[{"pubrep_id":"676","status":"public","conference":{"name":"ASIACRYPT: Theory and Application of Cryptology and Information Security","end_date":"2015-12-03","location":"Auckland, New Zealand","start_date":"2015-11-29"},"type":"conference","_id":"1654","series_title":"Lecture Notes in Computer Science","department":[{"_id":"KrPi"}],"file_date_updated":"2020-07-14T12:45:08Z","ddc":["004","005"],"date_updated":"2021-01-12T06:52:16Z","intvolume":" 9453","month":"12","scopus_import":1,"alternative_title":["LNCS"],"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"HMAC and its variant NMAC are the most popular approaches to deriving a MAC (and more generally, a PRF) from a cryptographic hash function. Despite nearly two decades of research, their exact security still remains far from understood in many different contexts. Indeed, recent works have re-surfaced interest for {\\em generic} attacks, i.e., attacks that treat the compression function of the underlying hash function as a black box.\r\n\r\nGeneric security can be proved in a model where the underlying compression function is modeled as a random function -- yet, to date, the question of proving tight, non-trivial bounds on the generic security of HMAC/NMAC even as a PRF remains a challenging open question.\r\n\r\nIn this paper, we ask the question of whether a small modification to HMAC and NMAC can allow us to exactly characterize the security of the resulting constructions, while only incurring little penalty with respect to efficiency. To this end, we present simple variants of NMAC and HMAC, for which we prove tight bounds on the generic PRF security, expressed in terms of numbers of construction and compression function queries necessary to break the construction. All of our constructions are obtained via a (near) {\\em black-box} modification of NMAC and HMAC, which can be interpreted as an initial step of key-dependent message pre-processing.\r\n\r\nWhile our focus is on PRF security, a further attractive feature of our new constructions is that they clearly defeat all recent generic attacks against properties such as state recovery and universal forgery. These exploit properties of the so-called ``functional graph'' which are not directly accessible in our new constructions. "}],"ec_funded":1,"volume":9453,"language":[{"iso":"eng"}],"file":[{"file_id":"4732","checksum":"d1e53203db2d8573a560995ccdffac62","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2016-676-v1+1_881.pdf","date_created":"2018-12-12T10:09:09Z","creator":"system","file_size":512071,"date_updated":"2020-07-14T12:45:08Z"}],"publication_status":"published","project":[{"name":"Provable Security for Physical Cryptography","grant_number":"259668","call_identifier":"FP7","_id":"258C570E-B435-11E9-9278-68D0E5697425"}],"title":"Generic security of NMAC and HMAC with input whitening","author":[{"full_name":"Gazi, Peter","last_name":"Gazi","id":"3E0BFE38-F248-11E8-B48F-1D18A9856A87","first_name":"Peter"},{"last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Tessaro","full_name":"Tessaro, Stefano","first_name":"Stefano"}],"publist_id":"5496","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"P. Gazi, K.Z. Pietrzak, S. Tessaro, 9453 (2015) 85–109.","ieee":"P. Gazi, K. Z. Pietrzak, and S. Tessaro, “Generic security of NMAC and HMAC with input whitening,” vol. 9453. Springer, pp. 85–109, 2015.","ama":"Gazi P, Pietrzak KZ, Tessaro S. Generic security of NMAC and HMAC with input whitening. 2015;9453:85-109. doi:10.1007/978-3-662-48800-3_4","apa":"Gazi, P., Pietrzak, K. Z., & Tessaro, S. (2015). Generic security of NMAC and HMAC with input whitening. Presented at the ASIACRYPT: Theory and Application of Cryptology and Information Security, Auckland, New Zealand: Springer. https://doi.org/10.1007/978-3-662-48800-3_4","mla":"Gazi, Peter, et al. Generic Security of NMAC and HMAC with Input Whitening. Vol. 9453, Springer, 2015, pp. 85–109, doi:10.1007/978-3-662-48800-3_4.","ista":"Gazi P, Pietrzak KZ, Tessaro S. 2015. Generic security of NMAC and HMAC with input whitening. 9453, 85–109.","chicago":"Gazi, Peter, Krzysztof Z Pietrzak, and Stefano Tessaro. “Generic Security of NMAC and HMAC with Input Whitening.” Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-662-48800-3_4."},"oa":1,"publisher":"Springer","quality_controlled":"1","date_created":"2018-12-11T11:53:17Z","doi":"10.1007/978-3-662-48800-3_4","date_published":"2015-12-30T00:00:00Z","page":"85 - 109","day":"30","year":"2015","has_accepted_license":"1"},{"year":"2015","has_accepted_license":"1","day":"20","page":"1046 - 1057","date_created":"2018-12-11T11:53:15Z","doi":"10.1007/978-3-662-47672-7_85","date_published":"2015-06-20T00:00:00Z","oa":1,"publisher":"Springer","quality_controlled":"1","citation":{"ista":"Skórski M, Golovnev A, Pietrzak KZ. 2015. Condensed unpredictability . ICALP: Automata, Languages and Programming, LNCS, vol. 9134, 1046–1057.","chicago":"Skórski, Maciej, Alexander Golovnev, and Krzysztof Z Pietrzak. “Condensed Unpredictability ,” 9134:1046–57. Springer, 2015. https://doi.org/10.1007/978-3-662-47672-7_85.","ama":"Skórski M, Golovnev A, Pietrzak KZ. Condensed unpredictability . In: Vol 9134. Springer; 2015:1046-1057. doi:10.1007/978-3-662-47672-7_85","apa":"Skórski, M., Golovnev, A., & Pietrzak, K. Z. (2015). Condensed unpredictability (Vol. 9134, pp. 1046–1057). Presented at the ICALP: Automata, Languages and Programming, Kyoto, Japan: Springer. https://doi.org/10.1007/978-3-662-47672-7_85","ieee":"M. Skórski, A. Golovnev, and K. Z. Pietrzak, “Condensed unpredictability ,” presented at the ICALP: Automata, Languages and Programming, Kyoto, Japan, 2015, vol. 9134, pp. 1046–1057.","short":"M. Skórski, A. Golovnev, K.Z. Pietrzak, in:, Springer, 2015, pp. 1046–1057.","mla":"Skórski, Maciej, et al. Condensed Unpredictability . Vol. 9134, Springer, 2015, pp. 1046–57, doi:10.1007/978-3-662-47672-7_85."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"5500","author":[{"first_name":"Maciej","full_name":"Skórski, Maciej","last_name":"Skórski"},{"full_name":"Golovnev, Alexander","last_name":"Golovnev","first_name":"Alexander"},{"full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z"}],"title":"Condensed unpredictability ","project":[{"grant_number":"259668","name":"Provable Security for Physical Cryptography","call_identifier":"FP7","_id":"258C570E-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"e808c7eecb631336fc9f9bf2e8d4ecae","file_id":"4693","date_updated":"2020-07-14T12:45:08Z","file_size":525503,"creator":"system","date_created":"2018-12-12T10:08:32Z","file_name":"IST-2016-675-v1+1_384.pdf"}],"ec_funded":1,"license":"https://creativecommons.org/licenses/by/4.0/","volume":9134,"abstract":[{"text":"We consider the task of deriving a key with high HILL entropy (i.e., being computationally indistinguishable from a key with high min-entropy) from an unpredictable source.\r\n\r\nPrevious to this work, the only known way to transform unpredictability into a key that was ϵ indistinguishable from having min-entropy was via pseudorandomness, for example by Goldreich-Levin (GL) hardcore bits. This approach has the inherent limitation that from a source with k bits of unpredictability entropy one can derive a key of length (and thus HILL entropy) at most k−2log(1/ϵ) bits. In many settings, e.g. when dealing with biometric data, such a 2log(1/ϵ) bit entropy loss in not an option. Our main technical contribution is a theorem that states that in the high entropy regime, unpredictability implies HILL entropy. Concretely, any variable K with |K|−d bits of unpredictability entropy has the same amount of so called metric entropy (against real-valued, deterministic distinguishers), which is known to imply the same amount of HILL entropy. The loss in circuit size in this argument is exponential in the entropy gap d, and thus this result only applies for small d (i.e., where the size of distinguishers considered is exponential in d).\r\n\r\nTo overcome the above restriction, we investigate if it’s possible to first “condense” unpredictability entropy and make the entropy gap small. We show that any source with k bits of unpredictability can be condensed into a source of length k with k−3 bits of unpredictability entropy. Our condenser simply “abuses" the GL construction and derives a k bit key from a source with k bits of unpredicatibily. The original GL theorem implies nothing when extracting that many bits, but we show that in this regime, GL still behaves like a “condenser" for unpredictability. This result comes with two caveats (1) the loss in circuit size is exponential in k and (2) we require that the source we start with has no HILL entropy (equivalently, one can efficiently check if a guess is correct). We leave it as an intriguing open problem to overcome these restrictions or to prove they’re inherent.","lang":"eng"}],"oa_version":"Published Version","scopus_import":1,"alternative_title":["LNCS"],"intvolume":" 9134","month":"06","date_updated":"2021-01-12T06:52:15Z","ddc":["000","005"],"file_date_updated":"2020-07-14T12:45:08Z","department":[{"_id":"KrPi"}],"_id":"1650","conference":{"name":"ICALP: Automata, Languages and Programming","start_date":"2015-07-06","location":"Kyoto, Japan","end_date":"2015-07-10"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"conference","pubrep_id":"675","status":"public"},{"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"isbn":["978-3-662-46446-5"]},"ec_funded":1,"volume":9020,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Cryptographic e-cash allows off-line electronic transactions between a bank, users and merchants in a secure and anonymous fashion. A plethora of e-cash constructions has been proposed in the literature; however, these traditional e-cash schemes only allow coins to be transferred once between users and merchants. Ideally, we would like users to be able to transfer coins between each other multiple times before deposit, as happens with physical cash. “Transferable” e-cash schemes are the solution to this problem. Unfortunately, the currently proposed schemes are either completely impractical or do not achieve the desirable anonymity properties without compromises, such as assuming the existence of a trusted “judge” who can trace all coins and users in the system. This paper presents the first efficient and fully anonymous transferable e-cash scheme without any trusted third parties. We start by revising the security and anonymity properties of transferable e-cash to capture issues that were previously overlooked. For our construction we use the recently proposed malleable signatures by Chase et al. to allow the secure and anonymous transfer of coins, combined with a new efficient double-spending detection mechanism. Finally, we discuss an instantiation of our construction."}],"intvolume":" 9020","month":"03","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/978-3-662-46447-2_5"}],"scopus_import":"1","alternative_title":["LNCS"],"date_updated":"2022-05-23T10:08:37Z","department":[{"_id":"KrPi"}],"_id":"1651","status":"public","conference":{"name":"PKC: Public Key Crypography","location":"Gaithersburg, MD, United States","end_date":"2015-04-01","start_date":"2015-03-30"},"type":"conference","publication":"Public-Key Cryptography - PKC 2015","day":"17","year":"2015","date_created":"2018-12-11T11:53:15Z","doi":"10.1007/978-3-662-46447-2_5","date_published":"2015-03-17T00:00:00Z","page":"101 - 124","acknowledgement":"Work done as an intern in Microsoft Research Redmond and as a student at Brown University, where supported by NSF grant 0964379. Supported by the European Research Council, ERC Starting Grant (259668-PSPC).","oa":1,"publisher":"Springer","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Baldimtsi, Foteini, Melissa Chase, Georg Fuchsbauer, and Markulf Kohlweiss. “Anonymous Transferable E-Cash.” In Public-Key Cryptography - PKC 2015, 9020:101–24. Springer, 2015. https://doi.org/10.1007/978-3-662-46447-2_5.","ista":"Baldimtsi F, Chase M, Fuchsbauer G, Kohlweiss M. 2015. Anonymous transferable e-cash. Public-Key Cryptography - PKC 2015. PKC: Public Key Crypography, LNCS, vol. 9020, 101–124.","mla":"Baldimtsi, Foteini, et al. “Anonymous Transferable E-Cash.” Public-Key Cryptography - PKC 2015, vol. 9020, Springer, 2015, pp. 101–24, doi:10.1007/978-3-662-46447-2_5.","short":"F. Baldimtsi, M. Chase, G. Fuchsbauer, M. Kohlweiss, in:, Public-Key Cryptography - PKC 2015, Springer, 2015, pp. 101–124.","ieee":"F. Baldimtsi, M. Chase, G. Fuchsbauer, and M. Kohlweiss, “Anonymous transferable e-cash,” in Public-Key Cryptography - PKC 2015, Gaithersburg, MD, United States, 2015, vol. 9020, pp. 101–124.","ama":"Baldimtsi F, Chase M, Fuchsbauer G, Kohlweiss M. Anonymous transferable e-cash. In: Public-Key Cryptography - PKC 2015. Vol 9020. Springer; 2015:101-124. doi:10.1007/978-3-662-46447-2_5","apa":"Baldimtsi, F., Chase, M., Fuchsbauer, G., & Kohlweiss, M. (2015). Anonymous transferable e-cash. In Public-Key Cryptography - PKC 2015 (Vol. 9020, pp. 101–124). Gaithersburg, MD, United States: Springer. https://doi.org/10.1007/978-3-662-46447-2_5"},"title":"Anonymous transferable e-cash","article_processing_charge":"No","publist_id":"5499","author":[{"last_name":"Baldimtsi","full_name":"Baldimtsi, Foteini","first_name":"Foteini"},{"full_name":"Chase, Melissa","last_name":"Chase","first_name":"Melissa"},{"last_name":"Fuchsbauer","full_name":"Fuchsbauer, Georg","id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","first_name":"Georg"},{"full_name":"Kohlweiss, Markulf","last_name":"Kohlweiss","first_name":"Markulf"}],"project":[{"_id":"258C570E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"259668","name":"Provable Security for Physical Cryptography"}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Alwen, Joel F., and Vladimir Serbinenko. “High Parallel Complexity Graphs and Memory-Hard Functions.” Proceedings of the 47th Annual ACM Symposium on Theory of Computing, ACM, 2015, pp. 595–603, doi:10.1145/2746539.2746622.","ieee":"J. F. Alwen and V. Serbinenko, “High parallel complexity graphs and memory-hard functions,” in Proceedings of the 47th annual ACM symposium on Theory of computing, Portland, OR, United States, 2015, pp. 595–603.","short":"J.F. Alwen, V. Serbinenko, in:, Proceedings of the 47th Annual ACM Symposium on Theory of Computing, ACM, 2015, pp. 595–603.","ama":"Alwen JF, Serbinenko V. High parallel complexity graphs and memory-hard functions. In: Proceedings of the 47th Annual ACM Symposium on Theory of Computing. ACM; 2015:595-603. doi:10.1145/2746539.2746622","apa":"Alwen, J. F., & Serbinenko, V. (2015). High parallel complexity graphs and memory-hard functions. In Proceedings of the 47th annual ACM symposium on Theory of computing (pp. 595–603). Portland, OR, United States: ACM. https://doi.org/10.1145/2746539.2746622","chicago":"Alwen, Joel F, and Vladimir Serbinenko. “High Parallel Complexity Graphs and Memory-Hard Functions.” In Proceedings of the 47th Annual ACM Symposium on Theory of Computing, 595–603. ACM, 2015. https://doi.org/10.1145/2746539.2746622.","ista":"Alwen JF, Serbinenko V. 2015. High parallel complexity graphs and memory-hard functions. Proceedings of the 47th annual ACM symposium on Theory of computing. STOC: Symposium on the Theory of Computing, 595–603."},"date_updated":"2021-01-12T06:52:16Z","title":"High parallel complexity graphs and memory-hard functions","department":[{"_id":"KrPi"}],"publist_id":"5498","author":[{"last_name":"Alwen","full_name":"Alwen, Joel F","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","first_name":"Joel F"},{"full_name":"Serbinenko, Vladimir","last_name":"Serbinenko","first_name":"Vladimir"}],"_id":"1652","project":[{"_id":"258C570E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Provable Security for Physical Cryptography","grant_number":"259668"}],"status":"public","type":"conference","conference":{"name":"STOC: Symposium on the Theory of Computing","location":"Portland, OR, United States","end_date":"2015-06-17","start_date":"2015-06-14"},"day":"01","language":[{"iso":"eng"}],"publication":"Proceedings of the 47th annual ACM symposium on Theory of computing","publication_status":"published","year":"2015","date_published":"2015-06-01T00:00:00Z","doi":"10.1145/2746539.2746622","ec_funded":1,"date_created":"2018-12-11T11:53:16Z","page":"595 - 603","oa_version":"Submitted Version","abstract":[{"text":"We develop new theoretical tools for proving lower-bounds on the (amortized) complexity of certain functions in models of parallel computation. We apply the tools to construct a class of functions with high amortized memory complexity in the parallel Random Oracle Model (pROM); a variant of the standard ROM allowing for batches of simultaneous queries. In particular we obtain a new, more robust, type of Memory-Hard Functions (MHF); a security primitive which has recently been gaining acceptance in practice as an effective means of countering brute-force attacks on security relevant functions. Along the way we also demonstrate an important shortcoming of previous definitions of MHFs and give a new definition addressing the problem. The tools we develop represent an adaptation of the powerful pebbling paradigm (initially introduced by Hewitt and Paterson [HP70] and Cook [Coo73]) to a simple and intuitive parallel setting. We define a simple pebbling game Gp over graphs which aims to abstract parallel computation in an intuitive way. As a conceptual contribution we define a measure of pebbling complexity for graphs called cumulative complexity (CC) and show how it overcomes a crucial shortcoming (in the parallel setting) exhibited by more traditional complexity measures used in the past. As a main technical contribution we give an explicit construction of a constant in-degree family of graphs whose CC in Gp approaches maximality to within a polylogarithmic factor for any graph of equal size (analogous to the graphs of Tarjan et. al. [PTC76, LT82] for sequential pebbling games). Finally, for a given graph G and related function fG, we derive a lower-bound on the amortized memory complexity of fG in the pROM in terms of the CC of G in the game Gp.","lang":"eng"}],"month":"06","scopus_import":1,"publisher":"ACM","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"http://eprint.iacr.org/2014/238"}],"oa":1},{"page":"77 - 89","doi":"10.1007/978-3-319-23401-4_8","date_published":"2015-09-01T00:00:00Z","date_created":"2018-12-11T11:53:18Z","year":"2015","day":"01","publisher":"Springer","quality_controlled":"1","author":[{"last_name":"Bogomolov","full_name":"Bogomolov, Sergiy","orcid":"0000-0002-0686-0365","first_name":"Sergiy","id":"369D9A44-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"last_name":"Podelski","full_name":"Podelski, Andreas","first_name":"Andreas"},{"id":"4A245D00-F248-11E8-B48F-1D18A9856A87","first_name":"Jakob","orcid":"0000-0003-1615-3282","full_name":"Ruess, Jakob","last_name":"Ruess"},{"full_name":"Schilling, Christian","last_name":"Schilling","first_name":"Christian"}],"publist_id":"5492","title":"Adaptive moment closure for parameter inference of biochemical reaction networks","citation":{"ista":"Bogomolov S, Henzinger TA, Podelski A, Ruess J, Schilling C. 2015. Adaptive moment closure for parameter inference of biochemical reaction networks. 9308, 77–89.","chicago":"Bogomolov, Sergiy, Thomas A Henzinger, Andreas Podelski, Jakob Ruess, and Christian Schilling. “Adaptive Moment Closure for Parameter Inference of Biochemical Reaction Networks.” Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-319-23401-4_8.","ieee":"S. Bogomolov, T. A. Henzinger, A. Podelski, J. Ruess, and C. Schilling, “Adaptive moment closure for parameter inference of biochemical reaction networks,” vol. 9308. Springer, pp. 77–89, 2015.","short":"S. Bogomolov, T.A. Henzinger, A. Podelski, J. Ruess, C. Schilling, 9308 (2015) 77–89.","ama":"Bogomolov S, Henzinger TA, Podelski A, Ruess J, Schilling C. Adaptive moment closure for parameter inference of biochemical reaction networks. 2015;9308:77-89. doi:10.1007/978-3-319-23401-4_8","apa":"Bogomolov, S., Henzinger, T. A., Podelski, A., Ruess, J., & Schilling, C. (2015). Adaptive moment closure for parameter inference of biochemical reaction networks. Presented at the CMSB: Computational Methods in Systems Biology, Nantes, France: Springer. https://doi.org/10.1007/978-3-319-23401-4_8","mla":"Bogomolov, Sergiy, et al. Adaptive Moment Closure for Parameter Inference of Biochemical Reaction Networks. Vol. 9308, Springer, 2015, pp. 77–89, doi:10.1007/978-3-319-23401-4_8."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","name":"Quantitative Reactive Modeling"},{"name":"The Wittgenstein Prize","grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"related_material":{"record":[{"relation":"later_version","status":"public","id":"1148"}]},"volume":9308,"ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}],"alternative_title":["LNCS"],"scopus_import":1,"month":"09","intvolume":" 9308","abstract":[{"lang":"eng","text":"Continuous-time Markov chain (CTMC) models have become a central tool for understanding the dynamics of complex reaction networks and the importance of stochasticity in the underlying biochemical processes. When such models are employed to answer questions in applications, in order to ensure that the model provides a sufficiently accurate representation of the real system, it is of vital importance that the model parameters are inferred from real measured data. This, however, is often a formidable task and all of the existing methods fail in one case or the other, usually because the underlying CTMC model is high-dimensional and computationally difficult to analyze. The parameter inference methods that tend to scale best in the dimension of the CTMC are based on so-called moment closure approximations. However, there exists a large number of different moment closure approximations and it is typically hard to say a priori which of the approximations is the most suitable for the inference procedure. Here, we propose a moment-based parameter inference method that automatically chooses the most appropriate moment closure method. Accordingly, contrary to existing methods, the user is not required to be experienced in moment closure techniques. In addition to that, our method adaptively changes the approximation during the parameter inference to ensure that always the best approximation is used, even in cases where different approximations are best in different regions of the parameter space."}],"oa_version":"None","department":[{"_id":"ToHe"},{"_id":"GaTk"}],"date_updated":"2023-02-21T16:17:24Z","type":"conference","conference":{"name":"CMSB: Computational Methods in Systems Biology","location":"Nantes, France","end_date":"2015-09-18","start_date":"2015-09-16"},"status":"public","series_title":"Lecture Notes in Computer Science","_id":"1658"},{"department":[{"_id":"KrCh"}],"title":"Long-run average behaviour of probabilistic vector addition systems","author":[{"full_name":"Brázdil, Tomáš","last_name":"Brázdil","first_name":"Tomáš"},{"full_name":"Kiefer, Stefan","last_name":"Kiefer","first_name":"Stefan"},{"first_name":"Antonín","last_name":"Kučera","full_name":"Kučera, Antonín"},{"first_name":"Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","full_name":"Novotny, Petr","last_name":"Novotny"}],"publist_id":"5490","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:52:20Z","citation":{"chicago":"Brázdil, Tomáš, Stefan Kiefer, Antonín Kučera, and Petr Novotný. “Long-Run Average Behaviour of Probabilistic Vector Addition Systems,” 44–55. IEEE, 2015. https://doi.org/10.1109/LICS.2015.15.","ista":"Brázdil T, Kiefer S, Kučera A, Novotný P. 2015. Long-run average behaviour of probabilistic vector addition systems. LICS: Logic in Computer Science, LICS, , 44–55.","mla":"Brázdil, Tomáš, et al. Long-Run Average Behaviour of Probabilistic Vector Addition Systems. IEEE, 2015, pp. 44–55, doi:10.1109/LICS.2015.15.","short":"T. Brázdil, S. Kiefer, A. Kučera, P. Novotný, in:, IEEE, 2015, pp. 44–55.","ieee":"T. Brázdil, S. Kiefer, A. Kučera, and P. Novotný, “Long-run average behaviour of probabilistic vector addition systems,” presented at the LICS: Logic in Computer Science, Kyoto, Japan, 2015, pp. 44–55.","apa":"Brázdil, T., Kiefer, S., Kučera, A., & Novotný, P. (2015). Long-run average behaviour of probabilistic vector addition systems (pp. 44–55). Presented at the LICS: Logic in Computer Science, Kyoto, Japan: IEEE. https://doi.org/10.1109/LICS.2015.15","ama":"Brázdil T, Kiefer S, Kučera A, Novotný P. Long-run average behaviour of probabilistic vector addition systems. In: IEEE; 2015:44-55. doi:10.1109/LICS.2015.15"},"project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"status":"public","conference":{"location":"Kyoto, Japan","end_date":"2015-07-10","start_date":"2015-07-06","name":"LICS: Logic in Computer Science"},"type":"conference","_id":"1660","ec_funded":1,"date_created":"2018-12-11T11:53:19Z","date_published":"2015-07-01T00:00:00Z","doi":"10.1109/LICS.2015.15","page":"44 - 55","language":[{"iso":"eng"}],"day":"01","publication_status":"published","year":"2015","month":"07","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1505.02655"}],"oa":1,"scopus_import":1,"quality_controlled":"1","alternative_title":["LICS"],"publisher":"IEEE","oa_version":"Preprint","abstract":[{"text":"We study the pattern frequency vector for runs in probabilistic Vector Addition Systems with States (pVASS). Intuitively, each configuration of a given pVASS is assigned one of finitely many patterns, and every run can thus be seen as an infinite sequence of these patterns. The pattern frequency vector assigns to each run the limit of pattern frequencies computed for longer and longer prefixes of the run. If the limit does not exist, then the vector is undefined. We show that for one-counter pVASS, the pattern frequency vector is defined and takes one of finitely many values for almost all runs. Further, these values and their associated probabilities can be approximated up to an arbitrarily small relative error in polynomial time. For stable two-counter pVASS, we show the same result, but we do not provide any upper complexity bound. As a byproduct of our study, we discover counterexamples falsifying some classical results about stochastic Petri nets published in the 80s.","lang":"eng"}]},{"year":"2015","day":"22","publication":"Nature","page":"525 - 530","doi":"10.1038/nature15395","date_published":"2015-10-22T00:00:00Z","date_created":"2018-12-11T11:53:21Z","quality_controlled":"1","publisher":"Nature Publishing Group","oa":1,"citation":{"ista":"Landau D, Tausch E, Taylor Weiner A, Stewart C, Reiter J, Bahlo J, Kluth S, Božić I, Lawrence M, Böttcher S, Carter S, Cibulskis K, Mertens D, Sougnez C, Rosenberg M, Hess J, Edelmann J, Kless S, Kneba M, Ritgen M, Fink A, Fischer K, Gabriel S, Lander E, Nowak M, Döhner H, Hallek M, Neuberg D, Getz G, Stilgenbauer S, Wu C. 2015. Mutations driving CLL and their evolution in progression and relapse. Nature. 526(7574), 525–530.","chicago":"Landau, Dan, Eugen Tausch, Amaro Taylor Weiner, Chip Stewart, Johannes Reiter, Jasmin Bahlo, Sandra Kluth, et al. “Mutations Driving CLL and Their Evolution in Progression and Relapse.” Nature. Nature Publishing Group, 2015. https://doi.org/10.1038/nature15395.","ieee":"D. Landau et al., “Mutations driving CLL and their evolution in progression and relapse,” Nature, vol. 526, no. 7574. Nature Publishing Group, pp. 525–530, 2015.","short":"D. Landau, E. Tausch, A. Taylor Weiner, C. Stewart, J. Reiter, J. Bahlo, S. Kluth, I. Božić, M. Lawrence, S. Böttcher, S. Carter, K. Cibulskis, D. Mertens, C. Sougnez, M. Rosenberg, J. Hess, J. Edelmann, S. Kless, M. Kneba, M. Ritgen, A. Fink, K. Fischer, S. Gabriel, E. Lander, M. Nowak, H. Döhner, M. Hallek, D. Neuberg, G. Getz, S. Stilgenbauer, C. Wu, Nature 526 (2015) 525–530.","ama":"Landau D, Tausch E, Taylor Weiner A, et al. Mutations driving CLL and their evolution in progression and relapse. Nature. 2015;526(7574):525-530. doi:10.1038/nature15395","apa":"Landau, D., Tausch, E., Taylor Weiner, A., Stewart, C., Reiter, J., Bahlo, J., … Wu, C. (2015). Mutations driving CLL and their evolution in progression and relapse. Nature. Nature Publishing Group. https://doi.org/10.1038/nature15395","mla":"Landau, Dan, et al. “Mutations Driving CLL and Their Evolution in Progression and Relapse.” Nature, vol. 526, no. 7574, Nature Publishing Group, 2015, pp. 525–30, doi:10.1038/nature15395."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"5484","author":[{"full_name":"Landau, Dan","last_name":"Landau","first_name":"Dan"},{"first_name":"Eugen","last_name":"Tausch","full_name":"Tausch, Eugen"},{"first_name":"Amaro","last_name":"Taylor Weiner","full_name":"Taylor Weiner, Amaro"},{"last_name":"Stewart","full_name":"Stewart, Chip","first_name":"Chip"},{"id":"4A918E98-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes","orcid":"0000-0002-0170-7353","full_name":"Reiter, Johannes","last_name":"Reiter"},{"first_name":"Jasmin","last_name":"Bahlo","full_name":"Bahlo, Jasmin"},{"last_name":"Kluth","full_name":"Kluth, Sandra","first_name":"Sandra"},{"first_name":"Ivana","full_name":"Božić, Ivana","last_name":"Božić"},{"first_name":"Michael","last_name":"Lawrence","full_name":"Lawrence, Michael"},{"first_name":"Sebastian","full_name":"Böttcher, Sebastian","last_name":"Böttcher"},{"first_name":"Scott","full_name":"Carter, Scott","last_name":"Carter"},{"first_name":"Kristian","last_name":"Cibulskis","full_name":"Cibulskis, Kristian"},{"last_name":"Mertens","full_name":"Mertens, Daniel","first_name":"Daniel"},{"full_name":"Sougnez, Carrie","last_name":"Sougnez","first_name":"Carrie"},{"first_name":"Mara","last_name":"Rosenberg","full_name":"Rosenberg, Mara"},{"first_name":"Julian","full_name":"Hess, Julian","last_name":"Hess"},{"first_name":"Jennifer","full_name":"Edelmann, Jennifer","last_name":"Edelmann"},{"first_name":"Sabrina","full_name":"Kless, Sabrina","last_name":"Kless"},{"first_name":"Michael","last_name":"Kneba","full_name":"Kneba, Michael"},{"last_name":"Ritgen","full_name":"Ritgen, Matthias","first_name":"Matthias"},{"last_name":"Fink","full_name":"Fink, Anna","first_name":"Anna"},{"last_name":"Fischer","full_name":"Fischer, Kirsten","first_name":"Kirsten"},{"first_name":"Stacey","full_name":"Gabriel, Stacey","last_name":"Gabriel"},{"first_name":"Eric","last_name":"Lander","full_name":"Lander, Eric"},{"first_name":"Martin","full_name":"Nowak, Martin","last_name":"Nowak"},{"last_name":"Döhner","full_name":"Döhner, Hartmut","first_name":"Hartmut"},{"last_name":"Hallek","full_name":"Hallek, Michael","first_name":"Michael"},{"last_name":"Neuberg","full_name":"Neuberg, Donna","first_name":"Donna"},{"full_name":"Getz, Gad","last_name":"Getz","first_name":"Gad"},{"first_name":"Stephan","full_name":"Stilgenbauer, Stephan","last_name":"Stilgenbauer"},{"first_name":"Catherine","full_name":"Wu, Catherine","last_name":"Wu"}],"external_id":{"pmid":["26466571"]},"article_processing_charge":"No","title":"Mutations driving CLL and their evolution in progression and relapse","project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","language":[{"iso":"eng"}],"volume":526,"issue":"7574","ec_funded":1,"abstract":[{"lang":"eng","text":"Which genetic alterations drive tumorigenesis and how they evolve over the course of disease and therapy are central questions in cancer biology. Here we identify 44 recurrently mutated genes and 11 recurrent somatic copy number variations through whole-exome sequencing of 538 chronic lymphocytic leukaemia (CLL) and matched germline DNA samples, 278 of which were collected in a prospective clinical trial. These include previously unrecognized putative cancer drivers (RPS15, IKZF3), and collectively identify RNA processing and export, MYC activity, and MAPK signalling as central pathways involved in CLL. Clonality analysis of this large data set further enabled reconstruction of temporal relationships between driver events. Direct comparison between matched pre-treatment and relapse samples from 59 patients demonstrated highly frequent clonal evolution. Thus, large sequencing data sets of clinically informative samples enable the discovery of novel genes associated with cancer, the network of relationships between the driver events, and their impact on disease relapse and clinical outcome."}],"pmid":1,"oa_version":"Submitted Version","scopus_import":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4815041/","open_access":"1"}],"month":"10","intvolume":" 526","date_updated":"2021-01-12T06:52:23Z","department":[{"_id":"KrCh"}],"_id":"1665","type":"journal_article","article_type":"original","status":"public"},{"scopus_import":1,"intvolume":" 27","month":"11","abstract":[{"lang":"eng","text":"CREB-binding protein (CBP) and p300 are transcriptional coactivators involved in numerous biological processes that affect cell growth, transformation, differentiation, and development. In this study, we provide evidence of the involvement of homeodomain-interacting protein kinase 2 (HIPK2) in the regulation of CBP activity. We show that HIPK2 interacts with and phosphorylates several regions of CBP. We demonstrate that serines 2361, 2363, 2371, 2376, and 2381 are responsible for the HIPK2-induced mobility shift of CBP C-terminal activation domain. Moreover, we show that HIPK2 strongly potentiates the transcriptional activity of CBP. However, our data suggest that HIPK2 activates CBP mainly by counteracting the repressive action of cell cycle regulatory domain 1 (CRD1), located between amino acids 977 and 1076, independently of CBP phosphorylation. Our findings thus highlight a complex regulation of CBP activity by HIPK2, which might be relevant for the control of specific sets of target genes involved in cellular proliferation, differentiation and apoptosis."}],"oa_version":"Published Version","ec_funded":1,"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","issue":"11","volume":27,"publication_status":"published","language":[{"iso":"eng"}],"file":[{"date_updated":"2020-07-14T12:45:10Z","file_size":1735337,"creator":"system","date_created":"2018-12-12T10:18:03Z","file_name":"IST-2016-578-v1+1_CLS-D-15-00072R1_.pdf","content_type":"application/pdf","access_level":"local","relation":"main_file","checksum":"4ee690b6444b7a43523237f0941457d1","file_id":"5321"}],"tmp":{"short":"CC BY-NC-ND (4.0)","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","image":"/images/cc_by_nc_nd.png"},"type":"journal_article","pubrep_id":"578","status":"public","_id":"1663","file_date_updated":"2020-07-14T12:45:10Z","department":[{"_id":"JoCs"}],"date_updated":"2021-01-12T06:52:22Z","ddc":["570"],"quality_controlled":"1","publisher":"Elsevier","page":"2252 - 2260","date_created":"2018-12-11T11:53:20Z","doi":"10.1016/j.cellsig.2015.08.001","date_published":"2015-11-01T00:00:00Z","year":"2015","has_accepted_license":"1","publication":"Cellular Signalling","day":"01","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"publist_id":"5487","author":[{"id":"2AB5821E-F248-11E8-B48F-1D18A9856A87","first_name":"Krisztián","full_name":"Kovács, Krisztián","last_name":"Kovács"},{"first_name":"Myriam","last_name":"Steinmann","full_name":"Steinmann, Myriam"},{"full_name":"Halfon, Olivier","last_name":"Halfon","first_name":"Olivier"},{"first_name":"Pierre","last_name":"Magistretti","full_name":"Magistretti, Pierre"},{"full_name":"Cardinaux, Jean","last_name":"Cardinaux","first_name":"Jean"}],"title":"Complex regulation of CREB-binding protein by homeodomain-interacting protein kinase 2","citation":{"ieee":"K. Kovács, M. Steinmann, O. Halfon, P. Magistretti, and J. Cardinaux, “Complex regulation of CREB-binding protein by homeodomain-interacting protein kinase 2,” Cellular Signalling, vol. 27, no. 11. Elsevier, pp. 2252–2260, 2015.","short":"K. Kovács, M. Steinmann, O. Halfon, P. Magistretti, J. Cardinaux, Cellular Signalling 27 (2015) 2252–2260.","apa":"Kovács, K., Steinmann, M., Halfon, O., Magistretti, P., & Cardinaux, J. (2015). Complex regulation of CREB-binding protein by homeodomain-interacting protein kinase 2. Cellular Signalling. Elsevier. https://doi.org/10.1016/j.cellsig.2015.08.001","ama":"Kovács K, Steinmann M, Halfon O, Magistretti P, Cardinaux J. Complex regulation of CREB-binding protein by homeodomain-interacting protein kinase 2. Cellular Signalling. 2015;27(11):2252-2260. doi:10.1016/j.cellsig.2015.08.001","mla":"Kovács, Krisztián, et al. “Complex Regulation of CREB-Binding Protein by Homeodomain-Interacting Protein Kinase 2.” Cellular Signalling, vol. 27, no. 11, Elsevier, 2015, pp. 2252–60, doi:10.1016/j.cellsig.2015.08.001.","ista":"Kovács K, Steinmann M, Halfon O, Magistretti P, Cardinaux J. 2015. Complex regulation of CREB-binding protein by homeodomain-interacting protein kinase 2. Cellular Signalling. 27(11), 2252–2260.","chicago":"Kovács, Krisztián, Myriam Steinmann, Olivier Halfon, Pierre Magistretti, and Jean Cardinaux. “Complex Regulation of CREB-Binding Protein by Homeodomain-Interacting Protein Kinase 2.” Cellular Signalling. Elsevier, 2015. https://doi.org/10.1016/j.cellsig.2015.08.001."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"status":"public","conference":{"start_date":"2015-09-01","location":"Madrid, Spain","end_date":"2015-09-03","name":"QEST: Quantitative Evaluation of Systems"},"type":"conference","series_title":"Lecture Notes in Computer Science","_id":"1667","department":[{"_id":"KrCh"}],"date_updated":"2021-01-12T06:52:24Z","intvolume":" 9259","month":"08","main_file_link":[{"url":"http://arxiv.org/abs/1407.4777","open_access":"1"}],"alternative_title":["LNCS"],"scopus_import":1,"oa_version":"Preprint","abstract":[{"text":"We consider parametric version of fixed-delay continuoustime Markov chains (or equivalently deterministic and stochastic Petri nets, DSPN) where fixed-delay transitions are specified by parameters, rather than concrete values. Our goal is to synthesize values of these parameters that, for a given cost function, minimise expected total cost incurred before reaching a given set of target states. We show that under mild assumptions, optimal values of parameters can be effectively approximated using translation to a Markov decision process (MDP) whose actions correspond to discretized values of these parameters. To this end we identify and overcome several interesting phenomena arising in systems with fixed delays.","lang":"eng"}],"ec_funded":1,"volume":9259,"language":[{"iso":"eng"}],"publication_status":"published","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"title":"Optimizing performance of continuous-time stochastic systems using timeout synthesis","author":[{"first_name":"Tomáš","last_name":"Brázdil","full_name":"Brázdil, Tomáš"},{"first_name":"L'Uboš","last_name":"Korenčiak","full_name":"Korenčiak, L'Uboš"},{"first_name":"Jan","full_name":"Krčál, Jan","last_name":"Krčál"},{"id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","first_name":"Petr","full_name":"Novotny, Petr","last_name":"Novotny"},{"last_name":"Řehák","full_name":"Řehák, Vojtěch","first_name":"Vojtěch"}],"publist_id":"5482","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Brázdil, Tomáš, L’Uboš Korenčiak, Jan Krčál, Petr Novotný, and Vojtěch Řehák. “Optimizing Performance of Continuous-Time Stochastic Systems Using Timeout Synthesis.” Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-319-22264-6_10.","ista":"Brázdil T, Korenčiak L, Krčál J, Novotný P, Řehák V. 2015. Optimizing performance of continuous-time stochastic systems using timeout synthesis. 9259, 141–159.","mla":"Brázdil, Tomáš, et al. Optimizing Performance of Continuous-Time Stochastic Systems Using Timeout Synthesis. Vol. 9259, Springer, 2015, pp. 141–59, doi:10.1007/978-3-319-22264-6_10.","apa":"Brázdil, T., Korenčiak, L., Krčál, J., Novotný, P., & Řehák, V. (2015). Optimizing performance of continuous-time stochastic systems using timeout synthesis. Presented at the QEST: Quantitative Evaluation of Systems, Madrid, Spain: Springer. https://doi.org/10.1007/978-3-319-22264-6_10","ama":"Brázdil T, Korenčiak L, Krčál J, Novotný P, Řehák V. Optimizing performance of continuous-time stochastic systems using timeout synthesis. 2015;9259:141-159. doi:10.1007/978-3-319-22264-6_10","short":"T. Brázdil, L. Korenčiak, J. Krčál, P. Novotný, V. Řehák, 9259 (2015) 141–159.","ieee":"T. Brázdil, L. Korenčiak, J. Krčál, P. Novotný, and V. Řehák, “Optimizing performance of continuous-time stochastic systems using timeout synthesis,” vol. 9259. Springer, pp. 141–159, 2015."},"oa":1,"quality_controlled":"1","publisher":"Springer","acknowledgement":"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 n∘ [291734]. This work is partly supported by the German Research Council (DFG) as part of the Transregional Collaborative Research Center AVACS (SFB/TR 14), by the EU 7th Framework Programme under grant agreement no. 295261 (MEALS) and 318490 (SENSATION), by the Czech Science Foundation, grant No. 15-17564S, and by the CAS/SAFEA International Partnership Program for Creative Research Teams.","date_created":"2018-12-11T11:53:22Z","doi":"10.1007/978-3-319-22264-6_10","date_published":"2015-08-22T00:00:00Z","page":"141 - 159","day":"22","year":"2015"},{"day":"21","publication":"Nature","year":"2015","date_published":"2015-10-21T00:00:00Z","doi":"10.1038/nature15701","date_created":"2018-12-11T11:53:20Z","page":"550 - 553","acknowledgement":"We acknowledge the Deutsche Forschungsgemeinschaft (Project No. FOR 1182), and the European Research Council under the European Union’s Seventh Framework Programme (FP/2007-2013)/ERC Grant Agreement 306589 for financial support. B.S. acknowledges financial support from the Chinese State Scholarship Fund under grant number 2010629145. B.S. acknowledges support from the International Max Planck Research School for the Physics of Biological and Complex Systems and the Göttingen Graduate School for Neurosciences and Molecular Biosciences. We acknowledge computing resources from GWDG (Gesellschaft für wissenschaftliche Datenverarbeitung Göttingen) and the Jülich Supercomputing Centre (grant HGU16) where the simulations were performed.","quality_controlled":"1","publisher":"Nature Publishing Group","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Barkley, D., Song, B., Vasudevan, M., Lemoult, G. M., Avila, M., & Hof, B. (2015). The rise of fully turbulent flow. Nature. Nature Publishing Group. https://doi.org/10.1038/nature15701","ama":"Barkley D, Song B, Vasudevan M, Lemoult GM, Avila M, Hof B. The rise of fully turbulent flow. Nature. 2015;526(7574):550-553. doi:10.1038/nature15701","ieee":"D. Barkley, B. Song, M. Vasudevan, G. M. Lemoult, M. Avila, and B. Hof, “The rise of fully turbulent flow,” Nature, vol. 526, no. 7574. Nature Publishing Group, pp. 550–553, 2015.","short":"D. Barkley, B. Song, M. Vasudevan, G.M. Lemoult, M. Avila, B. Hof, Nature 526 (2015) 550–553.","mla":"Barkley, Dwight, et al. “The Rise of Fully Turbulent Flow.” Nature, vol. 526, no. 7574, Nature Publishing Group, 2015, pp. 550–53, doi:10.1038/nature15701.","ista":"Barkley D, Song B, Vasudevan M, Lemoult GM, Avila M, Hof B. 2015. The rise of fully turbulent flow. Nature. 526(7574), 550–553.","chicago":"Barkley, Dwight, Baofang Song, Mukund Vasudevan, Grégoire M Lemoult, Marc Avila, and Björn Hof. “The Rise of Fully Turbulent Flow.” Nature. Nature Publishing Group, 2015. https://doi.org/10.1038/nature15701."},"title":"The rise of fully turbulent flow","author":[{"full_name":"Barkley, Dwight","last_name":"Barkley","first_name":"Dwight"},{"first_name":"Baofang","last_name":"Song","full_name":"Song, Baofang"},{"full_name":"Vasudevan, Mukund","last_name":"Vasudevan","id":"3C5A959A-F248-11E8-B48F-1D18A9856A87","first_name":"Mukund"},{"id":"4787FE80-F248-11E8-B48F-1D18A9856A87","first_name":"Grégoire M","full_name":"Lemoult, Grégoire M","last_name":"Lemoult"},{"full_name":"Avila, Marc","last_name":"Avila","first_name":"Marc"},{"orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn"}],"publist_id":"5485","project":[{"name":"Decoding the complexity of turbulence at its origin","grant_number":"306589","call_identifier":"FP7","_id":"25152F3A-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"publication_status":"published","issue":"7574","volume":526,"ec_funded":1,"oa_version":"Preprint","abstract":[{"text":"Over a century of research into the origin of turbulence in wall-bounded shear flows has resulted in a puzzling picture in which turbulence appears in a variety of different states competing with laminar background flow. At moderate flow speeds, turbulence is confined to localized patches; it is only at higher speeds that the entire flow becomes turbulent. The origin of the different states encountered during this transition, the front dynamics of the turbulent regions and the transformation to full turbulence have yet to be explained. By combining experiments, theory and computer simulations, here we uncover a bifurcation scenario that explains the transformation to fully turbulent pipe flow and describe the front dynamics of the different states encountered in the process. Key to resolving this problem is the interpretation of the flow as a bistable system with nonlinear propagation (advection) of turbulent fronts. These findings bridge the gap between our understanding of the onset of turbulence and fully turbulent flows.","lang":"eng"}],"month":"10","intvolume":" 526","scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1510.09143"}],"date_updated":"2021-01-12T06:52:22Z","department":[{"_id":"BjHo"}],"_id":"1664","status":"public","type":"journal_article"},{"acknowledgement":"Joël Alwen was supported by the ERC starting grant (259668-PSPC). Rafail Ostrovsky was supported in part by NSF grants 09165174, 1065276, 1118126 and 1136174, US-Israel BSF grant 2008411, OKAWA Foundation Research Award, IBM Faculty Research Award, Xerox Faculty Research Award, B. John Garrick Foundation Award, Teradata Research Award, Lockheed-Martin Corporation Research Award, and the Defense Advanced Research Projects Agency through the U.S. Office of Naval Research under Contract N00014 -11 -1-0392. The views expressed are those of the author and do not reflect the official policy or position of the Department of Defense or the U.S. Government. Vassilis Zikas was supported in part by the Swiss National Science Foundation (SNF) via the Ambizione grant PZ00P-2142549.","quality_controlled":"1","publisher":"Springer","oa":1,"day":"01","publication":"Advances in Cryptology - CRYPTO 2015","has_accepted_license":"1","year":"2015","doi":"10.1007/978-3-662-48000-7_37","date_published":"2015-08-01T00:00:00Z","date_created":"2018-12-11T11:53:23Z","page":"763 - 780","project":[{"_id":"258C570E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"259668","name":"Provable Security for Physical Cryptography"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Alwen JF, Ostrovsky R, Zhou H, Zikas V. 2015. Incoercible multi-party computation and universally composable receipt-free voting. Advances in Cryptology - CRYPTO 2015. CRYPTO: International Cryptology ConferenceLecture Notes in Computer Science, LNCS, vol. 9216, 763–780.","chicago":"Alwen, Joel F, Rafail Ostrovsky, Hongsheng Zhou, and Vassilis Zikas. “Incoercible Multi-Party Computation and Universally Composable Receipt-Free Voting.” In Advances in Cryptology - CRYPTO 2015, 9216:763–80. Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-662-48000-7_37.","ieee":"J. F. Alwen, R. Ostrovsky, H. Zhou, and V. Zikas, “Incoercible multi-party computation and universally composable receipt-free voting,” in Advances in Cryptology - CRYPTO 2015, Santa Barbara, CA, United States, 2015, vol. 9216, pp. 763–780.","short":"J.F. Alwen, R. Ostrovsky, H. Zhou, V. Zikas, in:, Advances in Cryptology - CRYPTO 2015, Springer, 2015, pp. 763–780.","apa":"Alwen, J. F., Ostrovsky, R., Zhou, H., & Zikas, V. (2015). Incoercible multi-party computation and universally composable receipt-free voting. In Advances in Cryptology - CRYPTO 2015 (Vol. 9216, pp. 763–780). Santa Barbara, CA, United States: Springer. https://doi.org/10.1007/978-3-662-48000-7_37","ama":"Alwen JF, Ostrovsky R, Zhou H, Zikas V. Incoercible multi-party computation and universally composable receipt-free voting. In: Advances in Cryptology - CRYPTO 2015. Vol 9216. Lecture Notes in Computer Science. Springer; 2015:763-780. doi:10.1007/978-3-662-48000-7_37","mla":"Alwen, Joel F., et al. “Incoercible Multi-Party Computation and Universally Composable Receipt-Free Voting.” Advances in Cryptology - CRYPTO 2015, vol. 9216, Springer, 2015, pp. 763–80, doi:10.1007/978-3-662-48000-7_37."},"title":"Incoercible multi-party computation and universally composable receipt-free voting","author":[{"last_name":"Alwen","full_name":"Alwen, Joel F","first_name":"Joel F","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Ostrovsky","full_name":"Ostrovsky, Rafail","first_name":"Rafail"},{"full_name":"Zhou, Hongsheng","last_name":"Zhou","first_name":"Hongsheng"},{"last_name":"Zikas","full_name":"Zikas, Vassilis","first_name":"Vassilis"}],"publist_id":"5476","article_processing_charge":"No","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Composable notions of incoercibility aim to forbid a coercer from using anything beyond the coerced parties’ inputs and outputs to catch them when they try to deceive him. Existing definitions are restricted to weak coercion types, and/or are not universally composable. Furthermore, they often make too strong assumptions on the knowledge of coerced parties—e.g., they assume they known the identities and/or the strategies of other coerced parties, or those of corrupted parties— which makes them unsuitable for applications of incoercibility such as e-voting, where colluding adversarial parties may attempt to coerce honest voters, e.g., by offering them money for a promised vote, and use their own view to check that the voter keeps his end of the bargain. In this work we put forward the first universally composable notion of incoercible multi-party computation, which satisfies the above intuition and does not assume collusions among coerced parties or knowledge of the corrupted set. We define natural notions of UC incoercibility corresponding to standard coercion-types, i.e., receipt-freeness and resistance to full-active coercion. Importantly, our suggested notion has the unique property that it builds on top of the well studied UC framework by Canetti instead of modifying it. This guarantees backwards compatibility, and allows us to inherit results from the rich UC literature. We then present MPC protocols which realize our notions of UC incoercibility given access to an arguably minimal setup—namely honestly generate tamper-proof hardware performing a very simple cryptographic operation—e.g., a smart card. This is, to our knowledge, the first proposed construction of an MPC protocol (for more than two parties) that is incoercibly secure and universally composable, and therefore the first construction of a universally composable receipt-free e-voting protocol."}],"month":"08","intvolume":" 9216","alternative_title":["LNCS"],"scopus_import":"1","file":[{"date_created":"2020-05-15T08:55:29Z","file_name":"2015_CRYPTO_Alwen.pdf","date_updated":"2020-07-14T12:45:11Z","file_size":397363,"creator":"dernst","file_id":"7853","checksum":"5b6649e80d1f781a8910f7cce6427f78","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-3-662-47999-5"],"eisbn":["978-3-662-48000-7"]},"publication_status":"published","volume":9216,"ec_funded":1,"_id":"1672","series_title":"Lecture Notes in Computer Science","status":"public","type":"conference","conference":{"name":"CRYPTO: International Cryptology Conference","start_date":"2015-08-16","location":"Santa Barbara, CA, United States","end_date":"2015-08-20"},"ddc":["000"],"date_updated":"2022-06-07T09:51:55Z","file_date_updated":"2020-07-14T12:45:11Z","department":[{"_id":"KrPi"}]},{"file":[{"creator":"system","file_size":443340,"date_updated":"2020-07-14T12:45:11Z","file_name":"IST-2016-669-v1+1_599.pdf","date_created":"2018-12-12T10:18:29Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"8cd4215b83efba720e8cf27c23ff4781","file_id":"5351"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":9230,"ec_funded":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Computational notions of entropy (a.k.a. pseudoentropy) have found many applications, including leakage-resilient cryptography, deterministic encryption or memory delegation. The most important tools to argue about pseudoentropy are chain rules, which quantify by how much (in terms of quantity and quality) the pseudoentropy of a given random variable X decreases when conditioned on some other variable Z (think for example of X as a secret key and Z as information leaked by a side-channel). In this paper we give a very simple and modular proof of the chain rule for HILL pseudoentropy, improving best known parameters. Our version allows for increasing the acceptable length of leakage in applications up to a constant factor compared to the best previous bounds. As a contribution of independent interest, we provide a comprehensive study of all known versions of the chain rule, comparing their worst-case strength and limitations."}],"month":"08","intvolume":" 9230","scopus_import":1,"alternative_title":["LNCS"],"ddc":["005"],"date_updated":"2021-01-12T06:52:24Z","department":[{"_id":"KrPi"}],"file_date_updated":"2020-07-14T12:45:11Z","series_title":"Lecture Notes in Computer Science","_id":"1669","status":"public","pubrep_id":"669","type":"conference","conference":{"name":"LATINCRYPT: Cryptology and Information Security in Latin America","start_date":"2015-08-23","end_date":"2015-08-26","location":"Guadalajara, Mexico"},"day":"15","has_accepted_license":"1","year":"2015","date_published":"2015-08-15T00:00:00Z","doi":"10.1007/978-3-319-22174-8_5","date_created":"2018-12-11T11:53:22Z","page":"81 - 98","quality_controlled":"1","publisher":"Springer","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Pietrzak, Krzysztof Z., and Maciej Skórski. The Chain Rule for HILL Pseudoentropy, Revisited. Vol. 9230, Springer, 2015, pp. 81–98, doi:10.1007/978-3-319-22174-8_5.","ieee":"K. Z. Pietrzak and M. Skórski, “The chain rule for HILL pseudoentropy, revisited,” vol. 9230. Springer, pp. 81–98, 2015.","short":"K.Z. Pietrzak, M. Skórski, 9230 (2015) 81–98.","ama":"Pietrzak KZ, Skórski M. The chain rule for HILL pseudoentropy, revisited. 2015;9230:81-98. doi:10.1007/978-3-319-22174-8_5","apa":"Pietrzak, K. Z., & Skórski, M. (2015). The chain rule for HILL pseudoentropy, revisited. Presented at the LATINCRYPT: Cryptology and Information Security in Latin America, Guadalajara, Mexico: Springer. https://doi.org/10.1007/978-3-319-22174-8_5","chicago":"Pietrzak, Krzysztof Z, and Maciej Skórski. “The Chain Rule for HILL Pseudoentropy, Revisited.” Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-319-22174-8_5.","ista":"Pietrzak KZ, Skórski M. 2015. The chain rule for HILL pseudoentropy, revisited. 9230, 81–98."},"title":"The chain rule for HILL pseudoentropy, revisited","publist_id":"5480","author":[{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z","full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654","last_name":"Pietrzak"},{"last_name":"Skórski","full_name":"Skórski, Maciej","first_name":"Maciej"}],"project":[{"name":"Provable Security for Physical Cryptography","grant_number":"259668","call_identifier":"FP7","_id":"258C570E-B435-11E9-9278-68D0E5697425"}]},{"project":[{"_id":"258C570E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Provable Security for Physical Cryptography","grant_number":"259668"}],"citation":{"chicago":"Gazi, Peter, Krzysztof Z Pietrzak, and Stefano Tessaro. “The Exact PRF Security of Truncation: Tight Bounds for Keyed Sponges and Truncated CBC,” 9215:368–87. Springer, 2015. https://doi.org/10.1007/978-3-662-47989-6_18.","ista":"Gazi P, Pietrzak KZ, Tessaro S. 2015. The exact PRF security of truncation: Tight bounds for keyed sponges and truncated CBC. CRYPTO: International Cryptology Conference, LNCS, vol. 9215, 368–387.","mla":"Gazi, Peter, et al. The Exact PRF Security of Truncation: Tight Bounds for Keyed Sponges and Truncated CBC. Vol. 9215, Springer, 2015, pp. 368–87, doi:10.1007/978-3-662-47989-6_18.","ieee":"P. Gazi, K. Z. Pietrzak, and S. Tessaro, “The exact PRF security of truncation: Tight bounds for keyed sponges and truncated CBC,” presented at the CRYPTO: International Cryptology Conference, Santa Barbara, CA, United States, 2015, vol. 9215, pp. 368–387.","short":"P. Gazi, K.Z. Pietrzak, S. Tessaro, in:, Springer, 2015, pp. 368–387.","ama":"Gazi P, Pietrzak KZ, Tessaro S. The exact PRF security of truncation: Tight bounds for keyed sponges and truncated CBC. In: Vol 9215. Springer; 2015:368-387. doi:10.1007/978-3-662-47989-6_18","apa":"Gazi, P., Pietrzak, K. Z., & Tessaro, S. (2015). The exact PRF security of truncation: Tight bounds for keyed sponges and truncated CBC (Vol. 9215, pp. 368–387). Presented at the CRYPTO: International Cryptology Conference, Santa Barbara, CA, United States: Springer. https://doi.org/10.1007/978-3-662-47989-6_18"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Gazi","full_name":"Gazi, Peter","id":"3E0BFE38-F248-11E8-B48F-1D18A9856A87","first_name":"Peter"},{"orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak","first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Stefano","full_name":"Tessaro, Stefano","last_name":"Tessaro"}],"publist_id":"5478","title":"The exact PRF security of truncation: Tight bounds for keyed sponges and truncated CBC","oa":1,"publisher":"Springer","quality_controlled":"1","year":"2015","has_accepted_license":"1","day":"01","page":"368 - 387","date_created":"2018-12-11T11:53:23Z","date_published":"2015-08-01T00:00:00Z","doi":"10.1007/978-3-662-47989-6_18","_id":"1671","conference":{"location":"Santa Barbara, CA, United States","end_date":"2015-08-20","start_date":"2015-08-16","name":"CRYPTO: International Cryptology Conference"},"type":"conference","pubrep_id":"673","status":"public","date_updated":"2021-01-12T06:52:25Z","ddc":["004","005"],"file_date_updated":"2020-07-14T12:45:11Z","department":[{"_id":"KrPi"}],"abstract":[{"lang":"eng","text":"This paper studies the concrete security of PRFs and MACs obtained by keying hash functions based on the sponge paradigm. One such hash function is KECCAK, selected as NIST’s new SHA-3 standard. In contrast to other approaches like HMAC, the exact security of keyed sponges is not well understood. Indeed, recent security analyses delivered concrete security bounds which are far from existing attacks. This paper aims to close this gap. We prove (nearly) exact bounds on the concrete PRF security of keyed sponges using a random permutation. These bounds are tight for the most relevant ranges of parameters, i.e., for messages of length (roughly) l ≤ min{2n/4, 2r} blocks, where n is the state size and r is the desired output length; and for l ≤ q queries (to the construction or the underlying permutation). Moreover, we also improve standard-model bounds. As an intermediate step of independent interest, we prove tight bounds on the PRF security of the truncated CBC-MAC construction, which operates as plain CBC-MAC, but only returns a prefix of the output."}],"oa_version":"Submitted Version","alternative_title":["LNCS"],"scopus_import":1,"intvolume":" 9215","month":"08","publication_status":"published","language":[{"iso":"eng"}],"file":[{"date_updated":"2020-07-14T12:45:11Z","file_size":592296,"creator":"system","date_created":"2018-12-12T10:10:38Z","file_name":"IST-2016-673-v1+1_053.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"4827","checksum":"17d854227b3b753fd34f5d29e5b5a32e"}],"ec_funded":1,"volume":9215},{"article_number":"20150114","project":[{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"}],"citation":{"ista":"Adlam B, Chatterjee K, Nowak M. 2015. Amplifiers of selection. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. 471(2181), 20150114.","chicago":"Adlam, Ben, Krishnendu Chatterjee, and Martin Nowak. “Amplifiers of Selection.” Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. Royal Society of London, 2015. https://doi.org/10.1098/rspa.2015.0114.","apa":"Adlam, B., Chatterjee, K., & Nowak, M. (2015). Amplifiers of selection. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. Royal Society of London. https://doi.org/10.1098/rspa.2015.0114","ama":"Adlam B, Chatterjee K, Nowak M. Amplifiers of selection. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. 2015;471(2181). doi:10.1098/rspa.2015.0114","short":"B. Adlam, K. Chatterjee, M. Nowak, Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 471 (2015).","ieee":"B. Adlam, K. Chatterjee, and M. Nowak, “Amplifiers of selection,” Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol. 471, no. 2181. Royal Society of London, 2015.","mla":"Adlam, Ben, et al. “Amplifiers of Selection.” Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol. 471, no. 2181, 20150114, Royal Society of London, 2015, doi:10.1098/rspa.2015.0114."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"5477","author":[{"first_name":"Ben","full_name":"Adlam, Ben","last_name":"Adlam"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"first_name":"Martin","full_name":"Nowak, Martin","last_name":"Nowak"}],"title":"Amplifiers of selection","acknowledgement":"K.C. gratefully acknowledges support from ERC Start grant no. (279307: Graph Games), Austrian Science Fund (FWF) grant no. P23499-N23, and FWF NFN grant no. S11407-N23 (RiSE). ","quality_controlled":"1","publisher":"Royal Society of London","oa":1,"has_accepted_license":"1","year":"2015","day":"08","publication":"Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences","doi":"10.1098/rspa.2015.0114","date_published":"2015-09-08T00:00:00Z","date_created":"2018-12-11T11:53:24Z","_id":"1673","type":"journal_article","status":"public","date_updated":"2021-01-12T06:52:26Z","ddc":["000"],"department":[{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:45:11Z","abstract":[{"lang":"eng","text":"When a new mutant arises in a population, there is a probability it outcompetes the residents and fixes. The structure of the population can affect this fixation probability. Suppressing population structures reduce the difference between two competing variants, while amplifying population structures enhance the difference. Suppressors are ubiquitous and easy to construct, but amplifiers for the large population limit are more elusive and only a few examples have been discovered. Whether or not a population structure is an amplifier of selection depends on the probability distribution for the placement of the invading mutant. First, we prove that there exist only bounded amplifiers for adversarial placement-that is, for arbitrary initial conditions. Next, we show that the Star population structure, which is known to amplify for mutants placed uniformly at random, does not amplify for mutants that arise through reproduction and are therefore placed proportional to the temperatures of the vertices. Finally, we construct population structures that amplify for all mutational events that arise through reproduction, uniformly at random, or through some combination of the two. "}],"oa_version":"Published Version","scopus_import":1,"month":"09","intvolume":" 471","publication_status":"published","file":[{"date_created":"2019-04-18T12:39:56Z","file_name":"2015_rspa_Adlam.pdf","date_updated":"2020-07-14T12:45:11Z","file_size":391466,"creator":"kschuh","file_id":"6342","checksum":"e613d94d283c776322403a28aad11bdd","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"issue":"2181","volume":471,"ec_funded":1},{"department":[{"_id":"KrPi"}],"date_updated":"2020-08-11T10:09:26Z","conference":{"start_date":"2015-03-08","end_date":"2015-03-11","location":"Istanbul, Turkey","name":"FSE: Fast Software Encryption"},"type":"conference","status":"public","_id":"1668","series_title":"Lecture Notes in Computer Science","ec_funded":1,"volume":9054,"publication_status":"published","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"http://eprint.iacr.org/2015/397"}],"alternative_title":["LNCS"],"scopus_import":1,"intvolume":" 9054","month":"08","abstract":[{"lang":"eng","text":"We revisit the security (as a pseudorandom permutation) of cascading-based constructions for block-cipher key-length extension. Previous works typically considered the extreme case where the adversary is given the entire codebook of the construction, the only complexity measure being the number qe of queries to the underlying ideal block cipher, representing adversary’s secret-key-independent computation. Here, we initiate a systematic study of the more natural case of an adversary restricted to adaptively learning a number qc of plaintext/ciphertext pairs that is less than the entire codebook. For any such qc, we aim to determine the highest number of block-cipher queries qe the adversary can issue without being able to successfully distinguish the construction (under a secret key) from a random permutation.\r\nMore concretely, we show the following results for key-length extension schemes using a block cipher with n-bit blocks and κ-bit keys:\r\nPlain cascades of length ℓ=2r+1 are secure whenever qcqre≪2r(κ+n), qc≪2κ and qe≪22κ. The bound for r=1 also applies to two-key triple encryption (as used within Triple DES).\r\nThe r-round XOR-cascade is secure as long as qcqre≪2r(κ+n), matching an attack by Gaži (CRYPTO 2013).\r\nWe fully characterize the security of Gaži and Tessaro’s two-call "}],"oa_version":"Submitted Version","author":[{"first_name":"Peter","id":"3E0BFE38-F248-11E8-B48F-1D18A9856A87","full_name":"Gazi, Peter","last_name":"Gazi"},{"last_name":"Lee","full_name":"Lee, Jooyoung","first_name":"Jooyoung"},{"first_name":"Yannick","full_name":"Seurin, Yannick","last_name":"Seurin"},{"first_name":"John","full_name":"Steinberger, John","last_name":"Steinberger"},{"last_name":"Tessaro","full_name":"Tessaro, Stefano","first_name":"Stefano"}],"publist_id":"5481","title":"Relaxing full-codebook security: A refined analysis of key-length extension schemes","citation":{"ista":"Gazi P, Lee J, Seurin Y, Steinberger J, Tessaro S. 2015. Relaxing full-codebook security: A refined analysis of key-length extension schemes. 9054, 319–341.","chicago":"Gazi, Peter, Jooyoung Lee, Yannick Seurin, John Steinberger, and Stefano Tessaro. “Relaxing Full-Codebook Security: A Refined Analysis of Key-Length Extension Schemes.” Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-662-48116-5_16.","apa":"Gazi, P., Lee, J., Seurin, Y., Steinberger, J., & Tessaro, S. (2015). Relaxing full-codebook security: A refined analysis of key-length extension schemes. Presented at the FSE: Fast Software Encryption, Istanbul, Turkey: Springer. https://doi.org/10.1007/978-3-662-48116-5_16","ama":"Gazi P, Lee J, Seurin Y, Steinberger J, Tessaro S. Relaxing full-codebook security: A refined analysis of key-length extension schemes. 2015;9054:319-341. doi:10.1007/978-3-662-48116-5_16","short":"P. Gazi, J. Lee, Y. Seurin, J. Steinberger, S. Tessaro, 9054 (2015) 319–341.","ieee":"P. Gazi, J. Lee, Y. Seurin, J. Steinberger, and S. Tessaro, “Relaxing full-codebook security: A refined analysis of key-length extension schemes,” vol. 9054. Springer, pp. 319–341, 2015.","mla":"Gazi, Peter, et al. Relaxing Full-Codebook Security: A Refined Analysis of Key-Length Extension Schemes. Vol. 9054, Springer, 2015, pp. 319–41, doi:10.1007/978-3-662-48116-5_16."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"name":"Provable Security for Physical Cryptography","grant_number":"259668","call_identifier":"FP7","_id":"258C570E-B435-11E9-9278-68D0E5697425"}],"page":"319 - 341","date_created":"2018-12-11T11:53:22Z","doi":"10.1007/978-3-662-48116-5_16","date_published":"2015-08-12T00:00:00Z","year":"2015","day":"12","oa":1,"publisher":"Springer","quality_controlled":"1"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Bogomolov, Sergiy, et al. PDDL+ Planning with Hybrid Automata: Foundations of Translating Must Behavior. AAAI Press, 2015, pp. 42–46.","ama":"Bogomolov S, Magazzeni D, Minopoli S, Wehrle M. PDDL+ planning with hybrid automata: Foundations of translating must behavior. In: AAAI Press; 2015:42-46.","apa":"Bogomolov, S., Magazzeni, D., Minopoli, S., & Wehrle, M. (2015). PDDL+ planning with hybrid automata: Foundations of translating must behavior (pp. 42–46). Presented at the ICAPS: International Conference on Automated Planning and Scheduling, Jerusalem, Israel: AAAI Press.","ieee":"S. Bogomolov, D. Magazzeni, S. Minopoli, and M. Wehrle, “PDDL+ planning with hybrid automata: Foundations of translating must behavior,” presented at the ICAPS: International Conference on Automated Planning and Scheduling, Jerusalem, Israel, 2015, pp. 42–46.","short":"S. Bogomolov, D. Magazzeni, S. Minopoli, M. Wehrle, in:, AAAI Press, 2015, pp. 42–46.","chicago":"Bogomolov, Sergiy, Daniele Magazzeni, Stefano Minopoli, and Martin Wehrle. “PDDL+ Planning with Hybrid Automata: Foundations of Translating Must Behavior,” 42–46. AAAI Press, 2015.","ista":"Bogomolov S, Magazzeni D, Minopoli S, Wehrle M. 2015. PDDL+ planning with hybrid automata: Foundations of translating must behavior. ICAPS: International Conference on Automated Planning and Scheduling, 42–46."},"date_updated":"2021-01-12T06:52:25Z","title":"PDDL+ planning with hybrid automata: Foundations of translating must behavior","department":[{"_id":"ToHe"}],"author":[{"id":"369D9A44-F248-11E8-B48F-1D18A9856A87","first_name":"Sergiy","last_name":"Bogomolov","orcid":"0000-0002-0686-0365","full_name":"Bogomolov, Sergiy"},{"full_name":"Magazzeni, Daniele","last_name":"Magazzeni","first_name":"Daniele"},{"last_name":"Minopoli","full_name":"Minopoli, Stefano","first_name":"Stefano"},{"first_name":"Martin","full_name":"Wehrle, Martin","last_name":"Wehrle"}],"publist_id":"5479","_id":"1670","project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989"},{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","grant_number":"Z211"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"status":"public","conference":{"start_date":"2015-06-07","location":"Jerusalem, Israel","end_date":"2015-06-11","name":"ICAPS: International Conference on Automated Planning and Scheduling"},"type":"conference","language":[{"iso":"eng"}],"day":"01","publication_status":"published","year":"2015","ec_funded":1,"date_created":"2018-12-11T11:53:23Z","date_published":"2015-06-01T00:00:00Z","page":"42 - 46","acknowledgement":"This work was partly supported by the German Research Foundation (DFG) as part of the Transregional Collaborative Research Center “Automatic Verification and Analysis of Complex Systems” (SFB/TR 14 AVACS, http://www.avacs.org/), by the European Research Council (ERC) under grant 267989 (QUAREM), by the Austrian Science Fund (FWF) under grants S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award), and by the Swiss National Science Foundation (SNSF) as part of the project “Automated Reformulation and Pruning in Factored State Spaces (ARAP)”.","oa_version":"None","abstract":[{"lang":"eng","text":"Planning in hybrid domains poses a special challenge due to the involved mixed discrete-continuous dynamics. A recent solving approach for such domains is based on applying model checking techniques on a translation of PDDL+ planning problems to hybrid automata. However, the proposed translation is limited because must behavior is only overapproximated, and hence, processes and events are not reflected exactly. In this paper, we present the theoretical foundation of an exact PDDL+ translation. We propose a schema to convert a hybrid automaton with must transitions into an equivalent hybrid automaton featuring only may transitions."}],"month":"06","main_file_link":[{"url":"https://www.aaai.org/ocs/index.php/ICAPS/ICAPS15/paper/view/10606/10394"}],"scopus_import":1,"publisher":"AAAI Press","quality_controlled":"1"},{"day":"01","language":[{"iso":"eng"}],"publication":"Reviews in Mathematical Physics","publication_status":"published","year":"2015","issue":"8","date_published":"2015-09-01T00:00:00Z","doi":"10.1142/S0129055X1550018X","volume":27,"date_created":"2018-12-11T11:53:24Z","oa_version":"Preprint","abstract":[{"text":"We consider N × N random matrices of the form H = W + V where W is a real symmetric Wigner matrix and V a random or deterministic, real, diagonal matrix whose entries are independent of W. We assume subexponential decay for the matrix entries of W and we choose V so that the eigenvalues of W and V are typically of the same order. For a large class of diagonal matrices V, we show that the rescaled distribution of the extremal eigenvalues is given by the Tracy-Widom distribution F1 in the limit of large N. Our proofs also apply to the complex Hermitian setting, i.e. when W is a complex Hermitian Wigner matrix.","lang":"eng"}],"month":"09","intvolume":" 27","quality_controlled":"1","scopus_import":1,"publisher":"World Scientific Publishing","main_file_link":[{"url":"http://arxiv.org/abs/1407.8015","open_access":"1"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Lee J, Schnelli K. 2015. Edge universality for deformed Wigner matrices. Reviews in Mathematical Physics. 27(8), 1550018.","chicago":"Lee, Jioon, and Kevin Schnelli. “Edge Universality for Deformed Wigner Matrices.” Reviews in Mathematical Physics. World Scientific Publishing, 2015. https://doi.org/10.1142/S0129055X1550018X.","short":"J. Lee, K. Schnelli, Reviews in Mathematical Physics 27 (2015).","ieee":"J. Lee and K. Schnelli, “Edge universality for deformed Wigner matrices,” Reviews in Mathematical Physics, vol. 27, no. 8. World Scientific Publishing, 2015.","apa":"Lee, J., & Schnelli, K. (2015). Edge universality for deformed Wigner matrices. Reviews in Mathematical Physics. World Scientific Publishing. https://doi.org/10.1142/S0129055X1550018X","ama":"Lee J, Schnelli K. Edge universality for deformed Wigner matrices. Reviews in Mathematical Physics. 2015;27(8). doi:10.1142/S0129055X1550018X","mla":"Lee, Jioon, and Kevin Schnelli. “Edge Universality for Deformed Wigner Matrices.” Reviews in Mathematical Physics, vol. 27, no. 8, 1550018, World Scientific Publishing, 2015, doi:10.1142/S0129055X1550018X."},"date_updated":"2021-01-12T06:52:26Z","title":"Edge universality for deformed Wigner matrices","department":[{"_id":"LaEr"}],"publist_id":"5475","author":[{"first_name":"Jioon","last_name":"Lee","full_name":"Lee, Jioon"},{"last_name":"Schnelli","full_name":"Schnelli, Kevin","orcid":"0000-0003-0954-3231","id":"434AD0AE-F248-11E8-B48F-1D18A9856A87","first_name":"Kevin"}],"article_number":"1550018","_id":"1674","status":"public","type":"journal_article"},{"_id":"1679","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"748","date_updated":"2021-01-12T06:52:28Z","ddc":["532"],"department":[{"_id":"BjHo"}],"file_date_updated":"2020-07-14T12:45:12Z","oa_version":"Published Version","scopus_import":1,"month":"09","intvolume":" 27","publication_status":"published","file":[{"file_id":"5019","checksum":"604bba3c2496aadb3efcff77de01ce6c","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:13:35Z","file_name":"IST-2017-748-v1+1_1.4930850.pdf","creator":"system","date_updated":"2020-07-14T12:45:12Z","file_size":872366}],"language":[{"iso":"eng"}],"volume":27,"issue":"9","article_number":"091102","citation":{"mla":"Lemoult, Grégoire M., et al. “Taylor’s Forest.” Physics of Fluids, vol. 27, no. 9, 091102, American Institute of Physics, 2015, doi:10.1063/1.4930850.","ama":"Lemoult GM, Maier P, Hof B. Taylor’s Forest. Physics of Fluids. 2015;27(9). doi:10.1063/1.4930850","apa":"Lemoult, G. M., Maier, P., & Hof, B. (2015). Taylor’s Forest. Physics of Fluids. American Institute of Physics. https://doi.org/10.1063/1.4930850","short":"G.M. Lemoult, P. Maier, B. Hof, Physics of Fluids 27 (2015).","ieee":"G. M. Lemoult, P. Maier, and B. Hof, “Taylor’s Forest,” Physics of Fluids, vol. 27, no. 9. American Institute of Physics, 2015.","chicago":"Lemoult, Grégoire M, Philipp Maier, and Björn Hof. “Taylor’s Forest.” Physics of Fluids. American Institute of Physics, 2015. https://doi.org/10.1063/1.4930850.","ista":"Lemoult GM, Maier P, Hof B. 2015. Taylor’s Forest. Physics of Fluids. 27(9), 091102."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"5469","author":[{"full_name":"Lemoult, Grégoire M","last_name":"Lemoult","id":"4787FE80-F248-11E8-B48F-1D18A9856A87","first_name":"Grégoire M"},{"first_name":"Philipp","id":"384F7C04-F248-11E8-B48F-1D18A9856A87","last_name":"Maier","full_name":"Maier, Philipp"},{"last_name":"Hof","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87"}],"title":"Taylor's Forest","publisher":"American Institute of Physics","quality_controlled":"1","oa":1,"has_accepted_license":"1","year":"2015","day":"24","publication":"Physics of Fluids","date_published":"2015-09-24T00:00:00Z","doi":"10.1063/1.4930850","date_created":"2018-12-11T11:53:26Z"},{"oa_version":"None","month":"10","intvolume":" 36","scopus_import":1,"publisher":"Elsevier","day":"01","language":[{"iso":"eng"}],"publication":"Current Opinion in Cell Biology","year":"2015","publication_status":"published","issue":"10","volume":36,"date_published":"2015-10-01T00:00:00Z","doi":"10.1016/j.ceb.2015.09.004","date_created":"2018-12-11T11:53:25Z","page":"4 - 6","_id":"1676","status":"public","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"M. K. Sixt and E. Raz, “Editorial overview: Cell adhesion and migration,” Current Opinion in Cell Biology, vol. 36, no. 10. Elsevier, pp. 4–6, 2015.","short":"M.K. Sixt, E. Raz, Current Opinion in Cell Biology 36 (2015) 4–6.","apa":"Sixt, M. K., & Raz, E. (2015). Editorial overview: Cell adhesion and migration. Current Opinion in Cell Biology. Elsevier. https://doi.org/10.1016/j.ceb.2015.09.004","ama":"Sixt MK, Raz E. Editorial overview: Cell adhesion and migration. Current Opinion in Cell Biology. 2015;36(10):4-6. doi:10.1016/j.ceb.2015.09.004","mla":"Sixt, Michael K., and Erez Raz. “Editorial Overview: Cell Adhesion and Migration.” Current Opinion in Cell Biology, vol. 36, no. 10, Elsevier, 2015, pp. 4–6, doi:10.1016/j.ceb.2015.09.004.","ista":"Sixt MK, Raz E. 2015. Editorial overview: Cell adhesion and migration. Current Opinion in Cell Biology. 36(10), 4–6.","chicago":"Sixt, Michael K, and Erez Raz. “Editorial Overview: Cell Adhesion and Migration.” Current Opinion in Cell Biology. Elsevier, 2015. https://doi.org/10.1016/j.ceb.2015.09.004."},"date_updated":"2021-01-12T06:52:27Z","title":"Editorial overview: Cell adhesion and migration","department":[{"_id":"MiSi"}],"author":[{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"},{"full_name":"Raz, Erez","last_name":"Raz","first_name":"Erez"}],"publist_id":"5473"},{"volume":13,"issue":"4","publication_status":"published","language":[{"iso":"eng"}],"file":[{"creator":"system","date_updated":"2020-07-14T12:45:12Z","file_size":1104701,"date_created":"2018-12-12T10:11:05Z","file_name":"IST-2016-492-v1+1_journal.pbio.1002078.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"92a300d7b97eafb477885303f7632fe1","file_id":"4858"}],"intvolume":" 13","month":"04","abstract":[{"text":"Many species groups, including mammals and many insects, determine sex using heteromorphic sex chromosomes. Diptera flies, which include the model Drosophila melanogaster, generally have XY sex chromosomes and a conserved karyotype consisting of six chromosomal arms (five large rods and a small dot), but superficially similar karyotypes may conceal the true extent of sex chromosome variation. Here, we use whole-genome analysis in 37 fly species belonging to 22 different families of Diptera and uncover tremendous hidden diversity in sex chromosome karyotypes among flies. We identify over a dozen different sex chromosome configurations, and the small dot chromosome is repeatedly used as the sex chromosome, which presumably reflects the ancestral karyotype of higher Diptera. However, we identify species with undifferentiated sex chromosomes, others in which a different chromosome replaced the dot as a sex chromosome or in which up to three chromosomal elements became incorporated into the sex chromosomes, and others yet with female heterogamety (ZW sex chromosomes). Transcriptome analysis shows that dosage compensation has evolved multiple times in flies, consistently through up-regulation of the single X in males. However, X chromosomes generally show a deficiency of genes with male-biased expression, possibly reflecting sex-specific selective pressures. These species thus provide a rich resource to study sex chromosome biology in a comparative manner and show that similar selective forces have shaped the unique evolution of sex chromosomes in diverse fly taxa.","lang":"eng"}],"oa_version":"Published Version","file_date_updated":"2020-07-14T12:45:12Z","date_updated":"2021-01-12T06:52:30Z","ddc":["570"],"extern":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"492","status":"public","_id":"1684","date_created":"2018-12-11T11:53:27Z","date_published":"2015-04-16T00:00:00Z","doi":"10.1371/journal.pbio.1002078","year":"2015","has_accepted_license":"1","publication":"PLoS Biology","day":"16","oa":1,"quality_controlled":"1","publisher":"Public Library of Science","acknowledgement":"This research was funded by NIH grants (R01GM076007 and R01GM093182) to DB. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.\r\nWe thank the people listed in S2 Table for samples, Jere Schweikert for identifying Tephritid species, and Zaak Walton for technical assistance.","author":[{"last_name":"Vicoso","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz"},{"last_name":"Bachtrog","full_name":"Bachtrog, Doris","first_name":"Doris"}],"publist_id":"5463","title":"Numerous transitions of sex chromosomes in Diptera","citation":{"chicago":"Vicoso, Beatriz, and Doris Bachtrog. “Numerous Transitions of Sex Chromosomes in Diptera.” PLoS Biology. Public Library of Science, 2015. https://doi.org/10.1371/journal.pbio.1002078.","ista":"Vicoso B, Bachtrog D. 2015. Numerous transitions of sex chromosomes in Diptera. PLoS Biology. 13(4), e1002078.","mla":"Vicoso, Beatriz, and Doris Bachtrog. “Numerous Transitions of Sex Chromosomes in Diptera.” PLoS Biology, vol. 13, no. 4, e1002078, Public Library of Science, 2015, doi:10.1371/journal.pbio.1002078.","short":"B. Vicoso, D. Bachtrog, PLoS Biology 13 (2015).","ieee":"B. Vicoso and D. Bachtrog, “Numerous transitions of sex chromosomes in Diptera,” PLoS Biology, vol. 13, no. 4. Public Library of Science, 2015.","apa":"Vicoso, B., & Bachtrog, D. (2015). Numerous transitions of sex chromosomes in Diptera. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.1002078","ama":"Vicoso B, Bachtrog D. Numerous transitions of sex chromosomes in Diptera. PLoS Biology. 2015;13(4). doi:10.1371/journal.pbio.1002078"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"e1002078"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Sarris M, Sixt MK. Navigating in tissue mazes: Chemoattractant interpretation in complex environments. Current Opinion in Cell Biology. 2015;36(10):93-102. doi:10.1016/j.ceb.2015.08.001","apa":"Sarris, M., & Sixt, M. K. (2015). Navigating in tissue mazes: Chemoattractant interpretation in complex environments. Current Opinion in Cell Biology. Elsevier. https://doi.org/10.1016/j.ceb.2015.08.001","short":"M. Sarris, M.K. Sixt, Current Opinion in Cell Biology 36 (2015) 93–102.","ieee":"M. Sarris and M. K. Sixt, “Navigating in tissue mazes: Chemoattractant interpretation in complex environments,” Current Opinion in Cell Biology, vol. 36, no. 10. Elsevier, pp. 93–102, 2015.","mla":"Sarris, Milka, and Michael K. Sixt. “Navigating in Tissue Mazes: Chemoattractant Interpretation in Complex Environments.” Current Opinion in Cell Biology, vol. 36, no. 10, Elsevier, 2015, pp. 93–102, doi:10.1016/j.ceb.2015.08.001.","ista":"Sarris M, Sixt MK. 2015. Navigating in tissue mazes: Chemoattractant interpretation in complex environments. Current Opinion in Cell Biology. 36(10), 93–102.","chicago":"Sarris, Milka, and Michael K Sixt. “Navigating in Tissue Mazes: Chemoattractant Interpretation in Complex Environments.” Current Opinion in Cell Biology. Elsevier, 2015. https://doi.org/10.1016/j.ceb.2015.08.001."},"title":"Navigating in tissue mazes: Chemoattractant interpretation in complex environments","publist_id":"5458","author":[{"first_name":"Milka","last_name":"Sarris","full_name":"Sarris, Milka"},{"first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"}],"project":[{"call_identifier":"FP7","_id":"25A603A2-B435-11E9-9278-68D0E5697425","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)","grant_number":"281556"}],"day":"01","publication":"Current Opinion in Cell Biology","has_accepted_license":"1","year":"2015","date_published":"2015-10-01T00:00:00Z","doi":"10.1016/j.ceb.2015.08.001","date_created":"2018-12-11T11:53:28Z","page":"93 - 102","quality_controlled":"1","publisher":"Elsevier","oa":1,"ddc":["570"],"date_updated":"2021-01-12T06:52:31Z","file_date_updated":"2020-07-14T12:45:12Z","department":[{"_id":"MiSi"}],"_id":"1687","status":"public","pubrep_id":"445","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"creator":"system","date_updated":"2020-07-14T12:45:12Z","file_size":797964,"date_created":"2018-12-12T10:11:21Z","file_name":"IST-2016-445-v1+1_1-s2.0-S0955067415001064-main.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"c29973924b790aab02fdd91857759cfb","file_id":"4875"}],"language":[{"iso":"eng"}],"publication_status":"published","issue":"10","volume":36,"ec_funded":1,"oa_version":"Published Version","abstract":[{"text":"Guided cell movement is essential for development and integrity of animals and crucially involved in cellular immune responses. Leukocytes are professional migratory cells that can navigate through most types of tissues and sense a wide range of directional cues. The responses of these cells to attractants have been mainly explored in tissue culture settings. How leukocytes make directional decisions in situ, within the challenging environment of a tissue maze, is less understood. Here we review recent advances in how leukocytes sense chemical cues in complex tissue settings and make links with paradigms of directed migration in development and Dictyostelium discoideum amoebae.","lang":"eng"}],"month":"10","intvolume":" 36","scopus_import":1},{"year":"2015","day":"01","page":"386 - 398","date_created":"2018-12-11T11:53:27Z","doi":"10.1007/978-3-662-48350-3_33","date_published":"2015-09-01T00:00:00Z","oa":1,"quality_controlled":"1","publisher":"Springer","citation":{"ieee":"V. Cohen Addad and A. N. de Mesmay, “A fixed parameter tractable approximation scheme for the optimal cut graph of a surface,” presented at the ESA: European Symposium on Algorithms, Patras, Greece, 2015, vol. 9294, pp. 386–398.","short":"V. Cohen Addad, A.N. de Mesmay, in:, Springer, 2015, pp. 386–398.","apa":"Cohen Addad, V., & de Mesmay, A. N. (2015). A fixed parameter tractable approximation scheme for the optimal cut graph of a surface (Vol. 9294, pp. 386–398). Presented at the ESA: European Symposium on Algorithms, Patras, Greece: Springer. https://doi.org/10.1007/978-3-662-48350-3_33","ama":"Cohen Addad V, de Mesmay AN. A fixed parameter tractable approximation scheme for the optimal cut graph of a surface. In: Vol 9294. Springer; 2015:386-398. doi:10.1007/978-3-662-48350-3_33","mla":"Cohen Addad, Vincent, and Arnaud N. de Mesmay. A Fixed Parameter Tractable Approximation Scheme for the Optimal Cut Graph of a Surface. Vol. 9294, Springer, 2015, pp. 386–98, doi:10.1007/978-3-662-48350-3_33.","ista":"Cohen Addad V, de Mesmay AN. 2015. A fixed parameter tractable approximation scheme for the optimal cut graph of a surface. ESA: European Symposium on Algorithms, LNCS, vol. 9294, 386–398.","chicago":"Cohen Addad, Vincent, and Arnaud N de Mesmay. “A Fixed Parameter Tractable Approximation Scheme for the Optimal Cut Graph of a Surface,” 9294:386–98. Springer, 2015. https://doi.org/10.1007/978-3-662-48350-3_33."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Vincent","full_name":"Cohen Addad, Vincent","last_name":"Cohen Addad"},{"id":"3DB2F25C-F248-11E8-B48F-1D18A9856A87","first_name":"Arnaud N","full_name":"De Mesmay, Arnaud N","last_name":"De Mesmay"}],"publist_id":"5462","title":"A fixed parameter tractable approximation scheme for the optimal cut graph of a surface","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"volume":9294,"abstract":[{"text":"Given a graph G cellularly embedded on a surface Σ of genus g, a cut graph is a subgraph of G such that cutting Σ along G yields a topological disk. We provide a fixed parameter tractable approximation scheme for the problem of computing the shortest cut graph, that is, for any ε > 0, we show how to compute a (1 + ε) approximation of the shortest cut graph in time f(ε, g)n3.\r\nOur techniques first rely on the computation of a spanner for the problem using the technique of brick decompositions, to reduce the problem to the case of bounded tree-width. Then, to solve the bounded tree-width case, we introduce a variant of the surface-cut decomposition of Rué, Sau and Thilikos, which may be of independent interest.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"url":"http://arxiv.org/abs/1507.01688","open_access":"1"}],"scopus_import":1,"alternative_title":["LNCS"],"intvolume":" 9294","month":"09","date_updated":"2021-01-12T06:52:31Z","department":[{"_id":"UlWa"}],"_id":"1685","conference":{"name":"ESA: European Symposium on Algorithms","start_date":"2015-09-14","end_date":"2015-09-16","location":"Patras, Greece"},"type":"conference","status":"public"},{"issue":"3","volume":54,"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1403.8147"}],"month":"10","intvolume":" 54","abstract":[{"lang":"eng","text":"We estimate the selection constant in the following geometric selection theorem by Pach: For every positive integer d, there is a constant (Formula presented.) such that whenever (Formula presented.) are n-element subsets of (Formula presented.), we can find a point (Formula presented.) and subsets (Formula presented.) for every i∈[d+1], each of size at least cdn, such that p belongs to all rainbowd-simplices determined by (Formula presented.) simplices with one vertex in each Yi. We show a super-exponentially decreasing upper bound (Formula presented.). The ideas used in the proof of the upper bound also help us to prove Pach’s theorem with (Formula presented.), which is a lower bound doubly exponentially decreasing in d (up to some polynomial in the exponent). For comparison, Pach’s original approach yields a triply exponentially decreasing lower bound. On the other hand, Fox, Pach, and Suk recently obtained a hypergraph density result implying a proof of Pach’s theorem with (Formula presented.). In our construction for the upper bound, we use the fact that the minimum solid angle of every d-simplex is super-exponentially small. This fact was previously unknown and might be of independent interest. For the lower bound, we improve the ‘separation’ part of the argument by showing that in one of the key steps only d+1 separations are necessary, compared to 2d separations in the original proof. We also provide a measure version of Pach’s theorem."}],"oa_version":"Preprint","department":[{"_id":"UlWa"}],"date_updated":"2021-01-12T06:52:32Z","type":"journal_article","status":"public","_id":"1688","page":"610 - 636","date_published":"2015-10-01T00:00:00Z","doi":"10.1007/s00454-015-9720-z","date_created":"2018-12-11T11:53:28Z","year":"2015","day":"01","publication":"Discrete & Computational Geometry","quality_controlled":"1","publisher":"Springer","oa":1,"acknowledgement":"R. K. was supported by the Russian Foundation for Basic Research Grant 15-31-20403 (mol_a_ved) and grant 15-01-99563. J. K., Z. P., and M. T. were partially supported by ERC Advanced Research Grant No. 267165 (DISCONV) and by the project CE-ITI (GAČR P202/12/G061) of the Czech Science Foundation. J. K. was also partially supported by Swiss National Science Foundation Grants 200021-137574 and 200020-14453. P. P., Z. P., and M. T. were partially supported by the Charles University Grant GAUK 421511. P. P. was also partially supported by the Charles University Grant SVV-2014-260107. Z. P. was also partially supported by the Charles University Grant SVV-2014-260103.","publist_id":"5457","author":[{"last_name":"Karasev","full_name":"Karasev, Roman","first_name":"Roman"},{"first_name":"Jan","last_name":"Kynčl","full_name":"Kynčl, Jan"},{"full_name":"Paták, Pavel","last_name":"Paták","first_name":"Pavel"},{"first_name":"Zuzana","full_name":"Patakova, Zuzana","orcid":"0000-0002-3975-1683","last_name":"Patakova"},{"id":"38AC689C-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Tancer","orcid":"0000-0002-1191-6714","full_name":"Tancer, Martin"}],"title":"Bounds for Pach's selection theorem and for the minimum solid angle in a simplex","citation":{"ieee":"R. Karasev, J. Kynčl, P. Paták, Z. Patakova, and M. Tancer, “Bounds for Pach’s selection theorem and for the minimum solid angle in a simplex,” Discrete & Computational Geometry, vol. 54, no. 3. Springer, pp. 610–636, 2015.","short":"R. Karasev, J. Kynčl, P. Paták, Z. Patakova, M. Tancer, Discrete & Computational Geometry 54 (2015) 610–636.","ama":"Karasev R, Kynčl J, Paták P, Patakova Z, Tancer M. Bounds for Pach’s selection theorem and for the minimum solid angle in a simplex. Discrete & Computational Geometry. 2015;54(3):610-636. doi:10.1007/s00454-015-9720-z","apa":"Karasev, R., Kynčl, J., Paták, P., Patakova, Z., & Tancer, M. (2015). Bounds for Pach’s selection theorem and for the minimum solid angle in a simplex. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-015-9720-z","mla":"Karasev, Roman, et al. “Bounds for Pach’s Selection Theorem and for the Minimum Solid Angle in a Simplex.” Discrete & Computational Geometry, vol. 54, no. 3, Springer, 2015, pp. 610–36, doi:10.1007/s00454-015-9720-z.","ista":"Karasev R, Kynčl J, Paták P, Patakova Z, Tancer M. 2015. Bounds for Pach’s selection theorem and for the minimum solid angle in a simplex. Discrete & Computational Geometry. 54(3), 610–636.","chicago":"Karasev, Roman, Jan Kynčl, Pavel Paták, Zuzana Patakova, and Martin Tancer. “Bounds for Pach’s Selection Theorem and for the Minimum Solid Angle in a Simplex.” Discrete & Computational Geometry. Springer, 2015. https://doi.org/10.1007/s00454-015-9720-z."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"project":[{"name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z211","name":"The Wittgenstein Prize"}],"status":"public","type":"journal_article","article_number":"2","_id":"1680","department":[{"_id":"ToHe"}],"title":"On the decidability of elementary modal logics","publist_id":"5468","author":[{"first_name":"Jakub","last_name":"Michaliszyn","full_name":"Michaliszyn, Jakub"},{"last_name":"Otop","full_name":"Otop, Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"},{"full_name":"Kieroňski, Emanuel","last_name":"Kieroňski","first_name":"Emanuel"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Michaliszyn, Jakub, et al. “On the Decidability of Elementary Modal Logics.” ACM Transactions on Computational Logic, vol. 17, no. 1, 2, ACM, 2015, doi:10.1145/2817825.","ieee":"J. Michaliszyn, J. Otop, and E. Kieroňski, “On the decidability of elementary modal logics,” ACM Transactions on Computational Logic, vol. 17, no. 1. ACM, 2015.","short":"J. Michaliszyn, J. Otop, E. Kieroňski, ACM Transactions on Computational Logic 17 (2015).","apa":"Michaliszyn, J., Otop, J., & Kieroňski, E. (2015). On the decidability of elementary modal logics. ACM Transactions on Computational Logic. ACM. https://doi.org/10.1145/2817825","ama":"Michaliszyn J, Otop J, Kieroňski E. On the decidability of elementary modal logics. ACM Transactions on Computational Logic. 2015;17(1). doi:10.1145/2817825","chicago":"Michaliszyn, Jakub, Jan Otop, and Emanuel Kieroňski. “On the Decidability of Elementary Modal Logics.” ACM Transactions on Computational Logic. ACM, 2015. https://doi.org/10.1145/2817825.","ista":"Michaliszyn J, Otop J, Kieroňski E. 2015. On the decidability of elementary modal logics. ACM Transactions on Computational Logic. 17(1), 2."},"date_updated":"2021-01-12T06:52:29Z","intvolume":" 17","month":"09","quality_controlled":"1","publisher":"ACM","oa_version":"None","abstract":[{"text":"We consider the satisfiability problem for modal logic over first-order definable classes of frames.We confirm the conjecture from Hemaspaandra and Schnoor [2008] that modal logic is decidable over classes definable by universal Horn formulae. We provide a full classification of Horn formulae with respect to the complexity of the corresponding satisfiability problem. It turns out, that except for the trivial case of inconsistent formulae, local satisfiability is eitherNP-complete or PSPACE-complete, and global satisfiability is NP-complete, PSPACE-complete, or ExpTime-complete. We also show that the finite satisfiability problem for modal logic over Horn definable classes of frames is decidable. On the negative side, we show undecidability of two related problems. First, we exhibit a simple universal three-variable formula defining the class of frames over which modal logic is undecidable. Second, we consider the satisfiability problem of bimodal logic over Horn definable classes of frames, and also present a formula leading to undecidability.","lang":"eng"}],"ec_funded":1,"date_created":"2018-12-11T11:53:26Z","issue":"1","doi":"10.1145/2817825","volume":17,"date_published":"2015-09-01T00:00:00Z","publication":"ACM Transactions on Computational Logic","language":[{"iso":"eng"}],"day":"01","publication_status":"published","year":"2015"},{"intvolume":" 62","month":"08","main_file_link":[{"url":"http://arxiv.org/abs/1402.0858","open_access":"1"}],"oa":1,"quality_controlled":"1","publisher":"ACM","scopus_import":1,"oa_version":"Preprint","abstract":[{"text":"We study the problem of robust satisfiability of systems of nonlinear equations, namely, whether for a given continuous function f:K→ ℝn on a finite simplicial complex K and α > 0, it holds that each function g: K → ℝn such that ||g - f || ∞ < α, has a root in K. Via a reduction to the extension problem of maps into a sphere, we particularly show that this problem is decidable in polynomial time for every fixed n, assuming dimK ≤ 2n - 3. This is a substantial extension of previous computational applications of topological degree and related concepts in numerical and interval analysis. Via a reverse reduction, we prove that the problem is undecidable when dim K > 2n - 2, where the threshold comes from the stable range in homotopy theory. For the lucidity of our exposition, we focus on the setting when f is simplexwise linear. Such functions can approximate general continuous functions, and thus we get approximation schemes and undecidability of the robust satisfiability in other possible settings.","lang":"eng"}],"date_created":"2018-12-11T11:53:27Z","issue":"4","volume":62,"doi":"10.1145/2751524","date_published":"2015-08-01T00:00:00Z","publication":"Journal of the ACM","language":[{"iso":"eng"}],"day":"01","year":"2015","publication_status":"published","status":"public","type":"journal_article","article_number":"26","_id":"1682","department":[{"_id":"UlWa"},{"_id":"HeEd"}],"title":"Robust satisfiability of systems of equations","author":[{"last_name":"Franek","full_name":"Franek, Peter","first_name":"Peter"},{"first_name":"Marek","id":"33E21118-F248-11E8-B48F-1D18A9856A87","full_name":"Krcál, Marek","last_name":"Krcál"}],"publist_id":"5466","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"P. Franek and M. Krcál, “Robust satisfiability of systems of equations,” Journal of the ACM, vol. 62, no. 4. ACM, 2015.","short":"P. Franek, M. Krcál, Journal of the ACM 62 (2015).","apa":"Franek, P., & Krcál, M. (2015). Robust satisfiability of systems of equations. Journal of the ACM. ACM. https://doi.org/10.1145/2751524","ama":"Franek P, Krcál M. Robust satisfiability of systems of equations. Journal of the ACM. 2015;62(4). doi:10.1145/2751524","mla":"Franek, Peter, and Marek Krcál. “Robust Satisfiability of Systems of Equations.” Journal of the ACM, vol. 62, no. 4, 26, ACM, 2015, doi:10.1145/2751524.","ista":"Franek P, Krcál M. 2015. Robust satisfiability of systems of equations. Journal of the ACM. 62(4), 26.","chicago":"Franek, Peter, and Marek Krcál. “Robust Satisfiability of Systems of Equations.” Journal of the ACM. ACM, 2015. https://doi.org/10.1145/2751524."},"date_updated":"2021-01-12T06:52:30Z"},{"title":"Gaining mass: The structure of respiratory complex I-from bacterial towards mitochondrial versions","department":[{"_id":"LeSa"}],"publist_id":"5465","author":[{"last_name":"Letts","orcid":"0000-0002-9864-3586","full_name":"Letts, Jame A","id":"322DA418-F248-11E8-B48F-1D18A9856A87","first_name":"Jame A"},{"last_name":"Sazanov","full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:52:30Z","citation":{"chicago":"Letts, James A, and Leonid A Sazanov. “Gaining Mass: The Structure of Respiratory Complex I-from Bacterial towards Mitochondrial Versions.” Current Opinion in Structural Biology. Elsevier, 2015. https://doi.org/10.1016/j.sbi.2015.08.008.","ista":"Letts JA, Sazanov LA. 2015. Gaining mass: The structure of respiratory complex I-from bacterial towards mitochondrial versions. Current Opinion in Structural Biology. 33(8), 135–145.","mla":"Letts, James A., and Leonid A. Sazanov. “Gaining Mass: The Structure of Respiratory Complex I-from Bacterial towards Mitochondrial Versions.” Current Opinion in Structural Biology, vol. 33, no. 8, Elsevier, 2015, pp. 135–45, doi:10.1016/j.sbi.2015.08.008.","ieee":"J. A. Letts and L. A. Sazanov, “Gaining mass: The structure of respiratory complex I-from bacterial towards mitochondrial versions,” Current Opinion in Structural Biology, vol. 33, no. 8. Elsevier, pp. 135–145, 2015.","short":"J.A. Letts, L.A. Sazanov, Current Opinion in Structural Biology 33 (2015) 135–145.","apa":"Letts, J. A., & Sazanov, L. A. (2015). Gaining mass: The structure of respiratory complex I-from bacterial towards mitochondrial versions. Current Opinion in Structural Biology. Elsevier. https://doi.org/10.1016/j.sbi.2015.08.008","ama":"Letts JA, Sazanov LA. Gaining mass: The structure of respiratory complex I-from bacterial towards mitochondrial versions. Current Opinion in Structural Biology. 2015;33(8):135-145. doi:10.1016/j.sbi.2015.08.008"},"status":"public","type":"journal_article","_id":"1683","volume":33,"doi":"10.1016/j.sbi.2015.08.008","issue":"8","date_published":"2015-08-01T00:00:00Z","date_created":"2018-12-11T11:53:27Z","page":"135 - 145","day":"01","language":[{"iso":"eng"}],"publication":"Current Opinion in Structural Biology","year":"2015","publication_status":"published","month":"08","intvolume":" 33","quality_controlled":"1","publisher":"Elsevier","scopus_import":1,"oa_version":"None","abstract":[{"lang":"eng","text":"The 1 MDa, 45-subunit proton-pumping NADH-ubiquinone oxidoreductase (complex I) is the largest complex of the mitochondrial electron transport chain. The molecular mechanism of complex I is central to the metabolism of cells, but has yet to be fully characterized. The last two years have seen steady progress towards this goal with the first atomic-resolution structure of the entire bacterial complex I, a 5 Å cryo-electron microscopy map of bovine mitochondrial complex I and a ∼3.8 Å resolution X-ray crystallographic study of mitochondrial complex I from yeast Yarrowia lipotytica. In this review we will discuss what we have learned from these studies and what remains to be elucidated."}]},{"page":"1055 - 1056","volume":349,"doi":"10.1126/science.aad0867","issue":"6252","date_published":"2015-09-04T00:00:00Z","date_created":"2018-12-11T11:53:28Z","publication_status":"published","year":"2015","day":"04","publication":"Science","language":[{"iso":"eng"}],"quality_controlled":"1","scopus_import":1,"publisher":"American Association for the Advancement of Science","month":"09","intvolume":" 349","oa_version":"None","author":[{"full_name":"Kiermaier, Eva","orcid":"0000-0001-6165-5738","last_name":"Kiermaier","id":"3EB04B78-F248-11E8-B48F-1D18A9856A87","first_name":"Eva"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","last_name":"Sixt"}],"publist_id":"5459","department":[{"_id":"MiSi"}],"title":"Fragmented communication between immune cells: Neutrophils blaze a trail with migratory cues for T cells to follow to sites of infection","citation":{"mla":"Kiermaier, Eva, and Michael K. Sixt. “Fragmented Communication between Immune Cells: Neutrophils Blaze a Trail with Migratory Cues for T Cells to Follow to Sites of Infection.” Science, vol. 349, no. 6252, American Association for the Advancement of Science, 2015, pp. 1055–56, doi:10.1126/science.aad0867.","ama":"Kiermaier E, Sixt MK. Fragmented communication between immune cells: Neutrophils blaze a trail with migratory cues for T cells to follow to sites of infection. Science. 2015;349(6252):1055-1056. doi:10.1126/science.aad0867","apa":"Kiermaier, E., & Sixt, M. K. (2015). Fragmented communication between immune cells: Neutrophils blaze a trail with migratory cues for T cells to follow to sites of infection. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aad0867","ieee":"E. Kiermaier and M. K. Sixt, “Fragmented communication between immune cells: Neutrophils blaze a trail with migratory cues for T cells to follow to sites of infection,” Science, vol. 349, no. 6252. American Association for the Advancement of Science, pp. 1055–1056, 2015.","short":"E. Kiermaier, M.K. Sixt, Science 349 (2015) 1055–1056.","chicago":"Kiermaier, Eva, and Michael K Sixt. “Fragmented Communication between Immune Cells: Neutrophils Blaze a Trail with Migratory Cues for T Cells to Follow to Sites of Infection.” Science. American Association for the Advancement of Science, 2015. https://doi.org/10.1126/science.aad0867.","ista":"Kiermaier E, Sixt MK. 2015. Fragmented communication between immune cells: Neutrophils blaze a trail with migratory cues for T cells to follow to sites of infection. Science. 349(6252), 1055–1056."},"date_updated":"2021-01-12T06:52:31Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","status":"public","_id":"1686"},{"publication_identifier":{"isbn":["978-1-4503-3433-4"]},"year":"2015","publication_status":"published","day":"14","language":[{"iso":"eng"}],"publication":"Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control","page":"149 - 158","date_published":"2015-04-14T00:00:00Z","doi":"10.1145/2728606.2728622","date_created":"2018-12-11T11:53:30Z","ec_funded":1,"abstract":[{"text":"Computing an approximation of the reachable states of a hybrid system is a challenge, mainly because overapproximating the solutions of ODEs with a finite number of sets does not scale well. Using template polyhedra can greatly reduce the computational complexity, since it replaces complex operations on sets with a small number of optimization problems. However, the use of templates may make the over-approximation too conservative. Spurious transitions, which are falsely considered reachable, are particularly detrimental to performance and accuracy, and may exacerbate the state explosion problem. In this paper, we examine how spurious transitions can be avoided with minimal computational effort. To this end, detecting spurious transitions is reduced to the well-known problem of showing that two convex sets are disjoint by finding a hyperplane that separates them. We generalize this to owpipes by considering hyperplanes that evolve with time in correspondence to the dynamics of the system. The approach is implemented in the model checker SpaceEx and demonstrated on examples.","lang":"eng"}],"oa_version":"None","publisher":"ACM","scopus_import":1,"quality_controlled":"1","month":"04","date_updated":"2021-01-12T06:52:33Z","citation":{"apa":"Frehse, G., Bogomolov, S., Greitschus, M., Strump, T., & Podelski, A. (2015). Eliminating spurious transitions in reachability with support functions. In Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control (pp. 149–158). Seattle, WA, United States: ACM. https://doi.org/10.1145/2728606.2728622","ama":"Frehse G, Bogomolov S, Greitschus M, Strump T, Podelski A. Eliminating spurious transitions in reachability with support functions. In: Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control. ACM; 2015:149-158. doi:10.1145/2728606.2728622","short":"G. Frehse, S. Bogomolov, M. Greitschus, T. Strump, A. Podelski, in:, Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control, ACM, 2015, pp. 149–158.","ieee":"G. Frehse, S. Bogomolov, M. Greitschus, T. Strump, and A. Podelski, “Eliminating spurious transitions in reachability with support functions,” in Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control, Seattle, WA, United States, 2015, pp. 149–158.","mla":"Frehse, Goran, et al. “Eliminating Spurious Transitions in Reachability with Support Functions.” Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control, ACM, 2015, pp. 149–58, doi:10.1145/2728606.2728622.","ista":"Frehse G, Bogomolov S, Greitschus M, Strump T, Podelski A. 2015. Eliminating spurious transitions in reachability with support functions. Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control. HSCC: Hybrid Systems - Computation and Control, 149–158.","chicago":"Frehse, Goran, Sergiy Bogomolov, Marius Greitschus, Thomas Strump, and Andreas Podelski. “Eliminating Spurious Transitions in Reachability with Support Functions.” In Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control, 149–58. ACM, 2015. https://doi.org/10.1145/2728606.2728622."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"5452","author":[{"full_name":"Frehse, Goran","last_name":"Frehse","first_name":"Goran"},{"last_name":"Bogomolov","full_name":"Bogomolov, Sergiy","orcid":"0000-0002-0686-0365","first_name":"Sergiy","id":"369D9A44-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Marius","last_name":"Greitschus","full_name":"Greitschus, Marius"},{"first_name":"Thomas","full_name":"Strump, Thomas","last_name":"Strump"},{"full_name":"Podelski, Andreas","last_name":"Podelski","first_name":"Andreas"}],"department":[{"_id":"ToHe"}],"title":"Eliminating spurious transitions in reachability with support functions","_id":"1692","type":"conference","conference":{"end_date":"2015-04-16","location":"Seattle, WA, United States","start_date":"2015-04-14","name":"HSCC: Hybrid Systems - Computation and Control"},"project":[{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","grant_number":"267989"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z211","name":"The Wittgenstein Prize"}],"status":"public"},{"project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"article_number":"022514","title":"Quantum interference effects in laser spectroscopy of muonic hydrogen, deuterium, and helium-3","author":[{"last_name":"Amaro","full_name":"Amaro, Pedro","first_name":"Pedro"},{"full_name":"Franke, Beatrice","last_name":"Franke","first_name":"Beatrice"},{"full_name":"Krauth, Julian","last_name":"Krauth","first_name":"Julian"},{"full_name":"Diepold, Marc","last_name":"Diepold","first_name":"Marc"},{"full_name":"Fratini, Filippo","last_name":"Fratini","first_name":"Filippo"},{"id":"3C325E5E-F248-11E8-B48F-1D18A9856A87","first_name":"Laleh","full_name":"Safari, Laleh","last_name":"Safari"},{"first_name":"Jorge","full_name":"Machado, Jorge","last_name":"Machado"},{"first_name":"Aldo","full_name":"Antognini, Aldo","last_name":"Antognini"},{"full_name":"Kottmann, Franz","last_name":"Kottmann","first_name":"Franz"},{"first_name":"Paul","full_name":"Indelicato, Paul","last_name":"Indelicato"},{"first_name":"Randolf","last_name":"Pohl","full_name":"Pohl, Randolf"},{"first_name":"José","full_name":"Santos, José","last_name":"Santos"}],"publist_id":"5451","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Amaro P, Franke B, Krauth J, Diepold M, Fratini F, Safari L, Machado J, Antognini A, Kottmann F, Indelicato P, Pohl R, Santos J. 2015. Quantum interference effects in laser spectroscopy of muonic hydrogen, deuterium, and helium-3. Physical Review A. 92(2), 022514.","chicago":"Amaro, Pedro, Beatrice Franke, Julian Krauth, Marc Diepold, Filippo Fratini, Laleh Safari, Jorge Machado, et al. “Quantum Interference Effects in Laser Spectroscopy of Muonic Hydrogen, Deuterium, and Helium-3.” Physical Review A. American Physical Society, 2015. https://doi.org/10.1103/PhysRevA.92.022514.","ama":"Amaro P, Franke B, Krauth J, et al. Quantum interference effects in laser spectroscopy of muonic hydrogen, deuterium, and helium-3. Physical Review A. 2015;92(2). doi:10.1103/PhysRevA.92.022514","apa":"Amaro, P., Franke, B., Krauth, J., Diepold, M., Fratini, F., Safari, L., … Santos, J. (2015). Quantum interference effects in laser spectroscopy of muonic hydrogen, deuterium, and helium-3. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.92.022514","ieee":"P. Amaro et al., “Quantum interference effects in laser spectroscopy of muonic hydrogen, deuterium, and helium-3,” Physical Review A, vol. 92, no. 2. American Physical Society, 2015.","short":"P. Amaro, B. Franke, J. Krauth, M. Diepold, F. Fratini, L. Safari, J. Machado, A. Antognini, F. Kottmann, P. Indelicato, R. Pohl, J. Santos, Physical Review A 92 (2015).","mla":"Amaro, Pedro, et al. “Quantum Interference Effects in Laser Spectroscopy of Muonic Hydrogen, Deuterium, and Helium-3.” Physical Review A, vol. 92, no. 2, 022514, American Physical Society, 2015, doi:10.1103/PhysRevA.92.022514."},"oa":1,"quality_controlled":"1","publisher":"American Physical Society","date_created":"2018-12-11T11:53:30Z","doi":"10.1103/PhysRevA.92.022514","date_published":"2015-08-28T00:00:00Z","publication":"Physical Review A","day":"28","year":"2015","status":"public","type":"journal_article","_id":"1693","department":[{"_id":"MiLe"}],"date_updated":"2021-01-12T06:52:34Z","intvolume":" 92","month":"08","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1506.02734"}],"scopus_import":1,"oa_version":"Preprint","abstract":[{"text":"Quantum interference between energetically close states is theoretically investigated, with the state structure being observed via laser spectroscopy. In this work, we focus on hyperfine states of selected hydrogenic muonic isotopes, and on how quantum interference affects the measured Lamb shift. The process of photon excitation and subsequent photon decay is implemented within the framework of nonrelativistic second-order perturbation theory. Due to its experimental interest, calculations are performed for muonic hydrogen, deuterium, and helium-3. We restrict our analysis to the case of photon scattering by incident linear polarized photons and the polarization of the scattered photons not being observed. We conclude that while quantum interference effects can be safely neglected in muonic hydrogen and helium-3, in the case of muonic deuterium there are resonances with close proximity, where quantum interference effects can induce shifts up to a few percent of the linewidth, assuming a pointlike detector. However, by taking into account the geometry of the setup used by the CREMA collaboration, this effect is reduced to less than 0.2% of the linewidth in all possible cases, which makes it irrelevant at the present level of accuracy. © 2015 American Physical Society.","lang":"eng"}],"ec_funded":1,"issue":"2","volume":92,"language":[{"iso":"eng"}],"publication_status":"published"},{"publist_id":"5454","author":[{"last_name":"Bak","full_name":"Bak, Stanley","first_name":"Stanley"},{"first_name":"Sergiy","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","last_name":"Bogomolov","orcid":"0000-0002-0686-0365","full_name":"Bogomolov, Sergiy"},{"last_name":"Johnson","full_name":"Johnson, Taylor","first_name":"Taylor"}],"title":"HYST: A source transformation and translation tool for hybrid automaton models","department":[{"_id":"ToHe"}],"citation":{"short":"S. Bak, S. Bogomolov, T. Johnson, in:, Springer, 2015, pp. 128–133.","ieee":"S. Bak, S. Bogomolov, and T. Johnson, “HYST: A source transformation and translation tool for hybrid automaton models,” presented at the HSCC: Hybrid Systems - Computation and Control, Seattle, WA, United States, 2015, pp. 128–133.","ama":"Bak S, Bogomolov S, Johnson T. HYST: A source transformation and translation tool for hybrid automaton models. In: Springer; 2015:128-133. doi:10.1145/2728606.2728630","apa":"Bak, S., Bogomolov, S., & Johnson, T. (2015). HYST: A source transformation and translation tool for hybrid automaton models (pp. 128–133). Presented at the HSCC: Hybrid Systems - Computation and Control, Seattle, WA, United States: Springer. https://doi.org/10.1145/2728606.2728630","mla":"Bak, Stanley, et al. HYST: A Source Transformation and Translation Tool for Hybrid Automaton Models. Springer, 2015, pp. 128–33, doi:10.1145/2728606.2728630.","ista":"Bak S, Bogomolov S, Johnson T. 2015. HYST: A source transformation and translation tool for hybrid automaton models. HSCC: Hybrid Systems - Computation and Control, 128–133.","chicago":"Bak, Stanley, Sergiy Bogomolov, and Taylor Johnson. “HYST: A Source Transformation and Translation Tool for Hybrid Automaton Models,” 128–33. Springer, 2015. https://doi.org/10.1145/2728606.2728630."},"date_updated":"2021-01-12T06:52:33Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","conference":{"name":"HSCC: Hybrid Systems - Computation and Control","start_date":"2015-04-14","end_date":"2015-04-16","location":"Seattle, WA, United States"},"project":[{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","grant_number":"267989"},{"name":"The Wittgenstein Prize","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"status":"public","_id":"1690","page":"128 - 133","doi":"10.1145/2728606.2728630","date_published":"2015-04-14T00:00:00Z","date_created":"2018-12-11T11:53:29Z","ec_funded":1,"year":"2015","publication_status":"published","day":"14","language":[{"iso":"eng"}],"quality_controlled":"1","publisher":"Springer","month":"04","abstract":[{"text":"A number of powerful and scalable hybrid systems model checkers have recently emerged. Although all of them honor roughly the same hybrid systems semantics, they have drastically different model description languages. This situation (a) makes it difficult to quickly evaluate a specific hybrid automaton model using the different tools, (b) obstructs comparisons of reachability approaches, and (c) impedes the widespread application of research results that perform model modification and could benefit many of the tools. In this paper, we present Hyst, a Hybrid Source Transformer. Hyst is a source-to-source translation tool, currently taking input in the SpaceEx model format, and translating to the formats of HyCreate, Flow∗, or dReach. Internally, the tool supports generic model-to-model transformation passes that serve to both ease the translation and potentially improve reachability results for the supported tools. Although these model transformation passes could be implemented within each tool, the Hyst approach provides a single place for model modification, generating modified input sources for the unmodified target tools. Our evaluation demonstrates Hyst is capable of automatically translating benchmarks in several classes (including affine and nonlinear hybrid automata) to the input formats of several tools. Additionally, we illustrate a general model transformation pass based on pseudo-invariants implemented in Hyst that illustrates the reachability improvement.","lang":"eng"}],"oa_version":"None","acknowledgement":"The material presented in this paper is based upon work sup-ported by the Air Force Research Laboratory’s Information Directorate (AFRL/RI) through the Visiting Faculty Research Program (VFRP) under contract number FA8750-13-2-0115 and the Air Force Office of Scientific Research (AFOSR). Any opinions,findings, and conclusions or recommendations expressed in this publication are those of the authors and do not necessarily reflect the views of the AFRL/RI or AFOSR. This work was also partly supported in part by the German Research Foundation (DFG) as part of the Transregional Collaborative Research Center “Automatic Verification and Analysis of Complex Systems” (SFB/TR14 AVACS, http://www.avacs.org/), by the European Research Council (ERC) under grant 267989 (QUAREM) and by the Austrian Science Fund (FWF) under grants S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award)."},{"year":"2015","publication_status":"published","publication":"Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control","language":[{"iso":"eng"}],"day":"14","page":"233 - 238","date_created":"2018-12-11T11:53:29Z","ec_funded":1,"doi":"10.1145/2728606.2728617","date_published":"2015-04-14T00:00:00Z","abstract":[{"lang":"eng","text":"We consider a case study of the problem of deploying an autonomous air vehicle in a partially observable, dynamic, indoor environment from a specification given as a linear temporal logic (LTL) formula over regions of interest. We model the motion and sensing capabilities of the vehicle as a partially observable Markov decision process (POMDP). We adapt recent results for solving POMDPs with parity objectives to generate a control policy. We also extend the existing framework with a policy minimization technique to obtain a better implementable policy, while preserving its correctness. The proposed techniques are illustrated in an experimental setup involving an autonomous quadrotor performing surveillance in a dynamic environment."}],"oa_version":"None","publisher":"ACM","scopus_import":1,"month":"04","date_updated":"2021-01-12T06:52:33Z","citation":{"ieee":"M. Svoreňová et al., “Temporal logic motion planning using POMDPs with parity objectives: Case study paper,” in Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control, Seattle, WA, United States, 2015, pp. 233–238.","short":"M. Svoreňová, M. Chmelik, K. Leahy, H. Eniser, K. Chatterjee, I. Cěrná, C. Belta, in:, Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control, ACM, 2015, pp. 233–238.","ama":"Svoreňová M, Chmelik M, Leahy K, et al. Temporal logic motion planning using POMDPs with parity objectives: Case study paper. In: Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control. ACM; 2015:233-238. doi:10.1145/2728606.2728617","apa":"Svoreňová, M., Chmelik, M., Leahy, K., Eniser, H., Chatterjee, K., Cěrná, I., & Belta, C. (2015). Temporal logic motion planning using POMDPs with parity objectives: Case study paper. In Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control (pp. 233–238). Seattle, WA, United States: ACM. https://doi.org/10.1145/2728606.2728617","mla":"Svoreňová, Mária, et al. “Temporal Logic Motion Planning Using POMDPs with Parity Objectives: Case Study Paper.” Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control, ACM, 2015, pp. 233–38, doi:10.1145/2728606.2728617.","ista":"Svoreňová M, Chmelik M, Leahy K, Eniser H, Chatterjee K, Cěrná I, Belta C. 2015. Temporal logic motion planning using POMDPs with parity objectives: Case study paper. Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control. HSCC: Hybrid Systems - Computation and Control, 233–238.","chicago":"Svoreňová, Mária, Martin Chmelik, Kevin Leahy, Hasan Eniser, Krishnendu Chatterjee, Ivana Cěrná, and Cǎlin Belta. “Temporal Logic Motion Planning Using POMDPs with Parity Objectives: Case Study Paper.” In Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control, 233–38. ACM, 2015. https://doi.org/10.1145/2728606.2728617."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Svoreňová, Mária","last_name":"Svoreňová","first_name":"Mária"},{"id":"3624234E-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","full_name":"Chmelik, Martin","last_name":"Chmelik"},{"first_name":"Kevin","full_name":"Leahy, Kevin","last_name":"Leahy"},{"full_name":"Eniser, Hasan","last_name":"Eniser","first_name":"Hasan"},{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"first_name":"Ivana","last_name":"Cěrná","full_name":"Cěrná, Ivana"},{"first_name":"Cǎlin","full_name":"Belta, Cǎlin","last_name":"Belta"}],"publist_id":"5453","department":[{"_id":"KrCh"}],"title":"Temporal logic motion planning using POMDPs with parity objectives: Case study paper","_id":"1691","conference":{"name":"HSCC: Hybrid Systems - Computation and Control","start_date":"2015-04-14","location":"Seattle, WA, United States","end_date":"2015-04-16"},"type":"conference","project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"}],"status":"public"},{"author":[{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"first_name":"Vinayak","full_name":"Prabhu, Vinayak","last_name":"Prabhu"}],"publist_id":"5450","title":"Quantitative temporal simulation and refinement distances for timed systems","department":[{"_id":"KrCh"}],"date_updated":"2021-01-12T06:52:34Z","citation":{"chicago":"Chatterjee, Krishnendu, and Vinayak Prabhu. “Quantitative Temporal Simulation and Refinement Distances for Timed Systems.” IEEE Transactions on Automatic Control. IEEE, 2015. https://doi.org/10.1109/TAC.2015.2404612.","ista":"Chatterjee K, Prabhu V. 2015. Quantitative temporal simulation and refinement distances for timed systems. IEEE Transactions on Automatic Control. 60(9), 2291–2306.","mla":"Chatterjee, Krishnendu, and Vinayak Prabhu. “Quantitative Temporal Simulation and Refinement Distances for Timed Systems.” IEEE Transactions on Automatic Control, vol. 60, no. 9, IEEE, 2015, pp. 2291–306, doi:10.1109/TAC.2015.2404612.","short":"K. Chatterjee, V. Prabhu, IEEE Transactions on Automatic Control 60 (2015) 2291–2306.","ieee":"K. Chatterjee and V. Prabhu, “Quantitative temporal simulation and refinement distances for timed systems,” IEEE Transactions on Automatic Control, vol. 60, no. 9. IEEE, pp. 2291–2306, 2015.","apa":"Chatterjee, K., & Prabhu, V. (2015). Quantitative temporal simulation and refinement distances for timed systems. IEEE Transactions on Automatic Control. IEEE. https://doi.org/10.1109/TAC.2015.2404612","ama":"Chatterjee K, Prabhu V. Quantitative temporal simulation and refinement distances for timed systems. IEEE Transactions on Automatic Control. 2015;60(9):2291-2306. doi:10.1109/TAC.2015.2404612"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","status":"public","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"_id":"1694","page":"2291 - 2306","ec_funded":1,"date_created":"2018-12-11T11:53:30Z","date_published":"2015-02-24T00:00:00Z","volume":60,"doi":"10.1109/TAC.2015.2404612","issue":"9","publication_status":"published","year":"2015","language":[{"iso":"eng"}],"publication":"IEEE Transactions on Automatic Control","day":"24","publisher":"IEEE","quality_controlled":"1","scopus_import":1,"intvolume":" 60","month":"02","abstract":[{"text":"\r\nWe introduce quantitative timed refinement and timed simulation (directed) metrics, incorporating zenoness checks, for timed systems. These metrics assign positive real numbers which quantify the timing mismatches between two timed systems, amongst non-zeno runs. We quantify timing mismatches in three ways: (1) the maximal timing mismatch that can arise, (2) the “steady-state” maximal timing mismatches, where initial transient timing mismatches are ignored; and (3) the (long-run) average timing mismatches amongst two systems. These three kinds of mismatches constitute three important types of timing differences. Our event times are the global times, measured from the start of the system execution, not just the time durations of individual steps. We present algorithms over timed automata for computing the three quantitative simulation distances to within any desired degree of accuracy. In order to compute the values of the quantitative simulation distances, we use a game theoretic formulation. We introduce two new kinds of objectives for two player games on finite-state game graphs: (1) eventual debit-sum level objectives, and (2) average debit-sum level objectives. We present algorithms for computing the optimal values for these objectives in graph games, and then use these algorithms to compute the values of the timed simulation distances over timed automata.\r\n","lang":"eng"}],"oa_version":"None"},{"status":"public","type":"journal_article","_id":"1695","department":[{"_id":"MiLe"}],"date_updated":"2021-01-12T06:52:34Z","month":"09","intvolume":" 252","scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1503.03738"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We give a comprehensive introduction into a diagrammatic method that allows for the evaluation of Gutzwiller wave functions in finite spatial dimensions. We discuss in detail some numerical schemes that turned out to be useful in the real-space evaluation of the diagrams. The method is applied to the problem of d-wave superconductivity in a two-dimensional single-band Hubbard model. Here, we discuss in particular the role of long-range contributions in our diagrammatic expansion. We further reconsider our previous analysis on the kinetic energy gain in the superconducting state."}],"volume":252,"issue":"9","ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"title":"Evaluation techniques for Gutzwiller wave functions in finite dimensions","author":[{"id":"46C405DE-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Kaczmarczyk","orcid":"0000-0002-1629-3675","full_name":"Kaczmarczyk, Jan"},{"last_name":"Schickling","full_name":"Schickling, Tobias","first_name":"Tobias"},{"first_name":"Jörg","full_name":"Bünemann, Jörg","last_name":"Bünemann"}],"publist_id":"5449","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Kaczmarczyk, Jan, Tobias Schickling, and Jörg Bünemann. “Evaluation Techniques for Gutzwiller Wave Functions in Finite Dimensions.” Physica Status Solidi (B): Basic Solid State Physics. Wiley, 2015. https://doi.org/10.1002/pssb.201552082.","ista":"Kaczmarczyk J, Schickling T, Bünemann J. 2015. Evaluation techniques for Gutzwiller wave functions in finite dimensions. Physica Status Solidi (B): Basic Solid State Physics. 252(9), 2059–2071.","mla":"Kaczmarczyk, Jan, et al. “Evaluation Techniques for Gutzwiller Wave Functions in Finite Dimensions.” Physica Status Solidi (B): Basic Solid State Physics, vol. 252, no. 9, Wiley, 2015, pp. 2059–71, doi:10.1002/pssb.201552082.","ieee":"J. Kaczmarczyk, T. Schickling, and J. Bünemann, “Evaluation techniques for Gutzwiller wave functions in finite dimensions,” Physica Status Solidi (B): Basic Solid State Physics, vol. 252, no. 9. Wiley, pp. 2059–2071, 2015.","short":"J. Kaczmarczyk, T. Schickling, J. Bünemann, Physica Status Solidi (B): Basic Solid State Physics 252 (2015) 2059–2071.","ama":"Kaczmarczyk J, Schickling T, Bünemann J. Evaluation techniques for Gutzwiller wave functions in finite dimensions. Physica Status Solidi (B): Basic Solid State Physics. 2015;252(9):2059-2071. doi:10.1002/pssb.201552082","apa":"Kaczmarczyk, J., Schickling, T., & Bünemann, J. (2015). Evaluation techniques for Gutzwiller wave functions in finite dimensions. Physica Status Solidi (B): Basic Solid State Physics. Wiley. https://doi.org/10.1002/pssb.201552082"},"publisher":"Wiley","quality_controlled":"1","oa":1,"date_published":"2015-09-01T00:00:00Z","doi":"10.1002/pssb.201552082","date_created":"2018-12-11T11:53:31Z","page":"2059 - 2071","day":"01","publication":"Physica Status Solidi (B): Basic Solid State Physics","year":"2015"},{"publication_status":"published","language":[{"iso":"eng"}],"file":[{"checksum":"472b979f3f1cffb37b3e503f085115ca","file_id":"5212","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:16:25Z","file_name":"IST-2016-455-v1+1_journal.pcbi.1004304.pdf","creator":"system","date_updated":"2020-07-14T12:45:12Z","file_size":4673930}],"issue":"7","volume":11,"abstract":[{"text":"Motion tracking is a challenge the visual system has to solve by reading out the retinal population. It is still unclear how the information from different neurons can be combined together to estimate the position of an object. Here we recorded a large population of ganglion cells in a dense patch of salamander and guinea pig retinas while displaying a bar moving diffusively. We show that the bar’s position can be reconstructed from retinal activity with a precision in the hyperacuity regime using a linear decoder acting on 100+ cells. We then took advantage of this unprecedented precision to explore the spatial structure of the retina’s population code. The classical view would have suggested that the firing rates of the cells form a moving hill of activity tracking the bar’s position. Instead, we found that most ganglion cells in the salamander fired sparsely and idiosyncratically, so that their neural image did not track the bar. Furthermore, ganglion cell activity spanned an area much larger than predicted by their receptive fields, with cells coding for motion far in their surround. As a result, population redundancy was high, and we could find multiple, disjoint subsets of neurons that encoded the trajectory with high precision. This organization allows for diverse collections of ganglion cells to represent high-accuracy motion information in a form easily read out by downstream neural circuits.","lang":"eng"}],"oa_version":"Published Version","scopus_import":1,"intvolume":" 11","month":"07","date_updated":"2021-01-12T06:52:35Z","ddc":["570"],"file_date_updated":"2020-07-14T12:45:12Z","department":[{"_id":"GaTk"}],"_id":"1697","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"455","status":"public","year":"2015","has_accepted_license":"1","publication":"PLoS Computational Biology","day":"01","date_created":"2018-12-11T11:53:31Z","doi":"10.1371/journal.pcbi.1004304","date_published":"2015-07-01T00:00:00Z","acknowledgement":"This work was supported by grants EY 014196 and EY 017934 to MJB, ANR OPTIMA, the French State program Investissements d’Avenir managed by the Agence Nationale de la Recherche [LIFESENSES: ANR-10-LABX-65], and by a EC grant from the Human Brain Project (CLAP) to OM, the Austrian Research Foundation FWF P25651 to VBS and GT. VBS is partially supported by contracts MEC, Spain (Grant No. AYA2010- 22111-C03-02, Grant No. AYA2013-48623-C2-2 and FEDER Funds).","oa":1,"publisher":"Public Library of Science","quality_controlled":"1","citation":{"apa":"Marre, O., Botella Soler, V., Simmons, K., Mora, T., Tkačik, G., & Berry, M. (2015). High accuracy decoding of dynamical motion from a large retinal population. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1004304","ama":"Marre O, Botella Soler V, Simmons K, Mora T, Tkačik G, Berry M. High accuracy decoding of dynamical motion from a large retinal population. PLoS Computational Biology. 2015;11(7). doi:10.1371/journal.pcbi.1004304","ieee":"O. Marre, V. Botella Soler, K. Simmons, T. Mora, G. Tkačik, and M. Berry, “High accuracy decoding of dynamical motion from a large retinal population,” PLoS Computational Biology, vol. 11, no. 7. Public Library of Science, 2015.","short":"O. Marre, V. Botella Soler, K. Simmons, T. Mora, G. Tkačik, M. Berry, PLoS Computational Biology 11 (2015).","mla":"Marre, Olivier, et al. “High Accuracy Decoding of Dynamical Motion from a Large Retinal Population.” PLoS Computational Biology, vol. 11, no. 7, e1004304, Public Library of Science, 2015, doi:10.1371/journal.pcbi.1004304.","ista":"Marre O, Botella Soler V, Simmons K, Mora T, Tkačik G, Berry M. 2015. High accuracy decoding of dynamical motion from a large retinal population. PLoS Computational Biology. 11(7), e1004304.","chicago":"Marre, Olivier, Vicente Botella Soler, Kristina Simmons, Thierry Mora, Gašper Tkačik, and Michael Berry. “High Accuracy Decoding of Dynamical Motion from a Large Retinal Population.” PLoS Computational Biology. Public Library of Science, 2015. https://doi.org/10.1371/journal.pcbi.1004304."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Olivier","full_name":"Marre, Olivier","last_name":"Marre"},{"first_name":"Vicente","id":"421234E8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8790-1914","full_name":"Botella Soler, Vicente","last_name":"Botella Soler"},{"last_name":"Simmons","full_name":"Simmons, Kristina","first_name":"Kristina"},{"first_name":"Thierry","last_name":"Mora","full_name":"Mora, Thierry"},{"last_name":"Tkacik","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper"},{"full_name":"Berry, Michael","last_name":"Berry","first_name":"Michael"}],"publist_id":"5447","title":"High accuracy decoding of dynamical motion from a large retinal population","article_number":"e1004304","project":[{"call_identifier":"FWF","_id":"254D1A94-B435-11E9-9278-68D0E5697425","grant_number":"P 25651-N26","name":"Sensitivity to higher-order statistics in natural scenes"}]},{"acknowledgement":"This work was made possible with financial support by the Vienna Science and Technology Fund (WWTF), by the Deutsche Forschungsgemeinschaft (DFG), Research Unit 1078 Natural selection in structured populations, by the Austrian Science Fund (FWF) via funding for the Vienna Graduate School for Population Genetics, and by a “For Women in Science” fellowship (L’Oréal Österreich in cooperation with the Austrian Commission for UNESCO and the Austrian Academy of Sciences with financial support from the Federal Ministry for Science and Research Austria).","oa":1,"publisher":"Springer","quality_controlled":"1","year":"2015","has_accepted_license":"1","publication":"Journal of Mathematical Biology","day":"01","page":"1523 - 1580","date_created":"2018-12-11T11:53:32Z","date_published":"2015-06-01T00:00:00Z","doi":"10.1007/s00285-014-0802-y","project":[{"_id":"25B67606-B435-11E9-9278-68D0E5697425","name":"L'OREAL Fellowship"}],"citation":{"mla":"Uecker, Hildegard, et al. “Adaptive Gene Introgression after Secondary Contact.” Journal of Mathematical Biology, vol. 70, no. 7, Springer, 2015, pp. 1523–80, doi:10.1007/s00285-014-0802-y.","apa":"Uecker, H., Setter, D., & Hermisson, J. (2015). Adaptive gene introgression after secondary contact. Journal of Mathematical Biology. Springer. https://doi.org/10.1007/s00285-014-0802-y","ama":"Uecker H, Setter D, Hermisson J. Adaptive gene introgression after secondary contact. Journal of Mathematical Biology. 2015;70(7):1523-1580. doi:10.1007/s00285-014-0802-y","short":"H. Uecker, D. Setter, J. Hermisson, Journal of Mathematical Biology 70 (2015) 1523–1580.","ieee":"H. Uecker, D. Setter, and J. Hermisson, “Adaptive gene introgression after secondary contact,” Journal of Mathematical Biology, vol. 70, no. 7. Springer, pp. 1523–1580, 2015.","chicago":"Uecker, Hildegard, Derek Setter, and Joachim Hermisson. “Adaptive Gene Introgression after Secondary Contact.” Journal of Mathematical Biology. Springer, 2015. https://doi.org/10.1007/s00285-014-0802-y.","ista":"Uecker H, Setter D, Hermisson J. 2015. Adaptive gene introgression after secondary contact. Journal of Mathematical Biology. 70(7), 1523–1580."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"2DB8F68A-F248-11E8-B48F-1D18A9856A87","first_name":"Hildegard","last_name":"Uecker","orcid":"0000-0001-9435-2813","full_name":"Uecker, Hildegard"},{"last_name":"Setter","full_name":"Setter, Derek","first_name":"Derek"},{"first_name":"Joachim","last_name":"Hermisson","full_name":"Hermisson, Joachim"}],"publist_id":"5442","title":"Adaptive gene introgression after secondary contact","abstract":[{"lang":"eng","text":"By hybridization and backcrossing, alleles can surmount species boundaries and be incorporated into the genome of a related species. This introgression of genes is of particular evolutionary relevance if it involves the transfer of adaptations between populations. However, any beneficial allele will typically be associated with other alien alleles that are often deleterious and hamper the introgression process. In order to describe the introgression of an adaptive allele, we set up a stochastic model with an explicit genetic makeup of linked and unlinked deleterious alleles. Based on the theory of reducible multitype branching processes, we derive a recursive expression for the establishment probability of the beneficial allele after a single hybridization event. We furthermore study the probability that slightly deleterious alleles hitchhike to fixation. The key to the analysis is a split of the process into a stochastic phase in which the advantageous alleles establishes and a deterministic phase in which it sweeps to fixation. We thereafter apply the theory to a set of biologically relevant scenarios such as introgression in the presence of many unlinked or few closely linked deleterious alleles. A comparison to computer simulations shows that the approximations work well over a large parameter range."}],"oa_version":"Published Version","scopus_import":1,"intvolume":" 70","month":"06","publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_size":1321527,"date_updated":"2020-07-14T12:45:12Z","creator":"system","file_name":"IST-2016-458-v1+1_s00285-014-0802-y.pdf","date_created":"2018-12-12T10:14:27Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5079","checksum":"00e3a67bda05d4cc165b3a48b41ef9ad"}],"volume":70,"issue":"7","_id":"1699","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"458","status":"public","date_updated":"2023-02-23T10:10:36Z","ddc":["576"],"file_date_updated":"2020-07-14T12:45:12Z","department":[{"_id":"NiBa"}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Wysokiński, Marcin, et al. “Gutzwiller Wave Function Solution for Anderson Lattice Model: Emerging Universal Regimes of Heavy Quasiparticle States.” Physical Review B, vol. 92, no. 12, 125135, American Physical Society, 2015, doi:10.1103/PhysRevB.92.125135.","short":"M. Wysokiński, J. Kaczmarczyk, J. Spałek, Physical Review B 92 (2015).","ieee":"M. Wysokiński, J. Kaczmarczyk, and J. Spałek, “Gutzwiller wave function solution for Anderson lattice model: Emerging universal regimes of heavy quasiparticle states,” Physical Review B, vol. 92, no. 12. American Physical Society, 2015.","ama":"Wysokiński M, Kaczmarczyk J, Spałek J. Gutzwiller wave function solution for Anderson lattice model: Emerging universal regimes of heavy quasiparticle states. Physical Review B. 2015;92(12). doi:10.1103/PhysRevB.92.125135","apa":"Wysokiński, M., Kaczmarczyk, J., & Spałek, J. (2015). Gutzwiller wave function solution for Anderson lattice model: Emerging universal regimes of heavy quasiparticle states. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.92.125135","chicago":"Wysokiński, Marcin, Jan Kaczmarczyk, and Jozef Spałek. “Gutzwiller Wave Function Solution for Anderson Lattice Model: Emerging Universal Regimes of Heavy Quasiparticle States.” Physical Review B. American Physical Society, 2015. https://doi.org/10.1103/PhysRevB.92.125135.","ista":"Wysokiński M, Kaczmarczyk J, Spałek J. 2015. Gutzwiller wave function solution for Anderson lattice model: Emerging universal regimes of heavy quasiparticle states. Physical Review B. 92(12), 125135."},"title":"Gutzwiller wave function solution for Anderson lattice model: Emerging universal regimes of heavy quasiparticle states","publist_id":"5448","author":[{"first_name":"Marcin","full_name":"Wysokiński, Marcin","last_name":"Wysokiński"},{"last_name":"Kaczmarczyk","orcid":"0000-0002-1629-3675","full_name":"Kaczmarczyk, Jan","first_name":"Jan","id":"46C405DE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jozef","full_name":"Spałek, Jozef","last_name":"Spałek"}],"article_number":"125135","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"publication":"Physical Review B","day":"18","year":"2015","date_created":"2018-12-11T11:53:31Z","doi":"10.1103/PhysRevB.92.125135","date_published":"2015-09-18T00:00:00Z","acknowledgement":"The work was partly supported by the National Science Centre (NCN) under MAESTRO, Grant No. DEC-2012/04/A/ST3/00342. M.W. acknowledges the hospitality of the Institute of Science and Technology Austria during the final stage of development of the present work, as well as partial financial support from the Society-Environment-Technology project of the Jagiellonian University for that stay. J.K. acknowledges support from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA Grant Agreement No. [291734 ].","oa":1,"quality_controlled":"1","publisher":"American Physical Society","date_updated":"2021-01-12T06:52:35Z","department":[{"_id":"MiLe"}],"_id":"1696","status":"public","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"issue":"12","volume":92,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"The recently proposed diagrammatic expansion (DE) technique for the full Gutzwiller wave function (GWF) is applied to the Anderson lattice model. This approach allows for a systematic evaluation of the expectation values with full Gutzwiller wave function in finite-dimensional systems. It introduces results extending in an essential manner those obtained by means of the standard Gutzwiller approximation (GA), which is variationally exact only in infinite dimensions. Within the DE-GWF approach we discuss the principal paramagnetic properties and their relevance to heavy-fermion systems. We demonstrate the formation of an effective, narrow f band originating from atomic f-electron states and subsequently interpret this behavior as a direct itineracy of f electrons; it represents a combined effect of both the hybridization and the correlations induced by the Coulomb repulsive interaction. Such a feature is absent on the level of GA, which is equivalent to the zeroth order of our expansion. Formation of the hybridization- and electron-concentration-dependent narrow f band rationalizes the common assumption of such dispersion of f levels in the phenomenological modeling of the band structure of CeCoIn5. Moreover, it is shown that the emerging f-electron direct itineracy leads in a natural manner to three physically distinct regimes within a single model that are frequently discussed for 4f- or 5f-electron compounds as separate model situations. We identify these regimes as (i) the mixed-valence regime, (ii) Kondo/almost-Kondo insulating regime, and (iii) the Kondo-lattice limit when the f-electron occupancy is very close to the f-state half filling, ⟨nˆf⟩→1. The nonstandard features of the emerging correlated quantum liquid state are stressed."}],"intvolume":" 92","month":"09","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1505.07003"}],"scopus_import":1},{"date_published":"2015-09-15T00:00:00Z","doi":"10.1073/pnas.1514188112","date_created":"2018-12-11T11:53:33Z","page":"11508 - 11513","day":"15","publication":"PNAS","year":"2015","quality_controlled":"1","publisher":"National Academy of Sciences","oa":1,"acknowledgement":"Research was supported in part by National Science Foundation Grants PHY-1305525, PHY-1451171, and CCF-0939370, by National Institutes of Health Grant R01 EY14196, and by Austrian Science Foundation Grant FWF P25651. Additional support was provided by the\r\nFannie and John Hertz Foundation, by the Swartz Foundation, by the W. M. Keck Foundation, and by the Simons Foundation.","title":"Thermodynamics and signatures of criticality in a network of neurons","author":[{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","last_name":"Tkacik","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455"},{"last_name":"Mora","full_name":"Mora, Thierry","first_name":"Thierry"},{"last_name":"Marre","full_name":"Marre, Olivier","first_name":"Olivier"},{"last_name":"Amodei","full_name":"Amodei, Dario","first_name":"Dario"},{"full_name":"Palmer, Stephanie","last_name":"Palmer","first_name":"Stephanie"},{"last_name":"Berry Ii","full_name":"Berry Ii, Michael","first_name":"Michael"},{"first_name":"William","last_name":"Bialek","full_name":"Bialek, William"}],"publist_id":"5440","external_id":{"pmid":["26330611"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Tkačik, Gašper, Thierry Mora, Olivier Marre, Dario Amodei, Stephanie Palmer, Michael Berry Ii, and William Bialek. “Thermodynamics and Signatures of Criticality in a Network of Neurons.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1514188112.","ista":"Tkačik G, Mora T, Marre O, Amodei D, Palmer S, Berry Ii M, Bialek W. 2015. Thermodynamics and signatures of criticality in a network of neurons. PNAS. 112(37), 11508–11513.","mla":"Tkačik, Gašper, et al. “Thermodynamics and Signatures of Criticality in a Network of Neurons.” PNAS, vol. 112, no. 37, National Academy of Sciences, 2015, pp. 11508–13, doi:10.1073/pnas.1514188112.","apa":"Tkačik, G., Mora, T., Marre, O., Amodei, D., Palmer, S., Berry Ii, M., & Bialek, W. (2015). Thermodynamics and signatures of criticality in a network of neurons. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1514188112","ama":"Tkačik G, Mora T, Marre O, et al. Thermodynamics and signatures of criticality in a network of neurons. PNAS. 2015;112(37):11508-11513. doi:10.1073/pnas.1514188112","short":"G. Tkačik, T. Mora, O. Marre, D. Amodei, S. Palmer, M. Berry Ii, W. Bialek, PNAS 112 (2015) 11508–11513.","ieee":"G. Tkačik et al., “Thermodynamics and signatures of criticality in a network of neurons,” PNAS, vol. 112, no. 37. National Academy of Sciences, pp. 11508–11513, 2015."},"project":[{"grant_number":"P 25651-N26","name":"Sensitivity to higher-order statistics in natural scenes","call_identifier":"FWF","_id":"254D1A94-B435-11E9-9278-68D0E5697425"}],"volume":112,"issue":"37","language":[{"iso":"eng"}],"publication_status":"published","month":"09","intvolume":" 112","scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4577210/"}],"pmid":1,"oa_version":"Submitted Version","abstract":[{"text":"The activity of a neural network is defined by patterns of spiking and silence from the individual neurons. Because spikes are (relatively) sparse, patterns of activity with increasing numbers of spikes are less probable, but, with more spikes, the number of possible patterns increases. This tradeoff between probability and numerosity is mathematically equivalent to the relationship between entropy and energy in statistical physics. We construct this relationship for populations of up to N = 160 neurons in a small patch of the vertebrate retina, using a combination of direct and model-based analyses of experiments on the response of this network to naturalistic movies. We see signs of a thermodynamic limit, where the entropy per neuron approaches a smooth function of the energy per neuron as N increases. The form of this function corresponds to the distribution of activity being poised near an unusual kind of critical point. We suggest further tests of criticality, and give a brief discussion of its functional significance. ","lang":"eng"}],"department":[{"_id":"GaTk"}],"date_updated":"2021-01-12T06:52:37Z","status":"public","type":"journal_article","_id":"1701"},{"scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1209.3234"}],"month":"04","intvolume":" 241","abstract":[{"lang":"eng","text":"In mean-payoff games, the objective of the protagonist is to ensure that the limit average of an infinite sequence of numeric weights is nonnegative. In energy games, the objective is to ensure that the running sum of weights is always nonnegative. Multi-mean-payoff and multi-energy games replace individual weights by tuples, and the limit average (resp., running sum) of each coordinate must be (resp., remain) nonnegative. We prove finite-memory determinacy of multi-energy games and show inter-reducibility of multi-mean-payoff and multi-energy games for finite-memory strategies. We improve the computational complexity for solving both classes with finite-memory strategies: we prove coNP-completeness improving the previous known EXPSPACE bound. For memoryless strategies, we show that deciding the existence of a winning strategy for the protagonist is NP-complete. We present the first solution of multi-mean-payoff games with infinite-memory strategies: we show that mean-payoff-sup objectives can be decided in NP∩coNP, whereas mean-payoff-inf objectives are coNP-complete."}],"oa_version":"Preprint","issue":"4","volume":241,"ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","status":"public","_id":"1698","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"date_updated":"2021-01-12T06:52:36Z","quality_controlled":"1","publisher":"Elsevier","oa":1,"acknowledgement":"The research was partly supported by Austrian Science Fund (FWF) Grant No P23499-N23, FWF NFN Grant No S11407-N23 and S11402-N23 (RiSE), ERC Start grant (279307: Graph Games), Microsoft faculty fellows award, the ERC Advanced Grant QUAREM (267989: Quantitative Reactive Modeling), European project Cassting (FP7-601148), ERC Start grant (279499: inVEST).","page":"177 - 196","doi":"10.1016/j.ic.2015.03.001","date_published":"2015-04-01T00:00:00Z","date_created":"2018-12-11T11:53:32Z","year":"2015","day":"01","publication":"Information and Computation","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","grant_number":"S11407"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"},{"grant_number":"267989","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"author":[{"first_name":"Yaron","full_name":"Velner, Yaron","last_name":"Velner"},{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Laurent","last_name":"Doyen","full_name":"Doyen, Laurent"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"first_name":"Alexander","full_name":"Rabinovich, Alexander","last_name":"Rabinovich"},{"last_name":"Raskin","full_name":"Raskin, Jean","first_name":"Jean"}],"publist_id":"5443","title":"The complexity of multi-mean-payoff and multi-energy games","citation":{"short":"Y. Velner, K. Chatterjee, L. Doyen, T.A. Henzinger, A. Rabinovich, J. Raskin, Information and Computation 241 (2015) 177–196.","ieee":"Y. Velner, K. Chatterjee, L. Doyen, T. A. Henzinger, A. Rabinovich, and J. Raskin, “The complexity of multi-mean-payoff and multi-energy games,” Information and Computation, vol. 241, no. 4. Elsevier, pp. 177–196, 2015.","apa":"Velner, Y., Chatterjee, K., Doyen, L., Henzinger, T. A., Rabinovich, A., & Raskin, J. (2015). The complexity of multi-mean-payoff and multi-energy games. Information and Computation. Elsevier. https://doi.org/10.1016/j.ic.2015.03.001","ama":"Velner Y, Chatterjee K, Doyen L, Henzinger TA, Rabinovich A, Raskin J. The complexity of multi-mean-payoff and multi-energy games. Information and Computation. 2015;241(4):177-196. doi:10.1016/j.ic.2015.03.001","mla":"Velner, Yaron, et al. “The Complexity of Multi-Mean-Payoff and Multi-Energy Games.” Information and Computation, vol. 241, no. 4, Elsevier, 2015, pp. 177–96, doi:10.1016/j.ic.2015.03.001.","ista":"Velner Y, Chatterjee K, Doyen L, Henzinger TA, Rabinovich A, Raskin J. 2015. The complexity of multi-mean-payoff and multi-energy games. Information and Computation. 241(4), 177–196.","chicago":"Velner, Yaron, Krishnendu Chatterjee, Laurent Doyen, Thomas A Henzinger, Alexander Rabinovich, and Jean Raskin. “The Complexity of Multi-Mean-Payoff and Multi-Energy Games.” Information and Computation. Elsevier, 2015. https://doi.org/10.1016/j.ic.2015.03.001."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"citation":{"ista":"Van Loon E, Katsnelson M, Lemeshko M. 2015. Ultralong-range order in the Fermi-Hubbard model with long-range interactions. Physical Review B. 92(8), 081106.","chicago":"Van Loon, Erik, Mikhail Katsnelson, and Mikhail Lemeshko. “Ultralong-Range Order in the Fermi-Hubbard Model with Long-Range Interactions.” Physical Review B. American Physical Society, 2015. https://doi.org/10.1103/PhysRevB.92.081106.","short":"E. Van Loon, M. Katsnelson, M. Lemeshko, Physical Review B 92 (2015).","ieee":"E. Van Loon, M. Katsnelson, and M. Lemeshko, “Ultralong-range order in the Fermi-Hubbard model with long-range interactions,” Physical Review B, vol. 92, no. 8. American Physical Society, 2015.","apa":"Van Loon, E., Katsnelson, M., & Lemeshko, M. (2015). Ultralong-range order in the Fermi-Hubbard model with long-range interactions. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.92.081106","ama":"Van Loon E, Katsnelson M, Lemeshko M. Ultralong-range order in the Fermi-Hubbard model with long-range interactions. Physical Review B. 2015;92(8). doi:10.1103/PhysRevB.92.081106","mla":"Van Loon, Erik, et al. “Ultralong-Range Order in the Fermi-Hubbard Model with Long-Range Interactions.” Physical Review B, vol. 92, no. 8, 081106, American Physical Society, 2015, doi:10.1103/PhysRevB.92.081106."},"date_updated":"2021-01-12T06:52:37Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"5441","author":[{"last_name":"Van Loon","full_name":"Van Loon, Erik","first_name":"Erik"},{"first_name":"Mikhail","last_name":"Katsnelson","full_name":"Katsnelson, Mikhail"},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","last_name":"Lemeshko"}],"department":[{"_id":"MiLe"}],"title":"Ultralong-range order in the Fermi-Hubbard model with long-range interactions","_id":"1700","article_number":"081106","type":"journal_article","status":"public","publication_status":"published","year":"2015","day":"10","publication":"Physical Review B","language":[{"iso":"eng"}],"issue":"8","doi":"10.1103/PhysRevB.92.081106","date_published":"2015-08-10T00:00:00Z","volume":92,"date_created":"2018-12-11T11:53:32Z","abstract":[{"text":"We use the dual boson approach to reveal the phase diagram of the Fermi-Hubbard model with long-range dipole-dipole interactions. By using a large-scale finite-temperature calculation on a 64×64 square lattice we demonstrate the existence of a novel phase, possessing an "ultralong-range" order. The fingerprint of this phase - the density correlation function - features a nontrivial behavior on a scale of tens of lattice sites. We study the properties and the stability of the ultralong-range-ordered phase, and show that it is accessible in modern experiments with ultracold polar molecules and magnetic atoms.","lang":"eng"}],"oa_version":"Preprint","acknowledgement":"The work is supported by European Research Council (ERC) Advanced Grant No. 338957 FEMTO/NANO.","publisher":"American Physical Society","scopus_import":1,"oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1506.06007","open_access":"1"}],"month":"08","intvolume":" 92"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Deuchert A, Hainzl C, Seiringer R. 2015. Note on a family of monotone quantum relative entropies. Letters in Mathematical Physics. 105(10), 1449–1466.","chicago":"Deuchert, Andreas, Christian Hainzl, and Robert Seiringer. “Note on a Family of Monotone Quantum Relative Entropies.” Letters in Mathematical Physics. Springer, 2015. https://doi.org/10.1007/s11005-015-0787-5.","ieee":"A. Deuchert, C. Hainzl, and R. Seiringer, “Note on a family of monotone quantum relative entropies,” Letters in Mathematical Physics, vol. 105, no. 10. Springer, pp. 1449–1466, 2015.","short":"A. Deuchert, C. Hainzl, R. Seiringer, Letters in Mathematical Physics 105 (2015) 1449–1466.","apa":"Deuchert, A., Hainzl, C., & Seiringer, R. (2015). Note on a family of monotone quantum relative entropies. Letters in Mathematical Physics. Springer. https://doi.org/10.1007/s11005-015-0787-5","ama":"Deuchert A, Hainzl C, Seiringer R. Note on a family of monotone quantum relative entropies. Letters in Mathematical Physics. 2015;105(10):1449-1466. doi:10.1007/s11005-015-0787-5","mla":"Deuchert, Andreas, et al. “Note on a Family of Monotone Quantum Relative Entropies.” Letters in Mathematical Physics, vol. 105, no. 10, Springer, 2015, pp. 1449–66, doi:10.1007/s11005-015-0787-5."},"title":"Note on a family of monotone quantum relative entropies","author":[{"first_name":"Andreas","last_name":"Deuchert","full_name":"Deuchert, Andreas","orcid":"0000-0003-3146-6746"},{"first_name":"Christian","last_name":"Hainzl","full_name":"Hainzl, Christian"},{"last_name":"Seiringer","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5432","oa":1,"quality_controlled":"1","publisher":"Springer","publication":"Letters in Mathematical Physics","day":"05","year":"2015","has_accepted_license":"1","date_created":"2018-12-11T11:53:34Z","date_published":"2015-08-05T00:00:00Z","doi":"10.1007/s11005-015-0787-5","page":"1449 - 1466","_id":"1704","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"type":"journal_article","ddc":["510"],"date_updated":"2021-01-12T06:52:38Z","department":[{"_id":"RoSe"}],"file_date_updated":"2020-07-14T12:45:13Z","oa_version":"Preprint","abstract":[{"lang":"eng","text":"Given a convex function (Formula presented.) and two hermitian matrices A and B, Lewin and Sabin study in (Lett Math Phys 104:691–705, 2014) the relative entropy defined by (Formula presented.). Among other things, they prove that the so-defined quantity is monotone if and only if (Formula presented.) is operator monotone. The monotonicity is then used to properly define (Formula presented.) for bounded self-adjoint operators acting on an infinite-dimensional Hilbert space by a limiting procedure. More precisely, for an increasing sequence of finite-dimensional projections (Formula presented.) with (Formula presented.) strongly, the limit (Formula presented.) is shown to exist and to be independent of the sequence of projections (Formula presented.). The question whether this sequence converges to its "obvious" limit, namely (Formula presented.), has been left open. We answer this question in principle affirmatively and show that (Formula presented.). If the operators A and B are regular enough, that is (A − B), (Formula presented.) and (Formula presented.) are trace-class, the identity (Formula presented.) holds."}],"intvolume":" 105","month":"08","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1502.07205"}],"scopus_import":1,"language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"5836","checksum":"fd7307282a314cc1fbbaef77b187516b","creator":"dernst","file_size":484967,"date_updated":"2020-07-14T12:45:13Z","file_name":"2015_LettersMathPhys_Deuchert.pdf","date_created":"2019-01-15T14:42:07Z"}],"publication_status":"published","license":"https://creativecommons.org/licenses/by-nc/4.0/","volume":105,"issue":"10"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:52:38Z","citation":{"ieee":"L. Broadhurst, G. Fifield, B. Vanzella, and M. Pickup, “An evaluation of the genetic structure of seed sources and the maintenance of genetic diversity during establishment of two yellow box (Eucalyptus melliodora) seed-production areas,” Australian Journal of Botany, vol. 63, no. 5. CSIRO, pp. 455–466, 2015.","short":"L. Broadhurst, G. Fifield, B. Vanzella, M. Pickup, Australian Journal of Botany 63 (2015) 455–466.","apa":"Broadhurst, L., Fifield, G., Vanzella, B., & Pickup, M. (2015). An evaluation of the genetic structure of seed sources and the maintenance of genetic diversity during establishment of two yellow box (Eucalyptus melliodora) seed-production areas. Australian Journal of Botany. CSIRO. https://doi.org/10.1071/BT15023","ama":"Broadhurst L, Fifield G, Vanzella B, Pickup M. An evaluation of the genetic structure of seed sources and the maintenance of genetic diversity during establishment of two yellow box (Eucalyptus melliodora) seed-production areas. Australian Journal of Botany. 2015;63(5):455-466. doi:10.1071/BT15023","mla":"Broadhurst, Linda, et al. “An Evaluation of the Genetic Structure of Seed Sources and the Maintenance of Genetic Diversity during Establishment of Two Yellow Box (Eucalyptus Melliodora) Seed-Production Areas.” Australian Journal of Botany, vol. 63, no. 5, CSIRO, 2015, pp. 455–66, doi:10.1071/BT15023.","ista":"Broadhurst L, Fifield G, Vanzella B, Pickup M. 2015. An evaluation of the genetic structure of seed sources and the maintenance of genetic diversity during establishment of two yellow box (Eucalyptus melliodora) seed-production areas. Australian Journal of Botany. 63(5), 455–466.","chicago":"Broadhurst, Linda, Graham Fifield, Bindi Vanzella, and Melinda Pickup. “An Evaluation of the Genetic Structure of Seed Sources and the Maintenance of Genetic Diversity during Establishment of Two Yellow Box (Eucalyptus Melliodora) Seed-Production Areas.” Australian Journal of Botany. CSIRO, 2015. https://doi.org/10.1071/BT15023."},"department":[{"_id":"NiBa"}],"title":"An evaluation of the genetic structure of seed sources and the maintenance of genetic diversity during establishment of two yellow box (Eucalyptus melliodora) seed-production areas","author":[{"last_name":"Broadhurst","full_name":"Broadhurst, Linda","first_name":"Linda"},{"last_name":"Fifield","full_name":"Fifield, Graham","first_name":"Graham"},{"full_name":"Vanzella, Bindi","last_name":"Vanzella","first_name":"Bindi"},{"first_name":"Melinda","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","last_name":"Pickup","orcid":"0000-0001-6118-0541","full_name":"Pickup, Melinda"}],"publist_id":"5434","_id":"1703","status":"public","type":"journal_article","language":[{"iso":"eng"}],"publication":"Australian Journal of Botany","day":"26","year":"2015","publication_status":"published","date_created":"2018-12-11T11:53:34Z","doi":"10.1071/BT15023","issue":"5","volume":63,"date_published":"2015-05-26T00:00:00Z","page":"455 - 466","oa_version":"None","abstract":[{"text":"Vegetation clearing and land-use change have depleted many natural plant communities to the point where restoration is required. A major impediment to the success of rebuilding complex vegetation communities is having regular access to sufficient quantities of high-quality seed. Seed-production areas (SPAs) can help generate this seed, but these must be underpinned by a broad genetic base to maximise the evolutionary potential of restored populations. However, genetic bottlenecks can occur at the collection, establishment and production stages in SPAs, requiring genetic evaluation. This is especially relevant for species that may take many years before a return on SPA investment is realised. Two recently established yellow box (Eucalyptus melliodora A.Cunn. ex Schauer, Myrtaceae) SPAs were evaluated to determine whether genetic bottlenecks had occurred between seed collection and SPA establishment. No evidence was found to suggest that a significant loss of genetic diversity had occurred at this stage, although there was a significant difference in diversity between the two SPAs. Complex population genetic structure was also observed in the seed used to source the SPAs, with up to eight groups identified. Plant survival in the SPAs was influenced by seed collection location but not by SPA location and was not associated with genetic diversity. There were also no associations between genetic diversity and plant growth. These data highlighted the importance of chance events when establishing SPAs and indicated that the two yellow box SPAs are likely to provide genetically diverse seed sources for future restoration projects, especially by pooling seed from both SPAs.","lang":"eng"}],"intvolume":" 63","month":"05","quality_controlled":"1","publisher":"CSIRO","scopus_import":1},{"title":"Multi-task and lifelong learning of kernels","author":[{"full_name":"Pentina, Anastasia","last_name":"Pentina","id":"42E87FC6-F248-11E8-B48F-1D18A9856A87","first_name":"Anastasia"},{"full_name":"Ben David, Shai","last_name":"Ben David","first_name":"Shai"}],"publist_id":"5430","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Pentina, Anastasia, and Shai Ben David. “Multi-Task and Lifelong Learning of Kernels,” 9355:194–208. Springer, 2015. https://doi.org/10.1007/978-3-319-24486-0_13.","ista":"Pentina A, Ben David S. 2015. Multi-task and lifelong learning of kernels. ALT: Algorithmic Learning Theory, LNCS, vol. 9355, 194–208.","mla":"Pentina, Anastasia, and Shai Ben David. Multi-Task and Lifelong Learning of Kernels. Vol. 9355, Springer, 2015, pp. 194–208, doi:10.1007/978-3-319-24486-0_13.","short":"A. Pentina, S. Ben David, in:, Springer, 2015, pp. 194–208.","ieee":"A. Pentina and S. Ben David, “Multi-task and lifelong learning of kernels,” presented at the ALT: Algorithmic Learning Theory, Banff, AB, Canada, 2015, vol. 9355, pp. 194–208.","ama":"Pentina A, Ben David S. Multi-task and lifelong learning of kernels. In: Vol 9355. Springer; 2015:194-208. doi:10.1007/978-3-319-24486-0_13","apa":"Pentina, A., & Ben David, S. (2015). Multi-task and lifelong learning of kernels (Vol. 9355, pp. 194–208). Presented at the ALT: Algorithmic Learning Theory, Banff, AB, Canada: Springer. https://doi.org/10.1007/978-3-319-24486-0_13"},"project":[{"grant_number":"308036","name":"Lifelong Learning of Visual Scene Understanding","_id":"2532554C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"date_created":"2018-12-11T11:53:35Z","date_published":"2015-01-01T00:00:00Z","doi":"10.1007/978-3-319-24486-0_13","page":"194 - 208","day":"01","year":"2015","oa":1,"publisher":"Springer","quality_controlled":"1","department":[{"_id":"ChLa"}],"date_updated":"2021-01-12T06:52:39Z","status":"public","conference":{"name":"ALT: Algorithmic Learning Theory","start_date":"2015-10-04","location":"Banff, AB, Canada","end_date":"2015-10-06"},"type":"conference","_id":"1706","ec_funded":1,"volume":9355,"language":[{"iso":"eng"}],"publication_status":"published","intvolume":" 9355","month":"01","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1602.06531"}],"scopus_import":1,"alternative_title":["LNCS"],"oa_version":"Preprint","abstract":[{"text":"We consider a problem of learning kernels for use in SVM classification in the multi-task and lifelong scenarios and provide generalization bounds on the error of a large margin classifier. Our results show that, under mild conditions on the family of kernels used for learning, solving several related tasks simultaneously is beneficial over single task learning. In particular, as the number of observed tasks grows, assuming that in the considered family of kernels there exists one that yields low approximation error on all tasks, the overhead associated with learning such a kernel vanishes and the complexity converges to that of learning when this good kernel is given to the learner.","lang":"eng"}]},{"project":[{"call_identifier":"FP7","_id":"2536F660-B435-11E9-9278-68D0E5697425","name":"Investigating the role of transporters in invasive migration through junctions","grant_number":"334077"}],"citation":{"chicago":"Ratheesh, Aparna, Vera Belyaeva, and Daria E Siekhaus. “Drosophila Immune Cell Migration and Adhesion during Embryonic Development and Larval Immune Responses.” Current Opinion in Cell Biology. Elsevier, 2015. https://doi.org/10.1016/j.ceb.2015.07.003.","ista":"Ratheesh A, Belyaeva V, Siekhaus DE. 2015. Drosophila immune cell migration and adhesion during embryonic development and larval immune responses. Current Opinion in Cell Biology. 36(10), 71–79.","mla":"Ratheesh, Aparna, et al. “Drosophila Immune Cell Migration and Adhesion during Embryonic Development and Larval Immune Responses.” Current Opinion in Cell Biology, vol. 36, no. 10, Elsevier, 2015, pp. 71–79, doi:10.1016/j.ceb.2015.07.003.","apa":"Ratheesh, A., Belyaeva, V., & Siekhaus, D. E. (2015). Drosophila immune cell migration and adhesion during embryonic development and larval immune responses. Current Opinion in Cell Biology. Elsevier. https://doi.org/10.1016/j.ceb.2015.07.003","ama":"Ratheesh A, Belyaeva V, Siekhaus DE. Drosophila immune cell migration and adhesion during embryonic development and larval immune responses. Current Opinion in Cell Biology. 2015;36(10):71-79. doi:10.1016/j.ceb.2015.07.003","short":"A. Ratheesh, V. Belyaeva, D.E. Siekhaus, Current Opinion in Cell Biology 36 (2015) 71–79.","ieee":"A. Ratheesh, V. Belyaeva, and D. E. Siekhaus, “Drosophila immune cell migration and adhesion during embryonic development and larval immune responses,” Current Opinion in Cell Biology, vol. 36, no. 10. Elsevier, pp. 71–79, 2015."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"5421","author":[{"last_name":"Ratheesh","full_name":"Ratheesh, Aparna","id":"2F064CFE-F248-11E8-B48F-1D18A9856A87","first_name":"Aparna"},{"id":"47F080FE-F248-11E8-B48F-1D18A9856A87","first_name":"Vera","full_name":"Belyaeva, Vera","last_name":"Belyaeva"},{"last_name":"Siekhaus","orcid":"0000-0001-8323-8353","full_name":"Siekhaus, Daria E","first_name":"Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87"}],"title":"Drosophila immune cell migration and adhesion during embryonic development and larval immune responses","publisher":"Elsevier","quality_controlled":"1","oa":1,"has_accepted_license":"1","year":"2015","day":"01","publication":"Current Opinion in Cell Biology","page":"71 - 79","doi":"10.1016/j.ceb.2015.07.003","date_published":"2015-10-01T00:00:00Z","date_created":"2018-12-11T11:53:36Z","_id":"1712","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","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","image":"/images/cc_by_nc_nd.png"},"status":"public","pubrep_id":"346","date_updated":"2021-01-12T06:52:41Z","ddc":["573"],"department":[{"_id":"DaSi"}],"file_date_updated":"2020-07-14T12:45:13Z","abstract":[{"lang":"eng","text":"The majority of immune cells in Drosophila melanogaster are plasmatocytes; they carry out similar functions to vertebrate macrophages, influencing development as well as protecting against infection and cancer. Plasmatocytes, sometimes referred to with the broader term of hemocytes, migrate widely during embryonic development and cycle in the larvae between sessile and circulating positions. Here we discuss the similarities of plasmatocyte developmental migration and its functions to that of vertebrate macrophages, considering the recent controversy regarding the functions of Drosophila PDGF/VEGF related ligands. We also examine recent findings on the significance of adhesion for plasmatocyte migration in the embryo, as well as proliferation, trans-differentiation, and tumor responses in the larva. We spotlight parallels throughout to vertebrate immune responses."}],"oa_version":"Published Version","scopus_import":1,"month":"10","intvolume":" 36","publication_status":"published","file":[{"checksum":"bbb1ee39ca52929aefe4f48752b166ee","file_id":"5098","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:14:44Z","file_name":"IST-2015-346-v1+1_Current_Opinion_Review_Ratheesh_et_al_2015.pdf","date_updated":"2020-07-14T12:45:13Z","file_size":1023680,"creator":"system"}],"language":[{"iso":"eng"}],"volume":36,"issue":"10","ec_funded":1},{"title":"Minimal resistance of curves under the single impact assumption","publist_id":"5423","author":[{"last_name":"Akopyan","orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","first_name":"Arseniy"},{"last_name":"Plakhov","full_name":"Plakhov, Alexander","first_name":"Alexander"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"A. Akopyan, A. Plakhov, Society for Industrial and Applied Mathematics 47 (2015) 2754–2769.","ieee":"A. Akopyan and A. Plakhov, “Minimal resistance of curves under the single impact assumption,” Society for Industrial and Applied Mathematics, vol. 47, no. 4. SIAM, pp. 2754–2769, 2015.","apa":"Akopyan, A., & Plakhov, A. (2015). Minimal resistance of curves under the single impact assumption. Society for Industrial and Applied Mathematics. SIAM. https://doi.org/10.1137/140993843","ama":"Akopyan A, Plakhov A. Minimal resistance of curves under the single impact assumption. Society for Industrial and Applied Mathematics. 2015;47(4):2754-2769. doi:10.1137/140993843","mla":"Akopyan, Arseniy, and Alexander Plakhov. “Minimal Resistance of Curves under the Single Impact Assumption.” Society for Industrial and Applied Mathematics, vol. 47, no. 4, SIAM, 2015, pp. 2754–69, doi:10.1137/140993843.","ista":"Akopyan A, Plakhov A. 2015. Minimal resistance of curves under the single impact assumption. Society for Industrial and Applied Mathematics. 47(4), 2754–2769.","chicago":"Akopyan, Arseniy, and Alexander Plakhov. “Minimal Resistance of Curves under the Single Impact Assumption.” Society for Industrial and Applied Mathematics. SIAM, 2015. https://doi.org/10.1137/140993843."},"project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"date_published":"2015-07-14T00:00:00Z","doi":"10.1137/140993843","date_created":"2018-12-11T11:53:36Z","page":"2754 - 2769","day":"14","publication":"Society for Industrial and Applied Mathematics","year":"2015","quality_controlled":"1","publisher":"SIAM","oa":1,"department":[{"_id":"HeEd"}],"date_updated":"2021-01-12T06:52:41Z","status":"public","type":"journal_article","_id":"1710","issue":"4","volume":47,"ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published","month":"07","intvolume":" 47","scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1410.3736"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We consider the hollow on the half-plane {(x, y) : y ≤ 0} ⊂ ℝ2 defined by a function u : (-1, 1) → ℝ, u(x) < 0, and a vertical flow of point particles incident on the hollow. It is assumed that u satisfies the so-called single impact condition (SIC): each incident particle is elastically reflected by graph(u) and goes away without hitting the graph of u anymore. We solve the problem: find the function u minimizing the force of resistance created by the flow. We show that the graph of the minimizer is formed by two arcs of parabolas symmetric to each other with respect to the y-axis. Assuming that the resistance of u ≡ 0 equals 1, we show that the minimal resistance equals π/2 - 2arctan(1/2) ≈ 0.6435. This result completes the previously obtained result [SIAM J. Math. Anal., 46 (2014), pp. 2730-2742] stating in particular that the minimal resistance of a hollow in higher dimensions equals 0.5. We additionally consider a similar problem of minimal resistance, where the hollow in the half-space {(x1,...,xd,y) : y ≤ 0} ⊂ ℝd+1 is defined by a radial function U satisfying the SIC, U(x) = u(|x|), with x = (x1,...,xd), u(ξ) < 0 for 0 ≤ ξ < 1, and u(ξ) = 0 for ξ ≥ 1, and the flow is parallel to the y-axis. The minimal resistance is greater than 0.5 (and coincides with 0.6435 when d = 1) and converges to 0.5 as d → ∞."}]},{"main_file_link":[{"url":"http://arxiv.org/abs/1408.4036","open_access":"1"}],"oa":1,"quality_controlled":"1","scopus_import":1,"publisher":"Springer","intvolume":" 53","month":"04","abstract":[{"text":"How much cutting is needed to simplify the topology of a surface? We provide bounds for several instances of this question, for the minimum length of topologically non-trivial closed curves, pants decompositions, and cut graphs with a given combinatorial map in triangulated combinatorial surfaces (or their dual cross-metric counterpart). Our work builds upon Riemannian systolic inequalities, which bound the minimum length of non-trivial closed curves in terms of the genus and the area of the surface. We first describe a systematic way to translate Riemannian systolic inequalities to a discrete setting, and vice-versa. This implies a conjecture by Przytycka and Przytycki (Graph structure theory. Contemporary Mathematics, vol. 147, 1993), a number of new systolic inequalities in the discrete setting, and the fact that a theorem of Hutchinson on the edge-width of triangulated surfaces and Gromov’s systolic inequality for surfaces are essentially equivalent. We also discuss how these proofs generalize to higher dimensions. Then we focus on topological decompositions of surfaces. Relying on ideas of Buser, we prove the existence of pants decompositions of length O(g^(3/2)n^(1/2)) for any triangulated combinatorial surface of genus g with n triangles, and describe an O(gn)-time algorithm to compute such a decomposition. Finally, we consider the problem of embedding a cut graph (or more generally a cellular graph) with a given combinatorial map on a given surface. Using random triangulations, we prove (essentially) that, for any choice of a combinatorial map, there are some surfaces on which any cellular embedding with that combinatorial map has length superlinear in the number of triangles of the triangulated combinatorial surface. There is also a similar result for graphs embedded on polyhedral triangulations.","lang":"eng"}],"oa_version":"Preprint","page":"587 - 620","date_created":"2018-12-11T11:53:42Z","issue":"3","doi":"10.1007/s00454-015-9679-9","date_published":"2015-04-02T00:00:00Z","volume":53,"year":"2015","publication_status":"published","language":[{"iso":"eng"}],"publication":"Discrete & Computational Geometry","day":"02","type":"journal_article","status":"public","_id":"1730","author":[{"first_name":"Éric","last_name":"Colin De Verdière","full_name":"Colin De Verdière, Éric"},{"first_name":"Alfredo","full_name":"Hubard, Alfredo","last_name":"Hubard"},{"first_name":"Arnaud N","id":"3DB2F25C-F248-11E8-B48F-1D18A9856A87","last_name":"De Mesmay","full_name":"De Mesmay, Arnaud N"}],"publist_id":"5397","department":[{"_id":"UlWa"}],"title":"Discrete systolic inequalities and decompositions of triangulated surfaces","date_updated":"2021-01-12T06:52:49Z","citation":{"ista":"Colin De Verdière É, Hubard A, de Mesmay AN. 2015. Discrete systolic inequalities and decompositions of triangulated surfaces. Discrete & Computational Geometry. 53(3), 587–620.","chicago":"Colin De Verdière, Éric, Alfredo Hubard, and Arnaud N de Mesmay. “Discrete Systolic Inequalities and Decompositions of Triangulated Surfaces.” Discrete & Computational Geometry. Springer, 2015. https://doi.org/10.1007/s00454-015-9679-9.","ama":"Colin De Verdière É, Hubard A, de Mesmay AN. Discrete systolic inequalities and decompositions of triangulated surfaces. Discrete & Computational Geometry. 2015;53(3):587-620. doi:10.1007/s00454-015-9679-9","apa":"Colin De Verdière, É., Hubard, A., & de Mesmay, A. N. (2015). Discrete systolic inequalities and decompositions of triangulated surfaces. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-015-9679-9","short":"É. Colin De Verdière, A. Hubard, A.N. de Mesmay, Discrete & Computational Geometry 53 (2015) 587–620.","ieee":"É. Colin De Verdière, A. Hubard, and A. N. de Mesmay, “Discrete systolic inequalities and decompositions of triangulated surfaces,” Discrete & Computational Geometry, vol. 53, no. 3. Springer, pp. 587–620, 2015.","mla":"Colin De Verdière, Éric, et al. “Discrete Systolic Inequalities and Decompositions of Triangulated Surfaces.” Discrete & Computational Geometry, vol. 53, no. 3, Springer, 2015, pp. 587–620, doi:10.1007/s00454-015-9679-9."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"date_created":"2018-12-11T11:53:42Z","doi":"10.1038/ncomms7709","date_published":"2015-04-02T00:00:00Z","volume":6,"publication":"Nature Communications","day":"02","publication_status":"published","year":"2015","intvolume":" 6","month":"04","quality_controlled":0,"publisher":"Nature Publishing Group","acknowledgement":"C.P.B. gratefully acknowledges funding from the Wellcome Trust through a Research Career Development Fellowship (097319/Z/11/Z). This work was supported by the Medical Research Council (U117560541) and Wellcome Trust (WT098326MA, WT098325MA).","abstract":[{"text":"In the vertebrate neural tube, the morphogen Sonic Hedgehog (Shh) establishes a characteristic pattern of gene expression. Here we quantify the Shh gradient in the developing mouse neural tube and show that while the amplitude of the gradient increases over time, the activity of the pathway transcriptional effectors, Gli proteins, initially increases but later decreases. Computational analysis of the pathway suggests three mechanisms that could contribute to this adaptation: transcriptional upregulation of the inhibitory receptor Ptch1, transcriptional downregulation of Gli and the differential stability of active and inactive Gli isoforms. Consistent with this, Gli2 protein expression is downregulated during neural tube patterning and adaptation continues when the pathway is stimulated downstream of Ptch1. Moreover, the Shh-induced upregulation of Gli2 transcription prevents Gli activity levels from adapting in a different cell type, NIH3T3 fibroblasts, despite the upregulation of Ptch1. Multiple mechanisms therefore contribute to the intracellular dynamics of Shh signalling, resulting in different signalling dynamics in different cell types.","lang":"eng"}],"title":"Ptch1 and Gli regulate Shh signalling dynamics via multiple mechanisms","publist_id":"5399","author":[{"first_name":"Michael","full_name":"Cohen, Michael H","last_name":"Cohen"},{"full_name":"Anna Kicheva","orcid":"0000-0003-4509-4998","last_name":"Kicheva","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","first_name":"Anna"},{"first_name":"Ana","last_name":"Ribeiro","full_name":"Ribeiro, Ana C"},{"full_name":"Blassberg, Robert A","last_name":"Blassberg","first_name":"Robert"},{"full_name":"Page, Karen M","last_name":"Page","first_name":"Karen"},{"first_name":"Chris","last_name":"Barnes","full_name":"Barnes, Chris P"},{"last_name":"Briscoe","full_name":"Briscoe, James","first_name":"James"}],"extern":1,"date_updated":"2021-01-12T06:52:48Z","citation":{"mla":"Cohen, Michael, et al. “Ptch1 and Gli Regulate Shh Signalling Dynamics via Multiple Mechanisms.” Nature Communications, vol. 6, Nature Publishing Group, 2015, doi:10.1038/ncomms7709.","ama":"Cohen M, Kicheva A, Ribeiro A, et al. Ptch1 and Gli regulate Shh signalling dynamics via multiple mechanisms. Nature Communications. 2015;6. doi:10.1038/ncomms7709","apa":"Cohen, M., Kicheva, A., Ribeiro, A., Blassberg, R., Page, K., Barnes, C., & Briscoe, J. (2015). Ptch1 and Gli regulate Shh signalling dynamics via multiple mechanisms. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms7709","short":"M. Cohen, A. Kicheva, A. Ribeiro, R. Blassberg, K. Page, C. Barnes, J. Briscoe, Nature Communications 6 (2015).","ieee":"M. Cohen et al., “Ptch1 and Gli regulate Shh signalling dynamics via multiple mechanisms,” Nature Communications, vol. 6. Nature Publishing Group, 2015.","chicago":"Cohen, Michael, Anna Kicheva, Ana Ribeiro, Robert Blassberg, Karen Page, Chris Barnes, and James Briscoe. “Ptch1 and Gli Regulate Shh Signalling Dynamics via Multiple Mechanisms.” Nature Communications. Nature Publishing Group, 2015. https://doi.org/10.1038/ncomms7709.","ista":"Cohen M, Kicheva A, Ribeiro A, Blassberg R, Page K, Barnes C, Briscoe J. 2015. Ptch1 and Gli regulate Shh signalling dynamics via multiple mechanisms. Nature Communications. 6."},"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"1728"},{"ddc":["000"],"date_updated":"2023-02-23T10:12:11Z","file_date_updated":"2020-07-14T12:45:15Z","department":[{"_id":"ChWo"}],"_id":"1735","pubrep_id":"607","status":"public","type":"journal_article","language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"590752bf977855b337a80f78a9bc2404","file_id":"5218","creator":"system","file_size":6312352,"date_updated":"2020-07-14T12:45:15Z","file_name":"IST-2016-607-v1+1_coarsegrid.pdf","date_created":"2018-12-12T10:16:30Z"}],"publication_status":"published","volume":34,"issue":"2","oa_version":"Submitted Version","abstract":[{"text":"This work presents a method for efficiently simplifying the pressure projection step in a liquid simulation. We first devise a straightforward dimension reduction technique that dramatically reduces the cost of solving the pressure projection. Next, we introduce a novel change of basis that satisfies free-surface boundary conditions exactly, regardless of the accuracy of the pressure solve. When combined, these ideas greatly reduce the computational complexity of the pressure solve without compromising free surface boundary conditions at the highest level of detail. Our techniques are easy to parallelize, and they effectively eliminate the computational bottleneck for large liquid simulations.","lang":"eng"}],"intvolume":" 34","month":"05","scopus_import":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Ando, Ryoichi, et al. “A Dimension-Reduced Pressure Solver for Liquid Simulations.” Computer Graphics Forum, vol. 34, no. 2, Wiley, 2015, pp. 473–80, doi:10.1111/cgf.12576.","apa":"Ando, R., Thürey, N., & Wojtan, C. (2015). A dimension-reduced pressure solver for liquid simulations. Computer Graphics Forum. Wiley. https://doi.org/10.1111/cgf.12576","ama":"Ando R, Thürey N, Wojtan C. A dimension-reduced pressure solver for liquid simulations. Computer Graphics Forum. 2015;34(2):473-480. doi:10.1111/cgf.12576","ieee":"R. Ando, N. Thürey, and C. Wojtan, “A dimension-reduced pressure solver for liquid simulations,” Computer Graphics Forum, vol. 34, no. 2. Wiley, pp. 473–480, 2015.","short":"R. Ando, N. Thürey, C. Wojtan, Computer Graphics Forum 34 (2015) 473–480.","chicago":"Ando, Ryoichi, Nils Thürey, and Chris Wojtan. “A Dimension-Reduced Pressure Solver for Liquid Simulations.” Computer Graphics Forum. Wiley, 2015. https://doi.org/10.1111/cgf.12576.","ista":"Ando R, Thürey N, Wojtan C. 2015. A dimension-reduced pressure solver for liquid simulations. Computer Graphics Forum. 34(2), 473–480."},"title":"A dimension-reduced pressure solver for liquid simulations","author":[{"last_name":"Ando","full_name":"Ando, Ryoichi","first_name":"Ryoichi"},{"first_name":"Nils","full_name":"Thürey, Nils","last_name":"Thürey"},{"last_name":"Wojtan","orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J","first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5389","publication":"Computer Graphics Forum","day":"01","year":"2015","has_accepted_license":"1","date_created":"2018-12-11T11:53:44Z","doi":"10.1111/cgf.12576","date_published":"2015-05-01T00:00:00Z","page":"473 - 480","acknowledgement":"The first author was supported by a JSPS Postdoctoral Fellowship for Research Abroad","oa":1,"quality_controlled":"1","publisher":"Wiley"},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Klehm, Oliver, Fabrice Rousselle, Marios Papas, Derek Bradley, Christophe Hery, Bernd Bickel, Wojciech Jarosz, and Thabo Beeler. “Recent Advances in Facial Appearance Capture.” Computer Graphics Forum. Wiley-Blackwell, 2015. https://doi.org/10.1111/cgf.12594.","ista":"Klehm O, Rousselle F, Papas M, Bradley D, Hery C, Bickel B, Jarosz W, Beeler T. 2015. Recent advances in facial appearance capture. Computer Graphics Forum. 34(2), 709–733.","mla":"Klehm, Oliver, et al. “Recent Advances in Facial Appearance Capture.” Computer Graphics Forum, vol. 34, no. 2, Wiley-Blackwell, 2015, pp. 709–33, doi:10.1111/cgf.12594.","ieee":"O. Klehm et al., “Recent advances in facial appearance capture,” Computer Graphics Forum, vol. 34, no. 2. Wiley-Blackwell, pp. 709–733, 2015.","short":"O. Klehm, F. Rousselle, M. Papas, D. Bradley, C. Hery, B. Bickel, W. Jarosz, T. Beeler, Computer Graphics Forum 34 (2015) 709–733.","apa":"Klehm, O., Rousselle, F., Papas, M., Bradley, D., Hery, C., Bickel, B., … Beeler, T. (2015). Recent advances in facial appearance capture. Computer Graphics Forum. Wiley-Blackwell. https://doi.org/10.1111/cgf.12594","ama":"Klehm O, Rousselle F, Papas M, et al. Recent advances in facial appearance capture. Computer Graphics Forum. 2015;34(2):709-733. doi:10.1111/cgf.12594"},"date_updated":"2021-01-12T06:52:52Z","department":[{"_id":"BeBi"}],"title":"Recent advances in facial appearance capture","publist_id":"5391","author":[{"last_name":"Klehm","full_name":"Klehm, Oliver","first_name":"Oliver"},{"first_name":"Fabrice","full_name":"Rousselle, Fabrice","last_name":"Rousselle"},{"full_name":"Papas, Marios","last_name":"Papas","first_name":"Marios"},{"full_name":"Bradley, Derek","last_name":"Bradley","first_name":"Derek"},{"last_name":"Hery","full_name":"Hery, Christophe","first_name":"Christophe"},{"last_name":"Bickel","full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd"},{"full_name":"Jarosz, Wojciech","last_name":"Jarosz","first_name":"Wojciech"},{"last_name":"Beeler","full_name":"Beeler, Thabo","first_name":"Thabo"}],"_id":"1734","status":"public","type":"journal_article","day":"01","language":[{"iso":"eng"}],"publication":"Computer Graphics Forum","publication_status":"published","year":"2015","issue":"2","doi":"10.1111/cgf.12594","date_published":"2015-05-01T00:00:00Z","volume":34,"date_created":"2018-12-11T11:53:43Z","page":"709 - 733","oa_version":"None","abstract":[{"lang":"eng","text":"Facial appearance capture is now firmly established within academic research and used extensively across various application domains, perhaps most prominently in the entertainment industry through the design of virtual characters in video games and films. While significant progress has occurred over the last two decades, no single survey currently exists that discusses the similarities, differences, and practical considerations of the available appearance capture techniques as applied to human faces. A central difficulty of facial appearance capture is the way light interacts with skin-which has a complex multi-layered structure-and the interactions that occur below the skin surface can, by definition, only be observed indirectly. In this report, we distinguish between two broad strategies for dealing with this complexity. "Image-based methods" try to exhaustively capture the exact face appearance under different lighting and viewing conditions, and then render the face through weighted image combinations. "Parametric methods" instead fit the captured reflectance data to some parametric appearance model used during rendering, allowing for a more lightweight and flexible representation but at the cost of potentially increased rendering complexity or inexact reproduction. The goal of this report is to provide an overview that can guide practitioners and researchers in assessing the tradeoffs between current approaches and identifying directions for future advances in facial appearance capture."}],"month":"05","intvolume":" 34","quality_controlled":"1","scopus_import":1,"publisher":"Wiley-Blackwell","main_file_link":[{"url":"https://graphics.ethz.ch/~mpapas/publications/fac_star.pdf"}]},{"publist_id":"5324","author":[{"full_name":"Kuechler, Alma","last_name":"Kuechler","first_name":"Alma"},{"full_name":"Zink, Alexander","last_name":"Zink","first_name":"Alexander"},{"first_name":"Thomas","full_name":"Wieland, Thomas","last_name":"Wieland"},{"last_name":"Lüdecke","full_name":"Lüdecke, Hermann","first_name":"Hermann"},{"full_name":"Cremer, Kirsten","last_name":"Cremer","first_name":"Kirsten"},{"first_name":"Leonardo","full_name":"Salviati, Leonardo","last_name":"Salviati"},{"first_name":"Pamela","full_name":"Magini, Pamela","last_name":"Magini"},{"first_name":"Kimia","last_name":"Najafi","full_name":"Najafi, Kimia"},{"last_name":"Zweier","full_name":"Zweier, Christiane","first_name":"Christiane"},{"full_name":"Czeschik, Johanna","last_name":"Czeschik","first_name":"Johanna"},{"full_name":"Aretz, Stefan","last_name":"Aretz","first_name":"Stefan"},{"first_name":"Sabine","last_name":"Endele","full_name":"Endele, Sabine"},{"first_name":"Federica","last_name":"Tamburrino","full_name":"Tamburrino, Federica"},{"full_name":"Pinato, Claudia","last_name":"Pinato","first_name":"Claudia"},{"first_name":"Maurizio","full_name":"Clementi, Maurizio","last_name":"Clementi"},{"full_name":"Gundlach, Jasmin","last_name":"Gundlach","first_name":"Jasmin"},{"first_name":"Carina","full_name":"Maylahn, Carina","last_name":"Maylahn"},{"first_name":"Laura","full_name":"Mazzanti, Laura","last_name":"Mazzanti"},{"first_name":"Eva","last_name":"Wohlleber","full_name":"Wohlleber, Eva"},{"first_name":"Thomas","last_name":"Schwarzmayr","full_name":"Schwarzmayr, Thomas"},{"first_name":"Roxana","full_name":"Kariminejad, Roxana","last_name":"Kariminejad"},{"first_name":"Avner","full_name":"Schlessinger, Avner","last_name":"Schlessinger"},{"full_name":"Wieczorek, Dagmar","last_name":"Wieczorek","first_name":"Dagmar"},{"last_name":"Strom","full_name":"Strom, Tim","first_name":"Tim"},{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","last_name":"Novarino","full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178"},{"full_name":"Engels, Hartmut","last_name":"Engels","first_name":"Hartmut"}],"external_id":{"pmid":["25138099"]},"title":"Loss-of-function variants of SETD5 cause intellectual disability and the core phenotype of microdeletion 3p25.3 syndrome","citation":{"ama":"Kuechler A, Zink A, Wieland T, et al. Loss-of-function variants of SETD5 cause intellectual disability and the core phenotype of microdeletion 3p25.3 syndrome. European Journal of Human Genetics. 2015;23(6):753-760. doi:10.1038/ejhg.2014.165","apa":"Kuechler, A., Zink, A., Wieland, T., Lüdecke, H., Cremer, K., Salviati, L., … Engels, H. (2015). Loss-of-function variants of SETD5 cause intellectual disability and the core phenotype of microdeletion 3p25.3 syndrome. European Journal of Human Genetics. Nature Publishing Group. https://doi.org/10.1038/ejhg.2014.165","short":"A. Kuechler, A. Zink, T. Wieland, H. Lüdecke, K. Cremer, L. Salviati, P. Magini, K. Najafi, C. Zweier, J. Czeschik, S. Aretz, S. Endele, F. Tamburrino, C. Pinato, M. Clementi, J. Gundlach, C. Maylahn, L. Mazzanti, E. Wohlleber, T. Schwarzmayr, R. Kariminejad, A. Schlessinger, D. Wieczorek, T. Strom, G. Novarino, H. Engels, European Journal of Human Genetics 23 (2015) 753–760.","ieee":"A. Kuechler et al., “Loss-of-function variants of SETD5 cause intellectual disability and the core phenotype of microdeletion 3p25.3 syndrome,” European Journal of Human Genetics, vol. 23, no. 6. Nature Publishing Group, pp. 753–760, 2015.","mla":"Kuechler, Alma, et al. “Loss-of-Function Variants of SETD5 Cause Intellectual Disability and the Core Phenotype of Microdeletion 3p25.3 Syndrome.” European Journal of Human Genetics, vol. 23, no. 6, Nature Publishing Group, 2015, pp. 753–60, doi:10.1038/ejhg.2014.165.","ista":"Kuechler A, Zink A, Wieland T, Lüdecke H, Cremer K, Salviati L, Magini P, Najafi K, Zweier C, Czeschik J, Aretz S, Endele S, Tamburrino F, Pinato C, Clementi M, Gundlach J, Maylahn C, Mazzanti L, Wohlleber E, Schwarzmayr T, Kariminejad R, Schlessinger A, Wieczorek D, Strom T, Novarino G, Engels H. 2015. Loss-of-function variants of SETD5 cause intellectual disability and the core phenotype of microdeletion 3p25.3 syndrome. European Journal of Human Genetics. 23(6), 753–760.","chicago":"Kuechler, Alma, Alexander Zink, Thomas Wieland, Hermann Lüdecke, Kirsten Cremer, Leonardo Salviati, Pamela Magini, et al. “Loss-of-Function Variants of SETD5 Cause Intellectual Disability and the Core Phenotype of Microdeletion 3p25.3 Syndrome.” European Journal of Human Genetics. Nature Publishing Group, 2015. https://doi.org/10.1038/ejhg.2014.165."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"753 - 760","doi":"10.1038/ejhg.2014.165","date_published":"2015-06-15T00:00:00Z","date_created":"2018-12-11T11:54:01Z","year":"2015","day":"15","publication":"European Journal of Human Genetics","publisher":"Nature Publishing Group","quality_controlled":"1","oa":1,"department":[{"_id":"GaNo"}],"date_updated":"2021-01-12T06:53:12Z","type":"journal_article","status":"public","_id":"1789","issue":"6","volume":23,"publication_status":"published","language":[{"iso":"eng"}],"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4795044/","open_access":"1"}],"month":"06","intvolume":" 23","abstract":[{"text":"Intellectual disability (ID) has an estimated prevalence of 2-3%. Due to its extreme heterogeneity, the genetic basis of ID remains elusive in many cases. Recently, whole exome sequencing (WES) studies revealed that a large proportion of sporadic cases are caused by de novo gene variants. To identify further genes involved in ID, we performed WES in 250 patients with unexplained ID and their unaffected parents and included exomes of 51 previously sequenced child-parents trios in the analysis. Exome analysis revealed de novo intragenic variants in SET domain-containing 5 (SETD5) in two patients. One patient carried a nonsense variant, and the other an 81 bp deletion located across a splice-donor site. Chromosomal microarray diagnostics further identified four de novo non-recurrent microdeletions encompassing SETD5. CRISPR/Cas9 mutation modelling of the two intragenic variants demonstrated nonsense-mediated decay of the resulting transcripts, pointing to a loss-of-function (LoF) and haploinsufficiency as the common disease-causing mechanism of intragenic SETD5 sequence variants and SETD5-containing microdeletions. In silico domain prediction of SETD5, a predicted SET domain-containing histone methyltransferase (HMT), substantiated the presence of a SET domain and identified a novel putative PHD domain, strengthening a functional link to well-known histone-modifying ID genes. All six patients presented with ID and certain facial dysmorphisms, suggesting that SETD5 sequence variants contribute substantially to the microdeletion 3p25.3 phenotype. The present report of two SETD5 LoF variants in 301 patients demonstrates a prevalence of 0.7% and thus SETD5 variants as a relatively frequent cause of ID.","lang":"eng"}],"pmid":1,"oa_version":"Submitted Version"},{"publication":"Optics Express","day":"09","year":"2015","publication_status":"published","date_created":"2018-12-11T11:54:01Z","doi":"10.1364/OE.23.003196","volume":23,"issue":"3","date_published":"2015-02-09T00:00:00Z","page":"3196 - 3208","acknowledgement":"This work was supported by the DARPA MESO program, the AFOSR Hybrid Nanophotonics MURI, the Institute for Quantum Information and Matter, an NSF Physics Frontiers Center with support of the Gordon and Betty Moore Foundation, and the Kavli Nanoscience Institute at Caltech. AP gratefully acknowledge funding from EU through Marie Curie Actions, project NEMO (GA 298861). AT acknowledges partial financial support from the ERC through the advanced grant SoulMan","abstract":[{"text":"We fabricate and characterize a microscale silicon opto-electromechanical system whose mechanical motion is coupled capacitively to an electrical circuit and optically via radiation pressure to a photonic crystal cavity. To achieve large electromechanical interaction strength, we implement an inverse shadow mask fabrication scheme which obtains capacitor gaps as small as 30 nm while maintaining a silicon surface quality necessary for minimizing optical loss. Using the sensitive optical read-out of the photonic crystal cavity, we characterize the linear and nonlinear capacitive coupling to the fundamental ωm=2π = 63 MHz in-plane flexural motion of the structure, showing that the large electromechanical coupling in such devices may be suitable for realizing efficient microwave-to-optical signal conversion.","lang":"eng"}],"intvolume":" 23","month":"02","publisher":"Optical Society of America","quality_controlled":0,"extern":1,"citation":{"ista":"Pitanti A, Fink JM, Safavi Naeini A, Hill J, Lei C, Tredicucci A, Painter O. 2015. Strong opto-electro-mechanical coupling in a silicon photonic crystal cavity. Optics Express. 23(3), 3196–3208.","chicago":"Pitanti, Alessandro, Johannes M Fink, Amir Safavi Naeini, Jeff Hill, Chan Lei, Alessandro Tredicucci, and Oskar Painter. “Strong Opto-Electro-Mechanical Coupling in a Silicon Photonic Crystal Cavity.” Optics Express. Optical Society of America, 2015. https://doi.org/10.1364/OE.23.003196.","apa":"Pitanti, A., Fink, J. M., Safavi Naeini, A., Hill, J., Lei, C., Tredicucci, A., & Painter, O. (2015). Strong opto-electro-mechanical coupling in a silicon photonic crystal cavity. Optics Express. Optical Society of America. https://doi.org/10.1364/OE.23.003196","ama":"Pitanti A, Fink JM, Safavi Naeini A, et al. Strong opto-electro-mechanical coupling in a silicon photonic crystal cavity. Optics Express. 2015;23(3):3196-3208. doi:10.1364/OE.23.003196","short":"A. Pitanti, J.M. Fink, A. Safavi Naeini, J. Hill, C. Lei, A. Tredicucci, O. Painter, Optics Express 23 (2015) 3196–3208.","ieee":"A. Pitanti et al., “Strong opto-electro-mechanical coupling in a silicon photonic crystal cavity,” Optics Express, vol. 23, no. 3. Optical Society of America, pp. 3196–3208, 2015.","mla":"Pitanti, Alessandro, et al. “Strong Opto-Electro-Mechanical Coupling in a Silicon Photonic Crystal Cavity.” Optics Express, vol. 23, no. 3, Optical Society of America, 2015, pp. 3196–208, doi:10.1364/OE.23.003196."},"date_updated":"2021-01-12T06:53:12Z","title":"Strong opto-electro-mechanical coupling in a silicon photonic crystal cavity","publist_id":"5325","author":[{"first_name":"Alessandro","last_name":"Pitanti","full_name":"Pitanti, Alessandro"},{"first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","full_name":"Johannes Fink","last_name":"Fink"},{"first_name":"Amir","last_name":"Safavi Naeini","full_name":"Safavi-Naeini, Amir H"},{"first_name":"Jeff","full_name":"Hill, Jeff T","last_name":"Hill"},{"first_name":"Chan","last_name":"Lei","full_name":"Lei, Chan U"},{"full_name":"Tredicucci, Alessandro","last_name":"Tredicucci","first_name":"Alessandro"},{"last_name":"Painter","full_name":"Painter, Oskar J","first_name":"Oskar"}],"_id":"1788","status":"public","type":"journal_article"}]