and X. G. was partially supported by the LabEx Bézout (ANR-10-LABX-58).","publisher":"Springer","department":[{"_id":"UlWa"}],"publication_status":"published","ec_funded":1,"publist_id":"7194","date_published":"2017-10-01T00:00:00Z","citation":{"ama":"Goaoc X, Mabillard I, Paták P, Patakova Z, Tancer M, Wagner U. On generalized Heawood inequalities for manifolds: A van Kampen–Flores type nonembeddability result. Israel Journal of Mathematics. 2017;222(2):841-866. doi:10.1007/s11856-017-1607-7","ista":"Goaoc X, Mabillard I, Paták P, Patakova Z, Tancer M, Wagner U. 2017. On generalized Heawood inequalities for manifolds: A van Kampen–Flores type nonembeddability result. Israel Journal of Mathematics. 222(2), 841–866.","ieee":"X. Goaoc, I. Mabillard, P. Paták, Z. Patakova, M. Tancer, and U. Wagner, “On generalized Heawood inequalities for manifolds: A van Kampen–Flores type nonembeddability result,” Israel Journal of Mathematics, vol. 222, no. 2. Springer, pp. 841–866, 2017.","apa":"Goaoc, X., Mabillard, I., Paták, P., Patakova, Z., Tancer, M., & Wagner, U. (2017). On generalized Heawood inequalities for manifolds: A van Kampen–Flores type nonembeddability result. Israel Journal of Mathematics. Springer. https://doi.org/10.1007/s11856-017-1607-7","mla":"Goaoc, Xavier, et al. “On Generalized Heawood Inequalities for Manifolds: A van Kampen–Flores Type Nonembeddability Result.” Israel Journal of Mathematics, vol. 222, no. 2, Springer, 2017, pp. 841–66, doi:10.1007/s11856-017-1607-7.","short":"X. Goaoc, I. Mabillard, P. Paták, Z. Patakova, M. Tancer, U. Wagner, Israel Journal of Mathematics 222 (2017) 841–866.","chicago":"Goaoc, Xavier, Isaac Mabillard, Pavel Paták, Zuzana Patakova, Martin Tancer, and Uli Wagner. “On Generalized Heawood Inequalities for Manifolds: A van Kampen–Flores Type Nonembeddability Result.” Israel Journal of Mathematics. Springer, 2017. https://doi.org/10.1007/s11856-017-1607-7."},"publication":"Israel Journal of Mathematics","page":"841 - 866","day":"01","scopus_import":1,"oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"610","intvolume":" 222","status":"public","title":"On generalized Heawood inequalities for manifolds: A van Kampen–Flores type nonembeddability result","issue":"2","abstract":[{"text":"The fact that the complete graph K5 does not embed in the plane has been generalized in two independent directions. On the one hand, the solution of the classical Heawood problem for graphs on surfaces established that the complete graph Kn embeds in a closed surface M (other than the Klein bottle) if and only if (n−3)(n−4) ≤ 6b1(M), where b1(M) is the first Z2-Betti number of M. On the other hand, van Kampen and Flores proved that the k-skeleton of the n-dimensional simplex (the higher-dimensional analogue of Kn+1) embeds in R2k if and only if n ≤ 2k + 1. Two decades ago, Kühnel conjectured that the k-skeleton of the n-simplex embeds in a compact, (k − 1)-connected 2k-manifold with kth Z2-Betti number bk only if the following generalized Heawood inequality holds: (k+1 n−k−1) ≤ (k+1 2k+1)bk. This is a common generalization of the case of graphs on surfaces as well as the van Kampen–Flores theorem. In the spirit of Kühnel’s conjecture, we prove that if the k-skeleton of the n-simplex embeds in a compact 2k-manifold with kth Z2-Betti number bk, then n ≤ 2bk(k 2k+2)+2k+4. This bound is weaker than the generalized Heawood inequality, but does not require the assumption that M is (k−1)-connected. Our results generalize to maps without q-covered points, in the spirit of Tverberg’s theorem, for q a prime power. Our proof uses a result of Volovikov about maps that satisfy a certain homological triviality condition.","lang":"eng"}],"type":"journal_article"},{"doi":"10.1126/science.aao3526","date_published":"2017-11-17T00:00:00Z","language":[{"iso":"eng"}],"citation":{"mla":"Bradley, Desmond, et al. “Evolution of Flower Color Pattern through Selection on Regulatory Small RNAs.” Science, vol. 358, no. 6365, American Association for the Advancement of Science, 2017, pp. 925–28, doi:10.1126/science.aao3526.","short":"D. Bradley, P. Xu, I. Mohorianu, A. Whibley, D. Field, H. Tavares, M. Couchman, L. Copsey, R. Carpenter, M. Li, Q. Li, Y. Xue, T. Dalmay, E. Coen, Science 358 (2017) 925–928.","chicago":"Bradley, Desmond, Ping Xu, Irina Mohorianu, Annabel Whibley, David Field, Hugo Tavares, Matthew Couchman, et al. “Evolution of Flower Color Pattern through Selection on Regulatory Small RNAs.” Science. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/science.aao3526.","ama":"Bradley D, Xu P, Mohorianu I, et al. Evolution of flower color pattern through selection on regulatory small RNAs. Science. 2017;358(6365):925-928. doi:10.1126/science.aao3526","ista":"Bradley D, Xu P, Mohorianu I, Whibley A, Field D, Tavares H, Couchman M, Copsey L, Carpenter R, Li M, Li Q, Xue Y, Dalmay T, Coen E. 2017. Evolution of flower color pattern through selection on regulatory small RNAs. Science. 358(6365), 925–928.","apa":"Bradley, D., Xu, P., Mohorianu, I., Whibley, A., Field, D., Tavares, H., … Coen, E. (2017). Evolution of flower color pattern through selection on regulatory small RNAs. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aao3526","ieee":"D. Bradley et al., “Evolution of flower color pattern through selection on regulatory small RNAs,” Science, vol. 358, no. 6365. American Association for the Advancement of Science, pp. 925–928, 2017."},"publication":"Science","page":"925 - 928","quality_controlled":"1","publication_identifier":{"issn":["00368075"]},"month":"11","day":"17","scopus_import":1,"author":[{"last_name":"Bradley","first_name":"Desmond","full_name":"Bradley, Desmond"},{"full_name":"Xu, Ping","first_name":"Ping","last_name":"Xu"},{"last_name":"Mohorianu","first_name":"Irina","full_name":"Mohorianu, Irina"},{"first_name":"Annabel","last_name":"Whibley","full_name":"Whibley, Annabel"},{"full_name":"Field, David","first_name":"David","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478"},{"first_name":"Hugo","last_name":"Tavares","full_name":"Tavares, Hugo"},{"last_name":"Couchman","first_name":"Matthew","full_name":"Couchman, Matthew"},{"full_name":"Copsey, Lucy","first_name":"Lucy","last_name":"Copsey"},{"full_name":"Carpenter, Rosemary","last_name":"Carpenter","first_name":"Rosemary"},{"last_name":"Li","first_name":"Miaomiao","full_name":"Li, Miaomiao"},{"full_name":"Li, Qun","first_name":"Qun","last_name":"Li"},{"full_name":"Xue, Yongbiao","last_name":"Xue","first_name":"Yongbiao"},{"full_name":"Dalmay, Tamas","last_name":"Dalmay","first_name":"Tamas"},{"full_name":"Coen, Enrico","first_name":"Enrico","last_name":"Coen"}],"volume":358,"oa_version":"None","date_created":"2018-12-11T11:47:29Z","date_updated":"2021-01-12T08:06:10Z","_id":"611","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2017","department":[{"_id":"NiBa"}],"publisher":"American Association for the Advancement of Science","intvolume":" 358","publication_status":"published","title":"Evolution of flower color pattern through selection on regulatory small RNAs","status":"public","publist_id":"7193","issue":"6365","abstract":[{"lang":"eng","text":"Small RNAs (sRNAs) regulate genes in plants and animals. Here, we show that population-wide differences in color patterns in snapdragon flowers are caused by an inverted duplication that generates sRNAs. The complexity and size of the transcripts indicate that the duplication represents an intermediate on the pathway to microRNA evolution. The sRNAs repress a pigment biosynthesis gene, creating a yellow highlight at the site of pollinator entry. The inverted duplication exhibits steep clines in allele frequency in a natural hybrid zone, showing that the allele is under selection. Thus, regulatory interactions of evolutionarily recent sRNAs can be acted upon by selection and contribute to the evolution of phenotypic diversity."}],"type":"journal_article"},{"date_published":"2017-12-01T00:00:00Z","publication":"Nature Communications","citation":{"chicago":"Chait, Remy P, Jakob Ruess, Tobias Bergmiller, Gašper Tkačik, and Calin C Guet. “Shaping Bacterial Population Behavior through Computer Interfaced Control of Individual Cells.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/s41467-017-01683-1.","short":"R.P. Chait, J. Ruess, T. Bergmiller, G. Tkačik, C.C. Guet, Nature Communications 8 (2017).","mla":"Chait, Remy P., et al. “Shaping Bacterial Population Behavior through Computer Interfaced Control of Individual Cells.” Nature Communications, vol. 8, no. 1, 1535, Nature Publishing Group, 2017, doi:10.1038/s41467-017-01683-1.","apa":"Chait, R. P., Ruess, J., Bergmiller, T., Tkačik, G., & Guet, C. C. (2017). Shaping bacterial population behavior through computer interfaced control of individual cells. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-01683-1","ieee":"R. P. Chait, J. Ruess, T. Bergmiller, G. Tkačik, and C. C. Guet, “Shaping bacterial population behavior through computer interfaced control of individual cells,” Nature Communications, vol. 8, no. 1. Nature Publishing Group, 2017.","ista":"Chait RP, Ruess J, Bergmiller T, Tkačik G, Guet CC. 2017. Shaping bacterial population behavior through computer interfaced control of individual cells. Nature Communications. 8(1), 1535.","ama":"Chait RP, Ruess J, Bergmiller T, Tkačik G, Guet CC. Shaping bacterial population behavior through computer interfaced control of individual cells. Nature Communications. 2017;8(1). doi:10.1038/s41467-017-01683-1"},"day":"01","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","scopus_import":1,"file":[{"date_created":"2018-12-12T10:16:05Z","date_updated":"2020-07-14T12:47:20Z","checksum":"44bb5d0229926c23a9955d9fe0f9723f","file_id":"5190","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":1951699,"file_name":"IST-2017-911-v1+1_s41467-017-01683-1.pdf","access_level":"open_access"}],"oa_version":"Published Version","pubrep_id":"911","status":"public","ddc":["576","579"],"title":"Shaping bacterial population behavior through computer interfaced control of individual cells","intvolume":" 8","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"613","abstract":[{"lang":"eng","text":"Bacteria in groups vary individually, and interact with other bacteria and the environment to produce population-level patterns of gene expression. Investigating such behavior in detail requires measuring and controlling populations at the single-cell level alongside precisely specified interactions and environmental characteristics. Here we present an automated, programmable platform that combines image-based gene expression and growth measurements with on-line optogenetic expression control for hundreds of individual Escherichia coli cells over days, in a dynamically adjustable environment. This integrated platform broadly enables experiments that bridge individual and population behaviors. We demonstrate: (i) population structuring by independent closed-loop control of gene expression in many individual cells, (ii) cell-cell variation control during antibiotic perturbation, (iii) hybrid bio-digital circuits in single cells, and freely specifiable digital communication between individual bacteria. These examples showcase the potential for real-time integration of theoretical models with measurement and control of many individual cells to investigate and engineer microbial population behavior."}],"issue":"1","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1038/s41467-017-01683-1","quality_controlled":"1","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"},{"grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425","name":"Biophysics of information processing in gene regulation","call_identifier":"FWF"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"month":"12","publication_identifier":{"issn":["20411723"]},"date_updated":"2021-01-12T08:06:15Z","date_created":"2018-12-11T11:47:30Z","volume":8,"author":[{"full_name":"Chait, Remy P","id":"3464AE84-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0876-3187","first_name":"Remy P","last_name":"Chait"},{"full_name":"Ruess, Jakob","orcid":"0000-0003-1615-3282","id":"4A245D00-F248-11E8-B48F-1D18A9856A87","last_name":"Ruess","first_name":"Jakob"},{"last_name":"Bergmiller","first_name":"Tobias","orcid":"0000-0001-5396-4346","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","full_name":"Bergmiller, Tobias"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","first_name":"Gasper","last_name":"Tkacik","full_name":"Tkacik, Gasper"},{"full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","first_name":"Calin C","last_name":"Guet"}],"publication_status":"published","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"publisher":"Nature Publishing Group","year":"2017","acknowledgement":"We are grateful to M. Lang, H. Janovjak, M. Khammash, A. Milias-Argeitis, M. Rullan, G. Batt, A. Bosma-Moody, Aryan, S. Leibler, and members of the Guet and Tkačik groups for helpful discussion, comments, and suggestions. We thank A. Moglich, T. Mathes, J. Tabor, and S. Schmidl for kind gifts of strains, and R. Hauschild, B. Knep, M. Lang, T. Asenov, E. Papusheva, T. Menner, T. Adletzberger, and J. Merrin for technical assistance. The research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007–2013) under REA grant agreement no. [291734]. (to R.C. and J.R.), Austrian Science Fund grant FWF P28844 (to G.T.), and internal IST Austria Interdisciplinary Project Support. J.R. acknowledges support from the Agence Nationale de la Recherche (ANR) under Grant Nos. ANR-16-CE33-0018 (MEMIP), ANR-16-CE12-0025 (COGEX) and ANR-10-BINF-06-01 (ICEBERG).","file_date_updated":"2020-07-14T12:47:20Z","ec_funded":1,"publist_id":"7191","article_number":"1535"},{"month":"11","publication_identifier":{"issn":["02460203"]},"quality_controlled":"1","project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804","name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1504.00650"}],"language":[{"iso":"eng"}],"doi":"10.1214/16-AIHP765","publist_id":"7189","ec_funded":1,"publication_status":"published","publisher":"Institute of Mathematical Statistics","department":[{"_id":"LaEr"}],"year":"2017","date_updated":"2021-01-12T08:06:22Z","date_created":"2018-12-11T11:47:30Z","volume":53,"author":[{"full_name":"Erdös, László","last_name":"Erdös","first_name":"László","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Schnelli, Kevin","orcid":"0000-0003-0954-3231","id":"434AD0AE-F248-11E8-B48F-1D18A9856A87","last_name":"Schnelli","first_name":"Kevin"}],"scopus_import":1,"day":"01","page":"1606 - 1656","publication":"Annales de l'institut Henri Poincare (B) Probability and Statistics","citation":{"mla":"Erdös, László, and Kevin Schnelli. “Universality for Random Matrix Flows with Time Dependent Density.” Annales de l’institut Henri Poincare (B) Probability and Statistics, vol. 53, no. 4, Institute of Mathematical Statistics, 2017, pp. 1606–56, doi:10.1214/16-AIHP765.","short":"L. Erdös, K. Schnelli, Annales de l’institut Henri Poincare (B) Probability and Statistics 53 (2017) 1606–1656.","chicago":"Erdös, László, and Kevin Schnelli. “Universality for Random Matrix Flows with Time Dependent Density.” Annales de l’institut Henri Poincare (B) Probability and Statistics. Institute of Mathematical Statistics, 2017. https://doi.org/10.1214/16-AIHP765.","ama":"Erdös L, Schnelli K. Universality for random matrix flows with time dependent density. Annales de l’institut Henri Poincare (B) Probability and Statistics. 2017;53(4):1606-1656. doi:10.1214/16-AIHP765","ista":"Erdös L, Schnelli K. 2017. Universality for random matrix flows with time dependent density. Annales de l’institut Henri Poincare (B) Probability and Statistics. 53(4), 1606–1656.","apa":"Erdös, L., & Schnelli, K. (2017). Universality for random matrix flows with time dependent density. Annales de l’institut Henri Poincare (B) Probability and Statistics. Institute of Mathematical Statistics. https://doi.org/10.1214/16-AIHP765","ieee":"L. Erdös and K. Schnelli, “Universality for random matrix flows with time dependent density,” Annales de l’institut Henri Poincare (B) Probability and Statistics, vol. 53, no. 4. Institute of Mathematical Statistics, pp. 1606–1656, 2017."},"date_published":"2017-11-01T00:00:00Z","type":"journal_article","abstract":[{"text":"We show that the Dyson Brownian Motion exhibits local universality after a very short time assuming that local rigidity and level repulsion of the eigenvalues hold. These conditions are verified, hence bulk spectral universality is proven, for a large class of Wigner-like matrices, including deformed Wigner ensembles and ensembles with non-stochastic variance matrices whose limiting densities differ from Wigner's semicircle law.","lang":"eng"}],"issue":"4","title":"Universality for random matrix flows with time dependent density","status":"public","intvolume":" 53","_id":"615","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version"},{"language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-52498-6_9","quality_controlled":"1","publication_identifier":{"isbn":["978-3-319-52496-2"],"issn":["03015556"]},"month":"05","volume":224,"date_updated":"2021-01-12T08:06:46Z","date_created":"2018-12-11T11:47:33Z","author":[{"last_name":"Hill Yardin","first_name":"Elisa","full_name":"Hill Yardin, Elisa"},{"full_name":"Mckeown, Sonja","first_name":"Sonja","last_name":"Mckeown"},{"first_name":"Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia"},{"full_name":"Grabrucker, Andreas","first_name":"Andreas","last_name":"Grabrucker"}],"department":[{"_id":"GaNo"}],"editor":[{"first_name":"Michael","last_name":"Schmeisser","full_name":"Schmeisser, Michael"},{"full_name":"Boekers, Tobias","last_name":"Boekers","first_name":"Tobias"}],"publisher":"Springer","publication_status":"published","year":"2017","publist_id":"7177","date_published":"2017-05-28T00:00:00Z","page":"159 - 187","citation":{"ama":"Hill Yardin E, Mckeown S, Novarino G, Grabrucker A. Extracerebral dysfunction in animal models of autism spectrum disorder. In: Schmeisser M, Boekers T, eds. Translational Anatomy and Cell Biology of Autism Spectrum Disorder. Vol 224. Advances in Anatomy Embryology and Cell Biology. Springer; 2017:159-187. doi:10.1007/978-3-319-52498-6_9","ista":"Hill Yardin E, Mckeown S, Novarino G, Grabrucker A. 2017.Extracerebral dysfunction in animal models of autism spectrum disorder. In: Translational Anatomy and Cell Biology of Autism Spectrum Disorder. ADVSANAT, vol. 224, 159–187.","ieee":"E. Hill Yardin, S. Mckeown, G. Novarino, and A. Grabrucker, “Extracerebral dysfunction in animal models of autism spectrum disorder,” in Translational Anatomy and Cell Biology of Autism Spectrum Disorder, vol. 224, M. Schmeisser and T. Boekers, Eds. Springer, 2017, pp. 159–187.","apa":"Hill Yardin, E., Mckeown, S., Novarino, G., & Grabrucker, A. (2017). Extracerebral dysfunction in animal models of autism spectrum disorder. In M. Schmeisser & T. Boekers (Eds.), Translational Anatomy and Cell Biology of Autism Spectrum Disorder (Vol. 224, pp. 159–187). Springer. https://doi.org/10.1007/978-3-319-52498-6_9","mla":"Hill Yardin, Elisa, et al. “Extracerebral Dysfunction in Animal Models of Autism Spectrum Disorder.” Translational Anatomy and Cell Biology of Autism Spectrum Disorder, edited by Michael Schmeisser and Tobias Boekers, vol. 224, Springer, 2017, pp. 159–87, doi:10.1007/978-3-319-52498-6_9.","short":"E. Hill Yardin, S. Mckeown, G. Novarino, A. Grabrucker, in:, M. Schmeisser, T. Boekers (Eds.), Translational Anatomy and Cell Biology of Autism Spectrum Disorder, Springer, 2017, pp. 159–187.","chicago":"Hill Yardin, Elisa, Sonja Mckeown, Gaia Novarino, and Andreas Grabrucker. “Extracerebral Dysfunction in Animal Models of Autism Spectrum Disorder.” In Translational Anatomy and Cell Biology of Autism Spectrum Disorder, edited by Michael Schmeisser and Tobias Boekers, 224:159–87. Advances in Anatomy Embryology and Cell Biology. Springer, 2017. https://doi.org/10.1007/978-3-319-52498-6_9."},"publication":"Translational Anatomy and Cell Biology of Autism Spectrum Disorder","day":"28","series_title":"Advances in Anatomy Embryology and Cell Biology","scopus_import":1,"oa_version":"None","intvolume":" 224","title":"Extracerebral dysfunction in animal models of autism spectrum disorder","status":"public","_id":"623","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Genetic factors might be largely responsible for the development of autism spectrum disorder (ASD) that alone or in combination with specific environmental risk factors trigger the pathology. Multiple mutations identified in ASD patients that impair synaptic function in the central nervous system are well studied in animal models. How these mutations might interact with other risk factors is not fully understood though. Additionally, how systems outside of the brain are altered in the context of ASD is an emerging area of research. Extracerebral influences on the physiology could begin in utero and contribute to changes in the brain and in the development of other body systems and further lead to epigenetic changes. Therefore, multiple recent studies have aimed at elucidating the role of gene-environment interactions in ASD. Here we provide an overview on the extracerebral systems that might play an important associative role in ASD and review evidence regarding the potential roles of inflammation, trace metals, metabolism, genetic susceptibility, enteric nervous system function and the microbiota of the gastrointestinal (GI) tract on the development of endophenotypes in animal models of ASD. By influencing environmental conditions, it might be possible to reduce or limit the severity of ASD pathology."}],"alternative_title":["ADVSANAT"],"type":"book_chapter"},{"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"doi":"10.1016/j.tpb.2017.06.001","month":"12","publication_identifier":{"issn":["00405809"]},"publication_status":"published","publisher":"Academic Press","department":[{"_id":"NiBa"}],"year":"2017","date_updated":"2021-01-12T08:06:50Z","date_created":"2018-12-11T11:47:34Z","volume":118,"author":[{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"},{"last_name":"Etheridge","first_name":"Alison","full_name":"Etheridge, Alison"},{"last_name":"Véber","first_name":"Amandine","full_name":"Véber, Amandine"}],"file_date_updated":"2020-07-14T12:47:25Z","publist_id":"7169","ec_funded":1,"page":"50 - 73","publication":"Theoretical Population Biology","citation":{"chicago":"Barton, Nicholas H, Alison Etheridge, and Amandine Véber. “The Infinitesimal Model: Definition Derivation and Implications.” Theoretical Population Biology. Academic Press, 2017. https://doi.org/10.1016/j.tpb.2017.06.001.","mla":"Barton, Nicholas H., et al. “The Infinitesimal Model: Definition Derivation and Implications.” Theoretical Population Biology, vol. 118, Academic Press, 2017, pp. 50–73, doi:10.1016/j.tpb.2017.06.001.","short":"N.H. Barton, A. Etheridge, A. Véber, Theoretical Population Biology 118 (2017) 50–73.","ista":"Barton NH, Etheridge A, Véber A. 2017. The infinitesimal model: Definition derivation and implications. Theoretical Population Biology. 118, 50–73.","apa":"Barton, N. H., Etheridge, A., & Véber, A. (2017). The infinitesimal model: Definition derivation and implications. Theoretical Population Biology. Academic Press. https://doi.org/10.1016/j.tpb.2017.06.001","ieee":"N. H. Barton, A. Etheridge, and A. Véber, “The infinitesimal model: Definition derivation and implications,” Theoretical Population Biology, vol. 118. Academic Press, pp. 50–73, 2017.","ama":"Barton NH, Etheridge A, Véber A. The infinitesimal model: Definition derivation and implications. Theoretical Population Biology. 2017;118:50-73. doi:10.1016/j.tpb.2017.06.001"},"date_published":"2017-12-01T00:00:00Z","scopus_import":1,"day":"01","has_accepted_license":"1","status":"public","ddc":["576"],"title":"The infinitesimal model: Definition derivation and implications","intvolume":" 118","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"626","oa_version":"Published Version","file":[{"file_id":"4964","relation":"main_file","checksum":"7dd02bfcfe8f244f4a6c19091aedf2c8","date_created":"2018-12-12T10:12:45Z","date_updated":"2020-07-14T12:47:25Z","access_level":"open_access","file_name":"IST-2017-908-v1+1_1-s2.0-S0040580917300886-main_1_.pdf","creator":"system","content_type":"application/pdf","file_size":1133924}],"pubrep_id":"908","type":"journal_article","abstract":[{"lang":"eng","text":"Our focus here is on the infinitesimal model. In this model, one or several quantitative traits are described as the sum of a genetic and a non-genetic component, the first being distributed within families as a normal random variable centred at the average of the parental genetic components, and with a variance independent of the parental traits. Thus, the variance that segregates within families is not perturbed by selection, and can be predicted from the variance components. This does not necessarily imply that the trait distribution across the whole population should be Gaussian, and indeed selection or population structure may have a substantial effect on the overall trait distribution. One of our main aims is to identify some general conditions on the allelic effects for the infinitesimal model to be accurate. We first review the long history of the infinitesimal model in quantitative genetics. Then we formulate the model at the phenotypic level in terms of individual trait values and relationships between individuals, but including different evolutionary processes: genetic drift, recombination, selection, mutation, population structure, …. We give a range of examples of its application to evolutionary questions related to stabilising selection, assortative mating, effective population size and response to selection, habitat preference and speciation. We provide a mathematical justification of the model as the limit as the number M of underlying loci tends to infinity of a model with Mendelian inheritance, mutation and environmental noise, when the genetic component of the trait is purely additive. We also show how the model generalises to include epistatic effects. We prove in particular that, within each family, the genetic components of the individual trait values in the current generation are indeed normally distributed with a variance independent of ancestral traits, up to an error of order 1∕M. Simulations suggest that in some cases the convergence may be as fast as 1∕M."}]},{"file_date_updated":"2020-07-14T12:47:25Z","publist_id":"7170","ec_funded":1,"acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grants S11402-N23 and S11407-N23 (RiSE/SHiNE), and Z211-N23 (Wittgenstein Award), ERC Start grant (279307: Graph Games), Vienna Science and Technology Fund (WWTF) through project ICT15-003.","year":"2017","publication_status":"published","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publisher":"Springer","editor":[{"first_name":"Luca","last_name":"Aceto","full_name":"Aceto, Luca"},{"full_name":"Bacci, Giorgio","last_name":"Bacci","first_name":"Giorgio"},{"full_name":"Ingólfsdóttir, Anna","last_name":"Ingólfsdóttir","first_name":"Anna"},{"last_name":"Legay","first_name":"Axel","full_name":"Legay, Axel"},{"last_name":"Mardare","first_name":"Radu","full_name":"Mardare, Radu"}],"author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"full_name":"Doyen, Laurent","first_name":"Laurent","last_name":"Doyen"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger"}],"date_updated":"2022-05-23T08:54:02Z","date_created":"2018-12-11T11:47:34Z","volume":10460,"month":"07","publication_identifier":{"isbn":["978-3-319-63120-2"],"issn":["0302-9743"]},"oa":1,"quality_controlled":"1","project":[{"name":"Moderne Concurrency Paradigms","call_identifier":"FWF","grant_number":"S11402-N23","_id":"25F5A88A-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"}],"doi":"10.1007/978-3-319-63121-9_18","language":[{"iso":"eng"}],"type":"book_chapter","alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"In the analysis of reactive systems a quantitative objective assigns a real value to every trace of the system. The value decision problem for a quantitative objective requires a trace whose value is at least a given threshold, and the exact value decision problem requires a trace whose value is exactly the threshold. We compare the computational complexity of the value and exact value decision problems for classical quantitative objectives, such as sum, discounted sum, energy, and mean-payoff for two standard models of reactive systems, namely, graphs and graph games."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"625","status":"public","ddc":["000"],"title":"The cost of exactness in quantitative reachability","intvolume":" 10460","file":[{"date_updated":"2020-07-14T12:47:25Z","date_created":"2019-11-19T08:06:50Z","checksum":"b2402766ec02c79801aac634bd8f9f6c","relation":"main_file","file_id":"7048","file_size":192826,"content_type":"application/pdf","creator":"dernst","file_name":"2017_ModelsAlgorithms_Chatterjee.pdf","access_level":"open_access"}],"oa_version":"Submitted Version","scopus_import":"1","series_title":"Theoretical Computer Science and General Issues","day":"25","has_accepted_license":"1","article_processing_charge":"No","publication":"Models, Algorithms, Logics and Tools","citation":{"ama":"Chatterjee K, Doyen L, Henzinger TA. The cost of exactness in quantitative reachability. In: Aceto L, Bacci G, Ingólfsdóttir A, Legay A, Mardare R, eds. Models, Algorithms, Logics and Tools. Vol 10460. Theoretical Computer Science and General Issues. Springer; 2017:367-381. doi:10.1007/978-3-319-63121-9_18","ista":"Chatterjee K, Doyen L, Henzinger TA. 2017.The cost of exactness in quantitative reachability. In: Models, Algorithms, Logics and Tools. LNCS, vol. 10460, 367–381.","ieee":"K. Chatterjee, L. Doyen, and T. A. Henzinger, “The cost of exactness in quantitative reachability,” in Models, Algorithms, Logics and Tools, vol. 10460, L. Aceto, G. Bacci, A. Ingólfsdóttir, A. Legay, and R. Mardare, Eds. Springer, 2017, pp. 367–381.","apa":"Chatterjee, K., Doyen, L., & Henzinger, T. A. (2017). The cost of exactness in quantitative reachability. In L. Aceto, G. Bacci, A. Ingólfsdóttir, A. Legay, & R. Mardare (Eds.), Models, Algorithms, Logics and Tools (Vol. 10460, pp. 367–381). Springer. https://doi.org/10.1007/978-3-319-63121-9_18","mla":"Chatterjee, Krishnendu, et al. “The Cost of Exactness in Quantitative Reachability.” Models, Algorithms, Logics and Tools, edited by Luca Aceto et al., vol. 10460, Springer, 2017, pp. 367–81, doi:10.1007/978-3-319-63121-9_18.","short":"K. Chatterjee, L. Doyen, T.A. Henzinger, in:, L. Aceto, G. Bacci, A. Ingólfsdóttir, A. Legay, R. Mardare (Eds.), Models, Algorithms, Logics and Tools, Springer, 2017, pp. 367–381.","chicago":"Chatterjee, Krishnendu, Laurent Doyen, and Thomas A Henzinger. “The Cost of Exactness in Quantitative Reachability.” In Models, Algorithms, Logics and Tools, edited by Luca Aceto, Giorgio Bacci, Anna Ingólfsdóttir, Axel Legay, and Radu Mardare, 10460:367–81. Theoretical Computer Science and General Issues. Springer, 2017. https://doi.org/10.1007/978-3-319-63121-9_18."},"page":"367 - 381","date_published":"2017-07-25T00:00:00Z"},{"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","doi":"10.7717/peerj.3830","language":[{"iso":"eng"}],"month":"09","publication_identifier":{"issn":["21678359"]},"year":"2017","acknowledgement":"Austrian Science Fund (FWF): M1697, P22249; Swiss National Science Foundation (SNF): 145706; European Commission;FWF Special Research Program: RNA-REG F43","publication_status":"published","publisher":"PeerJ","department":[{"_id":"CaGu"}],"author":[{"full_name":"Nikolic, Nela","orcid":"0000-0001-9068-6090","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","last_name":"Nikolic","first_name":"Nela"},{"first_name":"Zrinka","last_name":"Didara","full_name":"Didara, Zrinka"},{"last_name":"Moll","first_name":"Isabella","full_name":"Moll, Isabella"}],"date_created":"2018-12-11T11:47:33Z","date_updated":"2021-01-12T08:06:48Z","volume":2017,"article_number":"3830","file_date_updated":"2020-07-14T12:47:24Z","publist_id":"7172","publication":"PeerJ","citation":{"chicago":"Nikolic, Nela, Zrinka Didara, and Isabella Moll. “MazF Activation Promotes Translational Heterogeneity of the GrcA MRNA in Escherichia Coli Populations.” PeerJ. PeerJ, 2017. https://doi.org/10.7717/peerj.3830.","mla":"Nikolic, Nela, et al. “MazF Activation Promotes Translational Heterogeneity of the GrcA MRNA in Escherichia Coli Populations.” PeerJ, vol. 2017, no. 9, 3830, PeerJ, 2017, doi:10.7717/peerj.3830.","short":"N. Nikolic, Z. Didara, I. Moll, PeerJ 2017 (2017).","ista":"Nikolic N, Didara Z, Moll I. 2017. MazF activation promotes translational heterogeneity of the grcA mRNA in Escherichia coli populations. PeerJ. 2017(9), 3830.","apa":"Nikolic, N., Didara, Z., & Moll, I. (2017). MazF activation promotes translational heterogeneity of the grcA mRNA in Escherichia coli populations. PeerJ. PeerJ. https://doi.org/10.7717/peerj.3830","ieee":"N. Nikolic, Z. Didara, and I. Moll, “MazF activation promotes translational heterogeneity of the grcA mRNA in Escherichia coli populations,” PeerJ, vol. 2017, no. 9. PeerJ, 2017.","ama":"Nikolic N, Didara Z, Moll I. MazF activation promotes translational heterogeneity of the grcA mRNA in Escherichia coli populations. PeerJ. 2017;2017(9). doi:10.7717/peerj.3830"},"date_published":"2017-09-21T00:00:00Z","scopus_import":1,"day":"21","has_accepted_license":"1","_id":"624","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"MazF activation promotes translational heterogeneity of the grcA mRNA in Escherichia coli populations","status":"public","ddc":["579"],"intvolume":" 2017","pubrep_id":"909","file":[{"access_level":"open_access","file_name":"IST-2017-909-v1+1_peerj-3830.pdf","creator":"system","content_type":"application/pdf","file_size":682064,"file_id":"4908","relation":"main_file","checksum":"3d79ae6b6eabc90b0eaaed82ff3493b0","date_created":"2018-12-12T10:11:51Z","date_updated":"2020-07-14T12:47:24Z"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Bacteria adapt to adverse environmental conditions by altering gene expression patterns. Recently, a novel stress adaptation mechanism has been described that allows Escherichia coli to alter gene expression at the post-transcriptional level. The key player in this regulatory pathway is the endoribonuclease MazF, the toxin component of the toxin-antitoxin module mazEF that is triggered by various stressful conditions. In general, MazF degrades the majority of transcripts by cleaving at ACA sites, which results in the retardation of bacterial growth. Furthermore, MazF can process a small subset of mRNAs and render them leaderless by removing their ribosome binding site. MazF concomitantly modifies ribosomes, making them selective for the translation of leaderless mRNAs. In this study, we employed fluorescent reporter-systems to investigate mazEF expression during stressful conditions, and to infer consequences of the mRNA processing mediated by MazF on gene expression at the single-cell level. Our results suggest that mazEF transcription is maintained at low levels in single cells encountering adverse conditions, such as antibiotic stress or amino acid starvation. Moreover, using the grcA mRNA as a model for MazF-mediated mRNA processing, we found that MazF activation promotes heterogeneity in the grcA reporter expression, resulting in a subpopulation of cells with increased levels of GrcA reporter protein."}],"issue":"9"},{"publication_status":"published","publisher":"Springer","department":[{"_id":"KrCh"}],"editor":[{"first_name":"Rupak","last_name":"Majumdar","full_name":"Majumdar, Rupak"},{"last_name":"Kunčak","first_name":"Viktor","full_name":"Kunčak, Viktor"}],"year":"2017","date_updated":"2021-01-12T08:06:55Z","date_created":"2018-12-11T11:47:35Z","volume":10426,"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"last_name":"Fu","first_name":"Hongfei","full_name":"Fu, Hongfei"},{"full_name":"Murhekar, Aniket","last_name":"Murhekar","first_name":"Aniket"}],"ec_funded":1,"publist_id":"7166","quality_controlled":"1","project":[{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","call_identifier":"FWF","name":"Game Theory"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.00314"}],"language":[{"iso":"eng"}],"conference":{"name":"CAV: Computer Aided Verification","end_date":"2017-07-28","location":"Heidelberg, Germany","start_date":"2017-07-24"},"doi":"10.1007/978-3-319-63387-9_6","month":"01","publication_identifier":{"isbn":["978-331963386-2"]},"title":"Automated recurrence analysis for almost linear expected runtime bounds","status":"public","intvolume":" 10426","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"628","oa_version":"Submitted Version","alternative_title":["LNCS"],"type":"conference","abstract":[{"text":"We consider the problem of developing automated techniques for solving recurrence relations to aid the expected-runtime analysis of programs. The motivation is that several classical textbook algorithms have quite efficient expected-runtime complexity, whereas the corresponding worst-case bounds are either inefficient (e.g., Quick-Sort), or completely ineffective (e.g., Coupon-Collector). Since the main focus of expected-runtime analysis is to obtain efficient bounds, we consider bounds that are either logarithmic, linear or almost-linear (O(log n), O(n), O(n · log n), respectively, where n represents the input size). Our main contribution is an efficient (simple linear-time algorithm) sound approach for deriving such expected-runtime bounds for the analysis of recurrence relations induced by randomized algorithms. The experimental results show that our approach can efficiently derive asymptotically optimal expected-runtime bounds for recurrences of classical randomized algorithms, including Randomized-Search, Quick-Sort, Quick-Select, Coupon-Collector, where the worst-case bounds are either inefficient (such as linear as compared to logarithmic expected-runtime complexity, or quadratic as compared to linear or almost-linear expected-runtime complexity), or ineffective.","lang":"eng"}],"page":"118 - 139","citation":{"ama":"Chatterjee K, Fu H, Murhekar A. Automated recurrence analysis for almost linear expected runtime bounds. In: Majumdar R, Kunčak V, eds. Vol 10426. Springer; 2017:118-139. doi:10.1007/978-3-319-63387-9_6","apa":"Chatterjee, K., Fu, H., & Murhekar, A. (2017). Automated recurrence analysis for almost linear expected runtime bounds. In R. Majumdar & V. Kunčak (Eds.) (Vol. 10426, pp. 118–139). Presented at the CAV: Computer Aided Verification, Heidelberg, Germany: Springer. https://doi.org/10.1007/978-3-319-63387-9_6","ieee":"K. Chatterjee, H. Fu, and A. Murhekar, “Automated recurrence analysis for almost linear expected runtime bounds,” presented at the CAV: Computer Aided Verification, Heidelberg, Germany, 2017, vol. 10426, pp. 118–139.","ista":"Chatterjee K, Fu H, Murhekar A. 2017. Automated recurrence analysis for almost linear expected runtime bounds. CAV: Computer Aided Verification, LNCS, vol. 10426, 118–139.","short":"K. Chatterjee, H. Fu, A. Murhekar, in:, R. Majumdar, V. Kunčak (Eds.), Springer, 2017, pp. 118–139.","mla":"Chatterjee, Krishnendu, et al. Automated Recurrence Analysis for Almost Linear Expected Runtime Bounds. Edited by Rupak Majumdar and Viktor Kunčak, vol. 10426, Springer, 2017, pp. 118–39, doi:10.1007/978-3-319-63387-9_6.","chicago":"Chatterjee, Krishnendu, Hongfei Fu, and Aniket Murhekar. “Automated Recurrence Analysis for Almost Linear Expected Runtime Bounds.” edited by Rupak Majumdar and Viktor Kunčak, 10426:118–39. Springer, 2017. https://doi.org/10.1007/978-3-319-63387-9_6."},"date_published":"2017-01-01T00:00:00Z","scopus_import":1,"day":"01"},{"series_title":"Sub-Cellular Biochemistry","scopus_import":1,"day":"13","page":"419 - 444","citation":{"short":"M. Loose, K. Zieske, P. Schwille, in:, Prokaryotic Cytoskeletons, Springer, 2017, pp. 419–444.","mla":"Loose, Martin, et al. “Reconstitution of Protein Dynamics Involved in Bacterial Cell Division.” Prokaryotic Cytoskeletons, vol. 84, Springer, 2017, pp. 419–44, doi:10.1007/978-3-319-53047-5_15.","chicago":"Loose, Martin, Katja Zieske, and Petra Schwille. “Reconstitution of Protein Dynamics Involved in Bacterial Cell Division.” In Prokaryotic Cytoskeletons, 84:419–44. Sub-Cellular Biochemistry. Springer, 2017. https://doi.org/10.1007/978-3-319-53047-5_15.","ama":"Loose M, Zieske K, Schwille P. Reconstitution of protein dynamics involved in bacterial cell division. In: Prokaryotic Cytoskeletons. Vol 84. Sub-Cellular Biochemistry. Springer; 2017:419-444. doi:10.1007/978-3-319-53047-5_15","ieee":"M. Loose, K. Zieske, and P. Schwille, “Reconstitution of protein dynamics involved in bacterial cell division,” in Prokaryotic Cytoskeletons, vol. 84, Springer, 2017, pp. 419–444.","apa":"Loose, M., Zieske, K., & Schwille, P. (2017). Reconstitution of protein dynamics involved in bacterial cell division. In Prokaryotic Cytoskeletons (Vol. 84, pp. 419–444). Springer. https://doi.org/10.1007/978-3-319-53047-5_15","ista":"Loose M, Zieske K, Schwille P. 2017.Reconstitution of protein dynamics involved in bacterial cell division. In: Prokaryotic Cytoskeletons. vol. 84, 419–444."},"publication":"Prokaryotic Cytoskeletons","date_published":"2017-05-13T00:00:00Z","type":"book_chapter","abstract":[{"text":"Even simple cells like bacteria have precisely regulated cellular anatomies, which allow them to grow, divide and to respond to internal or external cues with high fidelity. How spatial and temporal intracellular organization in prokaryotic cells is achieved and maintained on the basis of locally interacting proteins still remains largely a mystery. Bulk biochemical assays with purified components and in vivo experiments help us to approach key cellular processes from two opposite ends, in terms of minimal and maximal complexity. However, to understand how cellular phenomena emerge, that are more than the sum of their parts, we have to assemble cellular subsystems step by step from the bottom up. Here, we review recent in vitro reconstitution experiments with proteins of the bacterial cell division machinery and illustrate how they help to shed light on fundamental cellular mechanisms that constitute spatiotemporal order and regulate cell division.","lang":"eng"}],"intvolume":" 84","status":"public","title":"Reconstitution of protein dynamics involved in bacterial cell division","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"629","oa_version":"None","publication_identifier":{"eisbn":["978-3-319-53047-5"]},"month":"05","quality_controlled":"1","external_id":{"pmid":["28500535"]},"language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-53047-5_15","publist_id":"7165","department":[{"_id":"MaLo"}],"publisher":"Springer","publication_status":"published","pmid":1,"year":"2017","volume":84,"date_created":"2018-12-11T11:47:35Z","date_updated":"2021-01-12T08:06:57Z","author":[{"orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose","first_name":"Martin","full_name":"Loose, Martin"},{"first_name":"Katja","last_name":"Zieske","full_name":"Zieske, Katja"},{"full_name":"Schwille, Petra","last_name":"Schwille","first_name":"Petra"}]},{"alternative_title":["Studies in Health Technology and Informatics"],"type":"conference","abstract":[{"lang":"eng","text":"Background: Standards have become available to share semantically encoded vital parameters from medical devices, as required for example by personal healthcare records. Standardised sharing of biosignal data largely remains open. Objectives: The goal of this work is to explore available biosignal file format and data exchange standards and profiles, and to conceptualise end-To-end solutions. Methods: The authors reviewed and discussed available biosignal file format standards with other members of international standards development organisations (SDOs). Results: A raw concept for standards based acquisition, storage, archiving and sharing of biosignals was developed. The GDF format may serve for storing biosignals. Signals can then be shared using FHIR resources and may be stored on FHIR servers or in DICOM archives, with DICOM waveforms as one possible format. Conclusion: Currently a group of international SDOs (e.g. HL7, IHE, DICOM, IEEE) is engaged in intensive discussions. This discussion extends existing work that already was adopted by large implementer communities. The concept presented here only reports the current status of the discussion in Austria. The discussion will continue internationally, with results to be expected over the coming years."}],"ddc":["005"],"status":"public","title":"Biosignals standards and FHIR: The way to go","intvolume":" 236","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"630","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"IST-2017-906-v1+1_SHTI236-0356.pdf","content_type":"application/pdf","file_size":443635,"creator":"system","relation":"main_file","file_id":"4913","checksum":"1254dcc5b04a996d97fad9a726b42727","date_created":"2018-12-12T10:11:56Z","date_updated":"2020-07-14T12:47:27Z"}],"pubrep_id":"906","scopus_import":1,"day":"01","has_accepted_license":"1","page":"356 - 362","citation":{"apa":"Sauermann, S., David, V., Schlögl, A., Egelkraut, R., Frohner, M., Pohn, B., … Mense, A. (2017). Biosignals standards and FHIR: The way to go (Vol. 236, pp. 356–362). Presented at the eHealth: Health Informatics Meets eHealth, Vienna, Austria: IOS Press. https://doi.org/10.3233/978-1-61499-759-7-356","ieee":"S. Sauermann et al., “Biosignals standards and FHIR: The way to go,” presented at the eHealth: Health Informatics Meets eHealth, Vienna, Austria, 2017, vol. 236, pp. 356–362.","ista":"Sauermann S, David V, Schlögl A, Egelkraut R, Frohner M, Pohn B, Urbauer P, Mense A. 2017. Biosignals standards and FHIR: The way to go. eHealth: Health Informatics Meets eHealth, Studies in Health Technology and Informatics, vol. 236, 356–362.","ama":"Sauermann S, David V, Schlögl A, et al. Biosignals standards and FHIR: The way to go. In: Vol 236. IOS Press; 2017:356-362. doi:10.3233/978-1-61499-759-7-356","chicago":"Sauermann, Stefan, Veronika David, Alois Schlögl, Reinhard Egelkraut, Matthias Frohner, Birgit Pohn, Philipp Urbauer, and Alexander Mense. “Biosignals Standards and FHIR: The Way to Go,” 236:356–62. IOS Press, 2017. https://doi.org/10.3233/978-1-61499-759-7-356.","short":"S. Sauermann, V. David, A. Schlögl, R. Egelkraut, M. Frohner, B. Pohn, P. Urbauer, A. Mense, in:, IOS Press, 2017, pp. 356–362.","mla":"Sauermann, Stefan, et al. Biosignals Standards and FHIR: The Way to Go. Vol. 236, IOS Press, 2017, pp. 356–62, doi:10.3233/978-1-61499-759-7-356."},"date_published":"2017-01-01T00:00:00Z","license":"https://creativecommons.org/licenses/by-nc/4.0/","file_date_updated":"2020-07-14T12:47:27Z","publist_id":"7164","publication_status":"published","department":[{"_id":"ScienComp"},{"_id":"PeJo"}],"publisher":"IOS Press","year":"2017","date_updated":"2021-01-12T08:06:59Z","date_created":"2018-12-11T11:47:36Z","volume":236,"author":[{"last_name":"Sauermann","first_name":"Stefan","full_name":"Sauermann, Stefan"},{"full_name":"David, Veronika","last_name":"David","first_name":"Veronika"},{"orcid":"0000-0002-5621-8100","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","last_name":"Schlögl","first_name":"Alois","full_name":"Schlögl, Alois"},{"last_name":"Egelkraut","first_name":"Reinhard","full_name":"Egelkraut, Reinhard"},{"full_name":"Frohner, Matthias","last_name":"Frohner","first_name":"Matthias"},{"last_name":"Pohn","first_name":"Birgit","full_name":"Pohn, Birgit"},{"last_name":"Urbauer","first_name":"Philipp","full_name":"Urbauer, Philipp"},{"full_name":"Mense, Alexander","last_name":"Mense","first_name":"Alexander"}],"month":"01","publication_identifier":{"isbn":["978-161499758-0"]},"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"language":[{"iso":"eng"}],"conference":{"name":"eHealth: Health Informatics Meets eHealth","end_date":"2017-05-24","start_date":"2017-05-23","location":"Vienna, Austria"},"doi":"10.3233/978-1-61499-759-7-356"},{"month":"01","quality_controlled":"1","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1509.09045","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1090/proc/13468","ec_funded":1,"publist_id":"7160","publication_status":"published","department":[{"_id":"RoSe"}],"publisher":"American Mathematical Society","year":"2017","date_updated":"2021-01-12T08:07:03Z","date_created":"2018-12-11T11:47:36Z","volume":145,"author":[{"full_name":"Lewin, Mathieu","first_name":"Mathieu","last_name":"Lewin"},{"id":"404092F4-F248-11E8-B48F-1D18A9856A87","first_name":"Phan","last_name":"Nam","full_name":"Nam, Phan"},{"full_name":"Rougerie, Nicolas","last_name":"Rougerie","first_name":"Nicolas"}],"scopus_import":1,"day":"01","page":"2441 - 2454","publication":"Proceedings of the American Mathematical Society","citation":{"mla":"Lewin, Mathieu, et al. “A Note on 2D Focusing Many Boson Systems.” Proceedings of the American Mathematical Society, vol. 145, no. 6, American Mathematical Society, 2017, pp. 2441–54, doi:10.1090/proc/13468.","short":"M. Lewin, P. Nam, N. Rougerie, Proceedings of the American Mathematical Society 145 (2017) 2441–2454.","chicago":"Lewin, Mathieu, Phan Nam, and Nicolas Rougerie. “A Note on 2D Focusing Many Boson Systems.” Proceedings of the American Mathematical Society. American Mathematical Society, 2017. https://doi.org/10.1090/proc/13468.","ama":"Lewin M, Nam P, Rougerie N. A note on 2D focusing many boson systems. Proceedings of the American Mathematical Society. 2017;145(6):2441-2454. doi:10.1090/proc/13468","ista":"Lewin M, Nam P, Rougerie N. 2017. A note on 2D focusing many boson systems. Proceedings of the American Mathematical Society. 145(6), 2441–2454.","ieee":"M. Lewin, P. Nam, and N. Rougerie, “A note on 2D focusing many boson systems,” Proceedings of the American Mathematical Society, vol. 145, no. 6. American Mathematical Society, pp. 2441–2454, 2017.","apa":"Lewin, M., Nam, P., & Rougerie, N. (2017). A note on 2D focusing many boson systems. Proceedings of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/proc/13468"},"date_published":"2017-01-01T00:00:00Z","type":"journal_article","abstract":[{"text":"We consider a 2D quantum system of N bosons in a trapping potential |x|s, interacting via a pair potential of the form N2β−1 w(Nβ x). We show that for all 0 < β < (s + 1)/(s + 2), the leading order behavior of ground states of the many-body system is described in the large N limit by the corresponding cubic nonlinear Schrödinger energy functional. Our result covers the focusing case (w < 0) where even the stability of the many-body system is not obvious. This answers an open question mentioned by X. Chen and J. Holmer for harmonic traps (s = 2). Together with the BBGKY hierarchy approach used by these authors, our result implies the convergence of the many-body quantum dynamics to the focusing NLS equation with harmonic trap for all 0 < β < 3/4. ","lang":"eng"}],"issue":"6","title":"A note on 2D focusing many boson systems","status":"public","intvolume":" 145","_id":"632","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version"},{"language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-52498-6_10","quality_controlled":"1","project":[{"name":"Transmembrane Transporters in Health and Disease","call_identifier":"FWF","_id":"25473368-B435-11E9-9278-68D0E5697425","grant_number":"F03523"}],"month":"05","publication_identifier":{"eisbn":["978-3-319-52498-6"]},"date_created":"2018-12-11T11:47:37Z","date_updated":"2021-01-12T08:07:08Z","volume":224,"author":[{"first_name":"Jan","last_name":"Schroeder","full_name":"Schroeder, Jan"},{"last_name":"Deliu","first_name":"Elena","orcid":"0000-0002-7370-5293","id":"37A40D7E-F248-11E8-B48F-1D18A9856A87","full_name":"Deliu, Elena"},{"last_name":"Novarino","first_name":"Gaia","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia"},{"full_name":"Schmeisser, Michael","first_name":"Michael","last_name":"Schmeisser"}],"publication_status":"published","publisher":"Springer","editor":[{"full_name":"Schmeisser, Michael","first_name":"Michael","last_name":"Schmeisser"},{"last_name":"Boekers","first_name":"Tobias","full_name":"Boekers, Tobias"}],"department":[{"_id":"GaNo"}],"year":"2017","publist_id":"7156","date_published":"2017-05-28T00:00:00Z","page":"189 - 211","publication":"Translational Anatomy and Cell Biology of Autism Spectrum Disorder","citation":{"chicago":"Schroeder, Jan, Elena Deliu, Gaia Novarino, and Michael Schmeisser. “Genetic and Pharmacological Reversibility of Phenotypes in Mouse Models of Autism Spectrum Disorder.” In Translational Anatomy and Cell Biology of Autism Spectrum Disorder, edited by Michael Schmeisser and Tobias Boekers, 224:189–211. Advances in Anatomy Embryology and Cell Biology. Springer, 2017. https://doi.org/10.1007/978-3-319-52498-6_10.","short":"J. Schroeder, E. Deliu, G. Novarino, M. Schmeisser, in:, M. Schmeisser, T. Boekers (Eds.), Translational Anatomy and Cell Biology of Autism Spectrum Disorder, Springer, 2017, pp. 189–211.","mla":"Schroeder, Jan, et al. “Genetic and Pharmacological Reversibility of Phenotypes in Mouse Models of Autism Spectrum Disorder.” Translational Anatomy and Cell Biology of Autism Spectrum Disorder, edited by Michael Schmeisser and Tobias Boekers, vol. 224, Springer, 2017, pp. 189–211, doi:10.1007/978-3-319-52498-6_10.","apa":"Schroeder, J., Deliu, E., Novarino, G., & Schmeisser, M. (2017). Genetic and pharmacological reversibility of phenotypes in mouse models of autism spectrum disorder. In M. Schmeisser & T. Boekers (Eds.), Translational Anatomy and Cell Biology of Autism Spectrum Disorder (Vol. 224, pp. 189–211). Springer. https://doi.org/10.1007/978-3-319-52498-6_10","ieee":"J. Schroeder, E. Deliu, G. Novarino, and M. Schmeisser, “Genetic and pharmacological reversibility of phenotypes in mouse models of autism spectrum disorder,” in Translational Anatomy and Cell Biology of Autism Spectrum Disorder, vol. 224, M. Schmeisser and T. Boekers, Eds. Springer, 2017, pp. 189–211.","ista":"Schroeder J, Deliu E, Novarino G, Schmeisser M. 2017.Genetic and pharmacological reversibility of phenotypes in mouse models of autism spectrum disorder. In: Translational Anatomy and Cell Biology of Autism Spectrum Disorder. ADVSANAT, vol. 224, 189–211.","ama":"Schroeder J, Deliu E, Novarino G, Schmeisser M. Genetic and pharmacological reversibility of phenotypes in mouse models of autism spectrum disorder. In: Schmeisser M, Boekers T, eds. Translational Anatomy and Cell Biology of Autism Spectrum Disorder. Vol 224. Advances in Anatomy Embryology and Cell Biology. Springer; 2017:189-211. doi:10.1007/978-3-319-52498-6_10"},"day":"28","series_title":"Advances in Anatomy Embryology and Cell Biology","scopus_import":1,"oa_version":"None","status":"public","title":"Genetic and pharmacological reversibility of phenotypes in mouse models of autism spectrum disorder","intvolume":" 224","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"634","abstract":[{"lang":"eng","text":"As autism spectrum disorder (ASD) is largely regarded as a neurodevelopmental condition, long-time consensus was that its hallmark features are irreversible. However, several studies from recent years using defined mouse models of ASD have provided clear evidence that in mice neurobiological and behavioural alterations can be ameliorated or even reversed by genetic restoration or pharmacological treatment either before or after symptom onset. Here, we review findings on genetic and pharmacological reversibility of phenotypes in mouse models of ASD. Our review should give a comprehensive overview on both aspects and encourage future studies to better understand the underlying molecular mechanisms that might be translatable from animals to humans."}],"alternative_title":["ADVSANAT"],"type":"book_chapter"},{"project":[{"call_identifier":"FWF","name":"Moderne Concurrency Paradigms","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","doi":"10.1007/978-3-319-63501-9_6","conference":{"name":"NSV: Numerical Software Verification","end_date":"2017-07-23","location":"Heidelberg, Germany","start_date":"2017-07-22"},"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-331963500-2"]},"month":"01","year":"2017","editor":[{"first_name":"Alessandro","last_name":"Abate","full_name":"Abate, Alessandro"},{"first_name":"Sylvie","last_name":"Bodo","full_name":"Bodo, Sylvie"}],"publisher":"Springer","department":[{"_id":"ToHe"}],"publication_status":"published","author":[{"first_name":"Stanley","last_name":"Bak","full_name":"Bak, Stanley"},{"orcid":"0000-0002-0686-0365","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","last_name":"Bogomolov","first_name":"Sergiy","full_name":"Bogomolov, Sergiy"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A"},{"full_name":"Kumar, Aviral","last_name":"Kumar","first_name":"Aviral"}],"volume":10381,"date_created":"2018-12-11T11:47:37Z","date_updated":"2021-01-12T08:07:06Z","publist_id":"7159","citation":{"chicago":"Bak, Stanley, Sergiy Bogomolov, Thomas A Henzinger, and Aviral Kumar. “Challenges and Tool Implementation of Hybrid Rapidly Exploring Random Trees.” edited by Alessandro Abate and Sylvie Bodo, 10381:83–89. Springer, 2017. https://doi.org/10.1007/978-3-319-63501-9_6.","mla":"Bak, Stanley, et al. Challenges and Tool Implementation of Hybrid Rapidly Exploring Random Trees. Edited by Alessandro Abate and Sylvie Bodo, vol. 10381, Springer, 2017, pp. 83–89, doi:10.1007/978-3-319-63501-9_6.","short":"S. Bak, S. Bogomolov, T.A. Henzinger, A. Kumar, in:, A. Abate, S. Bodo (Eds.), Springer, 2017, pp. 83–89.","ista":"Bak S, Bogomolov S, Henzinger TA, Kumar A. 2017. Challenges and tool implementation of hybrid rapidly exploring random trees. NSV: Numerical Software Verification, LNCS, vol. 10381, 83–89.","ieee":"S. Bak, S. Bogomolov, T. A. Henzinger, and A. Kumar, “Challenges and tool implementation of hybrid rapidly exploring random trees,” presented at the NSV: Numerical Software Verification, Heidelberg, Germany, 2017, vol. 10381, pp. 83–89.","apa":"Bak, S., Bogomolov, S., Henzinger, T. A., & Kumar, A. (2017). Challenges and tool implementation of hybrid rapidly exploring random trees. In A. Abate & S. Bodo (Eds.) (Vol. 10381, pp. 83–89). Presented at the NSV: Numerical Software Verification, Heidelberg, Germany: Springer. https://doi.org/10.1007/978-3-319-63501-9_6","ama":"Bak S, Bogomolov S, Henzinger TA, Kumar A. Challenges and tool implementation of hybrid rapidly exploring random trees. In: Abate A, Bodo S, eds. Vol 10381. Springer; 2017:83-89. doi:10.1007/978-3-319-63501-9_6"},"page":"83 - 89","date_published":"2017-01-01T00:00:00Z","scopus_import":1,"day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"633","intvolume":" 10381","status":"public","title":"Challenges and tool implementation of hybrid rapidly exploring random trees","oa_version":"None","type":"conference","alternative_title":["LNCS"],"abstract":[{"text":"A Rapidly-exploring Random Tree (RRT) is an algorithm which can search a non-convex region of space by incrementally building a space-filling tree. The tree is constructed from random points drawn from system’s state space and is biased to grow towards large unexplored areas in the system. RRT can provide better coverage of a system’s possible behaviors compared with random simulations, but is more lightweight than full reachability analysis. In this paper, we explore some of the design decisions encountered while implementing a hybrid extension of the RRT algorithm, which have not been elaborated on before. In particular, we focus on handling non-determinism, which arises due to discrete transitions. We introduce the notion of important points to account for this phenomena. We showcase our ideas using heater and navigation benchmarks.","lang":"eng"}]},{"oa_version":"Submitted Version","title":"Scrypt is maximally memory hard","status":"public","intvolume":" 10212","_id":"635","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Memory-hard functions (MHFs) are hash algorithms whose evaluation cost is dominated by memory cost. As memory, unlike computation, costs about the same across different platforms, MHFs cannot be evaluated at significantly lower cost on dedicated hardware like ASICs. MHFs have found widespread applications including password hashing, key derivation, and proofs-of-work. This paper focuses on scrypt, a simple candidate MHF designed by Percival, and described in RFC 7914. It has been used within a number of cryptocurrencies (e.g., Litecoin and Dogecoin) and has been an inspiration for Argon2d, one of the winners of the recent password-hashing competition. Despite its popularity, no rigorous lower bounds on its memory complexity are known. We prove that scrypt is optimally memory-hard, i.e., its cumulative memory complexity (cmc) in the parallel random oracle model is Ω(n2w), where w and n are the output length and number of invocations of the underlying hash function, respectively. High cmc is a strong security target for MHFs introduced by Alwen and Serbinenko (STOC’15) which implies high memory cost even for adversaries who can amortize the cost over many evaluations and evaluate the underlying hash functions many times in parallel. Our proof is the first showing optimal memory-hardness for any MHF. Our result improves both quantitatively and qualitatively upon the recent work by Alwen et al. (EUROCRYPT’16) who proved a weaker lower bound of Ω(n2w/ log2 n) for a restricted class of adversaries.","lang":"eng"}],"alternative_title":["LNCS"],"type":"conference","date_published":"2017-01-01T00:00:00Z","page":"33 - 62","citation":{"chicago":"Alwen, Joel F, Binchi Chen, Krzysztof Z Pietrzak, Leonid Reyzin, and Stefano Tessaro. “Scrypt Is Maximally Memory Hard.” edited by Jean-Sébastien Coron and Jesper Buus Nielsen, 10212:33–62. Springer, 2017. https://doi.org/10.1007/978-3-319-56617-7_2.","short":"J.F. Alwen, B. Chen, K.Z. Pietrzak, L. Reyzin, S. Tessaro, in:, J.-S. Coron, J. Buus Nielsen (Eds.), Springer, 2017, pp. 33–62.","mla":"Alwen, Joel F., et al. Scrypt Is Maximally Memory Hard. Edited by Jean-Sébastien Coron and Jesper Buus Nielsen, vol. 10212, Springer, 2017, pp. 33–62, doi:10.1007/978-3-319-56617-7_2.","apa":"Alwen, J. F., Chen, B., Pietrzak, K. Z., Reyzin, L., & Tessaro, S. (2017). Scrypt is maximally memory hard. In J.-S. Coron & J. Buus Nielsen (Eds.) (Vol. 10212, pp. 33–62). Presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Paris, France: Springer. https://doi.org/10.1007/978-3-319-56617-7_2","ieee":"J. F. Alwen, B. Chen, K. Z. Pietrzak, L. Reyzin, and S. Tessaro, “Scrypt is maximally memory hard,” presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Paris, France, 2017, vol. 10212, pp. 33–62.","ista":"Alwen JF, Chen B, Pietrzak KZ, Reyzin L, Tessaro S. 2017. Scrypt is maximally memory hard. EUROCRYPT: Theory and Applications of Cryptographic Techniques, LNCS, vol. 10212, 33–62.","ama":"Alwen JF, Chen B, Pietrzak KZ, Reyzin L, Tessaro S. Scrypt is maximally memory hard. In: Coron J-S, Buus Nielsen J, eds. Vol 10212. Springer; 2017:33-62. doi:10.1007/978-3-319-56617-7_2"},"day":"01","scopus_import":1,"date_created":"2018-12-11T11:47:37Z","date_updated":"2021-01-12T08:07:10Z","volume":10212,"author":[{"last_name":"Alwen","first_name":"Joel F","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","full_name":"Alwen, Joel F"},{"full_name":"Chen, Binchi","first_name":"Binchi","last_name":"Chen"},{"full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak","first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Leonid","last_name":"Reyzin","full_name":"Reyzin, Leonid"},{"full_name":"Tessaro, Stefano","first_name":"Stefano","last_name":"Tessaro"}],"publication_status":"published","editor":[{"first_name":"Jean-Sébastien","last_name":"Coron","full_name":"Coron, Jean-Sébastien"},{"full_name":"Buus Nielsen, Jesper","last_name":"Buus Nielsen","first_name":"Jesper"}],"publisher":"Springer","department":[{"_id":"KrPi"}],"year":"2017","ec_funded":1,"publist_id":"7154","language":[{"iso":"eng"}],"conference":{"name":"EUROCRYPT: Theory and Applications of Cryptographic Techniques","end_date":"2017-05-04","location":"Paris, France","start_date":"2017-04-30"},"doi":"10.1007/978-3-319-56617-7_2","quality_controlled":"1","project":[{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815","call_identifier":"H2020","name":"Teaching Old Crypto New Tricks"}],"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2016/989"}],"oa":1,"month":"01","publication_identifier":{"isbn":["978-331956616-0"]}},{"publist_id":"7152","volume":10419,"date_created":"2018-12-11T11:47:38Z","date_updated":"2021-01-12T08:07:14Z","author":[{"full_name":"Bakhirkin, Alexey","last_name":"Bakhirkin","first_name":"Alexey"},{"full_name":"Ferrere, Thomas","orcid":"0000-0001-5199-3143","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","last_name":"Ferrere","first_name":"Thomas"},{"first_name":"Oded","last_name":"Maler","full_name":"Maler, Oded"},{"last_name":"Ulus","first_name":"Dogan","full_name":"Ulus, Dogan"}],"department":[{"_id":"ToHe"}],"editor":[{"last_name":"Abate","first_name":"Alessandro","full_name":"Abate, Alessandro"},{"full_name":"Geeraerts, Gilles","last_name":"Geeraerts","first_name":"Gilles"}],"publisher":"Springer","publication_status":"published","year":"2017","publication_identifier":{"isbn":["978-331965764-6"]},"month":"08","language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-65765-3_11","conference":{"start_date":"2017-09-05","location":"Berlin, Germany","end_date":"2017-09-07","name":"FORMATS: Formal Modelling and Analysis of Timed Systems"},"project":[{"name":"Moderne Concurrency Paradigms","call_identifier":"FWF","grant_number":"S11402-N23","_id":"25F5A88A-B435-11E9-9278-68D0E5697425"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"}],"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://hal.archives-ouvertes.fr/hal-01552132"}],"abstract":[{"lang":"eng","text":"Signal regular expressions can specify sequential properties of real-valued signals based on threshold conditions, regular operations, and duration constraints. In this paper we endow them with a quantitative semantics which indicates how robustly a signal matches or does not match a given expression. First, we show that this semantics is a safe approximation of a distance between the signal and the language defined by the expression. Then, we consider the robust matching problem, that is, computing the quantitative semantics of every segment of a given signal relative to an expression. We present an algorithm that solves this problem for piecewise-constant and piecewise-linear signals and show that for such signals the robustness map is a piecewise-linear function. The availability of an indicator describing how robustly a signal segment matches some regular pattern provides a general framework for quantitative monitoring of cyber-physical systems."}],"alternative_title":["LNCS"],"type":"conference","oa_version":"Submitted Version","intvolume":" 10419","title":"On the quantitative semantics of regular expressions over real-valued signals","status":"public","_id":"636","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","day":"03","scopus_import":1,"date_published":"2017-08-03T00:00:00Z","page":"189 - 206","citation":{"chicago":"Bakhirkin, Alexey, Thomas Ferrere, Oded Maler, and Dogan Ulus. “On the Quantitative Semantics of Regular Expressions over Real-Valued Signals.” edited by Alessandro Abate and Gilles Geeraerts, 10419:189–206. Springer, 2017. https://doi.org/10.1007/978-3-319-65765-3_11.","mla":"Bakhirkin, Alexey, et al. On the Quantitative Semantics of Regular Expressions over Real-Valued Signals. Edited by Alessandro Abate and Gilles Geeraerts, vol. 10419, Springer, 2017, pp. 189–206, doi:10.1007/978-3-319-65765-3_11.","short":"A. Bakhirkin, T. Ferrere, O. Maler, D. Ulus, in:, A. Abate, G. Geeraerts (Eds.), Springer, 2017, pp. 189–206.","ista":"Bakhirkin A, Ferrere T, Maler O, Ulus D. 2017. On the quantitative semantics of regular expressions over real-valued signals. FORMATS: Formal Modelling and Analysis of Timed Systems, LNCS, vol. 10419, 189–206.","apa":"Bakhirkin, A., Ferrere, T., Maler, O., & Ulus, D. (2017). On the quantitative semantics of regular expressions over real-valued signals. In A. Abate & G. Geeraerts (Eds.) (Vol. 10419, pp. 189–206). Presented at the FORMATS: Formal Modelling and Analysis of Timed Systems, Berlin, Germany: Springer. https://doi.org/10.1007/978-3-319-65765-3_11","ieee":"A. Bakhirkin, T. Ferrere, O. Maler, and D. Ulus, “On the quantitative semantics of regular expressions over real-valued signals,” presented at the FORMATS: Formal Modelling and Analysis of Timed Systems, Berlin, Germany, 2017, vol. 10419, pp. 189–206.","ama":"Bakhirkin A, Ferrere T, Maler O, Ulus D. On the quantitative semantics of regular expressions over real-valued signals. In: Abate A, Geeraerts G, eds. Vol 10419. Springer; 2017:189-206. doi:10.1007/978-3-319-65765-3_11"}},{"abstract":[{"lang":"eng","text":"This book constitutes the refereed proceedings of the 9th InternationalWorkshop on Numerical Software Verification, NSV 2016, held in Toronto, ON, Canada in July 2011 - colocated with CAV 2016, the 28th International Conference on Computer Aided Verification.\r\nThe NSV workshop is dedicated to the development of logical and mathematical techniques for the reasoning about programmability and reliability."}],"publist_id":"7150","type":"conference_editor","date_updated":"2022-05-24T07:09:52Z","date_created":"2018-12-11T11:47:38Z","volume":10152,"oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"638","year":"2017","title":"Numerical Software Verification","status":"public","publication_status":"published","editor":[{"last_name":"Bogomolov","first_name":"Sergiy","orcid":"0000-0002-0686-0365","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","full_name":"Bogomolov, Sergiy"},{"full_name":"Martel, Matthieu","first_name":"Matthieu","last_name":"Martel"},{"full_name":"Prabhakar, Pavithra","first_name":"Pavithra","last_name":"Prabhakar"}],"publisher":"Springer","intvolume":" 10152","department":[{"_id":"ToHe"}],"month":"01","day":"01","publication_identifier":{"issn":["0302-9743"],"eisbn":["978-3-319-54292-8"]},"article_processing_charge":"No","series_title":"LNCS","conference":{"end_date":"2016-07-18","location":"Toronto, ON, Canada","start_date":"2016-07-17","name":"NSV: Numerical Software Verification"},"doi":"10.1007/978-3-319-54292-8","date_published":"2017-01-01T00:00:00Z","language":[{"iso":"eng"}],"citation":{"ama":"Bogomolov S, Martel M, Prabhakar P, eds. Numerical Software Verification. Vol 10152. Springer; 2017. doi:10.1007/978-3-319-54292-8","ista":"Bogomolov S, Martel M, Prabhakar P eds. 2017. Numerical Software Verification, Springer,p.","ieee":"S. Bogomolov, M. Martel, and P. Prabhakar, Eds., Numerical Software Verification, vol. 10152. Springer, 2017.","apa":"Bogomolov, S., Martel, M., & Prabhakar, P. (Eds.). (2017). Numerical Software Verification (Vol. 10152). Presented at the NSV: Numerical Software Verification, Toronto, ON, Canada: Springer. https://doi.org/10.1007/978-3-319-54292-8","mla":"Bogomolov, Sergiy, et al., editors. Numerical Software Verification. Vol. 10152, Springer, 2017, doi:10.1007/978-3-319-54292-8.","short":"S. Bogomolov, M. Martel, P. Prabhakar, eds., Numerical Software Verification, Springer, 2017.","chicago":"Bogomolov, Sergiy, Matthieu Martel, and Pavithra Prabhakar, eds. Numerical Software Verification. Vol. 10152. LNCS. Springer, 2017. https://doi.org/10.1007/978-3-319-54292-8."},"quality_controlled":"1"},{"conference":{"name":"EUROCRYPT: Theory and Applications of Cryptographic Techniques","location":"Paris, France","start_date":"2017-04-30","end_date":"2017-05-04"},"doi":"10.1007/978-3-319-56617-7_1","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"https://eprint.iacr.org/2016/875","open_access":"1"}],"quality_controlled":"1","project":[{"name":"Teaching Old Crypto New Tricks","call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815"}],"month":"04","publication_identifier":{"isbn":["978-331956616-0"]},"author":[{"full_name":"Alwen, Joel F","first_name":"Joel F","last_name":"Alwen","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Blocki","first_name":"Jeremiah","full_name":"Blocki, Jeremiah"},{"full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak","first_name":"Krzysztof Z"}],"date_created":"2018-12-11T11:47:39Z","date_updated":"2021-01-12T08:07:22Z","volume":10212,"year":"2017","publication_status":"published","department":[{"_id":"KrPi"}],"publisher":"Springer","editor":[{"full_name":"Coron, Jean-Sébastien","first_name":"Jean-Sébastien","last_name":"Coron"},{"last_name":"Buus Nielsen","first_name":"Jesper","full_name":"Buus Nielsen, Jesper"}],"publist_id":"7148","ec_funded":1,"date_published":"2017-04-01T00:00:00Z","citation":{"ama":"Alwen JF, Blocki J, Pietrzak KZ. Depth-robust graphs and their cumulative memory complexity. In: Coron J-S, Buus Nielsen J, eds. Vol 10212. Springer; 2017:3-32. doi:10.1007/978-3-319-56617-7_1","ista":"Alwen JF, Blocki J, Pietrzak KZ. 2017. Depth-robust graphs and their cumulative memory complexity. EUROCRYPT: Theory and Applications of Cryptographic Techniques, LNCS, vol. 10212, 3–32.","ieee":"J. F. Alwen, J. Blocki, and K. Z. Pietrzak, “Depth-robust graphs and their cumulative memory complexity,” presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Paris, France, 2017, vol. 10212, pp. 3–32.","apa":"Alwen, J. F., Blocki, J., & Pietrzak, K. Z. (2017). Depth-robust graphs and their cumulative memory complexity. In J.-S. Coron & J. Buus Nielsen (Eds.) (Vol. 10212, pp. 3–32). Presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Paris, France: Springer. https://doi.org/10.1007/978-3-319-56617-7_1","mla":"Alwen, Joel F., et al. Depth-Robust Graphs and Their Cumulative Memory Complexity. Edited by Jean-Sébastien Coron and Jesper Buus Nielsen, vol. 10212, Springer, 2017, pp. 3–32, doi:10.1007/978-3-319-56617-7_1.","short":"J.F. Alwen, J. Blocki, K.Z. Pietrzak, in:, J.-S. Coron, J. Buus Nielsen (Eds.), Springer, 2017, pp. 3–32.","chicago":"Alwen, Joel F, Jeremiah Blocki, and Krzysztof Z Pietrzak. “Depth-Robust Graphs and Their Cumulative Memory Complexity.” edited by Jean-Sébastien Coron and Jesper Buus Nielsen, 10212:3–32. Springer, 2017. https://doi.org/10.1007/978-3-319-56617-7_1."},"page":"3 - 32","day":"01","scopus_import":1,"oa_version":"Submitted Version","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"640","status":"public","title":"Depth-robust graphs and their cumulative memory complexity","intvolume":" 10212","abstract":[{"text":"Data-independent Memory Hard Functions (iMHFS) are finding a growing number of applications in security; especially in the domain of password hashing. An important property of a concrete iMHF is specified by fixing a directed acyclic graph (DAG) Gn on n nodes. The quality of that iMHF is then captured by the following two pebbling complexities of Gn: – The parallel cumulative pebbling complexity Π∥cc(Gn) must be as high as possible (to ensure that the amortized cost of computing the function on dedicated hardware is dominated by the cost of memory). – The sequential space-time pebbling complexity Πst(Gn) should be as close as possible to Π∥cc(Gn) (to ensure that using many cores in parallel and amortizing over many instances does not give much of an advantage). In this paper we construct a family of DAGs with best possible parameters in an asymptotic sense, i.e., where Π∥cc(Gn) = Ω(n2/ log(n)) (which matches a known upper bound) and Πst(Gn) is within a constant factor of Π∥cc(Gn). Our analysis relies on a new connection between the pebbling complexity of a DAG and its depth-robustness (DR) – a well studied combinatorial property. We show that high DR is sufficient for high Π∥cc. Alwen and Blocki (CRYPTO’16) showed that high DR is necessary and so, together, these results fully characterize DAGs with high Π∥cc in terms of DR. Complementing these results, we provide new upper and lower bounds on the Π∥cc of several important candidate iMHFs from the literature. We give the first lower bounds on the memory hardness of the Catena and Balloon Hashing functions in a parallel model of computation and we give the first lower bounds of any kind for (a version) of Argon2i. Finally we describe a new class of pebbling attacks improving on those of Alwen and Blocki (CRYPTO’16). By instantiating these attacks we upperbound the Π∥cc of the Password Hashing Competition winner Argon2i and one of the Balloon Hashing functions by O (n1.71). We also show an upper bound of O(n1.625) for the Catena functions and the two remaining Balloon Hashing functions.","lang":"eng"}],"type":"conference","alternative_title":["LNCS"]},{"month":"01","day":"01","publication_identifier":{"isbn":["978-331958770-7"]},"scopus_import":1,"language":[{"iso":"eng"}],"conference":{"name":"SSVM: Scale Space and Variational Methods in Computer Vision","location":"Kolding, Denmark","start_date":"2017-06-04","end_date":"2017-06-08"},"doi":"10.1007/978-3-319-58771-4_26","date_published":"2017-01-01T00:00:00Z","quality_controlled":"1","page":"323 - 334","citation":{"ista":"Trajkovska V, Swoboda P, Åström F, Petra S. 2017. Graphical model parameter learning by inverse linear programming. SSVM: Scale Space and Variational Methods in Computer Vision, LNCS, vol. 10302, 323–334.","ieee":"V. Trajkovska, P. Swoboda, F. Åström, and S. Petra, “Graphical model parameter learning by inverse linear programming,” presented at the SSVM: Scale Space and Variational Methods in Computer Vision, Kolding, Denmark, 2017, vol. 10302, pp. 323–334.","apa":"Trajkovska, V., Swoboda, P., Åström, F., & Petra, S. (2017). Graphical model parameter learning by inverse linear programming. In F. Lauze, Y. Dong, & A. Bjorholm Dahl (Eds.) (Vol. 10302, pp. 323–334). Presented at the SSVM: Scale Space and Variational Methods in Computer Vision, Kolding, Denmark: Springer. https://doi.org/10.1007/978-3-319-58771-4_26","ama":"Trajkovska V, Swoboda P, Åström F, Petra S. Graphical model parameter learning by inverse linear programming. In: Lauze F, Dong Y, Bjorholm Dahl A, eds. Vol 10302. Springer; 2017:323-334. doi:10.1007/978-3-319-58771-4_26","chicago":"Trajkovska, Vera, Paul Swoboda, Freddie Åström, and Stefanie Petra. “Graphical Model Parameter Learning by Inverse Linear Programming.” edited by François Lauze, Yiqiu Dong, and Anders Bjorholm Dahl, 10302:323–34. Springer, 2017. https://doi.org/10.1007/978-3-319-58771-4_26.","mla":"Trajkovska, Vera, et al. Graphical Model Parameter Learning by Inverse Linear Programming. Edited by François Lauze et al., vol. 10302, Springer, 2017, pp. 323–34, doi:10.1007/978-3-319-58771-4_26.","short":"V. Trajkovska, P. Swoboda, F. Åström, S. Petra, in:, F. Lauze, Y. Dong, A. Bjorholm Dahl (Eds.), Springer, 2017, pp. 323–334."},"abstract":[{"lang":"eng","text":"We introduce two novel methods for learning parameters of graphical models for image labelling. The following two tasks underline both methods: (i) perturb model parameters based on given features and ground truth labelings, so as to exactly reproduce these labelings as optima of the local polytope relaxation of the labelling problem; (ii) train a predictor for the perturbed model parameters so that improved model parameters can be applied to the labelling of novel data. Our first method implements task (i) by inverse linear programming and task (ii) using a regressor e.g. a Gaussian process. Our second approach simultaneously solves tasks (i) and (ii) in a joint manner, while being restricted to linearly parameterised predictors. Experiments demonstrate the merits of both approaches."}],"publist_id":"7147","alternative_title":["LNCS"],"type":"conference","date_updated":"2021-01-12T08:07:23Z","date_created":"2018-12-11T11:47:39Z","volume":10302,"oa_version":"None","author":[{"full_name":"Trajkovska, Vera","first_name":"Vera","last_name":"Trajkovska"},{"id":"446560C6-F248-11E8-B48F-1D18A9856A87","last_name":"Swoboda","first_name":"Paul","full_name":"Swoboda, Paul"},{"full_name":"Åström, Freddie","last_name":"Åström","first_name":"Freddie"},{"last_name":"Petra","first_name":"Stefanie","full_name":"Petra, Stefanie"}],"publication_status":"published","status":"public","title":"Graphical model parameter learning by inverse linear programming","publisher":"Springer","intvolume":" 10302","department":[{"_id":"VlKo"}],"editor":[{"last_name":"Lauze","first_name":"François","full_name":"Lauze, François"},{"full_name":"Dong, Yiqiu","last_name":"Dong","first_name":"Yiqiu"},{"last_name":"Bjorholm Dahl","first_name":"Anders","full_name":"Bjorholm Dahl, Anders"}],"_id":"641","year":"2017","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"language":[{"iso":"eng"}],"date_published":"2017-08-04T00:00:00Z","doi":"10.15479/AT:IST-2018-853-v2-2","page":"28","citation":{"chicago":"Henzinger, Thomas A, Bernhard Kragl, and Shaz Qadeer. Synchronizing the Asynchronous. IST Austria, 2017. https://doi.org/10.15479/AT:IST-2018-853-v2-2.","mla":"Henzinger, Thomas A., et al. Synchronizing the Asynchronous. IST Austria, 2017, doi:10.15479/AT:IST-2018-853-v2-2.","short":"T.A. Henzinger, B. Kragl, S. Qadeer, Synchronizing the Asynchronous, IST Austria, 2017.","ista":"Henzinger TA, Kragl B, Qadeer S. 2017. Synchronizing the asynchronous, IST Austria, 28p.","apa":"Henzinger, T. A., Kragl, B., & Qadeer, S. (2017). Synchronizing the asynchronous. IST Austria. https://doi.org/10.15479/AT:IST-2018-853-v2-2","ieee":"T. A. Henzinger, B. Kragl, and S. Qadeer, Synchronizing the asynchronous. IST Austria, 2017.","ama":"Henzinger TA, Kragl B, Qadeer S. Synchronizing the Asynchronous. IST Austria; 2017. doi:10.15479/AT:IST-2018-853-v2-2"},"oa":1,"has_accepted_license":"1","publication_identifier":{"issn":["2664-1690"]},"day":"04","month":"08","file":[{"access_level":"open_access","file_name":"main(1).pdf","creator":"dernst","file_size":971347,"content_type":"application/pdf","file_id":"6431","relation":"main_file","checksum":"b48d42725182d7ca10107a118815f4cf","date_created":"2019-05-13T08:14:44Z","date_updated":"2020-07-14T12:47:30Z"}],"oa_version":"Published Version","date_created":"2019-05-13T08:15:55Z","date_updated":"2023-02-21T16:59:21Z","related_material":{"record":[{"id":"133","relation":"later_version","status":"public"}]},"author":[{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-7745-9117","id":"320FC952-F248-11E8-B48F-1D18A9856A87","last_name":"Kragl","first_name":"Bernhard","full_name":"Kragl, Bernhard"},{"full_name":"Qadeer, Shaz","last_name":"Qadeer","first_name":"Shaz"}],"publisher":"IST Austria","department":[{"_id":"ToHe"}],"status":"public","publication_status":"published","ddc":["000"],"title":"Synchronizing the asynchronous","_id":"6426","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2017","abstract":[{"lang":"eng","text":"Synchronous programs are easy to specify because the side effects of an operation are finished by the time the invocation of the operation returns to the caller. Asynchronous programs, on the other hand, are difficult to specify because there are side effects due to pending computation scheduled as a result of the invocation of an operation. They are also difficult to verify because of the large number of possible interleavings of concurrent asynchronous computation threads. We show that specifications and correctness proofs for asynchronous programs can be structured by introducing the fiction, for proof purposes, that intermediate, non-quiescent states of asynchronous operations can be ignored. Then, the task of specification becomes relatively simple and the task of verification can be naturally decomposed into smaller sub-tasks. The sub-tasks iteratively summarize, guided by the structure of an asynchronous program, the atomic effect of non-atomic operations and the synchronous effect of asynchronous operations. This structuring of specifications and proofs corresponds to the introduction of multiple layers of stepwise refinement for asynchronous programs. We present the first proof rule, called synchronization, to reduce asynchronous invocations on a lower layer to synchronous invocations on a higher layer. We implemented our proof method in CIVL and evaluated it on a collection of benchmark programs."}],"file_date_updated":"2020-07-14T12:47:30Z","alternative_title":["IST Austria Technical Report"],"type":"technical_report"},{"quality_controlled":"1","external_id":{"pmid":["28847140"]},"language":[{"iso":"eng"}],"doi":"10.4077/CJP.2017.BAF469","month":"08","publication_identifier":{"issn":["03044920"]},"publication_status":"published","department":[{"_id":"RySh"}],"publisher":"Chinese Physiological Society","year":"2017","pmid":1,"date_created":"2018-12-11T11:47:40Z","date_updated":"2021-01-12T08:07:28Z","volume":60,"author":[{"first_name":"Wuping","last_name":"Sun","full_name":"Sun, Wuping"},{"id":"34009CFA-F248-11E8-B48F-1D18A9856A87","first_name":"Ming-Zhu","last_name":"Zhai","full_name":"Zhai, Ming-Zhu"},{"full_name":"Zhou, Qian","last_name":"Zhou","first_name":"Qian"},{"full_name":"Qian, Chengrui","first_name":"Chengrui","last_name":"Qian"},{"first_name":"Changyu","last_name":"Jiang","full_name":"Jiang, Changyu"}],"publist_id":"7142","article_type":"original","page":"207 - 214","publication":"Chinese Journal of Physiology","citation":{"chicago":"Sun, Wuping, Ming-Zhu Zhai, Qian Zhou, Chengrui Qian, and Changyu Jiang. “Effects of B Vitamins Overload on Plasma Insulin Level and Hydrogen Peroxide Generation in Rats.” Chinese Journal of Physiology. Chinese Physiological Society, 2017. https://doi.org/10.4077/CJP.2017.BAF469.","short":"W. Sun, M.-Z. Zhai, Q. Zhou, C. Qian, C. Jiang, Chinese Journal of Physiology 60 (2017) 207–214.","mla":"Sun, Wuping, et al. “Effects of B Vitamins Overload on Plasma Insulin Level and Hydrogen Peroxide Generation in Rats.” Chinese Journal of Physiology, vol. 60, no. 4, Chinese Physiological Society, 2017, pp. 207–14, doi:10.4077/CJP.2017.BAF469.","ieee":"W. Sun, M.-Z. Zhai, Q. Zhou, C. Qian, and C. Jiang, “Effects of B vitamins overload on plasma insulin level and hydrogen peroxide generation in rats,” Chinese Journal of Physiology, vol. 60, no. 4. Chinese Physiological Society, pp. 207–214, 2017.","apa":"Sun, W., Zhai, M.-Z., Zhou, Q., Qian, C., & Jiang, C. (2017). Effects of B vitamins overload on plasma insulin level and hydrogen peroxide generation in rats. Chinese Journal of Physiology. Chinese Physiological Society. https://doi.org/10.4077/CJP.2017.BAF469","ista":"Sun W, Zhai M-Z, Zhou Q, Qian C, Jiang C. 2017. Effects of B vitamins overload on plasma insulin level and hydrogen peroxide generation in rats. Chinese Journal of Physiology. 60(4), 207–214.","ama":"Sun W, Zhai M-Z, Zhou Q, Qian C, Jiang C. Effects of B vitamins overload on plasma insulin level and hydrogen peroxide generation in rats. Chinese Journal of Physiology. 2017;60(4):207-214. doi:10.4077/CJP.2017.BAF469"},"date_published":"2017-08-31T00:00:00Z","scopus_import":1,"day":"31","article_processing_charge":"No","status":"public","ddc":["570"],"title":"Effects of B vitamins overload on plasma insulin level and hydrogen peroxide generation in rats","intvolume":" 60","_id":"643","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"It has been reported that nicotinamide-overload induces oxidative stress associated with insulin resistance, the key feature of type 2 diabetes mellitus (T2DM). This study aimed to investigate the effects of B vitamins in T2DM. Glucose tolerance tests (GTT) were carried out in adult Sprague-Dawley rats treated with or without cumulative doses of B vitamins. More specifically, insulin tolerance tests (ITT) were also carried out in adult Sprague-Dawley rats treated with or without cumulative doses of Vitamin B3. We found that cumulative Vitamin B1 and Vitamin B3 administration significantly increased the plasma H2O2 levels associated with high insulin levels. Only Vitamin B3 reduced muscular and hepatic glycogen contents. Cumulative administration of nicotinic acid, another form of Vitamin B3, also significantly increased plasma insulin level and H2O2 generation. Moreover, cumulative administration of nicotinic acid or nicotinamide impaired glucose metabolism. This study suggested that excess Vitamin B1 and Vitamin B3 caused oxidative stress and insulin resistance."}],"issue":"4"},{"publist_id":"7144","author":[{"full_name":"Gerencser, Mate","id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87","first_name":"Mate","last_name":"Gerencser"},{"full_name":"Gyöngy, István","first_name":"István","last_name":"Gyöngy"}],"date_created":"2018-12-11T11:47:40Z","date_updated":"2021-01-12T08:07:26Z","volume":86,"year":"2017","publication_status":"published","publisher":"American Mathematical Society","department":[{"_id":"JaMa"}],"month":"01","publication_identifier":{"issn":["00255718"]},"doi":"10.1090/mcom/3201","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1508.05535"}],"quality_controlled":"1","abstract":[{"lang":"eng","text":"Cauchy problems with SPDEs on the whole space are localized to Cauchy problems on a ball of radius R. This localization reduces various kinds of spatial approximation schemes to finite dimensional problems. The error is shown to be exponentially small. As an application, a numerical scheme is presented which combines the localization and the space and time discretization, and thus is fully implementable."}],"issue":"307","type":"journal_article","oa_version":"Submitted Version","_id":"642","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Localization errors in solving stochastic partial differential equations in the whole space","intvolume":" 86","day":"01","scopus_import":1,"date_published":"2017-01-01T00:00:00Z","publication":"Mathematics of Computation","citation":{"ama":"Gerencser M, Gyöngy I. Localization errors in solving stochastic partial differential equations in the whole space. Mathematics of Computation. 2017;86(307):2373-2397. doi:10.1090/mcom/3201","ieee":"M. Gerencser and I. Gyöngy, “Localization errors in solving stochastic partial differential equations in the whole space,” Mathematics of Computation, vol. 86, no. 307. American Mathematical Society, pp. 2373–2397, 2017.","apa":"Gerencser, M., & Gyöngy, I. (2017). Localization errors in solving stochastic partial differential equations in the whole space. Mathematics of Computation. American Mathematical Society. https://doi.org/10.1090/mcom/3201","ista":"Gerencser M, Gyöngy I. 2017. Localization errors in solving stochastic partial differential equations in the whole space. Mathematics of Computation. 86(307), 2373–2397.","short":"M. Gerencser, I. Gyöngy, Mathematics of Computation 86 (2017) 2373–2397.","mla":"Gerencser, Mate, and István Gyöngy. “Localization Errors in Solving Stochastic Partial Differential Equations in the Whole Space.” Mathematics of Computation, vol. 86, no. 307, American Mathematical Society, 2017, pp. 2373–97, doi:10.1090/mcom/3201.","chicago":"Gerencser, Mate, and István Gyöngy. “Localization Errors in Solving Stochastic Partial Differential Equations in the Whole Space.” Mathematics of Computation. American Mathematical Society, 2017. https://doi.org/10.1090/mcom/3201."},"page":"2373 - 2397"},{"publist_id":"7135","ec_funded":1,"department":[{"_id":"KrCh"}],"publisher":"Springer","editor":[{"full_name":"Majumdar, Rupak","first_name":"Rupak","last_name":"Majumdar"},{"first_name":"Viktor","last_name":"Kunčak","full_name":"Kunčak, Viktor"}],"publication_status":"published","year":"2017","volume":10426,"date_created":"2018-12-11T11:47:41Z","date_updated":"2021-01-12T08:07:32Z","author":[{"full_name":"Ashok, Pranav","last_name":"Ashok","first_name":"Pranav"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"full_name":"Daca, Przemyslaw","id":"49351290-F248-11E8-B48F-1D18A9856A87","first_name":"Przemyslaw","last_name":"Daca"},{"full_name":"Kretinsky, Jan","last_name":"Kretinsky","first_name":"Jan","orcid":"0000-0002-8122-2881","id":"44CEF464-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Meggendorfer","first_name":"Tobias","full_name":"Meggendorfer, Tobias"}],"publication_identifier":{"isbn":["978-331963386-2"]},"month":"07","project":[{"grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification"},{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"}],"quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1705.02326","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-63387-9_10","conference":{"end_date":"2017-07-28","start_date":"2017-07-24","location":"Heidelberg, Germany","name":"CAV: Computer Aided Verification"},"alternative_title":["LNCS"],"type":"conference","abstract":[{"text":"Markov decision processes (MDPs) are standard models for probabilistic systems with non-deterministic behaviours. Long-run average rewards provide a mathematically elegant formalism for expressing long term performance. Value iteration (VI) is one of the simplest and most efficient algorithmic approaches to MDPs with other properties, such as reachability objectives. Unfortunately, a naive extension of VI does not work for MDPs with long-run average rewards, as there is no known stopping criterion. In this work our contributions are threefold. (1) We refute a conjecture related to stopping criteria for MDPs with long-run average rewards. (2) We present two practical algorithms for MDPs with long-run average rewards based on VI. First, we show that a combination of applying VI locally for each maximal end-component (MEC) and VI for reachability objectives can provide approximation guarantees. Second, extending the above approach with a simulation-guided on-demand variant of VI, we present an anytime algorithm that is able to deal with very large models. (3) Finally, we present experimental results showing that our methods significantly outperform the standard approaches on several benchmarks.","lang":"eng"}],"intvolume":" 10426","title":"Value iteration for long run average reward in markov decision processes","status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"645","oa_version":"Submitted Version","scopus_import":1,"day":"13","page":"201 - 221","citation":{"ama":"Ashok P, Chatterjee K, Daca P, Kretinsky J, Meggendorfer T. Value iteration for long run average reward in markov decision processes. In: Majumdar R, Kunčak V, eds. Vol 10426. Springer; 2017:201-221. doi:10.1007/978-3-319-63387-9_10","ista":"Ashok P, Chatterjee K, Daca P, Kretinsky J, Meggendorfer T. 2017. Value iteration for long run average reward in markov decision processes. CAV: Computer Aided Verification, LNCS, vol. 10426, 201–221.","apa":"Ashok, P., Chatterjee, K., Daca, P., Kretinsky, J., & Meggendorfer, T. (2017). Value iteration for long run average reward in markov decision processes. In R. Majumdar & V. Kunčak (Eds.) (Vol. 10426, pp. 201–221). Presented at the CAV: Computer Aided Verification, Heidelberg, Germany: Springer. https://doi.org/10.1007/978-3-319-63387-9_10","ieee":"P. Ashok, K. Chatterjee, P. Daca, J. Kretinsky, and T. Meggendorfer, “Value iteration for long run average reward in markov decision processes,” presented at the CAV: Computer Aided Verification, Heidelberg, Germany, 2017, vol. 10426, pp. 201–221.","mla":"Ashok, Pranav, et al. Value Iteration for Long Run Average Reward in Markov Decision Processes. Edited by Rupak Majumdar and Viktor Kunčak, vol. 10426, Springer, 2017, pp. 201–21, doi:10.1007/978-3-319-63387-9_10.","short":"P. Ashok, K. Chatterjee, P. Daca, J. Kretinsky, T. Meggendorfer, in:, R. Majumdar, V. Kunčak (Eds.), Springer, 2017, pp. 201–221.","chicago":"Ashok, Pranav, Krishnendu Chatterjee, Przemyslaw Daca, Jan Kretinsky, and Tobias Meggendorfer. “Value Iteration for Long Run Average Reward in Markov Decision Processes.” edited by Rupak Majumdar and Viktor Kunčak, 10426:201–21. Springer, 2017. https://doi.org/10.1007/978-3-319-63387-9_10."},"date_published":"2017-07-13T00:00:00Z"},{"publist_id":"7138","ec_funded":1,"publisher":"SIAM","department":[{"_id":"VlKo"}],"publication_status":"published","year":"2017","volume":46,"date_updated":"2023-02-23T10:07:49Z","date_created":"2018-12-11T11:47:40Z","related_material":{"record":[{"relation":"other","status":"public","id":"1637"}]},"author":[{"full_name":"Kolmogorov, Vladimir","last_name":"Kolmogorov","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Krokhin","first_name":"Andrei","full_name":"Krokhin, Andrei"},{"id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87","last_name":"Rolinek","first_name":"Michal","full_name":"Rolinek, Michal"}],"month":"06","project":[{"grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice"}],"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1502.07327"}],"language":[{"iso":"eng"}],"doi":"10.1137/16M1091836","type":"journal_article","issue":"3","abstract":[{"text":"An instance of the valued constraint satisfaction problem (VCSP) is given by a finite set of variables, a finite domain of labels, and a sum of functions, each function depending on a subset of the variables. Each function can take finite values specifying costs of assignments of labels to its variables or the infinite value, which indicates an infeasible assignment. The goal is to find an assignment of labels to the variables that minimizes the sum. We study, assuming that P 6= NP, how the complexity of this very general problem depends on the set of functions allowed in the instances, the so-called constraint language. The case when all allowed functions take values in f0;1g corresponds to ordinary CSPs, where one deals only with the feasibility issue, and there is no optimization. This case is the subject of the algebraic CSP dichotomy conjecture predicting for which constraint languages CSPs are tractable (i.e., solvable in polynomial time) and for which they are NP-hard. The case when all allowed functions take only finite values corresponds to a finitevalued CSP, where the feasibility aspect is trivial and one deals only with the optimization issue. The complexity of finite-valued CSPs was fully classified by Thapper and Živný. An algebraic necessary condition for tractability of a general-valued CSP with a fixed constraint language was recently given by Kozik and Ochremiak. As our main result, we prove that if a constraint language satisfies this algebraic necessary condition, and the feasibility CSP (i.e., the problem of deciding whether a given instance has a feasible solution) corresponding to the VCSP with this language is tractable, then the VCSP is tractable. The algorithm is a simple combination of the assumed algorithm for the feasibility CSP and the standard LP relaxation. As a corollary, we obtain that a dichotomy for ordinary CSPs would imply a dichotomy for general-valued CSPs.","lang":"eng"}],"intvolume":" 46","status":"public","title":"The complexity of general-valued CSPs","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"644","oa_version":"Preprint","scopus_import":1,"day":"29","page":"1087 - 1110","citation":{"chicago":"Kolmogorov, Vladimir, Andrei Krokhin, and Michal Rolinek. “The Complexity of General-Valued CSPs.” SIAM Journal on Computing. SIAM, 2017. https://doi.org/10.1137/16M1091836.","mla":"Kolmogorov, Vladimir, et al. “The Complexity of General-Valued CSPs.” SIAM Journal on Computing, vol. 46, no. 3, SIAM, 2017, pp. 1087–110, doi:10.1137/16M1091836.","short":"V. Kolmogorov, A. Krokhin, M. Rolinek, SIAM Journal on Computing 46 (2017) 1087–1110.","ista":"Kolmogorov V, Krokhin A, Rolinek M. 2017. The complexity of general-valued CSPs. SIAM Journal on Computing. 46(3), 1087–1110.","ieee":"V. Kolmogorov, A. Krokhin, and M. Rolinek, “The complexity of general-valued CSPs,” SIAM Journal on Computing, vol. 46, no. 3. SIAM, pp. 1087–1110, 2017.","apa":"Kolmogorov, V., Krokhin, A., & Rolinek, M. (2017). The complexity of general-valued CSPs. SIAM Journal on Computing. SIAM. https://doi.org/10.1137/16M1091836","ama":"Kolmogorov V, Krokhin A, Rolinek M. The complexity of general-valued CSPs. SIAM Journal on Computing. 2017;46(3):1087-1110. doi:10.1137/16M1091836"},"publication":"SIAM Journal on Computing","date_published":"2017-06-29T00:00:00Z"},{"date_published":"2017-06-01T00:00:00Z","citation":{"chicago":"Kuske, Jan, Paul Swoboda, and Stefanie Petra. “A Novel Convex Relaxation for Non Binary Discrete Tomography.” edited by François Lauze, Yiqiu Dong, and Anders Bjorholm Dahl, 10302:235–46. Springer, 2017. https://doi.org/10.1007/978-3-319-58771-4_19.","short":"J. Kuske, P. Swoboda, S. Petra, in:, F. Lauze, Y. Dong, A. Bjorholm Dahl (Eds.), Springer, 2017, pp. 235–246.","mla":"Kuske, Jan, et al. A Novel Convex Relaxation for Non Binary Discrete Tomography. Edited by François Lauze et al., vol. 10302, Springer, 2017, pp. 235–46, doi:10.1007/978-3-319-58771-4_19.","apa":"Kuske, J., Swoboda, P., & Petra, S. (2017). A novel convex relaxation for non binary discrete tomography. In F. Lauze, Y. Dong, & A. Bjorholm Dahl (Eds.) (Vol. 10302, pp. 235–246). Presented at the SSVM: Scale Space and Variational Methods in Computer Vision, Kolding, Denmark: Springer. https://doi.org/10.1007/978-3-319-58771-4_19","ieee":"J. Kuske, P. Swoboda, and S. Petra, “A novel convex relaxation for non binary discrete tomography,” presented at the SSVM: Scale Space and Variational Methods in Computer Vision, Kolding, Denmark, 2017, vol. 10302, pp. 235–246.","ista":"Kuske J, Swoboda P, Petra S. 2017. A novel convex relaxation for non binary discrete tomography. SSVM: Scale Space and Variational Methods in Computer Vision, LNCS, vol. 10302, 235–246.","ama":"Kuske J, Swoboda P, Petra S. A novel convex relaxation for non binary discrete tomography. In: Lauze F, Dong Y, Bjorholm Dahl A, eds. Vol 10302. Springer; 2017:235-246. doi:10.1007/978-3-319-58771-4_19"},"page":"235 - 246","day":"01","scopus_import":1,"oa_version":"Submitted Version","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"646","title":"A novel convex relaxation for non binary discrete tomography","status":"public","intvolume":" 10302","abstract":[{"text":"We present a novel convex relaxation and a corresponding inference algorithm for the non-binary discrete tomography problem, that is, reconstructing discrete-valued images from few linear measurements. In contrast to state of the art approaches that split the problem into a continuous reconstruction problem for the linear measurement constraints and a discrete labeling problem to enforce discrete-valued reconstructions, we propose a joint formulation that addresses both problems simultaneously, resulting in a tighter convex relaxation. For this purpose a constrained graphical model is set up and evaluated using a novel relaxation optimized by dual decomposition. We evaluate our approach experimentally and show superior solutions both mathematically (tighter relaxation) and experimentally in comparison to previously proposed relaxations.","lang":"eng"}],"type":"conference","alternative_title":["LNCS"],"conference":{"end_date":"2017-06-08","start_date":"2017-06-04","location":"Kolding, Denmark","name":"SSVM: Scale Space and Variational Methods in Computer Vision"},"doi":"10.1007/978-3-319-58771-4_19","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1703.03769"}],"oa":1,"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice","_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160"}],"month":"06","publication_identifier":{"isbn":["978-331958770-7"]},"author":[{"first_name":"Jan","last_name":"Kuske","full_name":"Kuske, Jan"},{"full_name":"Swoboda, Paul","first_name":"Paul","last_name":"Swoboda","id":"446560C6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Petra","first_name":"Stefanie","full_name":"Petra, Stefanie"}],"date_updated":"2021-01-12T08:07:34Z","date_created":"2018-12-11T11:47:41Z","volume":10302,"year":"2017","publication_status":"published","editor":[{"last_name":"Lauze","first_name":"François","full_name":"Lauze, François"},{"full_name":"Dong, Yiqiu","first_name":"Yiqiu","last_name":"Dong"},{"full_name":"Bjorholm Dahl, Anders","last_name":"Bjorholm Dahl","first_name":"Anders"}],"department":[{"_id":"VlKo"}],"publisher":"Springer","publist_id":"7132","ec_funded":1},{"page":"600 - 613","citation":{"chicago":"Skórski, Maciej. “On the Complexity of Breaking Pseudoentropy.” edited by Gerhard Jäger and Silvia Steila, 10185:600–613. Springer, 2017. https://doi.org/10.1007/978-3-319-55911-7_43.","mla":"Skórski, Maciej. On the Complexity of Breaking Pseudoentropy. Edited by Gerhard Jäger and Silvia Steila, vol. 10185, Springer, 2017, pp. 600–13, doi:10.1007/978-3-319-55911-7_43.","short":"M. Skórski, in:, G. Jäger, S. Steila (Eds.), Springer, 2017, pp. 600–613.","ista":"Skórski M. 2017. On the complexity of breaking pseudoentropy. TAMC: Theory and Applications of Models of Computation, LNCS, vol. 10185, 600–613.","apa":"Skórski, M. (2017). On the complexity of breaking pseudoentropy. In G. Jäger & S. Steila (Eds.) (Vol. 10185, pp. 600–613). Presented at the TAMC: Theory and Applications of Models of Computation, Bern, Switzerland: Springer. https://doi.org/10.1007/978-3-319-55911-7_43","ieee":"M. Skórski, “On the complexity of breaking pseudoentropy,” presented at the TAMC: Theory and Applications of Models of Computation, Bern, Switzerland, 2017, vol. 10185, pp. 600–613.","ama":"Skórski M. On the complexity of breaking pseudoentropy. In: Jäger G, Steila S, eds. Vol 10185. Springer; 2017:600-613. doi:10.1007/978-3-319-55911-7_43"},"date_published":"2017-04-01T00:00:00Z","scopus_import":1,"day":"01","title":"On the complexity of breaking pseudoentropy","status":"public","intvolume":" 10185","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"648","oa_version":"Submitted Version","alternative_title":["LNCS"],"type":"conference","abstract":[{"lang":"eng","text":"Pseudoentropy has found a lot of important applications to cryptography and complexity theory. In this paper we focus on the foundational problem that has not been investigated so far, namely by how much pseudoentropy (the amount seen by computationally bounded attackers) differs from its information-theoretic counterpart (seen by unbounded observers), given certain limits on attacker’s computational power? We provide the following answer for HILL pseudoentropy, which exhibits a threshold behavior around the size exponential in the entropy amount:– If the attacker size (s) and advantage () satisfy s (formula presented) where k is the claimed amount of pseudoentropy, then the pseudoentropy boils down to the information-theoretic smooth entropy. – If s (formula presented) then pseudoentropy could be arbitrarily bigger than the information-theoretic smooth entropy. Besides answering the posted question, we show an elegant application of our result to the complexity theory, namely that it implies the clas-sical result on the existence of functions hard to approximate (due to Pippenger). In our approach we utilize non-constructive techniques: the duality of linear programming and the probabilistic method."}],"quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://eprint.iacr.org/2016/1186.pdf","open_access":"1"}],"language":[{"iso":"eng"}],"conference":{"location":"Bern, Switzerland","start_date":"2017-04-20","end_date":"2017-04-22","name":"TAMC: Theory and Applications of Models of Computation"},"doi":"10.1007/978-3-319-55911-7_43","month":"04","publication_identifier":{"isbn":["978-331955910-0"]},"publication_status":"published","department":[{"_id":"KrPi"}],"publisher":"Springer","editor":[{"full_name":"Jäger, Gerhard","last_name":"Jäger","first_name":"Gerhard"},{"first_name":"Silvia","last_name":"Steila","full_name":"Steila, Silvia"}],"year":"2017","date_updated":"2021-01-12T08:07:39Z","date_created":"2018-12-11T11:47:42Z","volume":10185,"author":[{"id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","last_name":"Skórski","first_name":"Maciej","full_name":"Skórski, Maciej"}],"publist_id":"7125"},{"scopus_import":"1","series_title":"Lecture Notes in Mathematics","day":"05","article_processing_charge":"No","publication":"Modern Approaches to Discrete Curvature","citation":{"ama":"Maas J. Entropic Ricci curvature for discrete spaces. In: Najman L, Romon P, eds. Modern Approaches to Discrete Curvature. Vol 2184. Lecture Notes in Mathematics. Springer; 2017:159-174. doi:10.1007/978-3-319-58002-9_5","ista":"Maas J. 2017.Entropic Ricci curvature for discrete spaces. In: Modern Approaches to Discrete Curvature. vol. 2184, 159–174.","apa":"Maas, J. (2017). Entropic Ricci curvature for discrete spaces. In L. Najman & P. Romon (Eds.), Modern Approaches to Discrete Curvature (Vol. 2184, pp. 159–174). Springer. https://doi.org/10.1007/978-3-319-58002-9_5","ieee":"J. Maas, “Entropic Ricci curvature for discrete spaces,” in Modern Approaches to Discrete Curvature, vol. 2184, L. Najman and P. Romon, Eds. Springer, 2017, pp. 159–174.","mla":"Maas, Jan. “Entropic Ricci Curvature for Discrete Spaces.” Modern Approaches to Discrete Curvature, edited by Laurent Najman and Pascal Romon, vol. 2184, Springer, 2017, pp. 159–74, doi:10.1007/978-3-319-58002-9_5.","short":"J. Maas, in:, L. Najman, P. Romon (Eds.), Modern Approaches to Discrete Curvature, Springer, 2017, pp. 159–174.","chicago":"Maas, Jan. “Entropic Ricci Curvature for Discrete Spaces.” In Modern Approaches to Discrete Curvature, edited by Laurent Najman and Pascal Romon, 2184:159–74. Lecture Notes in Mathematics. Springer, 2017. https://doi.org/10.1007/978-3-319-58002-9_5."},"page":"159 - 174","date_published":"2017-10-05T00:00:00Z","type":"book_chapter","abstract":[{"text":"We give a short overview on a recently developed notion of Ricci curvature for discrete spaces. This notion relies on geodesic convexity properties of the relative entropy along geodesics in the space of probability densities, for a metric which is similar to (but different from) the 2-Wasserstein metric. The theory can be considered as a discrete counterpart to the theory of Ricci curvature for geodesic measure spaces developed by Lott–Sturm–Villani.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"649","title":"Entropic Ricci curvature for discrete spaces","status":"public","intvolume":" 2184","oa_version":"None","month":"10","publication_identifier":{"eissn":["978-3-319-58002-9"],"isbn":["978-3-319-58001-2"]},"quality_controlled":"1","doi":"10.1007/978-3-319-58002-9_5","language":[{"iso":"eng"}],"publist_id":"7123","year":"2017","publication_status":"published","publisher":"Springer","editor":[{"first_name":"Laurent","last_name":"Najman","full_name":"Najman, Laurent"},{"first_name":"Pascal","last_name":"Romon","full_name":"Romon, Pascal"}],"department":[{"_id":"JaMa"}],"author":[{"orcid":"0000-0002-0845-1338","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","last_name":"Maas","first_name":"Jan","full_name":"Maas, Jan"}],"date_updated":"2022-05-24T07:01:33Z","date_created":"2018-12-11T11:47:42Z","volume":2184},{"oa_version":"Submitted Version","status":"public","title":"A cryptographic view of regularity lemmas: Simpler unified proofs and refined bounds","intvolume":" 10185","_id":"650","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"In this work we present a short and unified proof for the Strong and Weak Regularity Lemma, based on the cryptographic tech-nique called low-complexity approximations. In short, both problems reduce to a task of finding constructively an approximation for a certain target function under a class of distinguishers (test functions), where dis-tinguishers are combinations of simple rectangle-indicators. In our case these approximations can be learned by a simple iterative procedure, which yields a unified and simple proof, achieving for any graph with density d and any approximation parameter the partition size. The novelty in our proof is: (a) a simple approach which yields both strong and weaker variant, and (b) improvements when d = o(1). At an abstract level, our proof can be seen a refinement and simplification of the “analytic” proof given by Lovasz and Szegedy.","lang":"eng"}],"alternative_title":["LNCS"],"type":"conference","date_published":"2017-01-01T00:00:00Z","page":"586 - 599","citation":{"chicago":"Skórski, Maciej. “A Cryptographic View of Regularity Lemmas: Simpler Unified Proofs and Refined Bounds.” edited by Gerhard Jäger and Silvia Steila, 10185:586–99. Springer, 2017. https://doi.org/10.1007/978-3-319-55911-7_42.","short":"M. Skórski, in:, G. Jäger, S. Steila (Eds.), Springer, 2017, pp. 586–599.","mla":"Skórski, Maciej. A Cryptographic View of Regularity Lemmas: Simpler Unified Proofs and Refined Bounds. Edited by Gerhard Jäger and Silvia Steila, vol. 10185, Springer, 2017, pp. 586–99, doi:10.1007/978-3-319-55911-7_42.","ieee":"M. Skórski, “A cryptographic view of regularity lemmas: Simpler unified proofs and refined bounds,” presented at the TAMC: Theory and Applications of Models of Computation, Bern, Switzerland, 2017, vol. 10185, pp. 586–599.","apa":"Skórski, M. (2017). A cryptographic view of regularity lemmas: Simpler unified proofs and refined bounds. In G. Jäger & S. Steila (Eds.) (Vol. 10185, pp. 586–599). Presented at the TAMC: Theory and Applications of Models of Computation, Bern, Switzerland: Springer. https://doi.org/10.1007/978-3-319-55911-7_42","ista":"Skórski M. 2017. A cryptographic view of regularity lemmas: Simpler unified proofs and refined bounds. TAMC: Theory and Applications of Models of Computation, LNCS, vol. 10185, 586–599.","ama":"Skórski M. A cryptographic view of regularity lemmas: Simpler unified proofs and refined bounds. In: Jäger G, Steila S, eds. Vol 10185. Springer; 2017:586-599. doi:10.1007/978-3-319-55911-7_42"},"day":"01","scopus_import":1,"date_updated":"2021-01-12T08:07:46Z","date_created":"2018-12-11T11:47:42Z","volume":10185,"author":[{"id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","first_name":"Maciej","last_name":"Skórski","full_name":"Skórski, Maciej"}],"publication_status":"published","department":[{"_id":"KrPi"}],"editor":[{"last_name":"Jäger","first_name":"Gerhard","full_name":"Jäger, Gerhard"},{"full_name":"Steila, Silvia","first_name":"Silvia","last_name":"Steila"}],"publisher":"Springer","year":"2017","publist_id":"7119","language":[{"iso":"eng"}],"conference":{"end_date":"2017-04-22","start_date":"2017-04-20","location":"Bern, Switzerland","name":"TAMC: Theory and Applications of Models of Computation"},"doi":"10.1007/978-3-319-55911-7_42","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2016/965.pdf"}],"oa":1,"month":"01","publication_identifier":{"issn":["03029743"]}},{"month":"08","conference":{"start_date":"2017-08-20","location":"Stockholm, Sweden","end_date":"2017-08-24","name":"CSL: Conference on Computer Science Logic"},"doi":"10.4230/LIPICS.CSL.2017.18","language":[{"iso":"eng"}],"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","short":"CC BY (3.0)","image":"/images/cc_by.png"},"quality_controlled":"1","project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003"}],"file_date_updated":"2020-07-14T12:47:33Z","ec_funded":1,"article_number":"18","author":[{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"last_name":"Dvorák","first_name":"Wolfgang","full_name":"Dvorák, Wolfgang"},{"full_name":"Henzinger, Monika H","last_name":"Henzinger","first_name":"Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"full_name":"Loitzenbauer, Veronika","last_name":"Loitzenbauer","first_name":"Veronika"}],"date_created":"2019-06-04T12:42:43Z","date_updated":"2023-02-14T10:08:25Z","volume":82,"year":"2017","publication_status":"published","publisher":"Schloss Dagstuhl -Leibniz-Zentrum fuer Informatik","department":[{"_id":"KrCh"}],"day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2017-08-01T00:00:00Z","citation":{"ama":"Chatterjee K, Dvorák W, Henzinger MH, Loitzenbauer V. Improved set-based symbolic algorithms for parity games. In: Vol 82. Schloss Dagstuhl -Leibniz-Zentrum fuer Informatik; 2017. doi:10.4230/LIPICS.CSL.2017.18","ista":"Chatterjee K, Dvorák W, Henzinger MH, Loitzenbauer V. 2017. Improved set-based symbolic algorithms for parity games. CSL: Conference on Computer Science Logic vol. 82, 18.","ieee":"K. Chatterjee, W. Dvorák, M. H. Henzinger, and V. Loitzenbauer, “Improved set-based symbolic algorithms for parity games,” presented at the CSL: Conference on Computer Science Logic, Stockholm, Sweden, 2017, vol. 82.","apa":"Chatterjee, K., Dvorák, W., Henzinger, M. H., & Loitzenbauer, V. (2017). Improved set-based symbolic algorithms for parity games (Vol. 82). Presented at the CSL: Conference on Computer Science Logic, Stockholm, Sweden: Schloss Dagstuhl -Leibniz-Zentrum fuer Informatik. https://doi.org/10.4230/LIPICS.CSL.2017.18","mla":"Chatterjee, Krishnendu, et al. Improved Set-Based Symbolic Algorithms for Parity Games. Vol. 82, 18, Schloss Dagstuhl -Leibniz-Zentrum fuer Informatik, 2017, doi:10.4230/LIPICS.CSL.2017.18.","short":"K. Chatterjee, W. Dvorák, M.H. Henzinger, V. Loitzenbauer, in:, Schloss Dagstuhl -Leibniz-Zentrum fuer Informatik, 2017.","chicago":"Chatterjee, Krishnendu, Wolfgang Dvorák, Monika H Henzinger, and Veronika Loitzenbauer. “Improved Set-Based Symbolic Algorithms for Parity Games,” Vol. 82. Schloss Dagstuhl -Leibniz-Zentrum fuer Informatik, 2017. https://doi.org/10.4230/LIPICS.CSL.2017.18."},"abstract":[{"text":"Graph games with omega-regular winning conditions provide a mathematical framework to analyze a wide range of problems in the analysis of reactive systems and programs (such as the synthesis of reactive systems, program repair, and the verification of branching time properties). Parity conditions are canonical forms to specify omega-regular winning conditions. Graph games with parity conditions are equivalent to mu-calculus model checking, and thus a very important algorithmic problem. Symbolic algorithms are of great significance because they provide scalable algorithms for the analysis of large finite-state systems, as well as algorithms for the analysis of infinite-state systems with finite quotient. A set-based symbolic algorithm uses the basic set operations and the one-step predecessor operators. We consider graph games with n vertices and parity conditions with c priorities (equivalently, a mu-calculus formula with c alternations of least and greatest fixed points). While many explicit algorithms exist for graph games with parity conditions, for set-based symbolic algorithms there are only two algorithms (notice that we use space to refer to the number of sets stored by a symbolic algorithm): (a) the basic algorithm that requires O(n^c) symbolic operations and linear space; and (b) an improved algorithm that requires O(n^{c/2+1}) symbolic operations but also O(n^{c/2+1}) space (i.e., exponential space). In this work we present two set-based symbolic algorithms for parity games: (a) our first algorithm requires O(n^{c/2+1}) symbolic operations and only requires linear space; and (b) developing on our first algorithm, we present an algorithm that requires O(n^{c/3+1}) symbolic operations and only linear space. We also present the first linear space set-based symbolic algorithm for parity games that requires at most a sub-exponential number of symbolic operations. ","lang":"eng"}],"type":"conference","file":[{"file_size":710185,"content_type":"application/pdf","creator":"kschuh","access_level":"open_access","file_name":"2017_LIPIcs-Chatterjee.pdf","checksum":"7c2c9d09970af79026d7e37d9b632ef8","date_created":"2019-06-04T12:56:52Z","date_updated":"2020-07-14T12:47:33Z","relation":"main_file","file_id":"6520"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6519","status":"public","ddc":["004"],"title":"Improved set-based symbolic algorithms for parity games","intvolume":" 82"},{"article_number":"34","ec_funded":1,"file_date_updated":"2020-07-14T12:47:33Z","department":[{"_id":"UlWa"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication_status":"published","year":"2017","volume":92,"date_created":"2019-06-04T12:11:52Z","date_updated":"2021-01-12T08:07:51Z","author":[{"full_name":"Fulek, Radoslav","first_name":"Radoslav","last_name":"Fulek","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8485-1774"}],"month":"12","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"},{"grant_number":"M02281","_id":"261FA626-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Eliminating intersections in drawings of graphs"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.4230/LIPICS.ISAAC.2017.34","conference":{"end_date":"2017-12-22","location":"Phuket, Thailand","start_date":"2017-12-09","name":"ISAAC: International Symposium on Algorithms and Computation"},"type":"conference","abstract":[{"lang":"eng","text":"A (possibly degenerate) drawing of a graph G in the plane is approximable by an embedding if it can be turned into an embedding by an arbitrarily small perturbation. We show that testing, whether a drawing of a planar graph G in the plane is approximable by an embedding, can be carried out in polynomial time, if a desired embedding of G belongs to a fixed isotopy class, i.e., the rotation system (or equivalently the faces) of the embedding of G and the choice of outer face are fixed. In other words, we show that c-planarity with embedded pipes is tractable for graphs with fixed embeddings. To the best of our knowledge an analogous result was previously known essentially only when G is a cycle."}],"intvolume":" 92","ddc":["510"],"title":"Embedding graphs into embedded graphs","status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"6517","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"6518","checksum":"fc7a643e29621c8bbe49d36b39081f31","date_updated":"2020-07-14T12:47:33Z","date_created":"2019-06-04T12:20:35Z","access_level":"open_access","file_name":"2017_LIPIcs-Fulek.pdf","content_type":"application/pdf","file_size":588982,"creator":"kschuh"}],"scopus_import":1,"has_accepted_license":"1","day":"01","citation":{"ama":"Fulek R. Embedding graphs into embedded graphs. In: Vol 92. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPICS.ISAAC.2017.34","apa":"Fulek, R. (2017). Embedding graphs into embedded graphs (Vol. 92). Presented at the ISAAC: International Symposium on Algorithms and Computation, Phuket, Thailand: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.ISAAC.2017.34","ieee":"R. Fulek, “Embedding graphs into embedded graphs,” presented at the ISAAC: International Symposium on Algorithms and Computation, Phuket, Thailand, 2017, vol. 92.","ista":"Fulek R. 2017. Embedding graphs into embedded graphs. ISAAC: International Symposium on Algorithms and Computation vol. 92, 34.","short":"R. Fulek, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","mla":"Fulek, Radoslav. Embedding Graphs into Embedded Graphs. Vol. 92, 34, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPICS.ISAAC.2017.34.","chicago":"Fulek, Radoslav. “Embedding Graphs into Embedded Graphs,” Vol. 92. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPICS.ISAAC.2017.34."},"date_published":"2017-12-01T00:00:00Z"},{"type":"conference","article_number":"7846789","publist_id":"7100","abstract":[{"lang":"eng","text":"We present an approach that enables robots to self-organize their sensorimotor behavior from scratch without providing specific information about neither the robot nor its environment. This is achieved by a simple neural control law that increases the consistency between external sensor dynamics and internal neural dynamics of the utterly simple controller. In this way, the embodiment and the agent-environment coupling are the only source of individual development. We show how an anthropomorphic tendon driven arm-shoulder system develops different behaviors depending on that coupling. For instance: Given a bottle half-filled with water, the arm starts to shake it, driven by the physical response of the water. When attaching a brush, the arm can be manipulated into wiping a table, and when connected to a revolvable wheel it finds out how to rotate it. Thus, the robot may be said to discover the affordances of the world. When allowing two (simulated) humanoid robots to interact physically, they engage into a joint behavior development leading to, for instance, spontaneous cooperation. More social effects are observed if the robots can visually perceive each other. Although, as an observer, it is tempting to attribute an apparent intentionality, there is nothing of the kind put in. As a conclusion, we argue that emergent behavior may be much less rooted in explicit intentions, internal motivations, or specific reward systems than is commonly believed."}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"652","year":"2017","department":[{"_id":"ChLa"},{"_id":"GaTk"}],"publisher":"IEEE","title":"Dynamical self consistency leads to behavioral development and emergent social interactions in robots","publication_status":"published","status":"public","author":[{"full_name":"Der, Ralf","first_name":"Ralf","last_name":"Der"},{"full_name":"Martius, Georg S","id":"3A276B68-F248-11E8-B48F-1D18A9856A87","last_name":"Martius","first_name":"Georg S"}],"oa_version":"None","date_updated":"2021-01-12T08:07:51Z","date_created":"2018-12-11T11:47:43Z","scopus_import":1,"publication_identifier":{"isbn":["978-150905069-7"]},"day":"07","month":"02","citation":{"ama":"Der R, Martius GS. Dynamical self consistency leads to behavioral development and emergent social interactions in robots. In: IEEE; 2017. doi:10.1109/DEVLRN.2016.7846789","apa":"Der, R., & Martius, G. S. (2017). Dynamical self consistency leads to behavioral development and emergent social interactions in robots. Presented at the ICDL EpiRob: International Conference on Development and Learning and Epigenetic Robotics , Cergy-Pontoise, France: IEEE. https://doi.org/10.1109/DEVLRN.2016.7846789","ieee":"R. Der and G. S. Martius, “Dynamical self consistency leads to behavioral development and emergent social interactions in robots,” presented at the ICDL EpiRob: International Conference on Development and Learning and Epigenetic Robotics , Cergy-Pontoise, France, 2017.","ista":"Der R, Martius GS. 2017. Dynamical self consistency leads to behavioral development and emergent social interactions in robots. ICDL EpiRob: International Conference on Development and Learning and Epigenetic Robotics , 7846789.","short":"R. Der, G.S. Martius, in:, IEEE, 2017.","mla":"Der, Ralf, and Georg S. Martius. Dynamical Self Consistency Leads to Behavioral Development and Emergent Social Interactions in Robots. 7846789, IEEE, 2017, doi:10.1109/DEVLRN.2016.7846789.","chicago":"Der, Ralf, and Georg S Martius. “Dynamical Self Consistency Leads to Behavioral Development and Emergent Social Interactions in Robots.” IEEE, 2017. https://doi.org/10.1109/DEVLRN.2016.7846789."},"quality_controlled":"1","date_published":"2017-02-07T00:00:00Z","doi":"10.1109/DEVLRN.2016.7846789","conference":{"start_date":"2016-09-19","location":"Cergy-Pontoise, France","end_date":"2016-09-22","name":"ICDL EpiRob: International Conference on Development and Learning and Epigenetic Robotics "},"language":[{"iso":"eng"}]},{"year":"2017","_id":"651","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Fluid dynamics: Water flows out of touch","publication_status":"published","department":[{"_id":"BjHo"}],"publisher":"Nature Publishing Group","intvolume":" 541","author":[{"full_name":"Hof, Björn","last_name":"Hof","first_name":"Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2018-12-11T11:47:43Z","date_updated":"2021-01-12T08:07:49Z","oa_version":"None","volume":541,"type":"journal_article","abstract":[{"text":"Superhydrophobic surfaces reduce the frictional drag between water and solid materials, but this effect is often temporary. The realization of sustained drag reduction has applications for water vehicles and pipeline flows.\r\n\r\n","lang":"eng"}],"issue":"7636","publist_id":"7116","publication":"Nature","citation":{"ama":"Hof B. Fluid dynamics: Water flows out of touch. Nature. 2017;541(7636):161-162. doi:10.1038/541161a","apa":"Hof, B. (2017). Fluid dynamics: Water flows out of touch. Nature. Nature Publishing Group. https://doi.org/10.1038/541161a","ieee":"B. Hof, “Fluid dynamics: Water flows out of touch,” Nature, vol. 541, no. 7636. Nature Publishing Group, pp. 161–162, 2017.","ista":"Hof B. 2017. Fluid dynamics: Water flows out of touch. Nature. 541(7636), 161–162.","short":"B. Hof, Nature 541 (2017) 161–162.","mla":"Hof, Björn. “Fluid Dynamics: Water Flows out of Touch.” Nature, vol. 541, no. 7636, Nature Publishing Group, 2017, pp. 161–62, doi:10.1038/541161a.","chicago":"Hof, Björn. “Fluid Dynamics: Water Flows out of Touch.” Nature. Nature Publishing Group, 2017. https://doi.org/10.1038/541161a."},"quality_controlled":"1","page":"161 - 162","date_published":"2017-01-11T00:00:00Z","doi":"10.1038/541161a","language":[{"iso":"eng"}],"scopus_import":1,"day":"11","month":"01","publication_identifier":{"issn":["00280836"]}},{"publist_id":"7092","ec_funded":1,"file_date_updated":"2020-07-14T12:47:33Z","department":[{"_id":"KrCh"}],"publisher":"Nature Publishing Group","publication_status":"published","pmid":1,"acknowledgement":"We thank the Memorial Sloan Kettering Cancer Center Molecular Cytology core facility for immunohistochemistry staining. This work was supported by Office of Naval Research grant N00014-16-1-2914, the Bill and Melinda Gates Foundation (OPP1148627), and a gift from B. Wu and E. Larson (M.A.N.), National Institutes of Health grants CA179991 (C.A.I.-D. and I.B.), F31 CA180682 (A.P.M.-M.), CA43460 (B.V.), and P50 CA62924, the Monastra Foundation, the Virginia and D.K. Ludwig Fund for Cancer Research, the Lustgarten Foundation for Pancreatic Cancer Research, the Sol Goldman Center for Pancreatic Cancer Research, the Sol Goldman Sequencing Center, ERC Start grant 279307: Graph Games (J.G.R., D.K., and C.K.), Austrian Science Fund (FWF) grant P23499-N23 (J.G.R., D.K., and C.K.), and FWF NFN grant S11407-N23 RiSE/SHiNE (J.G.R., D.K., and C.K.).","year":"2017","volume":49,"date_created":"2018-12-11T11:47:43Z","date_updated":"2022-06-10T09:55:08Z","author":[{"first_name":"Alvin","last_name":"Makohon Moore","full_name":"Makohon Moore, Alvin"},{"full_name":"Zhang, Ming","first_name":"Ming","last_name":"Zhang"},{"first_name":"Johannes","last_name":"Reiter","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0170-7353","full_name":"Reiter, Johannes"},{"full_name":"Božić, Ivana","first_name":"Ivana","last_name":"Božić"},{"full_name":"Allen, Benjamin","last_name":"Allen","first_name":"Benjamin"},{"full_name":"Kundu, Deepanjan","first_name":"Deepanjan","last_name":"Kundu","id":"1d4c0f4f-e8a3-11ec-a351-e36772758c45"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"full_name":"Wong, Fay","last_name":"Wong","first_name":"Fay"},{"last_name":"Jiao","first_name":"Yuchen","full_name":"Jiao, Yuchen"},{"full_name":"Kohutek, Zachary","last_name":"Kohutek","first_name":"Zachary"},{"full_name":"Hong, Jungeui","first_name":"Jungeui","last_name":"Hong"},{"first_name":"Marc","last_name":"Attiyeh","full_name":"Attiyeh, Marc"},{"last_name":"Javier","first_name":"Breanna","full_name":"Javier, Breanna"},{"full_name":"Wood, Laura","last_name":"Wood","first_name":"Laura"},{"first_name":"Ralph","last_name":"Hruban","full_name":"Hruban, Ralph"},{"full_name":"Nowak, Martin","first_name":"Martin","last_name":"Nowak"},{"full_name":"Papadopoulos, Nickolas","last_name":"Papadopoulos","first_name":"Nickolas"},{"first_name":"Kenneth","last_name":"Kinzler","full_name":"Kinzler, Kenneth"},{"full_name":"Vogelstein, Bert","first_name":"Bert","last_name":"Vogelstein"},{"last_name":"Iacobuzio Donahue","first_name":"Christine","full_name":"Iacobuzio Donahue, Christine"}],"publication_identifier":{"issn":["10614036"]},"month":"03","project":[{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"name":"Game Theory","call_identifier":"FWF","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","oa":1,"external_id":{"pmid":["28092682"]},"language":[{"iso":"eng"}],"doi":"10.1038/ng.3764","type":"journal_article","issue":"3","abstract":[{"text":"The extent of heterogeneity among driver gene mutations present in naturally occurring metastases - that is, treatment-naive metastatic disease - is largely unknown. To address this issue, we carried out 60× whole-genome sequencing of 26 metastases from four patients with pancreatic cancer. We found that identical mutations in known driver genes were present in every metastatic lesion for each patient studied. Passenger gene mutations, which do not have known or predicted functional consequences, accounted for all intratumoral heterogeneity. Even with respect to these passenger mutations, our analysis suggests that the genetic similarity among the founding cells of metastases was higher than that expected for any two cells randomly taken from a normal tissue. The uniformity of known driver gene mutations among metastases in the same patient has critical and encouraging implications for the success of future targeted therapies in advanced-stage disease.","lang":"eng"}],"intvolume":" 49","ddc":["000"],"status":"public","title":"Limited heterogeneity of known driver gene mutations among the metastases of individual patients with pancreatic cancer","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"653","oa_version":"Submitted Version","file":[{"relation":"main_file","file_id":"7050","checksum":"e442dc3b7420a36ec805e9bb45cc1a2e","date_updated":"2020-07-14T12:47:33Z","date_created":"2019-11-19T08:13:50Z","access_level":"open_access","file_name":"2017_NatureGenetics_Makohon.pdf","file_size":908099,"content_type":"application/pdf","creator":"dernst"}],"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"01","page":"358 - 366","article_type":"original","citation":{"ama":"Makohon Moore A, Zhang M, Reiter J, et al. Limited heterogeneity of known driver gene mutations among the metastases of individual patients with pancreatic cancer. Nature Genetics. 2017;49(3):358-366. doi:10.1038/ng.3764","apa":"Makohon Moore, A., Zhang, M., Reiter, J., Božić, I., Allen, B., Kundu, D., … Iacobuzio Donahue, C. (2017). Limited heterogeneity of known driver gene mutations among the metastases of individual patients with pancreatic cancer. Nature Genetics. Nature Publishing Group. https://doi.org/10.1038/ng.3764","ieee":"A. Makohon Moore et al., “Limited heterogeneity of known driver gene mutations among the metastases of individual patients with pancreatic cancer,” Nature Genetics, vol. 49, no. 3. Nature Publishing Group, pp. 358–366, 2017.","ista":"Makohon Moore A, Zhang M, Reiter J, Božić I, Allen B, Kundu D, Chatterjee K, Wong F, Jiao Y, Kohutek Z, Hong J, Attiyeh M, Javier B, Wood L, Hruban R, Nowak M, Papadopoulos N, Kinzler K, Vogelstein B, Iacobuzio Donahue C. 2017. Limited heterogeneity of known driver gene mutations among the metastases of individual patients with pancreatic cancer. Nature Genetics. 49(3), 358–366.","short":"A. Makohon Moore, M. Zhang, J. Reiter, I. Božić, B. Allen, D. Kundu, K. Chatterjee, F. Wong, Y. Jiao, Z. Kohutek, J. Hong, M. Attiyeh, B. Javier, L. Wood, R. Hruban, M. Nowak, N. Papadopoulos, K. Kinzler, B. Vogelstein, C. Iacobuzio Donahue, Nature Genetics 49 (2017) 358–366.","mla":"Makohon Moore, Alvin, et al. “Limited Heterogeneity of Known Driver Gene Mutations among the Metastases of Individual Patients with Pancreatic Cancer.” Nature Genetics, vol. 49, no. 3, Nature Publishing Group, 2017, pp. 358–66, doi:10.1038/ng.3764.","chicago":"Makohon Moore, Alvin, Ming Zhang, Johannes Reiter, Ivana Božić, Benjamin Allen, Deepanjan Kundu, Krishnendu Chatterjee, et al. “Limited Heterogeneity of Known Driver Gene Mutations among the Metastases of Individual Patients with Pancreatic Cancer.” Nature Genetics. Nature Publishing Group, 2017. https://doi.org/10.1038/ng.3764."},"publication":"Nature Genetics","date_published":"2017-03-01T00:00:00Z"},{"type":"conference","abstract":[{"lang":"eng","text":"A memory-hard function (MHF) ƒn with parameter n can be computed in sequential time and space n. Simultaneously, a high amortized parallel area-time complexity (aAT) is incurred per evaluation. In practice, MHFs are used to limit the rate at which an adversary (using a custom computational device) can evaluate a security sensitive function that still occasionally needs to be evaluated by honest users (using an off-the-shelf general purpose device). The most prevalent examples of such sensitive functions are Key Derivation Functions (KDFs) and password hashing algorithms where rate limits help mitigate off-line dictionary attacks. As the honest users' inputs to these functions are often (low-entropy) passwords special attention is given to a class of side-channel resistant MHFs called iMHFs.\r\n\r\nEssentially all iMHFs can be viewed as some mode of operation (making n calls to some round function) given by a directed acyclic graph (DAG) with very low indegree. Recently, a combinatorial property of a DAG has been identified (called \"depth-robustness\") which results in good provable security for an iMHF based on that DAG. Depth-robust DAGs have also proven useful in other cryptographic applications. Unfortunately, up till now, all known very depth-robust DAGs are impractically complicated and little is known about their exact (i.e. non-asymptotic) depth-robustness both in theory and in practice.\r\n\r\nIn this work we build and analyze (both formally and empirically) several exceedingly simple and efficient to navigate practical DAGs for use in iMHFs and other applications. For each DAG we:\r\n*Prove that their depth-robustness is asymptotically maximal.\r\n*Prove bounds of at least 3 orders of magnitude better on their exact depth-robustness compared to known bounds for other practical iMHF.\r\n*Implement and empirically evaluate their depth-robustness and aAT against a variety of state-of-the art (and several new) depth-reduction and low aAT attacks. \r\nWe find that, against all attacks, the new DAGs perform significantly better in practice than Argon2i, the most widely deployed iMHF in practice.\r\n\r\nAlong the way we also improve the best known empirical attacks on the aAT of Argon2i by implementing and testing several heuristic versions of a (hitherto purely theoretical) depth-reduction attack. Finally, we demonstrate practicality of our constructions by modifying the Argon2i code base to use one of the new high aAT DAGs. Experimental benchmarks on a standard off-the-shelf CPU show that the new modifications do not adversely affect the impressive throughput of Argon2i (despite seemingly enjoying significantly higher aAT).\r\n"}],"ec_funded":1,"year":"2017","_id":"6527","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Practical graphs for optimal side-channel resistant memory-hard functions","publication_status":"published","publisher":"ACM Press","department":[{"_id":"KrPi"}],"author":[{"first_name":"Joel F","last_name":"Alwen","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","full_name":"Alwen, Joel F"},{"last_name":"Blocki","first_name":"Jeremiah","full_name":"Blocki, Jeremiah"},{"full_name":"Harsha, Ben","last_name":"Harsha","first_name":"Ben"}],"date_created":"2019-06-06T13:21:29Z","date_updated":"2021-01-12T08:07:53Z","oa_version":"Submitted Version","scopus_import":1,"day":"30","month":"10","publication_identifier":{"isbn":["9781450349468"]},"publication":"Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security","citation":{"chicago":"Alwen, Joel F, Jeremiah Blocki, and Ben Harsha. “Practical Graphs for Optimal Side-Channel Resistant Memory-Hard Functions.” In Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security, 1001–17. ACM Press, 2017. https://doi.org/10.1145/3133956.3134031.","short":"J.F. Alwen, J. Blocki, B. Harsha, in:, Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security, ACM Press, 2017, pp. 1001–1017.","mla":"Alwen, Joel F., et al. “Practical Graphs for Optimal Side-Channel Resistant Memory-Hard Functions.” Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security, ACM Press, 2017, pp. 1001–17, doi:10.1145/3133956.3134031.","apa":"Alwen, J. F., Blocki, J., & Harsha, B. (2017). Practical graphs for optimal side-channel resistant memory-hard functions. In Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security (pp. 1001–1017). Dallas, TX, USA: ACM Press. https://doi.org/10.1145/3133956.3134031","ieee":"J. F. Alwen, J. Blocki, and B. Harsha, “Practical graphs for optimal side-channel resistant memory-hard functions,” in Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security, Dallas, TX, USA, 2017, pp. 1001–1017.","ista":"Alwen JF, Blocki J, Harsha B. 2017. Practical graphs for optimal side-channel resistant memory-hard functions. Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security. CCS: Conference on Computer and Communications Security, 1001–1017.","ama":"Alwen JF, Blocki J, Harsha B. Practical graphs for optimal side-channel resistant memory-hard functions. In: Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security. ACM Press; 2017:1001-1017. doi:10.1145/3133956.3134031"},"oa":1,"main_file_link":[{"url":"https://eprint.iacr.org/2017/443","open_access":"1"}],"quality_controlled":"1","page":"1001-1017","project":[{"name":"Teaching Old Crypto New Tricks","call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815"}],"conference":{"location":"Dallas, TX, USA","start_date":"2017-10-30","end_date":"2017-11-03","name":"CCS: Conference on Computer and Communications Security"},"date_published":"2017-10-30T00:00:00Z","doi":"10.1145/3133956.3134031","language":[{"iso":"eng"}]},{"status":"public","ddc":["571"],"title":"Creating to understand – developmental biology meets engineering in Paris","intvolume":" 144","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"654","oa_version":"Submitted Version","file":[{"date_created":"2018-12-12T10:15:20Z","date_updated":"2020-07-14T12:47:33Z","checksum":"eef22a0f42a55b232cb2d1188a2322cb","file_id":"5139","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":228206,"file_name":"IST-2018-987-v1+1_2017_KichevaRivron__Creating_to.pdf","access_level":"open_access"}],"pubrep_id":"987","type":"journal_article","abstract":[{"text":"In November 2016, developmental biologists, synthetic biologists and engineers gathered in Paris for a meeting called ‘Engineering the embryo’. The participants shared an interest in exploring how synthetic systems can reveal new principles of embryonic development, and how the in vitro manipulation and modeling of development using stem cells can be used to integrate ideas and expertise from physics, developmental biology and tissue engineering. As we review here, the conference pinpointed some of the challenges arising at the intersection of these fields, along with great enthusiasm for finding new approaches and collaborations.","lang":"eng"}],"issue":"5","page":"733 - 736","publication":"Development","citation":{"mla":"Kicheva, Anna, and Nicolas Rivron. “Creating to Understand – Developmental Biology Meets Engineering in Paris.” Development, vol. 144, no. 5, Company of Biologists, 2017, pp. 733–36, doi:10.1242/dev.144915.","short":"A. Kicheva, N. Rivron, Development 144 (2017) 733–736.","chicago":"Kicheva, Anna, and Nicolas Rivron. “Creating to Understand – Developmental Biology Meets Engineering in Paris.” Development. Company of Biologists, 2017. https://doi.org/10.1242/dev.144915.","ama":"Kicheva A, Rivron N. Creating to understand – developmental biology meets engineering in Paris. Development. 2017;144(5):733-736. doi:10.1242/dev.144915","ista":"Kicheva A, Rivron N. 2017. Creating to understand – developmental biology meets engineering in Paris. Development. 144(5), 733–736.","ieee":"A. Kicheva and N. Rivron, “Creating to understand – developmental biology meets engineering in Paris,” Development, vol. 144, no. 5. Company of Biologists, pp. 733–736, 2017.","apa":"Kicheva, A., & Rivron, N. (2017). Creating to understand – developmental biology meets engineering in Paris. Development. Company of Biologists. https://doi.org/10.1242/dev.144915"},"date_published":"2017-03-01T00:00:00Z","scopus_import":1,"day":"01","has_accepted_license":"1","publication_status":"published","department":[{"_id":"AnKi"}],"publisher":"Company of Biologists","year":"2017","date_updated":"2021-01-12T08:07:54Z","date_created":"2018-12-11T11:47:44Z","volume":144,"author":[{"orcid":"0000-0003-4509-4998","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","last_name":"Kicheva","first_name":"Anna","full_name":"Kicheva, Anna"},{"full_name":"Rivron, Nicolas","first_name":"Nicolas","last_name":"Rivron"}],"file_date_updated":"2020-07-14T12:47:33Z","ec_funded":1,"publist_id":"7089","quality_controlled":"1","project":[{"name":"Coordination of Patterning And Growth In the Spinal Cord","call_identifier":"H2020","grant_number":"680037","_id":"B6FC0238-B512-11E9-945C-1524E6697425"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1242/dev.144915","month":"03","publication_identifier":{"issn":["09501991"]}},{"ec_funded":1,"article_number":"8006529","date_updated":"2021-01-12T08:07:53Z","date_created":"2019-06-06T12:53:09Z","author":[{"id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","first_name":"Maciej","last_name":"Skórski","full_name":"Skórski, Maciej"}],"publication_status":"published","department":[{"_id":"KrPi"}],"publisher":"IEEE","year":"2017","month":"08","publication_identifier":{"isbn":["9781509040964"]},"language":[{"iso":"eng"}],"conference":{"name":"ISIT: International Symposium on Information Theory","start_date":"2017-06-25","location":"Aachen, Germany","end_date":"2017-06-30"},"doi":"10.1109/isit.2017.8006529","quality_controlled":"1","project":[{"grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Teaching Old Crypto New Tricks"}],"main_file_link":[{"url":"https://arxiv.org/abs/1702.01666","open_access":"1"}],"external_id":{"arxiv":["1702.01666"]},"oa":1,"abstract":[{"lang":"eng","text":"This paper studies the complexity of estimating Rényi divergences of discrete distributions: p observed from samples and the baseline distribution q known a priori. Extending the results of Acharya et al. (SODA'15) on estimating Rényi entropy, we present improved estimation techniques together with upper and lower bounds on the sample complexity. We show that, contrarily to estimating Rényi entropy where a sublinear (in the alphabet size) number of samples suffices, the sample complexity is heavily dependent on events occurring unlikely in q, and is unbounded in general (no matter what an estimation technique is used). For any divergence of integer order bigger than 1, we provide upper and lower bounds on the number of samples dependent on probabilities of p and q (the lower bounds hold for non-integer orders as well). We conclude that the worst-case sample complexity is polynomial in the alphabet size if and only if the probabilities of q are non-negligible. This gives theoretical insights into heuristics used in the applied literature to handle numerical instability, which occurs for small probabilities of q. Our result shows that they should be handled with care not only because of numerical issues, but also because of a blow up in the sample complexity."}],"type":"conference","oa_version":"Preprint","title":"On the complexity of estimating Rènyi divergences","status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"6526","day":"09","scopus_import":1,"date_published":"2017-08-09T00:00:00Z","publication":"2017 IEEE International Symposium on Information Theory (ISIT)","citation":{"chicago":"Skórski, Maciej. “On the Complexity of Estimating Rènyi Divergences.” In 2017 IEEE International Symposium on Information Theory (ISIT). IEEE, 2017. https://doi.org/10.1109/isit.2017.8006529.","short":"M. Skórski, in:, 2017 IEEE International Symposium on Information Theory (ISIT), IEEE, 2017.","mla":"Skórski, Maciej. “On the Complexity of Estimating Rènyi Divergences.” 2017 IEEE International Symposium on Information Theory (ISIT), 8006529, IEEE, 2017, doi:10.1109/isit.2017.8006529.","apa":"Skórski, M. (2017). On the complexity of estimating Rènyi divergences. In 2017 IEEE International Symposium on Information Theory (ISIT). Aachen, Germany: IEEE. https://doi.org/10.1109/isit.2017.8006529","ieee":"M. Skórski, “On the complexity of estimating Rènyi divergences,” in 2017 IEEE International Symposium on Information Theory (ISIT), Aachen, Germany, 2017.","ista":"Skórski M. 2017. On the complexity of estimating Rènyi divergences. 2017 IEEE International Symposium on Information Theory (ISIT). ISIT: International Symposium on Information Theory, 8006529.","ama":"Skórski M. On the complexity of estimating Rènyi divergences. In: 2017 IEEE International Symposium on Information Theory (ISIT). IEEE; 2017. doi:10.1109/isit.2017.8006529"}},{"scopus_import":1,"has_accepted_license":"1","day":"06","citation":{"short":"T. Renault, A. Abraham, T. Bergmiller, G. Paradis, S. Rainville, E. Charpentier, C.C. Guet, Y. Tu, K. Namba, J. Keener, T. Minamino, M. Erhardt, ELife 6 (2017).","mla":"Renault, Thibaud, et al. “Bacterial Flagella Grow through an Injection Diffusion Mechanism.” ELife, vol. 6, e23136, eLife Sciences Publications, 2017, doi:10.7554/eLife.23136.","chicago":"Renault, Thibaud, Anthony Abraham, Tobias Bergmiller, Guillaume Paradis, Simon Rainville, Emmanuelle Charpentier, Calin C Guet, et al. “Bacterial Flagella Grow through an Injection Diffusion Mechanism.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.23136.","ama":"Renault T, Abraham A, Bergmiller T, et al. Bacterial flagella grow through an injection diffusion mechanism. eLife. 2017;6. doi:10.7554/eLife.23136","ieee":"T. Renault et al., “Bacterial flagella grow through an injection diffusion mechanism,” eLife, vol. 6. eLife Sciences Publications, 2017.","apa":"Renault, T., Abraham, A., Bergmiller, T., Paradis, G., Rainville, S., Charpentier, E., … Erhardt, M. (2017). Bacterial flagella grow through an injection diffusion mechanism. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.23136","ista":"Renault T, Abraham A, Bergmiller T, Paradis G, Rainville S, Charpentier E, Guet CC, Tu Y, Namba K, Keener J, Minamino T, Erhardt M. 2017. Bacterial flagella grow through an injection diffusion mechanism. eLife. 6, e23136."},"publication":"eLife","date_published":"2017-03-06T00:00:00Z","type":"journal_article","abstract":[{"text":"The bacterial flagellum is a self-assembling nanomachine. The external flagellar filament, several times longer than a bacterial cell body, is made of a few tens of thousands subunits of a single protein: flagellin. A fundamental problem concerns the molecular mechanism of how the flagellum grows outside the cell, where no discernible energy source is available. Here, we monitored the dynamic assembly of individual flagella using in situ labelling and real-time immunostaining of elongating flagellar filaments. We report that the rate of flagellum growth, initially ~1,700 amino acids per second, decreases with length and that the previously proposed chain mechanism does not contribute to the filament elongation dynamics. Inhibition of the proton motive force-dependent export apparatus revealed a major contribution of substrate injection in driving filament elongation. The combination of experimental and mathematical evidence demonstrates that a simple, injection-diffusion mechanism controls bacterial flagella growth outside the cell.","lang":"eng"}],"_id":"655","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 6","ddc":["579"],"title":"Bacterial flagella grow through an injection diffusion mechanism","status":"public","pubrep_id":"904","file":[{"file_id":"4716","relation":"main_file","checksum":"39e1c3e82ddac83a30422fa72fa1a383","date_created":"2018-12-12T10:08:53Z","date_updated":"2020-07-14T12:47:33Z","access_level":"open_access","file_name":"IST-2017-904-v1+1_elife-23136-v2.pdf","creator":"system","content_type":"application/pdf","file_size":5520359},{"checksum":"a6d542253028f52e00aa29739ddffe8f","date_created":"2018-12-12T10:08:54Z","date_updated":"2020-07-14T12:47:33Z","relation":"main_file","file_id":"4717","content_type":"application/pdf","file_size":11242920,"creator":"system","access_level":"open_access","file_name":"IST-2017-904-v1+2_elife-23136-figures-v2.pdf"}],"oa_version":"Published Version","publication_identifier":{"issn":["2050084X"]},"month":"03","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","doi":"10.7554/eLife.23136","language":[{"iso":"eng"}],"article_number":"e23136","publist_id":"7082","file_date_updated":"2020-07-14T12:47:33Z","year":"2017","department":[{"_id":"CaGu"}],"publisher":"eLife Sciences Publications","publication_status":"published","author":[{"full_name":"Renault, Thibaud","last_name":"Renault","first_name":"Thibaud"},{"full_name":"Abraham, Anthony","last_name":"Abraham","first_name":"Anthony"},{"id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5396-4346","first_name":"Tobias","last_name":"Bergmiller","full_name":"Bergmiller, Tobias"},{"full_name":"Paradis, Guillaume","last_name":"Paradis","first_name":"Guillaume"},{"first_name":"Simon","last_name":"Rainville","full_name":"Rainville, Simon"},{"first_name":"Emmanuelle","last_name":"Charpentier","full_name":"Charpentier, Emmanuelle"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","first_name":"Calin C","last_name":"Guet","full_name":"Guet, Calin C"},{"first_name":"Yuhai","last_name":"Tu","full_name":"Tu, Yuhai"},{"first_name":"Keiichi","last_name":"Namba","full_name":"Namba, Keiichi"},{"full_name":"Keener, James","first_name":"James","last_name":"Keener"},{"full_name":"Minamino, Tohru","last_name":"Minamino","first_name":"Tohru"},{"last_name":"Erhardt","first_name":"Marc","full_name":"Erhardt, Marc"}],"volume":6,"date_updated":"2021-01-12T08:07:55Z","date_created":"2018-12-11T11:47:44Z"},{"issue":"12","abstract":[{"lang":"eng","text":"Plant organs are typically organized into three main tissue layers. The middle ground tissue layer comprises the majority of the plant body and serves a wide range of functions, including photosynthesis, selective nutrient uptake and storage, and gravity sensing. Ground tissue patterning and maintenance in Arabidopsis are controlled by a well-established gene network revolving around the key regulator SHORT-ROOT (SHR). In contrast, it is completely unknown how ground tissue identity is first specified from totipotent precursor cells in the embryo. The plant signaling molecule auxin, acting through AUXIN RESPONSE FACTOR (ARF) transcription factors, is critical for embryo patterning. The auxin effector ARF5/MONOPTEROS (MP) acts both cell-autonomously and noncell-autonomously to control embryonic vascular tissue formation and root initiation, respectively. Here we show that auxin response and ARF activity cell-autonomously control the asymmetric division of the first ground tissue cells. By identifying embryonic target genes, we show that MP transcriptionally initiates the ground tissue lineage and acts upstream of the regulatory network that controls ground tissue patterning and maintenance. Strikingly, whereas the SHR network depends on MP, this MP function is, at least in part, SHR independent. Our study therefore identifies auxin response as a regulator of ground tissue specification in the embryonic root, and reveals that ground tissue initiation and maintenance use different regulators and mechanisms. Moreover, our data provide a framework for the simultaneous formation of multiple cell types by the same transcriptional regulator."}],"type":"journal_article","oa_version":"Submitted Version","_id":"657","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 114","status":"public","title":"Auxin response cell autonomously controls ground tissue initiation in the early arabidopsis embryo","day":"21","scopus_import":1,"date_published":"2017-03-21T00:00:00Z","citation":{"chicago":"Möller, Barbara, Colette Ten Hove, Daoquan Xiang, Nerys Williams, Lorena López, Saiko Yoshida, Margot Smit, Raju Datla, and Dolf Weijers. “Auxin Response Cell Autonomously Controls Ground Tissue Initiation in the Early Arabidopsis Embryo.” PNAS. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1616493114.","short":"B. Möller, C. Ten Hove, D. Xiang, N. Williams, L. López, S. Yoshida, M. Smit, R. Datla, D. Weijers, PNAS 114 (2017) E2533–E2539.","mla":"Möller, Barbara, et al. “Auxin Response Cell Autonomously Controls Ground Tissue Initiation in the Early Arabidopsis Embryo.” PNAS, vol. 114, no. 12, National Academy of Sciences, 2017, pp. E2533–39, doi:10.1073/pnas.1616493114.","ieee":"B. Möller et al., “Auxin response cell autonomously controls ground tissue initiation in the early arabidopsis embryo,” PNAS, vol. 114, no. 12. National Academy of Sciences, pp. E2533–E2539, 2017.","apa":"Möller, B., Ten Hove, C., Xiang, D., Williams, N., López, L., Yoshida, S., … Weijers, D. (2017). Auxin response cell autonomously controls ground tissue initiation in the early arabidopsis embryo. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1616493114","ista":"Möller B, Ten Hove C, Xiang D, Williams N, López L, Yoshida S, Smit M, Datla R, Weijers D. 2017. Auxin response cell autonomously controls ground tissue initiation in the early arabidopsis embryo. PNAS. 114(12), E2533–E2539.","ama":"Möller B, Ten Hove C, Xiang D, et al. Auxin response cell autonomously controls ground tissue initiation in the early arabidopsis embryo. PNAS. 2017;114(12):E2533-E2539. doi:10.1073/pnas.1616493114"},"publication":"PNAS","page":"E2533 - E2539","publist_id":"7076","author":[{"first_name":"Barbara","last_name":"Möller","full_name":"Möller, Barbara"},{"full_name":"Ten Hove, Colette","first_name":"Colette","last_name":"Ten Hove"},{"last_name":"Xiang","first_name":"Daoquan","full_name":"Xiang, Daoquan"},{"full_name":"Williams, Nerys","first_name":"Nerys","last_name":"Williams"},{"last_name":"López","first_name":"Lorena","full_name":"López, Lorena"},{"id":"2E46069C-F248-11E8-B48F-1D18A9856A87","first_name":"Saiko","last_name":"Yoshida","full_name":"Yoshida, Saiko"},{"first_name":"Margot","last_name":"Smit","full_name":"Smit, Margot"},{"first_name":"Raju","last_name":"Datla","full_name":"Datla, Raju"},{"last_name":"Weijers","first_name":"Dolf","full_name":"Weijers, Dolf"}],"volume":114,"date_updated":"2021-01-12T08:08:02Z","date_created":"2018-12-11T11:47:45Z","pmid":1,"year":"2017","department":[{"_id":"JiFr"}],"publisher":"National Academy of Sciences","publication_status":"published","publication_identifier":{"issn":["00278424"]},"month":"03","doi":"10.1073/pnas.1616493114","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5373392/"}],"external_id":{"pmid":["28265057"]},"quality_controlled":"1"},{"scopus_import":1,"month":"03","day":"15","publication_identifier":{"issn":["19466234"]},"publication":"Science Translational Medicine","citation":{"apa":"Novarino, G. (2017). Modeling Alzheimer’s disease in mice with human neurons. Science Translational Medicine. American Association for the Advancement of Science. https://doi.org/10.1126/scitranslmed.aam9867","ieee":"G. Novarino, “Modeling Alzheimer’s disease in mice with human neurons,” Science Translational Medicine, vol. 9, no. 381. American Association for the Advancement of Science, 2017.","ista":"Novarino G. 2017. Modeling Alzheimer’s disease in mice with human neurons. Science Translational Medicine. 9(381), eaam9867.","ama":"Novarino G. Modeling Alzheimer’s disease in mice with human neurons. Science Translational Medicine. 2017;9(381). doi:10.1126/scitranslmed.aam9867","chicago":"Novarino, Gaia. “Modeling Alzheimer’s Disease in Mice with Human Neurons.” Science Translational Medicine. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/scitranslmed.aam9867.","short":"G. Novarino, Science Translational Medicine 9 (2017).","mla":"Novarino, Gaia. “Modeling Alzheimer’s Disease in Mice with Human Neurons.” Science Translational Medicine, vol. 9, no. 381, eaam9867, American Association for the Advancement of Science, 2017, doi:10.1126/scitranslmed.aam9867."},"quality_controlled":"1","doi":"10.1126/scitranslmed.aam9867","date_published":"2017-03-15T00:00:00Z","language":[{"iso":"eng"}],"article_number":"eaam9867","type":"journal_article","abstract":[{"lang":"eng","text":"Human neurons transplanted into a mouse model for Alzheimer’s disease show human-specific vulnerability to β-amyloid plaques and may help to identify new therapeutic targets."}],"issue":"381","publist_id":"7079","_id":"656","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","year":"2017","status":"public","title":"Modeling Alzheimer's disease in mice with human neurons","publication_status":"published","intvolume":" 9","publisher":"American Association for the Advancement of Science","department":[{"_id":"GaNo"}],"author":[{"full_name":"Novarino, Gaia","first_name":"Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178"}],"date_created":"2018-12-11T11:47:45Z","date_updated":"2021-01-12T08:07:59Z","volume":9,"oa_version":"None"},{"oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:47:33Z","date_created":"2018-12-12T10:18:49Z","checksum":"b1bc43f96d1df3313c03032c2a46388d","relation":"main_file","file_id":"5371","file_size":8439566,"content_type":"application/pdf","creator":"system","file_name":"IST-2017-903-v1+1_fnbot-11-00008.pdf","access_level":"open_access"}],"pubrep_id":"903","status":"public","ddc":["006"],"title":"Self organized behavior generation for musculoskeletal robots","intvolume":" 11","user_id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","_id":"658","abstract":[{"text":"With the accelerated development of robot technologies, control becomes one of the central themes of research. In traditional approaches, the controller, by its internal functionality, finds appropriate actions on the basis of specific objectives for the task at hand. While very successful in many applications, self-organized control schemes seem to be favored in large complex systems with unknown dynamics or which are difficult to model. Reasons are the expected scalability, robustness, and resilience of self-organizing systems. The paper presents a self-learning neurocontroller based on extrinsic differential plasticity introduced recently, applying it to an anthropomorphic musculoskeletal robot arm with attached objects of unknown physical dynamics. The central finding of the paper is the following effect: by the mere feedback through the internal dynamics of the object, the robot is learning to relate each of the objects with a very specific sensorimotor pattern. Specifically, an attached pendulum pilots the arm into a circular motion, a half-filled bottle produces axis oriented shaking behavior, a wheel is getting rotated, and wiping patterns emerge automatically in a table-plus-brush setting. By these object-specific dynamical patterns, the robot may be said to recognize the object's identity, or in other words, it discovers dynamical affordances of objects. Furthermore, when including hand coordinates obtained from a camera, a dedicated hand-eye coordination self-organizes spontaneously. These phenomena are discussed from a specific dynamical system perspective. Central is the dedicated working regime at the border to instability with its potentially infinite reservoir of (limit cycle) attractors "waiting" to be excited. Besides converging toward one of these attractors, variate behavior is also arising from a self-induced attractor morphing driven by the learning rule. We claim that experimental investigations with this anthropomorphic, self-learning robot not only generate interesting and potentially useful behaviors, but may also help to better understand what subjective human muscle feelings are, how they can be rooted in sensorimotor patterns, and how these concepts may feed back on robotics.","lang":"eng"}],"issue":"MAR","type":"journal_article","date_published":"2017-03-16T00:00:00Z","publication":"Frontiers in Neurorobotics","citation":{"chicago":"Der, Ralf, and Georg S Martius. “Self Organized Behavior Generation for Musculoskeletal Robots.” Frontiers in Neurorobotics. Frontiers Research Foundation, 2017. https://doi.org/10.3389/fnbot.2017.00008.","mla":"Der, Ralf, and Georg S. Martius. “Self Organized Behavior Generation for Musculoskeletal Robots.” Frontiers in Neurorobotics, vol. 11, no. MAR, 00008, Frontiers Research Foundation, 2017, doi:10.3389/fnbot.2017.00008.","short":"R. Der, G.S. Martius, Frontiers in Neurorobotics 11 (2017).","ista":"Der R, Martius GS. 2017. Self organized behavior generation for musculoskeletal robots. Frontiers in Neurorobotics. 11(MAR), 00008.","apa":"Der, R., & Martius, G. S. (2017). Self organized behavior generation for musculoskeletal robots. Frontiers in Neurorobotics. Frontiers Research Foundation. https://doi.org/10.3389/fnbot.2017.00008","ieee":"R. Der and G. S. Martius, “Self organized behavior generation for musculoskeletal robots,” Frontiers in Neurorobotics, vol. 11, no. MAR. Frontiers Research Foundation, 2017.","ama":"Der R, Martius GS. Self organized behavior generation for musculoskeletal robots. Frontiers in Neurorobotics. 2017;11(MAR). doi:10.3389/fnbot.2017.00008"},"day":"16","has_accepted_license":"1","article_processing_charge":"Yes","scopus_import":1,"date_updated":"2021-01-12T08:08:04Z","date_created":"2018-12-11T11:47:45Z","volume":11,"author":[{"full_name":"Der, Ralf","last_name":"Der","first_name":"Ralf"},{"full_name":"Martius, Georg S","last_name":"Martius","first_name":"Georg S","id":"3A276B68-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","publisher":"Frontiers Research Foundation","department":[{"_id":"ChLa"},{"_id":"GaTk"}],"year":"2017","file_date_updated":"2020-07-14T12:47:33Z","publist_id":"7078","ec_funded":1,"article_number":"00008","language":[{"iso":"eng"}],"doi":"10.3389/fnbot.2017.00008","quality_controlled":"1","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"month":"03","publication_identifier":{"issn":["16625218"]}},{"date_published":"2017-03-22T00:00:00Z","publication":"Nature Communications","citation":{"ama":"Kage F, Winterhoff M, Dimchev V, et al. FMNL formins boost lamellipodial force generation. Nature Communications. 2017;8. doi:10.1038/ncomms14832","ista":"Kage F, Winterhoff M, Dimchev V, Müller J, Thalheim T, Freise A, Brühmann S, Kollasser J, Block J, Dimchev GA, Geyer M, Schnittler H, Brakebusch C, Stradal T, Carlier M, Sixt MK, Käs J, Faix J, Rottner K. 2017. FMNL formins boost lamellipodial force generation. Nature Communications. 8, 14832.","ieee":"F. Kage et al., “FMNL formins boost lamellipodial force generation,” Nature Communications, vol. 8. Nature Publishing Group, 2017.","apa":"Kage, F., Winterhoff, M., Dimchev, V., Müller, J., Thalheim, T., Freise, A., … Rottner, K. (2017). FMNL formins boost lamellipodial force generation. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms14832","mla":"Kage, Frieda, et al. “FMNL Formins Boost Lamellipodial Force Generation.” Nature Communications, vol. 8, 14832, Nature Publishing Group, 2017, doi:10.1038/ncomms14832.","short":"F. Kage, M. Winterhoff, V. Dimchev, J. Müller, T. Thalheim, A. Freise, S. Brühmann, J. Kollasser, J. Block, G.A. Dimchev, M. Geyer, H. Schnittler, C. Brakebusch, T. Stradal, M. Carlier, M.K. Sixt, J. Käs, J. Faix, K. Rottner, Nature Communications 8 (2017).","chicago":"Kage, Frieda, Moritz Winterhoff, Vanessa Dimchev, Jan Müller, Tobias Thalheim, Anika Freise, Stefan Brühmann, et al. “FMNL Formins Boost Lamellipodial Force Generation.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/ncomms14832."},"day":"22","article_processing_charge":"No","has_accepted_license":"1","scopus_import":1,"file":[{"creator":"system","content_type":"application/pdf","file_size":9523746,"access_level":"open_access","file_name":"IST-2017-902-v1+1_Kage_et_al-2017-Nature_Communications.pdf","checksum":"dae30190291c3630e8102d8714a8d23e","date_created":"2018-12-12T10:14:21Z","date_updated":"2020-07-14T12:47:34Z","file_id":"5072","relation":"main_file"}],"oa_version":"Published Version","pubrep_id":"902","title":"FMNL formins boost lamellipodial force generation","ddc":["570"],"status":"public","intvolume":" 8","_id":"659","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Migration frequently involves Rac-mediated protrusion of lamellipodia, formed by Arp2/3 complex-dependent branching thought to be crucial for force generation and stability of these networks. The formins FMNL2 and FMNL3 are Cdc42 effectors targeting to the lamellipodium tip and shown here to nucleate and elongate actin filaments with complementary activities in vitro. In migrating B16-F1 melanoma cells, both formins contribute to the velocity of lamellipodium protrusion. Loss of FMNL2/3 function in melanoma cells and fibroblasts reduces lamellipodial width, actin filament density and -bundling, without changing patterns of Arp2/3 complex incorporation. Strikingly, in melanoma cells, FMNL2/3 gene inactivation almost completely abolishes protrusion forces exerted by lamellipodia and modifies their ultrastructural organization. Consistently, CRISPR/Cas-mediated depletion of FMNL2/3 in fibroblasts reduces both migration and capability of cells to move against viscous media. Together, we conclude that force generation in lamellipodia strongly depends on FMNL formin activity, operating in addition to Arp2/3 complex-dependent filament branching.","lang":"eng"}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1038/ncomms14832","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"month":"03","publication_identifier":{"issn":["20411723"]},"date_created":"2018-12-11T11:47:46Z","date_updated":"2021-01-12T08:08:06Z","volume":8,"author":[{"first_name":"Frieda","last_name":"Kage","full_name":"Kage, Frieda"},{"full_name":"Winterhoff, Moritz","last_name":"Winterhoff","first_name":"Moritz"},{"last_name":"Dimchev","first_name":"Vanessa","full_name":"Dimchev, Vanessa"},{"last_name":"Müller","first_name":"Jan","id":"AD07FDB4-0F61-11EA-8158-C4CC64CEAA8D","full_name":"Müller, Jan"},{"full_name":"Thalheim, Tobias","first_name":"Tobias","last_name":"Thalheim"},{"full_name":"Freise, Anika","last_name":"Freise","first_name":"Anika"},{"full_name":"Brühmann, Stefan","last_name":"Brühmann","first_name":"Stefan"},{"full_name":"Kollasser, Jana","first_name":"Jana","last_name":"Kollasser"},{"first_name":"Jennifer","last_name":"Block","full_name":"Block, Jennifer"},{"full_name":"Dimchev, Georgi A","last_name":"Dimchev","first_name":"Georgi A"},{"first_name":"Matthias","last_name":"Geyer","full_name":"Geyer, Matthias"},{"full_name":"Schnittler, Hams","last_name":"Schnittler","first_name":"Hams"},{"first_name":"Cord","last_name":"Brakebusch","full_name":"Brakebusch, Cord"},{"last_name":"Stradal","first_name":"Theresia","full_name":"Stradal, Theresia"},{"full_name":"Carlier, Marie","last_name":"Carlier","first_name":"Marie"},{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt"},{"first_name":"Josef","last_name":"Käs","full_name":"Käs, Josef"},{"full_name":"Faix, Jan","first_name":"Jan","last_name":"Faix"},{"last_name":"Rottner","first_name":"Klemens","full_name":"Rottner, Klemens"}],"publication_status":"published","publisher":"Nature Publishing Group","department":[{"_id":"MiSi"}],"year":"2017","file_date_updated":"2020-07-14T12:47:34Z","publist_id":"7075","article_number":"14832"},{"abstract":[{"lang":"eng","text":"Growing microtubules are protected from depolymerization by the presence of a GTP or GDP/Pi cap. End-binding proteins of the EB1 family bind to the stabilizing cap, allowing monitoring of its size in real time. The cap size has been shown to correlate with instantaneous microtubule stability. Here we have quantitatively characterized the properties of cap size fluctuations during steadystate growth and have developed a theory predicting their timescale and amplitude from the kinetics of microtubule growth and cap maturation. In contrast to growth speed fluctuations, cap size fluctuations show a characteristic timescale, which is defined by the lifetime of the cap sites. Growth fluctuations affect the amplitude of cap size fluctuations; however, cap size does not affect growth speed, indicating that microtubules are far from instability during most of their time of growth. Our theory provides the basis for a quantitative understanding of microtubule stability fluctuations during steady-state growth."}],"issue":"13","type":"journal_article","oa_version":"Submitted Version","title":"Steady state EB cap size fluctuations are determined by stochastic microtubule growth and maturation","status":"public","intvolume":" 114","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"660","day":"28","scopus_import":1,"date_published":"2017-03-28T00:00:00Z","page":"3427 - 3432","publication":"PNAS","citation":{"ama":"Rickman J, Düllberg CF, Cade N, Griffin L, Surrey T. Steady state EB cap size fluctuations are determined by stochastic microtubule growth and maturation. PNAS. 2017;114(13):3427-3432. doi:10.1073/pnas.1620274114","apa":"Rickman, J., Düllberg, C. F., Cade, N., Griffin, L., & Surrey, T. (2017). Steady state EB cap size fluctuations are determined by stochastic microtubule growth and maturation. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1620274114","ieee":"J. Rickman, C. F. Düllberg, N. Cade, L. Griffin, and T. Surrey, “Steady state EB cap size fluctuations are determined by stochastic microtubule growth and maturation,” PNAS, vol. 114, no. 13. National Academy of Sciences, pp. 3427–3432, 2017.","ista":"Rickman J, Düllberg CF, Cade N, Griffin L, Surrey T. 2017. Steady state EB cap size fluctuations are determined by stochastic microtubule growth and maturation. PNAS. 114(13), 3427–3432.","short":"J. Rickman, C.F. Düllberg, N. Cade, L. Griffin, T. Surrey, PNAS 114 (2017) 3427–3432.","mla":"Rickman, Jamie, et al. “Steady State EB Cap Size Fluctuations Are Determined by Stochastic Microtubule Growth and Maturation.” PNAS, vol. 114, no. 13, National Academy of Sciences, 2017, pp. 3427–32, doi:10.1073/pnas.1620274114.","chicago":"Rickman, Jamie, Christian F Düllberg, Nicholas Cade, Lewis Griffin, and Thomas Surrey. “Steady State EB Cap Size Fluctuations Are Determined by Stochastic Microtubule Growth and Maturation.” PNAS. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1620274114."},"publist_id":"7073","date_created":"2018-12-11T11:47:46Z","date_updated":"2021-01-12T08:08:09Z","volume":114,"author":[{"first_name":"Jamie","last_name":"Rickman","full_name":"Rickman, Jamie"},{"full_name":"Düllberg, Christian F","last_name":"Düllberg","first_name":"Christian F","orcid":"0000-0001-6335-9748","id":"459064DC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Cade","first_name":"Nicholas","full_name":"Cade, Nicholas"},{"last_name":"Griffin","first_name":"Lewis","full_name":"Griffin, Lewis"},{"full_name":"Surrey, Thomas","last_name":"Surrey","first_name":"Thomas"}],"publication_status":"published","publisher":"National Academy of Sciences","department":[{"_id":"MaLo"}],"year":"2017","acknowledgement":"We thank Philippe Cluzel for helpful discussions and Gunnar Pruessner for data analysis advice. This work was supported by the Francis Crick Institute, which receives its core funding from Cancer Research UK Grant FC001163, Medical Research Council Grant FC001163, and Wellcome Trust Grant FC001163. This work was also supported by European Research Council Advanced Grant Project 323042 (to C.D. and T.S.).","pmid":1,"month":"03","publication_identifier":{"issn":["00278424"]},"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1620274114","quality_controlled":"1","external_id":{"pmid":["28280102"]},"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5380103/","open_access":"1"}],"oa":1},{"day":"01","scopus_import":1,"date_published":"2017-04-01T00:00:00Z","citation":{"ama":"Shi L, Hof B, Rampp M, Avila M. Hydrodynamic turbulence in quasi Keplerian rotating flows. Physics of Fluids. 2017;29(4). doi:10.1063/1.4981525","apa":"Shi, L., Hof, B., Rampp, M., & Avila, M. (2017). Hydrodynamic turbulence in quasi Keplerian rotating flows. Physics of Fluids. American Institute of Physics. https://doi.org/10.1063/1.4981525","ieee":"L. Shi, B. Hof, M. Rampp, and M. Avila, “Hydrodynamic turbulence in quasi Keplerian rotating flows,” Physics of Fluids, vol. 29, no. 4. American Institute of Physics, 2017.","ista":"Shi L, Hof B, Rampp M, Avila M. 2017. Hydrodynamic turbulence in quasi Keplerian rotating flows. Physics of Fluids. 29(4), 044107.","short":"L. Shi, B. Hof, M. Rampp, M. Avila, Physics of Fluids 29 (2017).","mla":"Shi, Liang, et al. “Hydrodynamic Turbulence in Quasi Keplerian Rotating Flows.” Physics of Fluids, vol. 29, no. 4, 044107, American Institute of Physics, 2017, doi:10.1063/1.4981525.","chicago":"Shi, Liang, Björn Hof, Markus Rampp, and Marc Avila. “Hydrodynamic Turbulence in Quasi Keplerian Rotating Flows.” Physics of Fluids. American Institute of Physics, 2017. https://doi.org/10.1063/1.4981525."},"publication":"Physics of Fluids","issue":"4","abstract":[{"text":"We report a direct-numerical-simulation study of the Taylor-Couette flow in the quasi-Keplerian regime at shear Reynolds numbers up to (105). Quasi-Keplerian rotating flow has been investigated for decades as a simplified model system to study the origin of turbulence in accretion disks that is not fully understood. The flow in this study is axially periodic and thus the experimental end-wall effects on the stability of the flow are avoided. Using optimal linear perturbations as initial conditions, our simulations find no sustained turbulence: the strong initial perturbations distort the velocity profile and trigger turbulence that eventually decays.","lang":"eng"}],"type":"journal_article","oa_version":"Submitted Version","intvolume":" 29","title":"Hydrodynamic turbulence in quasi Keplerian rotating flows","status":"public","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"662","publication_identifier":{"issn":["10706631"]},"month":"04","language":[{"iso":"eng"}],"doi":"10.1063/1.4981525","project":[{"grant_number":"SFB 963 TP A8","_id":"2511D90C-B435-11E9-9278-68D0E5697425","name":"Astrophysical instability of currents and turbulences"}],"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1703.01714"}],"publist_id":"7072","article_number":"044107","volume":29,"date_created":"2018-12-11T11:47:47Z","date_updated":"2021-01-12T08:08:15Z","author":[{"full_name":"Shi, Liang","first_name":"Liang","last_name":"Shi"},{"first_name":"Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn"},{"last_name":"Rampp","first_name":"Markus","full_name":"Rampp, Markus"},{"first_name":"Marc","last_name":"Avila","full_name":"Avila, Marc"}],"publisher":"American Institute of Physics","department":[{"_id":"BjHo"}],"publication_status":"published","year":"2017"},{"month":"04","publication_identifier":{"isbn":["978-145034590-3"]},"quality_controlled":"1","oa":1,"language":[{"iso":"eng"}],"conference":{"name":"HSCC: Hybrid Systems Computation and Control ","location":"Pittsburgh, PA, United States","start_date":"2017-04-18","end_date":"2017-04-20"},"doi":"10.1145/3049797.3049814","file_date_updated":"2020-07-14T12:47:34Z","publist_id":"7067","publication_status":"published","publisher":"ACM","department":[{"_id":"ToHe"}],"year":"2017","date_updated":"2021-01-12T08:08:17Z","date_created":"2018-12-11T11:47:47Z","author":[{"last_name":"Kong","first_name":"Hui","orcid":"0000-0002-3066-6941","id":"3BDE25AA-F248-11E8-B48F-1D18A9856A87","full_name":"Kong, Hui"},{"last_name":"Bogomolov","first_name":"Sergiy","orcid":"0000-0002-0686-0365","full_name":"Bogomolov, Sergiy"},{"full_name":"Schilling, Christian","last_name":"Schilling","first_name":"Christian"},{"full_name":"Jiang, Yu","first_name":"Yu","last_name":"Jiang"},{"first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"}],"scopus_import":1,"day":"01","has_accepted_license":"1","page":"163 - 172","publication":"Proceedings of the 20th International Conference on Hybrid Systems","citation":{"chicago":"Kong, Hui, Sergiy Bogomolov, Christian Schilling, Yu Jiang, and Thomas A Henzinger. “Safety Verification of Nonlinear Hybrid Systems Based on Invariant Clusters.” In Proceedings of the 20th International Conference on Hybrid Systems, 163–72. ACM, 2017. https://doi.org/10.1145/3049797.3049814.","mla":"Kong, Hui, et al. “Safety Verification of Nonlinear Hybrid Systems Based on Invariant Clusters.” Proceedings of the 20th International Conference on Hybrid Systems, ACM, 2017, pp. 163–72, doi:10.1145/3049797.3049814.","short":"H. Kong, S. Bogomolov, C. Schilling, Y. Jiang, T.A. Henzinger, in:, Proceedings of the 20th International Conference on Hybrid Systems, ACM, 2017, pp. 163–172.","ista":"Kong H, Bogomolov S, Schilling C, Jiang Y, Henzinger TA. 2017. Safety verification of nonlinear hybrid systems based on invariant clusters. Proceedings of the 20th International Conference on Hybrid Systems. HSCC: Hybrid Systems Computation and Control , 163–172.","ieee":"H. Kong, S. Bogomolov, C. Schilling, Y. Jiang, and T. A. Henzinger, “Safety verification of nonlinear hybrid systems based on invariant clusters,” in Proceedings of the 20th International Conference on Hybrid Systems, Pittsburgh, PA, United States, 2017, pp. 163–172.","apa":"Kong, H., Bogomolov, S., Schilling, C., Jiang, Y., & Henzinger, T. A. (2017). Safety verification of nonlinear hybrid systems based on invariant clusters. In Proceedings of the 20th International Conference on Hybrid Systems (pp. 163–172). Pittsburgh, PA, United States: ACM. https://doi.org/10.1145/3049797.3049814","ama":"Kong H, Bogomolov S, Schilling C, Jiang Y, Henzinger TA. Safety verification of nonlinear hybrid systems based on invariant clusters. In: Proceedings of the 20th International Conference on Hybrid Systems. ACM; 2017:163-172. doi:10.1145/3049797.3049814"},"date_published":"2017-04-01T00:00:00Z","type":"conference","abstract":[{"text":"In this paper, we propose an approach to automatically compute invariant clusters for nonlinear semialgebraic hybrid systems. An invariant cluster for an ordinary differential equation (ODE) is a multivariate polynomial invariant g(u→, x→) = 0, parametric in u→, which can yield an infinite number of concrete invariants by assigning different values to u→ so that every trajectory of the system can be overapproximated precisely by the intersection of a group of concrete invariants. For semialgebraic systems, which involve ODEs with multivariate polynomial right-hand sides, given a template multivariate polynomial g(u→, x→), an invariant cluster can be obtained by first computing the remainder of the Lie derivative of g(u→, x→) divided by g(u→, x→) and then solving the system of polynomial equations obtained from the coefficients of the remainder. Based on invariant clusters and sum-of-squares (SOS) programming, we present a new method for the safety verification of hybrid systems. Experiments on nonlinear benchmark systems from biology and control theory show that our approach is efficient. ","lang":"eng"}],"title":"Safety verification of nonlinear hybrid systems based on invariant clusters","status":"public","ddc":["000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"663","file":[{"relation":"main_file","file_id":"4873","checksum":"b7667434cbf5b5f0ade3bea1dbe5bf63","date_updated":"2020-07-14T12:47:34Z","date_created":"2018-12-12T10:11:20Z","access_level":"open_access","file_name":"IST-2017-817-v1+1_p163-kong.pdf","content_type":"application/pdf","file_size":1650530,"creator":"system"}],"oa_version":"Submitted Version","pubrep_id":"817"},{"publication_identifier":{"issn":["19466234"]},"day":"26","month":"04","scopus_import":1,"date_published":"2017-04-26T00:00:00Z","doi":"10.1126/scitranslmed.aan2786","language":[{"iso":"eng"}],"citation":{"short":"G. Novarino, Science Translational Medicine 9 (2017).","mla":"Novarino, Gaia. “The Antisocial Side of Antibiotics.” Science Translational Medicine, vol. 9, no. 387, 2786, American Association for the Advancement of Science, 2017, doi:10.1126/scitranslmed.aan2786.","chicago":"Novarino, Gaia. “The Antisocial Side of Antibiotics.” Science Translational Medicine. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/scitranslmed.aan2786.","ama":"Novarino G. The antisocial side of antibiotics. Science Translational Medicine. 2017;9(387). doi:10.1126/scitranslmed.aan2786","ieee":"G. Novarino, “The antisocial side of antibiotics,” Science Translational Medicine, vol. 9, no. 387. American Association for the Advancement of Science, 2017.","apa":"Novarino, G. (2017). The antisocial side of antibiotics. Science Translational Medicine. American Association for the Advancement of Science. https://doi.org/10.1126/scitranslmed.aan2786","ista":"Novarino G. 2017. The antisocial side of antibiotics. Science Translational Medicine. 9(387), 2786."},"publication":"Science Translational Medicine","quality_controlled":"1","issue":"387","publist_id":"7060","abstract":[{"text":"Perinatal exposure to penicillin may result in longlasting gut and behavioral changes.","lang":"eng"}],"type":"journal_article","article_number":"2786","author":[{"full_name":"Novarino, Gaia","last_name":"Novarino","first_name":"Gaia","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"None","volume":9,"date_updated":"2021-01-12T08:08:30Z","date_created":"2018-12-11T11:47:48Z","_id":"667","year":"2017","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"GaNo"}],"publisher":"American Association for the Advancement of Science","intvolume":" 9","status":"public","title":"The antisocial side of antibiotics","publication_status":"published"},{"_id":"668","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Multiple roles of filopodial dynamics in particle capture and phagocytosis and phenotypes of Cdc42 and Myo10 deletion","ddc":["570"],"intvolume":" 292","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":5647880,"creator":"dernst","file_name":"2017_JBC_Horsthemke.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:37Z","date_created":"2019-10-24T15:25:42Z","checksum":"d488162874326a4bb056065fa549dc4a","relation":"main_file","file_id":"6971"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Macrophage filopodia, finger-like membrane protrusions, were first implicated in phagocytosis more than 100 years ago, but little is still known about the involvement of these actin-dependent structures in particle clearance. Using spinning disk confocal microscopy to image filopodial dynamics in mouse resident Lifeact-EGFP macrophages, we show that filopodia, or filopodia-like structures, support pathogen clearance by multiple means. Filopodia supported the phagocytic uptake of bacterial (Escherichia coli) particles by (i) capturing along the filopodial shaft and surfing toward the cell body, the most common mode of capture; (ii) capturing via the tip followed by retraction; (iii) combinations of surfing and retraction; or (iv) sweeping actions. In addition, filopodia supported the uptake of zymosan (Saccharomyces cerevisiae) particles by (i) providing fixation, (ii) capturing at the tip and filopodia-guided actin anterograde flow with phagocytic cup formation, and (iii) the rapid growth of new protrusions. To explore the role of filopodia-inducing Cdc42, we generated myeloid-restricted Cdc42 knock-out mice. Cdc42-deficient macrophages exhibited rapid phagocytic cup kinetics, but reduced particle clearance, which could be explained by the marked rounded-up morphology of these cells. Macrophages lacking Myo10, thought to act downstream of Cdc42, had normal morphology, motility, and phagocytic cup formation, but displayed markedly reduced filopodia formation. In conclusion, live-cell imaging revealed multiple mechanisms involving macrophage filopodia in particle capture and engulfment. Cdc42 is not critical for filopodia or phagocytic cup formation, but plays a key role in driving macrophage lamellipodial spreading."}],"issue":"17","publication":"Journal of Biological Chemistry","citation":{"ista":"Horsthemke M, Bachg A, Groll K, Moyzio S, Müther B, Hemkemeyer S, Wedlich Söldner R, Sixt MK, Tacke S, Bähler M, Hanley P. 2017. Multiple roles of filopodial dynamics in particle capture and phagocytosis and phenotypes of Cdc42 and Myo10 deletion. Journal of Biological Chemistry. 292(17), 7258–7273.","ieee":"M. Horsthemke et al., “Multiple roles of filopodial dynamics in particle capture and phagocytosis and phenotypes of Cdc42 and Myo10 deletion,” Journal of Biological Chemistry, vol. 292, no. 17. American Society for Biochemistry and Molecular Biology, pp. 7258–7273, 2017.","apa":"Horsthemke, M., Bachg, A., Groll, K., Moyzio, S., Müther, B., Hemkemeyer, S., … Hanley, P. (2017). Multiple roles of filopodial dynamics in particle capture and phagocytosis and phenotypes of Cdc42 and Myo10 deletion. Journal of Biological Chemistry. American Society for Biochemistry and Molecular Biology. https://doi.org/10.1074/jbc.M116.766923","ama":"Horsthemke M, Bachg A, Groll K, et al. Multiple roles of filopodial dynamics in particle capture and phagocytosis and phenotypes of Cdc42 and Myo10 deletion. Journal of Biological Chemistry. 2017;292(17):7258-7273. doi:10.1074/jbc.M116.766923","chicago":"Horsthemke, Markus, Anne Bachg, Katharina Groll, Sven Moyzio, Barbara Müther, Sandra Hemkemeyer, Roland Wedlich Söldner, et al. “Multiple Roles of Filopodial Dynamics in Particle Capture and Phagocytosis and Phenotypes of Cdc42 and Myo10 Deletion.” Journal of Biological Chemistry. American Society for Biochemistry and Molecular Biology, 2017. https://doi.org/10.1074/jbc.M116.766923.","mla":"Horsthemke, Markus, et al. “Multiple Roles of Filopodial Dynamics in Particle Capture and Phagocytosis and Phenotypes of Cdc42 and Myo10 Deletion.” Journal of Biological Chemistry, vol. 292, no. 17, American Society for Biochemistry and Molecular Biology, 2017, pp. 7258–73, doi:10.1074/jbc.M116.766923.","short":"M. Horsthemke, A. Bachg, K. Groll, S. Moyzio, B. Müther, S. Hemkemeyer, R. Wedlich Söldner, M.K. Sixt, S. Tacke, M. Bähler, P. Hanley, Journal of Biological Chemistry 292 (2017) 7258–7273."},"article_type":"original","page":"7258 - 7273","date_published":"2017-04-28T00:00:00Z","scopus_import":1,"day":"28","has_accepted_license":"1","year":"2017","publication_status":"published","department":[{"_id":"MiSi"}],"publisher":"American Society for Biochemistry and Molecular Biology","author":[{"last_name":"Horsthemke","first_name":"Markus","full_name":"Horsthemke, Markus"},{"full_name":"Bachg, Anne","first_name":"Anne","last_name":"Bachg"},{"full_name":"Groll, Katharina","last_name":"Groll","first_name":"Katharina"},{"last_name":"Moyzio","first_name":"Sven","full_name":"Moyzio, Sven"},{"first_name":"Barbara","last_name":"Müther","full_name":"Müther, Barbara"},{"full_name":"Hemkemeyer, Sandra","first_name":"Sandra","last_name":"Hemkemeyer"},{"full_name":"Wedlich Söldner, Roland","first_name":"Roland","last_name":"Wedlich Söldner"},{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K"},{"full_name":"Tacke, Sebastian","first_name":"Sebastian","last_name":"Tacke"},{"full_name":"Bähler, Martin","last_name":"Bähler","first_name":"Martin"},{"last_name":"Hanley","first_name":"Peter","full_name":"Hanley, Peter"}],"date_updated":"2021-01-12T08:08:34Z","date_created":"2018-12-11T11:47:49Z","volume":292,"file_date_updated":"2020-07-14T12:47:37Z","publist_id":"7059","oa":1,"quality_controlled":"1","doi":"10.1074/jbc.M116.766923","language":[{"iso":"eng"}],"month":"04","publication_identifier":{"issn":["00219258"]}},{"date_published":"2017-05-01T00:00:00Z","publication":"Plant Physiology","citation":{"short":"L. Synek, N. Vukašinović, I. Kulich, M. Hála, K. Aldorfová, M. Fendrych, V. Žárský, Plant Physiology 174 (2017) 223–240.","mla":"Synek, Lukáš, et al. “EXO70C2 Is a Key Regulatory Factor for Optimal Tip Growth of Pollen.” Plant Physiology, vol. 174, no. 1, American Society of Plant Biologists, 2017, pp. 223–40, doi:10.1104/pp.16.01282.","chicago":"Synek, Lukáš, Nemanja Vukašinović, Ivan Kulich, Michal Hála, Klára Aldorfová, Matyas Fendrych, and Viktor Žárský. “EXO70C2 Is a Key Regulatory Factor for Optimal Tip Growth of Pollen.” Plant Physiology. American Society of Plant Biologists, 2017. https://doi.org/10.1104/pp.16.01282.","ama":"Synek L, Vukašinović N, Kulich I, et al. EXO70C2 is a key regulatory factor for optimal tip growth of pollen. Plant Physiology. 2017;174(1):223-240. doi:10.1104/pp.16.01282","apa":"Synek, L., Vukašinović, N., Kulich, I., Hála, M., Aldorfová, K., Fendrych, M., & Žárský, V. (2017). EXO70C2 is a key regulatory factor for optimal tip growth of pollen. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1104/pp.16.01282","ieee":"L. Synek et al., “EXO70C2 is a key regulatory factor for optimal tip growth of pollen,” Plant Physiology, vol. 174, no. 1. American Society of Plant Biologists, pp. 223–240, 2017.","ista":"Synek L, Vukašinović N, Kulich I, Hála M, Aldorfová K, Fendrych M, Žárský V. 2017. EXO70C2 is a key regulatory factor for optimal tip growth of pollen. Plant Physiology. 174(1), 223–240."},"article_type":"original","page":"223 - 240","day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":1,"oa_version":"Submitted Version","file":[{"checksum":"97155acc6aa5f0d0a78e0589a932fe02","date_created":"2019-11-18T16:16:18Z","date_updated":"2020-07-14T12:47:37Z","relation":"main_file","file_id":"7041","content_type":"application/pdf","file_size":2176903,"creator":"dernst","access_level":"open_access","file_name":"2017_PlantPhysio_Synek.pdf"}],"_id":"669","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"EXO70C2 is a key regulatory factor for optimal tip growth of pollen","ddc":["580"],"status":"public","intvolume":" 174","abstract":[{"lang":"eng","text":"The exocyst, a eukaryotic tethering complex, coregulates targeted exocytosis as an effector of small GTPases in polarized cell growth. In land plants, several exocyst subunits are encoded by double or triple paralogs, culminating in tens of EXO70 paralogs. Out of 23 Arabidopsis thaliana EXO70 isoforms, we analyzed seven isoforms expressed in pollen. Genetic and microscopic analyses of single mutants in EXO70A2, EXO70C1, EXO70C2, EXO70F1, EXO70H3, EXO70H5, and EXO70H6 genes revealed that only a loss-of-function EXO70C2 allele resulted in a significant male-specific transmission defect (segregation 40%:51%:9%) due to aberrant pollen tube growth. Mutant pollen tubes grown in vitro exhibited an enhanced growth rate and a decreased thickness of the tip cell wall, causing tip bursts. However, exo70C2 pollen tubes could frequently recover and restart their speedy elongation, resulting in a repetitive stop-and-go growth dynamics. A pollenspecific depletion of the closest paralog, EXO70C1, using artificial microRNA in the exo70C2 mutant background, resulted in a complete pollen-specific transmission defect, suggesting redundant functions of EXO70C1 and EXO70C2. Both EXO70C1 and EXO70C2, GFP tagged and expressed under the control of their native promoters, localized in the cytoplasm of pollen grains, pollen tubes, and also root trichoblast cells. The expression of EXO70C2-GFP complemented the aberrant growth of exo70C2 pollen tubes. The absent EXO70C2 interactions with core exocyst subunits in the yeast two-hybrid assay, cytoplasmic localization, and genetic effect suggest an unconventional EXO70 function possibly as a regulator of exocytosis outside the exocyst complex. In conclusion, EXO70C2 is a novel factor contributing to the regulation of optimal tip growth of Arabidopsis pollen tubes. "}],"issue":"1","type":"journal_article","doi":"10.1104/pp.16.01282","language":[{"iso":"eng"}],"oa":1,"external_id":{"pmid":["28356503"]},"quality_controlled":"1","month":"05","publication_identifier":{"issn":["00320889"]},"author":[{"full_name":"Synek, Lukáš","first_name":"Lukáš","last_name":"Synek"},{"last_name":"Vukašinović","first_name":"Nemanja","full_name":"Vukašinović, Nemanja"},{"full_name":"Kulich, Ivan","last_name":"Kulich","first_name":"Ivan"},{"full_name":"Hála, Michal","first_name":"Michal","last_name":"Hála"},{"full_name":"Aldorfová, Klára","first_name":"Klára","last_name":"Aldorfová"},{"full_name":"Fendrych, Matyas","orcid":"0000-0002-9767-8699","id":"43905548-F248-11E8-B48F-1D18A9856A87","last_name":"Fendrych","first_name":"Matyas"},{"full_name":"Žárský, Viktor","last_name":"Žárský","first_name":"Viktor"}],"date_updated":"2021-01-12T08:08:35Z","date_created":"2018-12-11T11:47:49Z","volume":174,"year":"2017","pmid":1,"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"American Society of Plant Biologists","file_date_updated":"2020-07-14T12:47:37Z","publist_id":"7058"},{"scopus_import":1,"article_processing_charge":"Yes (in subscription journal)","day":"02","page":"4715 - 4720","citation":{"short":"C. Hilbe, V. Martinez, K. Chatterjee, M. Nowak, PNAS 114 (2017) 4715–4720.","mla":"Hilbe, Christian, et al. “Memory-n Strategies of Direct Reciprocity.” PNAS, vol. 114, no. 18, National Academy of Sciences, 2017, pp. 4715–20, doi:10.1073/pnas.1621239114.","chicago":"Hilbe, Christian, Vaquero Martinez, Krishnendu Chatterjee, and Martin Nowak. “Memory-n Strategies of Direct Reciprocity.” PNAS. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1621239114.","ama":"Hilbe C, Martinez V, Chatterjee K, Nowak M. Memory-n strategies of direct reciprocity. PNAS. 2017;114(18):4715-4720. doi:10.1073/pnas.1621239114","ieee":"C. Hilbe, V. Martinez, K. Chatterjee, and M. Nowak, “Memory-n strategies of direct reciprocity,” PNAS, vol. 114, no. 18. National Academy of Sciences, pp. 4715–4720, 2017.","apa":"Hilbe, C., Martinez, V., Chatterjee, K., & Nowak, M. (2017). Memory-n strategies of direct reciprocity. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1621239114","ista":"Hilbe C, Martinez V, Chatterjee K, Nowak M. 2017. Memory-n strategies of direct reciprocity. PNAS. 114(18), 4715–4720."},"publication":"PNAS","date_published":"2017-05-02T00:00:00Z","type":"journal_article","issue":"18","abstract":[{"lang":"eng","text":"Humans routinely use conditionally cooperative strategies when interacting in repeated social dilemmas. They are more likely to cooperate if others cooperated before, and are ready to retaliate if others defected. To capture the emergence of reciprocity, most previous models consider subjects who can only choose from a restricted set of representative strategies, or who react to the outcome of the very last round only. As players memorize more rounds, the dimension of the strategy space increases exponentially. This increasing computational complexity renders simulations for individuals with higher cognitive abilities infeasible, especially if multiplayer interactions are taken into account. Here, we take an axiomatic approach instead. We propose several properties that a robust cooperative strategy for a repeated multiplayer dilemma should have. These properties naturally lead to a unique class of cooperative strategies, which contains the classical Win-Stay Lose-Shift rule as a special case. A comprehensive numerical analysis for the prisoner's dilemma and for the public goods game suggests that strategies of this class readily evolve across various memory-n spaces. Our results reveal that successful strategies depend not only on how cooperative others were in the past but also on the respective context of cooperation."}],"intvolume":" 114","status":"public","title":"Memory-n strategies of direct reciprocity","_id":"671","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","publication_identifier":{"issn":["00278424"]},"month":"05","project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"name":"Game Theory","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407"}],"quality_controlled":"1","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5422766/","open_access":"1"}],"external_id":{"pmid":["28420786"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1621239114","publist_id":"7053","ec_funded":1,"department":[{"_id":"KrCh"}],"publisher":"National Academy of Sciences","publication_status":"published","pmid":1,"year":"2017","volume":114,"date_updated":"2021-01-12T08:08:37Z","date_created":"2018-12-11T11:47:50Z","author":[{"last_name":"Hilbe","first_name":"Christian","orcid":"0000-0001-5116-955X","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","full_name":"Hilbe, Christian"},{"full_name":"Martinez, Vaquero","first_name":"Vaquero","last_name":"Martinez"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"full_name":"Nowak, Martin","last_name":"Nowak","first_name":"Martin"}]},{"issue":"2","abstract":[{"text":"We propose an efficient method to model paper tearing in the context of interactive modeling. The method uses geometrical information to automatically detect potential starting points of tears. We further introduce a new hybrid geometrical and physical-based method to compute the trajectory of tears while procedurally synthesizing high resolution details of the tearing path using a texture based approach. The results obtained are compared with real paper and with previous studies on the expected geometric paths of paper that tears.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","intvolume":" 36","title":"Interactive paper tearing","status":"public","ddc":["000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"670","article_processing_charge":"No","day":"01","scopus_import":1,"date_published":"2017-05-01T00:00:00Z","page":"95 - 106","article_type":"original","citation":{"chicago":"Schreck, Camille, Damien Rohmer, and Stefanie Hahmann. “Interactive Paper Tearing.” Computer Graphics Forum. Wiley, 2017. https://doi.org/10.1111/cgf.13110.","mla":"Schreck, Camille, et al. “Interactive Paper Tearing.” Computer Graphics Forum, vol. 36, no. 2, Wiley, 2017, pp. 95–106, doi:10.1111/cgf.13110.","short":"C. Schreck, D. Rohmer, S. Hahmann, Computer Graphics Forum 36 (2017) 95–106.","ista":"Schreck C, Rohmer D, Hahmann S. 2017. Interactive paper tearing. Computer Graphics Forum. 36(2), 95–106.","apa":"Schreck, C., Rohmer, D., & Hahmann, S. (2017). Interactive paper tearing. Computer Graphics Forum. Wiley. https://doi.org/10.1111/cgf.13110","ieee":"C. Schreck, D. Rohmer, and S. Hahmann, “Interactive paper tearing,” Computer Graphics Forum, vol. 36, no. 2. Wiley, pp. 95–106, 2017.","ama":"Schreck C, Rohmer D, Hahmann S. Interactive paper tearing. Computer Graphics Forum. 2017;36(2):95-106. doi:10.1111/cgf.13110"},"publication":"Computer Graphics Forum","publist_id":"7056","volume":36,"date_created":"2018-12-11T11:47:49Z","date_updated":"2021-01-12T08:08:37Z","author":[{"full_name":"Schreck, Camille","last_name":"Schreck","first_name":"Camille","id":"2B14B676-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Rohmer, Damien","first_name":"Damien","last_name":"Rohmer"},{"full_name":"Hahmann, Stefanie","last_name":"Hahmann","first_name":"Stefanie"}],"department":[{"_id":"ChWo"}],"publisher":"Wiley","publication_status":"published","year":"2017","publication_identifier":{"issn":["01677055"]},"month":"05","language":[{"iso":"eng"}],"doi":"10.1111/cgf.13110","project":[{"_id":"25357BD2-B435-11E9-9278-68D0E5697425","grant_number":"P 24352-N23","call_identifier":"FWF","name":"Deep Pictures: Creating Visual and Haptic Vector Images"}],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://hal.inria.fr/hal-01647113/file/eg_2017_schreck_paper_tearing.pdf"}],"oa":1},{"language":[{"iso":"eng"}],"doi":"10.1016/j.celrep.2017.04.027","quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)","grant_number":"281556","_id":"25A603A2-B435-11E9-9278-68D0E5697425"},{"name":"Cytoskeletal force generation and transduction of leukocytes (FWF)","call_identifier":"FWF","grant_number":"Y 564-B12","_id":"25A8E5EA-B435-11E9-9278-68D0E5697425"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"month":"05","publication_identifier":{"issn":["22111247"]},"date_created":"2018-12-11T11:47:50Z","date_updated":"2023-02-23T12:50:09Z","volume":19,"author":[{"id":"368EE576-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7829-3518","first_name":"Kari","last_name":"Vaahtomeri","full_name":"Vaahtomeri, Kari"},{"full_name":"Brown, Markus","first_name":"Markus","last_name":"Brown","id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","first_name":"Robert"},{"full_name":"De Vries, Ingrid","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","last_name":"De Vries","first_name":"Ingrid"},{"last_name":"Leithner","first_name":"Alexander F","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","full_name":"Leithner, Alexander F"},{"full_name":"Mehling, Matthias","first_name":"Matthias","last_name":"Mehling","id":"3C23B994-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8599-1226"},{"full_name":"Kaufmann, Walter","last_name":"Kaufmann","first_name":"Walter","orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sixt, Michael K","first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179"}],"publication_status":"published","publisher":"Cell Press","department":[{"_id":"MiSi"},{"_id":"Bio"},{"_id":"EM-Fac"}],"year":"2017","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","file_date_updated":"2020-07-14T12:47:38Z","ec_funded":1,"publist_id":"7052","date_published":"2017-05-02T00:00:00Z","page":"902 - 909","publication":"Cell Reports","citation":{"ama":"Vaahtomeri K, Brown M, Hauschild R, et al. Locally triggered release of the chemokine CCL21 promotes dendritic cell transmigration across lymphatic endothelia. Cell Reports. 2017;19(5):902-909. doi:10.1016/j.celrep.2017.04.027","ista":"Vaahtomeri K, Brown M, Hauschild R, de Vries I, Leithner AF, Mehling M, Kaufmann W, Sixt MK. 2017. Locally triggered release of the chemokine CCL21 promotes dendritic cell transmigration across lymphatic endothelia. Cell Reports. 19(5), 902–909.","apa":"Vaahtomeri, K., Brown, M., Hauschild, R., de Vries, I., Leithner, A. F., Mehling, M., … Sixt, M. K. (2017). Locally triggered release of the chemokine CCL21 promotes dendritic cell transmigration across lymphatic endothelia. Cell Reports. Cell Press. https://doi.org/10.1016/j.celrep.2017.04.027","ieee":"K. Vaahtomeri et al., “Locally triggered release of the chemokine CCL21 promotes dendritic cell transmigration across lymphatic endothelia,” Cell Reports, vol. 19, no. 5. Cell Press, pp. 902–909, 2017.","mla":"Vaahtomeri, Kari, et al. “Locally Triggered Release of the Chemokine CCL21 Promotes Dendritic Cell Transmigration across Lymphatic Endothelia.” Cell Reports, vol. 19, no. 5, Cell Press, 2017, pp. 902–09, doi:10.1016/j.celrep.2017.04.027.","short":"K. Vaahtomeri, M. Brown, R. Hauschild, I. de Vries, A.F. Leithner, M. Mehling, W. Kaufmann, M.K. Sixt, Cell Reports 19 (2017) 902–909.","chicago":"Vaahtomeri, Kari, Markus Brown, Robert Hauschild, Ingrid de Vries, Alexander F Leithner, Matthias Mehling, Walter Kaufmann, and Michael K Sixt. “Locally Triggered Release of the Chemokine CCL21 Promotes Dendritic Cell Transmigration across Lymphatic Endothelia.” Cell Reports. Cell Press, 2017. https://doi.org/10.1016/j.celrep.2017.04.027."},"day":"02","has_accepted_license":"1","article_processing_charge":"Yes","scopus_import":1,"oa_version":"Published Version","file":[{"relation":"main_file","file_id":"5109","date_created":"2018-12-12T10:14:54Z","date_updated":"2020-07-14T12:47:38Z","checksum":"8fdddaab1f1d76a6ec9ca94dcb6b07a2","file_name":"IST-2017-900-v1+1_1-s2.0-S2211124717305211-main.pdf","access_level":"open_access","file_size":2248814,"content_type":"application/pdf","creator":"system"}],"pubrep_id":"900","title":"Locally triggered release of the chemokine CCL21 promotes dendritic cell transmigration across lymphatic endothelia","status":"public","ddc":["570"],"intvolume":" 19","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"672","abstract":[{"lang":"eng","text":"Trafficking cells frequently transmigrate through epithelial and endothelial monolayers. How monolayers cooperate with the penetrating cells to support their transit is poorly understood. We studied dendritic cell (DC) entry into lymphatic capillaries as a model system for transendothelial migration. We find that the chemokine CCL21, which is the decisive guidance cue for intravasation, mainly localizes in the trans-Golgi network and intracellular vesicles of lymphatic endothelial cells. Upon DC transmigration, these Golgi deposits disperse and CCL21 becomes extracellularly enriched at the sites of endothelial cell-cell junctions. When we reconstitute the transmigration process in vitro, we find that secretion of CCL21-positive vesicles is triggered by a DC contact-induced calcium signal, and selective calcium chelation in lymphatic endothelium attenuates transmigration. Altogether, our data demonstrate a chemokine-mediated feedback between DCs and lymphatic endothelium, which facilitates transendothelial migration."}],"issue":"5","type":"journal_article"},{"date_published":"2017-05-09T00:00:00Z","page":"1314 - 1325","citation":{"ama":"Schwarz J, Bierbaum V, Vaahtomeri K, et al. Dendritic cells interpret haptotactic chemokine gradients in a manner governed by signal to noise ratio and dependent on GRK6. Current Biology. 2017;27(9):1314-1325. doi:10.1016/j.cub.2017.04.004","ista":"Schwarz J, Bierbaum V, Vaahtomeri K, Hauschild R, Brown M, de Vries I, Leithner AF, Reversat A, Merrin J, Tarrant T, Bollenbach MT, Sixt MK. 2017. Dendritic cells interpret haptotactic chemokine gradients in a manner governed by signal to noise ratio and dependent on GRK6. Current Biology. 27(9), 1314–1325.","ieee":"J. Schwarz et al., “Dendritic cells interpret haptotactic chemokine gradients in a manner governed by signal to noise ratio and dependent on GRK6,” Current Biology, vol. 27, no. 9. Cell Press, pp. 1314–1325, 2017.","apa":"Schwarz, J., Bierbaum, V., Vaahtomeri, K., Hauschild, R., Brown, M., de Vries, I., … Sixt, M. K. (2017). Dendritic cells interpret haptotactic chemokine gradients in a manner governed by signal to noise ratio and dependent on GRK6. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2017.04.004","mla":"Schwarz, Jan, et al. “Dendritic Cells Interpret Haptotactic Chemokine Gradients in a Manner Governed by Signal to Noise Ratio and Dependent on GRK6.” Current Biology, vol. 27, no. 9, Cell Press, 2017, pp. 1314–25, doi:10.1016/j.cub.2017.04.004.","short":"J. Schwarz, V. Bierbaum, K. Vaahtomeri, R. Hauschild, M. Brown, I. de Vries, A.F. Leithner, A. Reversat, J. Merrin, T. Tarrant, M.T. Bollenbach, M.K. Sixt, Current Biology 27 (2017) 1314–1325.","chicago":"Schwarz, Jan, Veronika Bierbaum, Kari Vaahtomeri, Robert Hauschild, Markus Brown, Ingrid de Vries, Alexander F Leithner, et al. “Dendritic Cells Interpret Haptotactic Chemokine Gradients in a Manner Governed by Signal to Noise Ratio and Dependent on GRK6.” Current Biology. Cell Press, 2017. https://doi.org/10.1016/j.cub.2017.04.004."},"publication":"Current Biology","day":"09","scopus_import":1,"oa_version":"None","intvolume":" 27","status":"public","title":"Dendritic cells interpret haptotactic chemokine gradients in a manner governed by signal to noise ratio and dependent on GRK6","_id":"674","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","issue":"9","abstract":[{"lang":"eng","text":"Navigation of cells along gradients of guidance cues is a determining step in many developmental and immunological processes. Gradients can either be soluble or immobilized to tissues as demonstrated for the haptotactic migration of dendritic cells (DCs) toward higher concentrations of immobilized chemokine CCL21. To elucidate how gradient characteristics govern cellular response patterns, we here introduce an in vitro system allowing to track migratory responses of DCs to precisely controlled immobilized gradients of CCL21. We find that haptotactic sensing depends on the absolute CCL21 concentration and local steepness of the gradient, consistent with a scenario where DC directionality is governed by the signal-to-noise ratio of CCL21 binding to the receptor CCR7. We find that the conditions for optimal DC guidance are perfectly provided by the CCL21 gradients we measure in vivo. Furthermore, we find that CCR7 signal termination by the G-protein-coupled receptor kinase 6 (GRK6) is crucial for haptotactic but dispensable for chemotactic CCL21 gradient sensing in vitro and confirm those observations in vivo. These findings suggest that stable, tissue-bound CCL21 gradients as sustainable “roads” ensure optimal guidance in vivo."}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1016/j.cub.2017.04.004","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Cytoskeletal force generation and transduction of leukocytes (FWF)","grant_number":"Y 564-B12","_id":"25A8E5EA-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","publication_identifier":{"issn":["09609822"]},"month":"05","volume":27,"date_updated":"2023-02-23T12:50:44Z","date_created":"2018-12-11T11:47:51Z","author":[{"full_name":"Schwarz, Jan","first_name":"Jan","last_name":"Schwarz","id":"346C1EC6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Bierbaum","first_name":"Veronika","id":"3FD04378-F248-11E8-B48F-1D18A9856A87","full_name":"Bierbaum, Veronika"},{"orcid":"0000-0001-7829-3518","id":"368EE576-F248-11E8-B48F-1D18A9856A87","last_name":"Vaahtomeri","first_name":"Kari","full_name":"Vaahtomeri, Kari"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","first_name":"Robert","last_name":"Hauschild","full_name":"Hauschild, Robert"},{"last_name":"Brown","first_name":"Markus","id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87","full_name":"Brown, Markus"},{"full_name":"De Vries, Ingrid","first_name":"Ingrid","last_name":"De Vries","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Leithner, Alexander F","last_name":"Leithner","first_name":"Alexander F","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Reversat, Anne","first_name":"Anne","last_name":"Reversat","id":"35B76592-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0666-8928"},{"last_name":"Merrin","first_name":"Jack","orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87","full_name":"Merrin, Jack"},{"first_name":"Teresa","last_name":"Tarrant","full_name":"Tarrant, Teresa"},{"full_name":"Bollenbach, Tobias","last_name":"Bollenbach","first_name":"Tobias","orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sixt, Michael K","last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Cell Press","department":[{"_id":"MiSi"},{"_id":"Bio"},{"_id":"NanoFab"}],"publication_status":"published","year":"2017","publist_id":"7050","ec_funded":1},{"date_updated":"2021-01-12T08:08:57Z","date_created":"2018-12-11T11:47:52Z","volume":19,"author":[{"last_name":"Lademann","first_name":"Claudio","full_name":"Lademann, Claudio"},{"full_name":"Renkawitz, Jörg","orcid":"0000-0003-2856-3369","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","last_name":"Renkawitz","first_name":"Jörg"},{"last_name":"Pfander","first_name":"Boris","full_name":"Pfander, Boris"},{"last_name":"Jentsch","first_name":"Stefan","full_name":"Jentsch, Stefan"}],"publication_status":"published","department":[{"_id":"MiSi"}],"publisher":"Cell Press","year":"2017","file_date_updated":"2020-07-14T12:47:40Z","publist_id":"7046","language":[{"iso":"eng"}],"doi":"10.1016/j.celrep.2017.04.051","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"month":"05","publication_identifier":{"issn":["22111247"]},"file":[{"access_level":"open_access","file_name":"IST-2017-899-v1+1_1-s2.0-S2211124717305454-main.pdf","content_type":"application/pdf","file_size":3005610,"creator":"system","relation":"main_file","file_id":"5171","checksum":"efc7287d9c6354983cb151880e9ad72a","date_created":"2018-12-12T10:15:48Z","date_updated":"2020-07-14T12:47:40Z"}],"oa_version":"Published Version","pubrep_id":"899","title":"The INO80 complex removes H2A.Z to promote presynaptic filament formation during homologous recombination","ddc":["570"],"status":"public","intvolume":" 19","_id":"677","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"The INO80 complex (INO80-C) is an evolutionarily conserved nucleosome remodeler that acts in transcription, replication, and genome stability. It is required for resistance against genotoxic agents and is involved in the repair of DNA double-strand breaks (DSBs) by homologous recombination (HR). However, the causes of the HR defect in INO80-C mutant cells are controversial. Here, we unite previous findings using a system to study HR with high spatial resolution in budding yeast. We find that INO80-C has at least two distinct functions during HR—DNA end resection and presynaptic filament formation. Importantly, the second function is linked to the histone variant H2A.Z. In the absence of H2A.Z, presynaptic filament formation and HR are restored in INO80-C-deficient mutants, suggesting that presynaptic filament formation is the crucial INO80-C function during HR."}],"issue":"7","type":"journal_article","date_published":"2017-05-16T00:00:00Z","page":"1294 - 1303","publication":"Cell Reports","citation":{"ista":"Lademann C, Renkawitz J, Pfander B, Jentsch S. 2017. The INO80 complex removes H2A.Z to promote presynaptic filament formation during homologous recombination. Cell Reports. 19(7), 1294–1303.","apa":"Lademann, C., Renkawitz, J., Pfander, B., & Jentsch, S. (2017). The INO80 complex removes H2A.Z to promote presynaptic filament formation during homologous recombination. Cell Reports. Cell Press. https://doi.org/10.1016/j.celrep.2017.04.051","ieee":"C. Lademann, J. Renkawitz, B. Pfander, and S. Jentsch, “The INO80 complex removes H2A.Z to promote presynaptic filament formation during homologous recombination,” Cell Reports, vol. 19, no. 7. Cell Press, pp. 1294–1303, 2017.","ama":"Lademann C, Renkawitz J, Pfander B, Jentsch S. The INO80 complex removes H2A.Z to promote presynaptic filament formation during homologous recombination. Cell Reports. 2017;19(7):1294-1303. doi:10.1016/j.celrep.2017.04.051","chicago":"Lademann, Claudio, Jörg Renkawitz, Boris Pfander, and Stefan Jentsch. “The INO80 Complex Removes H2A.Z to Promote Presynaptic Filament Formation during Homologous Recombination.” Cell Reports. Cell Press, 2017. https://doi.org/10.1016/j.celrep.2017.04.051.","mla":"Lademann, Claudio, et al. “The INO80 Complex Removes H2A.Z to Promote Presynaptic Filament Formation during Homologous Recombination.” Cell Reports, vol. 19, no. 7, Cell Press, 2017, pp. 1294–303, doi:10.1016/j.celrep.2017.04.051.","short":"C. Lademann, J. Renkawitz, B. Pfander, S. Jentsch, Cell Reports 19 (2017) 1294–1303."},"day":"16","has_accepted_license":"1","scopus_import":1},{"abstract":[{"lang":"eng","text":"The seminal observation that mechanical signals can elicit changes in biochemical signalling within cells, a process commonly termed mechanosensation and mechanotransduction, has revolutionized our understanding of the role of cell mechanics in various fundamental biological processes, such as cell motility, adhesion, proliferation and differentiation. In this Review, we will discuss how the interplay and feedback between mechanical and biochemical signals control tissue morphogenesis and cell fate specification in embryonic development."}],"publist_id":"7040","issue":"6","type":"journal_article","author":[{"last_name":"Petridou","first_name":"Nicoletta","orcid":"0000-0002-8451-1195","id":"2A003F6C-F248-11E8-B48F-1D18A9856A87","full_name":"Petridou, Nicoletta"},{"full_name":"Spiro, Zoltan P","id":"426AD026-F248-11E8-B48F-1D18A9856A87","last_name":"Spiro","first_name":"Zoltan P"},{"first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J"}],"date_created":"2018-12-11T11:47:53Z","date_updated":"2021-01-12T08:08:59Z","volume":19,"oa_version":"None","_id":"678","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","year":"2017","publication_status":"published","title":"Multiscale force sensing in development","status":"public","intvolume":" 19","department":[{"_id":"CaHe"}],"publisher":"Nature Publishing Group","month":"05","day":"31","publication_identifier":{"issn":["14657392"]},"scopus_import":1,"date_published":"2017-05-31T00:00:00Z","doi":"10.1038/ncb3524","language":[{"iso":"eng"}],"publication":"Nature Cell Biology","citation":{"mla":"Petridou, Nicoletta, et al. “Multiscale Force Sensing in Development.” Nature Cell Biology, vol. 19, no. 6, Nature Publishing Group, 2017, pp. 581–88, doi:10.1038/ncb3524.","short":"N. Petridou, Z.P. Spiro, C.-P.J. Heisenberg, Nature Cell Biology 19 (2017) 581–588.","chicago":"Petridou, Nicoletta, Zoltan P Spiro, and Carl-Philipp J Heisenberg. “Multiscale Force Sensing in Development.” Nature Cell Biology. Nature Publishing Group, 2017. https://doi.org/10.1038/ncb3524.","ama":"Petridou N, Spiro ZP, Heisenberg C-PJ. Multiscale force sensing in development. Nature Cell Biology. 2017;19(6):581-588. doi:10.1038/ncb3524","ista":"Petridou N, Spiro ZP, Heisenberg C-PJ. 2017. Multiscale force sensing in development. Nature Cell Biology. 19(6), 581–588.","ieee":"N. Petridou, Z. P. Spiro, and C.-P. J. Heisenberg, “Multiscale force sensing in development,” Nature Cell Biology, vol. 19, no. 6. Nature Publishing Group, pp. 581–588, 2017.","apa":"Petridou, N., Spiro, Z. P., & Heisenberg, C.-P. J. (2017). Multiscale force sensing in development. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb3524"},"quality_controlled":"1","project":[{"name":"The generation and function of anisotropic tissue tension in zebrafish epiboly (EMBO Fellowship)","_id":"25236028-B435-11E9-9278-68D0E5697425","grant_number":"ALTF534-2016"}],"page":"581 - 588"},{"date_published":"2017-06-01T00:00:00Z","citation":{"ista":"Chatterjee K, Doyen L, Filiot E, Raskin J. 2017. Doomsday equilibria for omega-regular games. Information and Computation. 254, 296–315.","apa":"Chatterjee, K., Doyen, L., Filiot, E., & Raskin, J. (2017). Doomsday equilibria for omega-regular games. Information and Computation. Elsevier. https://doi.org/10.1016/j.ic.2016.10.012","ieee":"K. Chatterjee, L. Doyen, E. Filiot, and J. Raskin, “Doomsday equilibria for omega-regular games,” Information and Computation, vol. 254. Elsevier, pp. 296–315, 2017.","ama":"Chatterjee K, Doyen L, Filiot E, Raskin J. Doomsday equilibria for omega-regular games. Information and Computation. 2017;254:296-315. doi:10.1016/j.ic.2016.10.012","chicago":"Chatterjee, Krishnendu, Laurent Doyen, Emmanuel Filiot, and Jean Raskin. “Doomsday Equilibria for Omega-Regular Games.” Information and Computation. Elsevier, 2017. https://doi.org/10.1016/j.ic.2016.10.012.","mla":"Chatterjee, Krishnendu, et al. “Doomsday Equilibria for Omega-Regular Games.” Information and Computation, vol. 254, Elsevier, 2017, pp. 296–315, doi:10.1016/j.ic.2016.10.012.","short":"K. Chatterjee, L. Doyen, E. Filiot, J. Raskin, Information and Computation 254 (2017) 296–315."},"publication":"Information and Computation","page":"296 - 315","article_type":"original","article_processing_charge":"No","day":"01","scopus_import":"1","oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"681","intvolume":" 254","status":"public","title":"Doomsday equilibria for omega-regular games","abstract":[{"lang":"eng","text":"Two-player games on graphs provide the theoretical framework for many important problems such as reactive synthesis. While the traditional study of two-player zero-sum games has been extended to multi-player games with several notions of equilibria, they are decidable only for perfect-information games, whereas several applications require imperfect-information. In this paper we propose a new notion of equilibria, called doomsday equilibria, which is a strategy profile where all players satisfy their own objective, and if any coalition of players deviates and violates even one of the players' objective, then the objective of every player is violated. We present algorithms and complexity results for deciding the existence of doomsday equilibria for various classes of ω-regular objectives, both for imperfect-information games, and for perfect-information games. We provide optimal complexity bounds for imperfect-information games, and in most cases for perfect-information games."}],"type":"journal_article","doi":"10.1016/j.ic.2016.10.012","language":[{"iso":"eng"}],"external_id":{"arxiv":["1311.3238"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1311.3238"}],"oa":1,"project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Game Theory"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"quality_controlled":"1","publication_identifier":{"issn":["08905401"]},"month":"06","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"10885"}]},"author":[{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"last_name":"Doyen","first_name":"Laurent","full_name":"Doyen, Laurent"},{"first_name":"Emmanuel","last_name":"Filiot","full_name":"Filiot, Emmanuel"},{"first_name":"Jean","last_name":"Raskin","full_name":"Raskin, Jean"}],"volume":254,"date_updated":"2023-02-21T16:06:02Z","date_created":"2018-12-11T11:47:53Z","year":"2017","publisher":"Elsevier","department":[{"_id":"KrCh"}],"publication_status":"published","ec_funded":1,"publist_id":"7036"},{"author":[{"full_name":"Martius, Georg S","first_name":"Georg S","last_name":"Martius","id":"3A276B68-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","first_name":"Christoph","last_name":"Lampert"}],"oa_version":"Preprint","date_updated":"2021-01-12T08:09:17Z","date_created":"2019-09-01T22:01:00Z","year":"2017","_id":"6841","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"International Conference on Learning Representations","department":[{"_id":"ChLa"}],"title":"Extrapolation and learning equations","status":"public","publication_status":"published","ec_funded":1,"abstract":[{"lang":"eng","text":"In classical machine learning, regression is treated as a black box process of identifying a suitable function from a hypothesis set without attempting to gain insight into the mechanism connecting inputs and outputs. In the natural sciences, however, finding an interpretable function for a phenomenon is the prime goal as it allows to understand and generalize results. This paper proposes a novel type of function learning network, called equation learner (EQL), that can learn analytical expressions and is able to extrapolate to unseen domains. It is implemented as an end-to-end differentiable feed-forward network and allows for efficient gradient based training. Due to sparsity regularization concise interpretable expressions can be obtained. Often the true underlying source expression is identified."}],"type":"conference","date_published":"2017-02-21T00:00:00Z","conference":{"name":"ICLR: International Conference on Learning Representations","end_date":"2017-04-26","start_date":"2017-04-24","location":"Toulon, France"},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1610.02995"}],"citation":{"chicago":"Martius, Georg S, and Christoph Lampert. “Extrapolation and Learning Equations.” In 5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings. International Conference on Learning Representations, 2017.","short":"G.S. Martius, C. Lampert, in:, 5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings, International Conference on Learning Representations, 2017.","mla":"Martius, Georg S., and Christoph Lampert. “Extrapolation and Learning Equations.” 5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings, International Conference on Learning Representations, 2017.","apa":"Martius, G. S., & Lampert, C. (2017). Extrapolation and learning equations. In 5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings. Toulon, France: International Conference on Learning Representations.","ieee":"G. S. Martius and C. Lampert, “Extrapolation and learning equations,” in 5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings, Toulon, France, 2017.","ista":"Martius GS, Lampert C. 2017. Extrapolation and learning equations. 5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings. ICLR: International Conference on Learning Representations.","ama":"Martius GS, Lampert C. Extrapolation and learning equations. In: 5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings. International Conference on Learning Representations; 2017."},"oa":1,"external_id":{"arxiv":["1610.02995"]},"publication":"5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings","project":[{"grant_number":"308036","_id":"2532554C-B435-11E9-9278-68D0E5697425","name":"Lifelong Learning of Visual Scene Understanding","call_identifier":"FP7"}],"quality_controlled":"1","month":"02","day":"21","scopus_import":1},{"publist_id":"7026","department":[{"_id":"KrCh"}],"publisher":"Cambridge University Press","publication_status":"published","year":"2017","volume":82,"date_updated":"2021-04-16T12:10:53Z","date_created":"2018-12-11T11:47:54Z","author":[{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"last_name":"Piterman","first_name":"Nir","full_name":"Piterman, Nir"}],"publication_identifier":{"eissn":["1943-5886"],"issn":["0022-4812"]},"month":"06","quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1206.5174","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1017/jsl.2016.71","type":"journal_article","issue":"2","abstract":[{"lang":"eng","text":"We generalize winning conditions in two-player games by adding a structural acceptance condition called obligations. Obligations are orthogonal to the linear winning conditions that define whether a play is winning. Obligations are a declaration that player 0 can achieve a certain value from a configuration. If the obligation is met, the value of that configuration for player 0 is 1. We define the value in such games and show that obligation games are determined. For Markov chains with Borel objectives and obligations, and finite turn-based stochastic parity games with obligations we give an alternative and simpler characterization of the value function. Based on this simpler definition we show that the decision problem of winning finite turn-based stochastic parity games with obligations is in NP∩co-NP. We also show that obligation games provide a game framework for reasoning about p-automata. © 2017 The Association for Symbolic Logic."}],"intvolume":" 82","status":"public","title":"Obligation blackwell games and p-automata","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"684","oa_version":"Submitted Version","scopus_import":"1","article_processing_charge":"No","day":"01","page":"420 - 452","citation":{"ama":"Chatterjee K, Piterman N. Obligation blackwell games and p-automata. Journal of Symbolic Logic. 2017;82(2):420-452. doi:10.1017/jsl.2016.71","ista":"Chatterjee K, Piterman N. 2017. Obligation blackwell games and p-automata. Journal of Symbolic Logic. 82(2), 420–452.","apa":"Chatterjee, K., & Piterman, N. (2017). Obligation blackwell games and p-automata. Journal of Symbolic Logic. Cambridge University Press. https://doi.org/10.1017/jsl.2016.71","ieee":"K. Chatterjee and N. Piterman, “Obligation blackwell games and p-automata,” Journal of Symbolic Logic, vol. 82, no. 2. Cambridge University Press, pp. 420–452, 2017.","mla":"Chatterjee, Krishnendu, and Nir Piterman. “Obligation Blackwell Games and P-Automata.” Journal of Symbolic Logic, vol. 82, no. 2, Cambridge University Press, 2017, pp. 420–52, doi:10.1017/jsl.2016.71.","short":"K. Chatterjee, N. Piterman, Journal of Symbolic Logic 82 (2017) 420–452.","chicago":"Chatterjee, Krishnendu, and Nir Piterman. “Obligation Blackwell Games and P-Automata.” Journal of Symbolic Logic. Cambridge University Press, 2017. https://doi.org/10.1017/jsl.2016.71."},"publication":"Journal of Symbolic Logic","date_published":"2017-06-01T00:00:00Z"},{"external_id":{"pmid":["28366718"]},"oa":1,"project":[{"name":"Coordination of Patterning And Growth In the Spinal Cord","call_identifier":"H2020","grant_number":"680037","_id":"B6FC0238-B512-11E9-945C-1524E6697425"}],"quality_controlled":"1","doi":"10.1016/j.mod.2017.03.005","language":[{"iso":"eng"}],"publication_identifier":{"issn":["09254773"]},"month":"06","pmid":1,"year":"2017","publisher":"Elsevier","department":[{"_id":"AnKi"}],"publication_status":"published","author":[{"first_name":"James","last_name":"Briscoe","full_name":"Briscoe, James"},{"orcid":"0000-0003-4509-4998","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","last_name":"Kicheva","first_name":"Anna","full_name":"Kicheva, Anna"}],"volume":145,"date_updated":"2021-01-12T08:09:20Z","date_created":"2018-12-11T11:47:55Z","publist_id":"7025","ec_funded":1,"file_date_updated":"2020-07-14T12:47:42Z","citation":{"mla":"Briscoe, James, and Anna Kicheva. “The Physics of Development 100 Years after D’Arcy Thompson’s ‘on Growth and Form.’” Mechanisms of Development, vol. 145, Elsevier, 2017, pp. 26–31, doi:10.1016/j.mod.2017.03.005.","short":"J. Briscoe, A. Kicheva, Mechanisms of Development 145 (2017) 26–31.","chicago":"Briscoe, James, and Anna Kicheva. “The Physics of Development 100 Years after D’Arcy Thompson’s ‘on Growth and Form.’” Mechanisms of Development. Elsevier, 2017. https://doi.org/10.1016/j.mod.2017.03.005.","ama":"Briscoe J, Kicheva A. The physics of development 100 years after D’Arcy Thompson’s “on growth and form.” Mechanisms of Development. 2017;145:26-31. doi:10.1016/j.mod.2017.03.005","ista":"Briscoe J, Kicheva A. 2017. The physics of development 100 years after D’Arcy Thompson’s “on growth and form”. Mechanisms of Development. 145, 26–31.","ieee":"J. Briscoe and A. Kicheva, “The physics of development 100 years after D’Arcy Thompson’s ‘on growth and form,’” Mechanisms of Development, vol. 145. Elsevier, pp. 26–31, 2017.","apa":"Briscoe, J., & Kicheva, A. (2017). The physics of development 100 years after D’Arcy Thompson’s “on growth and form.” Mechanisms of Development. Elsevier. https://doi.org/10.1016/j.mod.2017.03.005"},"publication":"Mechanisms of Development","page":"26 - 31","date_published":"2017-06-01T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"01","_id":"685","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 145","title":"The physics of development 100 years after D'Arcy Thompson's “on growth and form”","ddc":["571"],"status":"public","pubrep_id":"985","file":[{"content_type":"application/pdf","file_size":652313,"creator":"dernst","file_name":"2017_Briscoe_Kicheva_and_DArcy_accepted_version.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:42Z","date_created":"2019-04-17T07:58:48Z","checksum":"727043d2e4199fbef6b3704e6d1ac105","relation":"main_file","file_id":"6335"}],"oa_version":"Submitted Version","type":"journal_article","abstract":[{"lang":"eng","text":"By applying methods and principles from the physical sciences to biological problems, D'Arcy Thompson's On Growth and Form demonstrated how mathematical reasoning reveals elegant, simple explanations for seemingly complex processes. This has had a profound influence on subsequent generations of developmental biologists. We discuss how this influence can be traced through twentieth century morphologists, embryologists and theoreticians to current research that explores the molecular and cellular mechanisms of tissue growth and patterning, including our own studies of the vertebrate neural tube."}]},{"publication_status":"published","department":[{"_id":"HeEd"},{"_id":"UlWa"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","year":"2017","date_updated":"2021-01-12T08:09:26Z","date_created":"2018-12-11T11:47:56Z","volume":77,"author":[{"last_name":"Edelsbrunner","first_name":"Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert"},{"last_name":"Wagner","first_name":"Hubert","id":"379CA8B8-F248-11E8-B48F-1D18A9856A87","full_name":"Wagner, Hubert"}],"file_date_updated":"2020-07-14T12:47:42Z","publist_id":"7021","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"conference":{"end_date":"2017-07-07","start_date":"2017-07-04","location":"Brisbane, Australia","name":"Symposium on Computational Geometry, SoCG"},"doi":"10.4230/LIPIcs.SoCG.2017.39","month":"06","publication_identifier":{"issn":["18688969"]},"status":"public","ddc":["514","516"],"title":"Topological data analysis with Bregman divergences","intvolume":" 77","_id":"688","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":990546,"creator":"system","file_name":"IST-2017-895-v1+1_LIPIcs-SoCG-2017-39.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:42Z","date_created":"2018-12-12T10:11:03Z","checksum":"067ab0cb3f962bae6c3af6bf0094e0f3","relation":"main_file","file_id":"4856"}],"pubrep_id":"895","alternative_title":["LIPIcs"],"type":"conference","abstract":[{"text":"We show that the framework of topological data analysis can be extended from metrics to general Bregman divergences, widening the scope of possible applications. Examples are the Kullback - Leibler divergence, which is commonly used for comparing text and images, and the Itakura - Saito divergence, popular for speech and sound. In particular, we prove that appropriately generalized čech and Delaunay (alpha) complexes capture the correct homotopy type, namely that of the corresponding union of Bregman balls. Consequently, their filtrations give the correct persistence diagram, namely the one generated by the uniformly growing Bregman balls. Moreover, we show that unlike the metric setting, the filtration of Vietoris-Rips complexes may fail to approximate the persistence diagram. We propose algorithms to compute the thus generalized čech, Vietoris-Rips and Delaunay complexes and experimentally test their efficiency. Lastly, we explain their surprisingly good performance by making a connection with discrete Morse theory. ","lang":"eng"}],"page":"391-3916","citation":{"apa":"Edelsbrunner, H., & Wagner, H. (2017). Topological data analysis with Bregman divergences (Vol. 77, pp. 391–3916). Presented at the Symposium on Computational Geometry, SoCG, Brisbane, Australia: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2017.39","ieee":"H. Edelsbrunner and H. Wagner, “Topological data analysis with Bregman divergences,” presented at the Symposium on Computational Geometry, SoCG, Brisbane, Australia, 2017, vol. 77, pp. 391–3916.","ista":"Edelsbrunner H, Wagner H. 2017. Topological data analysis with Bregman divergences. Symposium on Computational Geometry, SoCG, LIPIcs, vol. 77, 391–3916.","ama":"Edelsbrunner H, Wagner H. Topological data analysis with Bregman divergences. In: Vol 77. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017:391-3916. doi:10.4230/LIPIcs.SoCG.2017.39","chicago":"Edelsbrunner, Herbert, and Hubert Wagner. “Topological Data Analysis with Bregman Divergences,” 77:391–3916. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.SoCG.2017.39.","short":"H. Edelsbrunner, H. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, pp. 391–3916.","mla":"Edelsbrunner, Herbert, and Hubert Wagner. Topological Data Analysis with Bregman Divergences. Vol. 77, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, pp. 391–3916, doi:10.4230/LIPIcs.SoCG.2017.39."},"date_published":"2017-06-01T00:00:00Z","scopus_import":1,"day":"01","has_accepted_license":"1"},{"day":"01","scopus_import":1,"date_published":"2017-06-01T00:00:00Z","citation":{"ama":"Davison B. The critical CoHA of a quiver with potential. Quarterly Journal of Mathematics. 2017;68(2):635-703. doi:10.1093/qmath/haw053","ista":"Davison B. 2017. The critical CoHA of a quiver with potential. Quarterly Journal of Mathematics. 68(2), 635–703.","apa":"Davison, B. (2017). The critical CoHA of a quiver with potential. Quarterly Journal of Mathematics. Oxford University Press. https://doi.org/10.1093/qmath/haw053","ieee":"B. Davison, “The critical CoHA of a quiver with potential,” Quarterly Journal of Mathematics, vol. 68, no. 2. Oxford University Press, pp. 635–703, 2017.","mla":"Davison, Ben. “The Critical CoHA of a Quiver with Potential.” Quarterly Journal of Mathematics, vol. 68, no. 2, Oxford University Press, 2017, pp. 635–703, doi:10.1093/qmath/haw053.","short":"B. Davison, Quarterly Journal of Mathematics 68 (2017) 635–703.","chicago":"Davison, Ben. “The Critical CoHA of a Quiver with Potential.” Quarterly Journal of Mathematics. Oxford University Press, 2017. https://doi.org/10.1093/qmath/haw053."},"publication":"Quarterly Journal of Mathematics","page":"635 - 703","issue":"2","abstract":[{"lang":"eng","text":"Pursuing the similarity between the Kontsevich-Soibelman construction of the cohomological Hall algebra (CoHA) of BPS states and Lusztig's construction of canonical bases for quantum enveloping algebras, and the similarity between the integrality conjecture for motivic Donaldson-Thomas invariants and the PBW theorem for quantum enveloping algebras, we build a coproduct on the CoHA associated to a quiver with potential. We also prove a cohomological dimensional reduction theorem, further linking a special class of CoHAs with Yangians, and explaining how to connect the study of character varieties with the study of CoHAs."}],"type":"journal_article","oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"687","intvolume":" 68","status":"public","title":"The critical CoHA of a quiver with potential","publication_identifier":{"issn":["00335606"]},"month":"06","doi":"10.1093/qmath/haw053","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1311.7172"}],"oa":1,"project":[{"grant_number":"320593","_id":"25E549F4-B435-11E9-9278-68D0E5697425","name":"Arithmetic and physics of Higgs moduli spaces","call_identifier":"FP7"}],"quality_controlled":"1","publist_id":"7022","ec_funded":1,"author":[{"full_name":"Davison, Ben","first_name":"Ben","last_name":"Davison","id":"4634AB1E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8944-4390"}],"volume":68,"date_updated":"2021-01-12T08:09:24Z","date_created":"2018-12-11T11:47:55Z","year":"2017","department":[{"_id":"TaHa"}],"publisher":"Oxford University Press","publication_status":"published"},{"scopus_import":1,"month":"06","day":"01","publication_identifier":{"issn":["09254773"]},"publication":"Mechanisms of Development","citation":{"ama":"Heisenberg C-PJ. D’Arcy Thompson’s ‘on growth and form’: From soap bubbles to tissue self organization. Mechanisms of Development. 2017;145:32-37. doi:10.1016/j.mod.2017.03.006","ista":"Heisenberg C-PJ. 2017. D’Arcy Thompson’s ‘on growth and form’: From soap bubbles to tissue self organization. Mechanisms of Development. 145, 32–37.","apa":"Heisenberg, C.-P. J. (2017). D’Arcy Thompson’s ‘on growth and form’: From soap bubbles to tissue self organization. Mechanisms of Development. Elsevier. https://doi.org/10.1016/j.mod.2017.03.006","ieee":"C.-P. J. Heisenberg, “D’Arcy Thompson’s ‘on growth and form’: From soap bubbles to tissue self organization,” Mechanisms of Development, vol. 145. Elsevier, pp. 32–37, 2017.","mla":"Heisenberg, Carl-Philipp J. “D’Arcy Thompson’s ‘on Growth and Form’: From Soap Bubbles to Tissue Self Organization.” Mechanisms of Development, vol. 145, Elsevier, 2017, pp. 32–37, doi:10.1016/j.mod.2017.03.006.","short":"C.-P.J. Heisenberg, Mechanisms of Development 145 (2017) 32–37.","chicago":"Heisenberg, Carl-Philipp J. “D’Arcy Thompson’s ‘on Growth and Form’: From Soap Bubbles to Tissue Self Organization.” Mechanisms of Development. Elsevier, 2017. https://doi.org/10.1016/j.mod.2017.03.006."},"quality_controlled":"1","page":"32 - 37","doi":"10.1016/j.mod.2017.03.006","date_published":"2017-06-01T00:00:00Z","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"text":"Tissues are thought to behave like fluids with a given surface tension. Differences in tissue surface tension (TST) have been proposed to trigger cell sorting and tissue envelopment. D'Arcy Thompson in his seminal book ‘On Growth and Form’ has introduced this concept of differential TST as a key physical mechanism dictating tissue formation and organization within the developing organism. Over the past century, many studies have picked up the concept of differential TST and analyzed the role and cell biological basis of TST in development, underlining the importance and influence of this concept in developmental biology.","lang":"eng"}],"publist_id":"7024","year":"2017","_id":"686","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"D'Arcy Thompson's ‘on growth and form’: From soap bubbles to tissue self organization","publication_status":"published","intvolume":" 145","department":[{"_id":"CaHe"}],"publisher":"Elsevier","author":[{"first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J"}],"date_updated":"2021-01-12T08:09:23Z","date_created":"2018-12-11T11:47:55Z","oa_version":"None","volume":145},{"article_number":"eaan8196","type":"journal_article","abstract":[{"text":"Rett syndrome modeling in monkey mirrors the human disorder.","lang":"eng"}],"publist_id":"7019","issue":"393","year":"2017","_id":"689","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","status":"public","publication_status":"published","title":"Rett syndrome modeling goes simian","intvolume":" 9","publisher":"American Association for the Advancement of Science","department":[{"_id":"GaNo"}],"author":[{"last_name":"Novarino","first_name":"Gaia","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia"}],"date_updated":"2021-01-12T08:09:29Z","date_created":"2018-12-11T11:47:56Z","oa_version":"None","volume":9,"scopus_import":1,"month":"06","day":"07","publication_identifier":{"issn":["19466234"]},"publication":"Science Translational Medicine","citation":{"mla":"Novarino, Gaia. “Rett Syndrome Modeling Goes Simian.” Science Translational Medicine, vol. 9, no. 393, eaan8196, American Association for the Advancement of Science, 2017, doi:10.1126/scitranslmed.aan8196.","short":"G. Novarino, Science Translational Medicine 9 (2017).","chicago":"Novarino, Gaia. “Rett Syndrome Modeling Goes Simian.” Science Translational Medicine. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/scitranslmed.aan8196.","ama":"Novarino G. Rett syndrome modeling goes simian. Science Translational Medicine. 2017;9(393). doi:10.1126/scitranslmed.aan8196","ista":"Novarino G. 2017. Rett syndrome modeling goes simian. Science Translational Medicine. 9(393), eaan8196.","apa":"Novarino, G. (2017). Rett syndrome modeling goes simian. Science Translational Medicine. American Association for the Advancement of Science. https://doi.org/10.1126/scitranslmed.aan8196","ieee":"G. Novarino, “Rett syndrome modeling goes simian,” Science Translational Medicine, vol. 9, no. 393. American Association for the Advancement of Science, 2017."},"quality_controlled":"1","doi":"10.1126/scitranslmed.aan8196","date_published":"2017-06-07T00:00:00Z","language":[{"iso":"eng"}]},{"file_date_updated":"2020-07-14T12:47:44Z","publist_id":"7013","publication_status":"published","publisher":"National Academy of Sciences","department":[{"_id":"EM-Fac"},{"_id":"RySh"}],"year":"2017","pmid":1,"date_updated":"2023-02-23T12:54:57Z","date_created":"2018-12-11T11:47:57Z","volume":114,"author":[{"full_name":"Miki, Takafumi","first_name":"Takafumi","last_name":"Miki"},{"full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","last_name":"Kaufmann","first_name":"Walter"},{"first_name":"Gerardo","last_name":"Malagon","full_name":"Malagon, Gerardo"},{"last_name":"Gomez","first_name":"Laura","full_name":"Gomez, Laura"},{"full_name":"Tabuchi, Katsuhiko","first_name":"Katsuhiko","last_name":"Tabuchi"},{"last_name":"Watanabe","first_name":"Masahiko","full_name":"Watanabe, Masahiko"},{"full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444"},{"full_name":"Marty, Alain","last_name":"Marty","first_name":"Alain"}],"month":"06","publication_identifier":{"issn":["00278424"]},"quality_controlled":"1","external_id":{"pmid":["28607047"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1704470114","type":"journal_article","abstract":[{"lang":"eng","text":"Many central synapses contain a single presynaptic active zone and a single postsynaptic density. Vesicular release statistics at such “simple synapses” indicate that they contain a small complement of docking sites where vesicles repetitively dock and fuse. In this work, we investigate functional and morphological aspects of docking sites at simple synapses made between cerebellar parallel fibers and molecular layer interneurons. Using immunogold labeling of SDS-treated freeze-fracture replicas, we find that Cav2.1 channels form several clusters per active zone with about nine channels per cluster. The mean value and range of intersynaptic variation are similar for Cav2.1 cluster numbers and for functional estimates of docking-site numbers obtained from the maximum numbers of released vesicles per action potential. Both numbers grow in relation with synaptic size and decrease by a similar extent with age between 2 wk and 4 wk postnatal. Thus, the mean docking-site numbers were 3.15 at 2 wk (range: 1–10) and 2.03 at 4 wk (range: 1–4), whereas the mean numbers of Cav2.1 clusters were 2.84 at 2 wk (range: 1–8) and 2.37 at 4 wk (range: 1–5). These changes were accompanied by decreases of miniature current amplitude (from 93 pA to 56 pA), active-zone surface area (from 0.0427 μm2 to 0.0234 μm2), and initial success rate (from 0.609 to 0.353), indicating a tightening of synaptic transmission with development. Altogether, these results suggest a close correspondence between the number of functionally defined vesicular docking sites and that of clusters of voltage-gated calcium channels. "}],"issue":"26","ddc":["570"],"title":"Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses","status":"public","intvolume":" 114","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"693","file":[{"relation":"main_file","file_id":"7223","date_updated":"2020-07-14T12:47:44Z","date_created":"2020-01-03T13:27:29Z","checksum":"2ab75d554f3df4a34d20fa8040589b7e","file_name":"2017_PNAS_Miki.pdf","access_level":"open_access","content_type":"application/pdf","file_size":2721544,"creator":"kschuh"}],"oa_version":"Published Version","scopus_import":1,"day":"27","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","page":"E5246 - E5255","publication":"PNAS","citation":{"chicago":"Miki, Takafumi, Walter Kaufmann, Gerardo Malagon, Laura Gomez, Katsuhiko Tabuchi, Masahiko Watanabe, Ryuichi Shigemoto, and Alain Marty. “Numbers of Presynaptic Ca2+ Channel Clusters Match Those of Functionally Defined Vesicular Docking Sites in Single Central Synapses.” PNAS. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1704470114.","mla":"Miki, Takafumi, et al. “Numbers of Presynaptic Ca2+ Channel Clusters Match Those of Functionally Defined Vesicular Docking Sites in Single Central Synapses.” PNAS, vol. 114, no. 26, National Academy of Sciences, 2017, pp. E5246–55, doi:10.1073/pnas.1704470114.","short":"T. Miki, W. Kaufmann, G. Malagon, L. Gomez, K. Tabuchi, M. Watanabe, R. Shigemoto, A. Marty, PNAS 114 (2017) E5246–E5255.","ista":"Miki T, Kaufmann W, Malagon G, Gomez L, Tabuchi K, Watanabe M, Shigemoto R, Marty A. 2017. Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses. PNAS. 114(26), E5246–E5255.","apa":"Miki, T., Kaufmann, W., Malagon, G., Gomez, L., Tabuchi, K., Watanabe, M., … Marty, A. (2017). Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1704470114","ieee":"T. Miki et al., “Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses,” PNAS, vol. 114, no. 26. National Academy of Sciences, pp. E5246–E5255, 2017.","ama":"Miki T, Kaufmann W, Malagon G, et al. Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses. PNAS. 2017;114(26):E5246-E5255. doi:10.1073/pnas.1704470114"},"date_published":"2017-06-27T00:00:00Z"},{"quality_controlled":"1","oa":1,"external_id":{"pmid":["28515231"]},"language":[{"iso":"eng"}],"doi":"10.1242/jcs.200899","month":"07","publication_identifier":{"issn":["00219533"]},"publication_status":"published","publisher":"Company of Biologists","department":[{"_id":"MiSi"}],"year":"2017","pmid":1,"date_created":"2018-12-11T11:47:58Z","date_updated":"2021-01-12T08:09:41Z","volume":130,"author":[{"full_name":"Veß, Astrid","first_name":"Astrid","last_name":"Veß"},{"full_name":"Blache, Ulrich","first_name":"Ulrich","last_name":"Blache"},{"full_name":"Leitner, Laura","first_name":"Laura","last_name":"Leitner"},{"full_name":"Kurz, Angela","first_name":"Angela","last_name":"Kurz"},{"full_name":"Ehrenpfordt, Anja","first_name":"Anja","last_name":"Ehrenpfordt"},{"full_name":"Sixt, Michael K","first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179"},{"last_name":"Posern","first_name":"Guido","full_name":"Posern, Guido"}],"file_date_updated":"2020-07-14T12:47:45Z","publist_id":"7008","article_type":"original","page":"2172 - 2184","publication":"Journal of Cell Science","citation":{"apa":"Veß, A., Blache, U., Leitner, L., Kurz, A., Ehrenpfordt, A., Sixt, M. K., & Posern, G. (2017). A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity. Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.200899","ieee":"A. Veß et al., “A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity,” Journal of Cell Science, vol. 130, no. 13. Company of Biologists, pp. 2172–2184, 2017.","ista":"Veß A, Blache U, Leitner L, Kurz A, Ehrenpfordt A, Sixt MK, Posern G. 2017. A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity. Journal of Cell Science. 130(13), 2172–2184.","ama":"Veß A, Blache U, Leitner L, et al. A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity. Journal of Cell Science. 2017;130(13):2172-2184. doi:10.1242/jcs.200899","chicago":"Veß, Astrid, Ulrich Blache, Laura Leitner, Angela Kurz, Anja Ehrenpfordt, Michael K Sixt, and Guido Posern. “A Dual Phenotype of MDA MB 468 Cancer Cells Reveals Mutual Regulation of Tensin3 and Adhesion Plasticity.” Journal of Cell Science. Company of Biologists, 2017. https://doi.org/10.1242/jcs.200899.","short":"A. Veß, U. Blache, L. Leitner, A. Kurz, A. Ehrenpfordt, M.K. Sixt, G. Posern, Journal of Cell Science 130 (2017) 2172–2184.","mla":"Veß, Astrid, et al. “A Dual Phenotype of MDA MB 468 Cancer Cells Reveals Mutual Regulation of Tensin3 and Adhesion Plasticity.” Journal of Cell Science, vol. 130, no. 13, Company of Biologists, 2017, pp. 2172–84, doi:10.1242/jcs.200899."},"date_published":"2017-07-01T00:00:00Z","scopus_import":1,"day":"01","has_accepted_license":"1","status":"public","title":"A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity","ddc":["570"],"intvolume":" 130","_id":"694","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_size":10847596,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2017_CellScience_Vess.pdf","checksum":"42c81a0a4fc3128883b391c3af3f74bc","date_created":"2019-10-24T09:43:56Z","date_updated":"2020-07-14T12:47:45Z","relation":"main_file","file_id":"6966"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"A change regarding the extent of adhesion - hereafter referred to as adhesion plasticity - between adhesive and less-adhesive states of mammalian cells is important for their behavior. To investigate adhesion plasticity, we have selected a stable isogenic subpopulation of human MDA-MB-468 breast carcinoma cells growing in suspension. These suspension cells are unable to re-adhere to various matrices or to contract three-dimensional collagen lattices. By using transcriptome analysis, we identified the focal adhesion protein tensin3 (Tns3) as a determinant of adhesion plasticity. Tns3 is strongly reduced at mRNA and protein levels in suspension cells. Furthermore, by transiently challenging breast cancer cells to grow under non-adherent conditions markedly reduces Tns3 protein expression, which is regained upon re-adhesion. Stable knockdown of Tns3 in parental MDA-MB-468 cells results in defective adhesion, spreading and migration. Tns3-knockdown cells display impaired structure and dynamics of focal adhesion complexes as determined by immunostaining. Restoration of Tns3 protein expression in suspension cells partially rescues adhesion and focal contact composition. Our work identifies Tns3 as a crucial focal adhesion component regulated by, and functionally contributing to, the switch between adhesive and non-adhesive states in MDA-MB-468 cancer cells.","lang":"eng"}],"issue":"13"},{"alternative_title":["LIPIcs"],"type":"conference","abstract":[{"lang":"eng","text":"De, Trevisan and Tulsiani [CRYPTO 2010] show that every distribution over n-bit strings which has constant statistical distance to uniform (e.g., the output of a pseudorandom generator mapping n-1 to n bit strings), can be distinguished from the uniform distribution with advantage epsilon by a circuit of size O( 2^n epsilon^2). We generalize this result, showing that a distribution which has less than k bits of min-entropy, can be distinguished from any distribution with k bits of delta-smooth min-entropy with advantage epsilon by a circuit of size O(2^k epsilon^2/delta^2). As a special case, this implies that any distribution with support at most 2^k (e.g., the output of a pseudoentropy generator mapping k to n bit strings) can be distinguished from any given distribution with min-entropy k+1 with advantage epsilon by a circuit of size O(2^k epsilon^2). Our result thus shows that pseudoentropy distributions face basically the same non-uniform attacks as pseudorandom distributions. "}],"status":"public","title":"Non uniform attacks against pseudoentropy","ddc":["005"],"intvolume":" 80","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"697","file":[{"file_id":"4701","relation":"main_file","checksum":"e95618a001692f1af2d68f5fde43bc1f","date_created":"2018-12-12T10:08:40Z","date_updated":"2020-07-14T12:47:46Z","access_level":"open_access","file_name":"IST-2017-893-v1+1_LIPIcs-ICALP-2017-39.pdf","creator":"system","file_size":601004,"content_type":"application/pdf"}],"oa_version":"Published Version","pubrep_id":"893","scopus_import":1,"day":"01","has_accepted_license":"1","citation":{"ama":"Pietrzak KZ, Skórski M. Non uniform attacks against pseudoentropy. In: Vol 80. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.ICALP.2017.39","ista":"Pietrzak KZ, Skórski M. 2017. Non uniform attacks against pseudoentropy. ICALP: International Colloquium on Automata, Languages, and Programming, LIPIcs, vol. 80, 39.","apa":"Pietrzak, K. Z., & Skórski, M. (2017). Non uniform attacks against pseudoentropy (Vol. 80). Presented at the ICALP: International Colloquium on Automata, Languages, and Programming, Warsaw, Poland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2017.39","ieee":"K. Z. Pietrzak and M. Skórski, “Non uniform attacks against pseudoentropy,” presented at the ICALP: International Colloquium on Automata, Languages, and Programming, Warsaw, Poland, 2017, vol. 80.","mla":"Pietrzak, Krzysztof Z., and Maciej Skórski. Non Uniform Attacks against Pseudoentropy. Vol. 80, 39, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.ICALP.2017.39.","short":"K.Z. Pietrzak, M. Skórski, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","chicago":"Pietrzak, Krzysztof Z, and Maciej Skórski. “Non Uniform Attacks against Pseudoentropy,” Vol. 80. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.ICALP.2017.39."},"date_published":"2017-07-01T00:00:00Z","article_number":"39","file_date_updated":"2020-07-14T12:47:46Z","publist_id":"7003","ec_funded":1,"publication_status":"published","department":[{"_id":"KrPi"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","year":"2017","date_updated":"2021-01-12T08:11:15Z","date_created":"2018-12-11T11:47:59Z","volume":80,"author":[{"orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak","first_name":"Krzysztof Z","full_name":"Pietrzak, Krzysztof Z"},{"id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","first_name":"Maciej","last_name":"Skórski","full_name":"Skórski, Maciej"}],"month":"07","publication_identifier":{"issn":["18688969"]},"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Teaching Old Crypto New Tricks","grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"conference":{"end_date":"2017-07-14","location":"Warsaw, Poland","start_date":"2017-07-10","name":"ICALP: International Colloquium on Automata, Languages, and Programming"},"doi":"10.4230/LIPIcs.ICALP.2017.39"},{"publication_identifier":{"issn":["10591524"]},"month":"07","language":[{"iso":"eng"}],"doi":"10.1091/mbc.E16-12-0825","project":[{"grant_number":"Y 903-N35","_id":"2530CA10-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Gaussian Graphical Models: Theory and Applications"}],"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","publist_id":"7001","file_date_updated":"2020-07-14T12:47:46Z","volume":28,"date_updated":"2021-01-12T08:11:17Z","date_created":"2018-12-11T11:47:59Z","author":[{"full_name":"Wang, Yejun","first_name":"Yejun","last_name":"Wang"},{"first_name":"Mallika","last_name":"Nagarajan","full_name":"Nagarajan, Mallika"},{"full_name":"Uhler, Caroline","last_name":"Uhler","first_name":"Caroline","orcid":"0000-0002-7008-0216","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Shivashankar, Gv","first_name":"Gv","last_name":"Shivashankar"}],"department":[{"_id":"CaUh"}],"publisher":"American Society for Cell Biology","publication_status":"published","year":"2017","has_accepted_license":"1","day":"07","scopus_import":1,"date_published":"2017-07-07T00:00:00Z","page":"1997 - 2009","citation":{"short":"Y. Wang, M. Nagarajan, C. Uhler, G. Shivashankar, Molecular Biology of the Cell 28 (2017) 1997–2009.","mla":"Wang, Yejun, et al. “Orientation and Repositioning of Chromosomes Correlate with Cell Geometry Dependent Gene Expression.” Molecular Biology of the Cell, vol. 28, no. 14, American Society for Cell Biology, 2017, pp. 1997–2009, doi:10.1091/mbc.E16-12-0825.","chicago":"Wang, Yejun, Mallika Nagarajan, Caroline Uhler, and Gv Shivashankar. “Orientation and Repositioning of Chromosomes Correlate with Cell Geometry Dependent Gene Expression.” Molecular Biology of the Cell. American Society for Cell Biology, 2017. https://doi.org/10.1091/mbc.E16-12-0825.","ama":"Wang Y, Nagarajan M, Uhler C, Shivashankar G. Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression. Molecular Biology of the Cell. 2017;28(14):1997-2009. doi:10.1091/mbc.E16-12-0825","apa":"Wang, Y., Nagarajan, M., Uhler, C., & Shivashankar, G. (2017). Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression. Molecular Biology of the Cell. American Society for Cell Biology. https://doi.org/10.1091/mbc.E16-12-0825","ieee":"Y. Wang, M. Nagarajan, C. Uhler, and G. Shivashankar, “Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression,” Molecular Biology of the Cell, vol. 28, no. 14. American Society for Cell Biology, pp. 1997–2009, 2017.","ista":"Wang Y, Nagarajan M, Uhler C, Shivashankar G. 2017. Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression. Molecular Biology of the Cell. 28(14), 1997–2009."},"publication":"Molecular Biology of the Cell","issue":"14","abstract":[{"lang":"eng","text":"Extracellular matrix signals from the microenvironment regulate gene expression patterns and cell behavior. Using a combination of experiments and geometric models, we demonstrate correlations between cell geometry, three-dimensional (3D) organization of chromosome territories, and gene expression. Fluorescence in situ hybridization experiments showed that micropatterned fibroblasts cultured on anisotropic versus isotropic substrates resulted in repositioning of specific chromosomes, which contained genes that were differentially regulated by cell geometries. Experiments combined with ellipsoid packing models revealed that the mechanosensitivity of chromosomes was correlated with their orientation in the nucleus. Transcription inhibition experiments suggested that the intermingling degree was more sensitive to global changes in transcription than to chromosome radial positioning and its orientations. These results suggested that cell geometry modulated 3D chromosome arrangement, and their neighborhoods correlated with gene expression patterns in a predictable manner. This is central to understanding geometric control of genetic programs involved in cellular homeostasis and the associated diseases. "}],"type":"journal_article","file":[{"file_id":"4844","relation":"main_file","checksum":"de01dac9e30970cfa6ae902480a4e04d","date_updated":"2020-07-14T12:47:46Z","date_created":"2018-12-12T10:10:53Z","access_level":"open_access","file_name":"IST-2017-892-v1+1_Mol._Biol._Cell-2017-Wang-1997-2009.pdf","creator":"system","content_type":"application/pdf","file_size":1086097}],"oa_version":"Published Version","pubrep_id":"892","intvolume":" 28","status":"public","ddc":["519"],"title":"Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"698"},{"volume":114,"date_created":"2018-12-11T11:48:00Z","date_updated":"2021-01-12T08:11:21Z","author":[{"full_name":"Veller, Carl","last_name":"Veller","first_name":"Carl"},{"first_name":"Laura","last_name":"Hayward","full_name":"Hayward, Laura"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"},{"full_name":"Hilbe, Christian","last_name":"Hilbe","first_name":"Christian","orcid":"0000-0001-5116-955X","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"KrCh"}],"publisher":"National Academy of Sciences","publication_status":"published","pmid":1,"year":"2017","publist_id":"7002","language":[{"iso":"eng"}],"doi":"10.1073/pnas.1702020114","quality_controlled":"1","external_id":{"pmid":["28630336"]},"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5502615/","open_access":"1"}],"oa":1,"publication_identifier":{"issn":["00278424"]},"month":"07","oa_version":"Submitted Version","intvolume":" 114","title":"The red queen and king in finite populations","status":"public","_id":"699","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"27","abstract":[{"lang":"eng","text":"In antagonistic symbioses, such as host–parasite interactions, one population’s success is the other’s loss. In mutualistic symbioses, such as division of labor, both parties can gain, but they might have different preferences over the possible mutualistic arrangements. The rates of evolution of the two populations in a symbiosis are important determinants of which population will be more successful: Faster evolution is thought to be favored in antagonistic symbioses (the “Red Queen effect”), but disfavored in certain mutualistic symbioses (the “Red King effect”). However, it remains unclear which biological parameters drive these effects. Here, we analyze the effects of the various determinants of evolutionary rate: generation time, mutation rate, population size, and the intensity of natural selection. Our main results hold for the case where mutation is infrequent. Slower evolution causes a long-term advantage in an important class of mutualistic interactions. Surprisingly, less intense selection is the strongest driver of this Red King effect, whereas relative mutation rates and generation times have little effect. In antagonistic interactions, faster evolution by any means is beneficial. Our results provide insight into the demographic evolution of symbionts. "}],"type":"journal_article","date_published":"2017-07-03T00:00:00Z","page":"E5396 - E5405","citation":{"ista":"Veller C, Hayward L, Nowak M, Hilbe C. 2017. The red queen and king in finite populations. PNAS. 114(27), E5396–E5405.","ieee":"C. Veller, L. Hayward, M. Nowak, and C. Hilbe, “The red queen and king in finite populations,” PNAS, vol. 114, no. 27. National Academy of Sciences, pp. E5396–E5405, 2017.","apa":"Veller, C., Hayward, L., Nowak, M., & Hilbe, C. (2017). The red queen and king in finite populations. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1702020114","ama":"Veller C, Hayward L, Nowak M, Hilbe C. The red queen and king in finite populations. PNAS. 2017;114(27):E5396-E5405. doi:10.1073/pnas.1702020114","chicago":"Veller, Carl, Laura Hayward, Martin Nowak, and Christian Hilbe. “The Red Queen and King in Finite Populations.” PNAS. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1702020114.","mla":"Veller, Carl, et al. “The Red Queen and King in Finite Populations.” PNAS, vol. 114, no. 27, National Academy of Sciences, 2017, pp. E5396–405, doi:10.1073/pnas.1702020114.","short":"C. Veller, L. Hayward, M. Nowak, C. Hilbe, PNAS 114 (2017) E5396–E5405."},"publication":"PNAS","day":"03","scopus_import":1},{"year":"2017","publication_status":"published","publisher":"American Institute of Physics","department":[{"_id":"JoFi"}],"author":[{"last_name":"Barzanjeh","first_name":"Shabir","orcid":"0000-0003-0415-1423","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","full_name":"Barzanjeh, Shabir"},{"full_name":"Salari, Vahid","last_name":"Salari","first_name":"Vahid"},{"full_name":"Tuszynski, Jack","first_name":"Jack","last_name":"Tuszynski"},{"first_name":"Michal","last_name":"Cifra","full_name":"Cifra, Michal"},{"first_name":"Christoph","last_name":"Simon","full_name":"Simon, Christoph"}],"date_created":"2018-12-11T11:48:00Z","date_updated":"2023-02-23T12:56:35Z","volume":96,"article_number":"012404","publist_id":"6997","ec_funded":1,"oa":1,"main_file_link":[{"url":"https://arxiv.org/pdf/1612.07061.pdf","open_access":"1"}],"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics","_id":"258047B6-B435-11E9-9278-68D0E5697425","grant_number":"707438"}],"doi":"10.1103/PhysRevE.96.012404","language":[{"iso":"eng"}],"month":"07","publication_identifier":{"issn":["24700045"]},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"700","title":"Optomechanical proposal for monitoring microtubule mechanical vibrations","status":"public","intvolume":" 96","oa_version":"Submitted Version","type":"journal_article","abstract":[{"text":"Microtubules provide the mechanical force required for chromosome separation during mitosis. However, little is known about the dynamic (high-frequency) mechanical properties of microtubules. Here, we theoretically propose to control the vibrations of a doubly clamped microtubule by tip electrodes and to detect its motion via the optomechanical coupling between the vibrational modes of the microtubule and an optical cavity. In the presence of a red-detuned strong pump laser, this coupling leads to optomechanical-induced transparency of an optical probe field, which can be detected with state-of-the art technology. The center frequency and line width of the transparency peak give the resonance frequency and damping rate of the microtubule, respectively, while the height of the peak reveals information about the microtubule-cavity field coupling. Our method opens the new possibilities to gain information about the physical properties of microtubules, which will enhance our capability to design physical cancer treatment protocols as alternatives to chemotherapeutic drugs.","lang":"eng"}],"issue":"1","publication":" Physical Review E Statistical Nonlinear and Soft Matter Physics ","citation":{"ama":"Barzanjeh S, Salari V, Tuszynski J, Cifra M, Simon C. Optomechanical proposal for monitoring microtubule mechanical vibrations. Physical Review E Statistical Nonlinear and Soft Matter Physics . 2017;96(1). doi:10.1103/PhysRevE.96.012404","ieee":"S. Barzanjeh, V. Salari, J. Tuszynski, M. Cifra, and C. Simon, “Optomechanical proposal for monitoring microtubule mechanical vibrations,” Physical Review E Statistical Nonlinear and Soft Matter Physics , vol. 96, no. 1. American Institute of Physics, 2017.","apa":"Barzanjeh, S., Salari, V., Tuszynski, J., Cifra, M., & Simon, C. (2017). Optomechanical proposal for monitoring microtubule mechanical vibrations. Physical Review E Statistical Nonlinear and Soft Matter Physics . American Institute of Physics. https://doi.org/10.1103/PhysRevE.96.012404","ista":"Barzanjeh S, Salari V, Tuszynski J, Cifra M, Simon C. 2017. Optomechanical proposal for monitoring microtubule mechanical vibrations. Physical Review E Statistical Nonlinear and Soft Matter Physics . 96(1), 012404.","short":"S. Barzanjeh, V. Salari, J. Tuszynski, M. Cifra, C. Simon, Physical Review E Statistical Nonlinear and Soft Matter Physics 96 (2017).","mla":"Barzanjeh, Shabir, et al. “Optomechanical Proposal for Monitoring Microtubule Mechanical Vibrations.” Physical Review E Statistical Nonlinear and Soft Matter Physics , vol. 96, no. 1, 012404, American Institute of Physics, 2017, doi:10.1103/PhysRevE.96.012404.","chicago":"Barzanjeh, Shabir, Vahid Salari, Jack Tuszynski, Michal Cifra, and Christoph Simon. “Optomechanical Proposal for Monitoring Microtubule Mechanical Vibrations.” Physical Review E Statistical Nonlinear and Soft Matter Physics . American Institute of Physics, 2017. https://doi.org/10.1103/PhysRevE.96.012404."},"date_published":"2017-07-12T00:00:00Z","scopus_import":1,"day":"12"},{"has_accepted_license":"1","day":"14","date_published":"2017-07-14T00:00:00Z","citation":{"ieee":"J. Kynčl and Z. Patakova, “On the nonexistence of k reptile simplices in ℝ^3 and ℝ^4,” The Electronic Journal of Combinatorics, vol. 24, no. 3. International Press, pp. 1–44, 2017.","apa":"Kynčl, J., & Patakova, Z. (2017). On the nonexistence of k reptile simplices in ℝ^3 and ℝ^4. The Electronic Journal of Combinatorics. International Press.","ista":"Kynčl J, Patakova Z. 2017. On the nonexistence of k reptile simplices in ℝ^3 and ℝ^4. The Electronic Journal of Combinatorics. 24(3), 1–44.","ama":"Kynčl J, Patakova Z. On the nonexistence of k reptile simplices in ℝ^3 and ℝ^4. The Electronic Journal of Combinatorics. 2017;24(3):1-44.","chicago":"Kynčl, Jan, and Zuzana Patakova. “On the Nonexistence of k Reptile Simplices in ℝ^3 and ℝ^4.” The Electronic Journal of Combinatorics. International Press, 2017.","short":"J. Kynčl, Z. Patakova, The Electronic Journal of Combinatorics 24 (2017) 1–44.","mla":"Kynčl, Jan, and Zuzana Patakova. “On the Nonexistence of k Reptile Simplices in ℝ^3 and ℝ^4.” The Electronic Journal of Combinatorics, vol. 24, no. 3, International Press, 2017, pp. 1–44."},"publication":"The Electronic Journal of Combinatorics","page":"1-44","issue":"3","abstract":[{"lang":"eng","text":"A d-dimensional simplex S is called a k-reptile (or a k-reptile simplex) if it can be tiled by k simplices with disjoint interiors that are all mutually congruent and similar to S. For d = 2, triangular k-reptiles exist for all k of the form a^2, 3a^2 or a^2+b^2 and they have been completely characterized by Snover, Waiveris, and Williams. On the other hand, the only k-reptile simplices that are known for d ≥ 3, have k = m^d, where m is a positive integer. We substantially simplify the proof by Matoušek and the second author that for d = 3, k-reptile tetrahedra can exist only for k = m^3. We then prove a weaker analogue of this result for d = 4 by showing that four-dimensional k-reptile simplices can exist only for k = m^2."}],"type":"journal_article","pubrep_id":"984","file":[{"date_updated":"2020-07-14T12:47:47Z","date_created":"2018-12-12T10:14:25Z","checksum":"a431e573e31df13bc0f66de3061006ec","relation":"main_file","file_id":"5077","content_type":"application/pdf","file_size":544042,"creator":"system","file_name":"IST-2018-984-v1+1_Patakova_on_the_nonexistence_of_k-reptile_simplices_in_R_3_and_R_4_2017.pdf","access_level":"open_access"}],"oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"701","intvolume":" 24","status":"public","title":"On the nonexistence of k reptile simplices in ℝ^3 and ℝ^4","ddc":["500"],"publication_identifier":{"issn":["10778926"]},"month":"07","language":[{"iso":"eng"}],"oa":1,"quality_controlled":"1","publist_id":"6996","file_date_updated":"2020-07-14T12:47:47Z","author":[{"first_name":"Jan","last_name":"Kynčl","full_name":"Kynčl, Jan"},{"full_name":"Patakova, Zuzana","orcid":"0000-0002-3975-1683","id":"48B57058-F248-11E8-B48F-1D18A9856A87","last_name":"Patakova","first_name":"Zuzana"}],"volume":24,"date_created":"2018-12-11T11:48:00Z","date_updated":"2021-01-12T08:11:28Z","year":"2017","department":[{"_id":"UlWa"}],"publisher":"International Press","publication_status":"published"},{"scopus_import":1,"publication_identifier":{"issn":["19466234"]},"day":"19","month":"07","page":"eaao0972","quality_controlled":"1","citation":{"chicago":"Novarino, Gaia. “The Riddle of CHD8 Haploinsufficiency in Autism Spectrum Disorder.” Science Translational Medicine. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/scitranslmed.aao0972.","short":"G. Novarino, Science Translational Medicine 9 (2017) eaao0972.","mla":"Novarino, Gaia. “The Riddle of CHD8 Haploinsufficiency in Autism Spectrum Disorder.” Science Translational Medicine, vol. 9, no. 399, American Association for the Advancement of Science, 2017, p. eaao0972, doi:10.1126/scitranslmed.aao0972.","ieee":"G. Novarino, “The riddle of CHD8 haploinsufficiency in autism spectrum disorder,” Science Translational Medicine, vol. 9, no. 399. American Association for the Advancement of Science, p. eaao0972, 2017.","apa":"Novarino, G. (2017). The riddle of CHD8 haploinsufficiency in autism spectrum disorder. Science Translational Medicine. American Association for the Advancement of Science. https://doi.org/10.1126/scitranslmed.aao0972","ista":"Novarino G. 2017. The riddle of CHD8 haploinsufficiency in autism spectrum disorder. Science Translational Medicine. 9(399), eaao0972.","ama":"Novarino G. The riddle of CHD8 haploinsufficiency in autism spectrum disorder. Science Translational Medicine. 2017;9(399):eaao0972. doi:10.1126/scitranslmed.aao0972"},"publication":"Science Translational Medicine","language":[{"iso":"eng"}],"date_published":"2017-07-19T00:00:00Z","doi":"10.1126/scitranslmed.aao0972","type":"journal_article","issue":"399","publist_id":"6993","abstract":[{"text":"Leading autism-associated mutation in mouse partially mimics human disorder.\r\n\r\n","lang":"eng"}],"publisher":"American Association for the Advancement of Science","department":[{"_id":"GaNo"}],"intvolume":" 9","publication_status":"published","title":"The riddle of CHD8 haploinsufficiency in autism spectrum disorder","status":"public","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"702","year":"2017","volume":9,"oa_version":"None","date_created":"2018-12-11T11:48:01Z","date_updated":"2021-01-12T08:11:31Z","author":[{"first_name":"Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia"}]},{"type":"journal_article","issue":"8","publist_id":"6987","abstract":[{"lang":"eng","text":"A hippocampal mossy fiber synapse has a complex structure and is implicated in learning and memory. In this synapse, the mossy fiber boutons attach to the dendritic shaft by puncta adherentia junctions and wrap around a multiply-branched spine, forming synaptic junctions. We have recently shown using transmission electron microscopy, immunoelectron microscopy and serial block face-scanning electron microscopy that atypical puncta adherentia junctions are formed in the afadin-deficient mossy fiber synapse and that the complexity of postsynaptic spines and mossy fiber boutons, the number of spine heads, the area of postsynaptic densities and the density of synaptic vesicles docked to active zones are decreased in the afadin-deficient synapse. We investigated here the roles of afadin in the functional differentiations of the mossy fiber synapse using the afadin-deficient mice. The electrophysiological studies showed that both the release probability of glutamate and the postsynaptic responsiveness to glutamate were markedly reduced, but not completely lost, in the afadin-deficient mossy fiber synapse, whereas neither long-term potentiation nor long-term depression was affected. These results indicate that afadin plays roles in the functional differentiations of the presynapse and the postsynapse of the hippocampal mossy fiber synapse."}],"department":[{"_id":"PeJo"}],"publisher":"Wiley-Blackwell","intvolume":" 22","status":"public","title":"Roles of afadin in functional differentiations of hippocampal mossy fiber synapse","publication_status":"published","_id":"706","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2017","volume":22,"oa_version":"None","date_updated":"2021-01-12T08:11:37Z","date_created":"2018-12-11T11:48:02Z","author":[{"last_name":"Geng","first_name":"Xiaoqi","id":"3395256A-F248-11E8-B48F-1D18A9856A87","full_name":"Geng, Xiaoqi"},{"full_name":"Maruo, Tomohiko","last_name":"Maruo","first_name":"Tomohiko"},{"full_name":"Mandai, Kenji","first_name":"Kenji","last_name":"Mandai"},{"full_name":"Supriyanto, Irwan","last_name":"Supriyanto","first_name":"Irwan"},{"first_name":"Muneaki","last_name":"Miyata","full_name":"Miyata, Muneaki"},{"last_name":"Sakakibara","first_name":"Shotaro","full_name":"Sakakibara, Shotaro"},{"full_name":"Mizoguchi, Akira","first_name":"Akira","last_name":"Mizoguchi"},{"last_name":"Takai","first_name":"Yoshimi","full_name":"Takai, Yoshimi"},{"full_name":"Mori, Masahiro","last_name":"Mori","first_name":"Masahiro"}],"scopus_import":1,"publication_identifier":{"issn":["13569597"]},"day":"01","month":"08","page":"715 - 722","quality_controlled":"1","citation":{"chicago":"Geng, Xiaoqi, Tomohiko Maruo, Kenji Mandai, Irwan Supriyanto, Muneaki Miyata, Shotaro Sakakibara, Akira Mizoguchi, Yoshimi Takai, and Masahiro Mori. “Roles of Afadin in Functional Differentiations of Hippocampal Mossy Fiber Synapse.” Genes to Cells. Wiley-Blackwell, 2017. https://doi.org/10.1111/gtc.12508.","short":"X. Geng, T. Maruo, K. Mandai, I. Supriyanto, M. Miyata, S. Sakakibara, A. Mizoguchi, Y. Takai, M. Mori, Genes to Cells 22 (2017) 715–722.","mla":"Geng, Xiaoqi, et al. “Roles of Afadin in Functional Differentiations of Hippocampal Mossy Fiber Synapse.” Genes to Cells, vol. 22, no. 8, Wiley-Blackwell, 2017, pp. 715–22, doi:10.1111/gtc.12508.","ieee":"X. Geng et al., “Roles of afadin in functional differentiations of hippocampal mossy fiber synapse,” Genes to Cells, vol. 22, no. 8. Wiley-Blackwell, pp. 715–722, 2017.","apa":"Geng, X., Maruo, T., Mandai, K., Supriyanto, I., Miyata, M., Sakakibara, S., … Mori, M. (2017). Roles of afadin in functional differentiations of hippocampal mossy fiber synapse. Genes to Cells. Wiley-Blackwell. https://doi.org/10.1111/gtc.12508","ista":"Geng X, Maruo T, Mandai K, Supriyanto I, Miyata M, Sakakibara S, Mizoguchi A, Takai Y, Mori M. 2017. Roles of afadin in functional differentiations of hippocampal mossy fiber synapse. Genes to Cells. 22(8), 715–722.","ama":"Geng X, Maruo T, Mandai K, et al. Roles of afadin in functional differentiations of hippocampal mossy fiber synapse. Genes to Cells. 2017;22(8):715-722. doi:10.1111/gtc.12508"},"publication":"Genes to Cells","language":[{"iso":"eng"}],"date_published":"2017-08-01T00:00:00Z","doi":"10.1111/gtc.12508"},{"date_published":"2017-08-01T00:00:00Z","citation":{"ama":"Akopyan A, Karasev R. A tight estimate for the waist of the ball . Bulletin of the London Mathematical Society. 2017;49(4):690-693. doi:10.1112/blms.12062","apa":"Akopyan, A., & Karasev, R. (2017). A tight estimate for the waist of the ball . Bulletin of the London Mathematical Society. Wiley-Blackwell. https://doi.org/10.1112/blms.12062","ieee":"A. Akopyan and R. Karasev, “A tight estimate for the waist of the ball ,” Bulletin of the London Mathematical Society, vol. 49, no. 4. Wiley-Blackwell, pp. 690–693, 2017.","ista":"Akopyan A, Karasev R. 2017. A tight estimate for the waist of the ball . Bulletin of the London Mathematical Society. 49(4), 690–693.","short":"A. Akopyan, R. Karasev, Bulletin of the London Mathematical Society 49 (2017) 690–693.","mla":"Akopyan, Arseniy, and Roman Karasev. “A Tight Estimate for the Waist of the Ball .” Bulletin of the London Mathematical Society, vol. 49, no. 4, Wiley-Blackwell, 2017, pp. 690–93, doi:10.1112/blms.12062.","chicago":"Akopyan, Arseniy, and Roman Karasev. “A Tight Estimate for the Waist of the Ball .” Bulletin of the London Mathematical Society. Wiley-Blackwell, 2017. https://doi.org/10.1112/blms.12062."},"publication":"Bulletin of the London Mathematical Society","page":"690 - 693","day":"01","scopus_import":1,"oa_version":"Preprint","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"707","intvolume":" 49","title":"A tight estimate for the waist of the ball ","status":"public","issue":"4","abstract":[{"text":"We answer a question of M. Gromov on the waist of the unit ball.","lang":"eng"}],"type":"journal_article","doi":"10.1112/blms.12062","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1608.06279","open_access":"1"}],"oa":1,"project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"quality_controlled":"1","publication_identifier":{"issn":["00246093"]},"month":"08","author":[{"orcid":"0000-0002-2548-617X","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","last_name":"Akopyan","first_name":"Arseniy","full_name":"Akopyan, Arseniy"},{"last_name":"Karasev","first_name":"Roman","full_name":"Karasev, Roman"}],"volume":49,"date_created":"2018-12-11T11:48:02Z","date_updated":"2021-01-12T08:11:41Z","year":"2017","publisher":"Wiley-Blackwell","department":[{"_id":"HeEd"}],"publication_status":"published","publist_id":"6982","ec_funded":1},{"abstract":[{"lang":"eng","text":"In the developing and adult brain, oligodendrocyte precursor cells (OPCs) are influenced by neuronal activity: they are involved in synaptic signaling with neurons, and their proliferation and differentiation into myelinating glia can be altered by transient changes in neuronal firing. An important question that has been unanswered is whether OPCs can discriminate different patterns of neuronal activity and respond to them in a distinct way. Here, we demonstrate in brain slices that the pattern of neuronal activity determines the functional changes triggered at synapses between axons and OPCs. Furthermore, we show that stimulation of the corpus callosum at different frequencies in vivo affects proliferation and differentiation of OPCs in a dissimilar way. Our findings suggest that neurons do not influence OPCs in “all-or-none” fashion but use their firing pattern to tune the response and behavior of these nonneuronal cells."}],"issue":"8","type":"journal_article","file":[{"creator":"system","file_size":18155365,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2017-889-v1+1_journal.pbio.2001993.pdf","checksum":"0c974f430682dc832ea7b27ab5a93124","date_created":"2018-12-12T10:15:35Z","date_updated":"2020-07-14T12:47:49Z","file_id":"5156","relation":"main_file"}],"oa_version":"Published Version","pubrep_id":"889","ddc":["576","610"],"status":"public","title":"Different patterns of neuronal activity trigger distinct responses of oligodendrocyte precursor cells in the corpus callosum","intvolume":" 15","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"708","day":"22","has_accepted_license":"1","scopus_import":1,"date_published":"2017-08-22T00:00:00Z","publication":"PLoS Biology","citation":{"ama":"Nagy B, Hovhannisyan A, Barzan R, Chen T, Kukley M. Different patterns of neuronal activity trigger distinct responses of oligodendrocyte precursor cells in the corpus callosum. PLoS Biology. 2017;15(8). doi:10.1371/journal.pbio.2001993","ista":"Nagy B, Hovhannisyan A, Barzan R, Chen T, Kukley M. 2017. Different patterns of neuronal activity trigger distinct responses of oligodendrocyte precursor cells in the corpus callosum. PLoS Biology. 15(8), e2001993.","apa":"Nagy, B., Hovhannisyan, A., Barzan, R., Chen, T., & Kukley, M. (2017). Different patterns of neuronal activity trigger distinct responses of oligodendrocyte precursor cells in the corpus callosum. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2001993","ieee":"B. Nagy, A. Hovhannisyan, R. Barzan, T. Chen, and M. Kukley, “Different patterns of neuronal activity trigger distinct responses of oligodendrocyte precursor cells in the corpus callosum,” PLoS Biology, vol. 15, no. 8. Public Library of Science, 2017.","mla":"Nagy, Balint, et al. “Different Patterns of Neuronal Activity Trigger Distinct Responses of Oligodendrocyte Precursor Cells in the Corpus Callosum.” PLoS Biology, vol. 15, no. 8, e2001993, Public Library of Science, 2017, doi:10.1371/journal.pbio.2001993.","short":"B. Nagy, A. Hovhannisyan, R. Barzan, T. Chen, M. Kukley, PLoS Biology 15 (2017).","chicago":"Nagy, Balint, Anahit Hovhannisyan, Ruxandra Barzan, Ting Chen, and Maria Kukley. “Different Patterns of Neuronal Activity Trigger Distinct Responses of Oligodendrocyte Precursor Cells in the Corpus Callosum.” PLoS Biology. Public Library of Science, 2017. https://doi.org/10.1371/journal.pbio.2001993."},"file_date_updated":"2020-07-14T12:47:49Z","publist_id":"6983","article_number":"e2001993","date_updated":"2021-01-12T08:11:45Z","date_created":"2018-12-11T11:48:03Z","volume":15,"author":[{"full_name":"Nagy, Balint","id":"30F830CE-02D1-11E9-9BAA-DAF4881429F2","orcid":"0000-0002-4002-4686","first_name":"Balint","last_name":"Nagy"},{"full_name":"Hovhannisyan, Anahit","first_name":"Anahit","last_name":"Hovhannisyan"},{"last_name":"Barzan","first_name":"Ruxandra","full_name":"Barzan, Ruxandra"},{"first_name":"Ting","last_name":"Chen","full_name":"Chen, Ting"},{"last_name":"Kukley","first_name":"Maria","full_name":"Kukley, Maria"}],"publication_status":"published","publisher":"Public Library of Science","department":[{"_id":"SaSi"}],"year":"2017","month":"08","publication_identifier":{"issn":["15449173"]},"language":[{"iso":"eng"}],"doi":"10.1371/journal.pbio.2001993","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"}}]