[{"month":"01","doi":"10.1007/978-3-642-45221-5_13","conference":{"name":"LPAR: Logic for Programming, Artificial Intelligence, and Reasoning","start_date":"2013-12-14","location":"Stellenbosch, South Africa","end_date":"2013-12-19"},"language":[{"iso":"eng"}],"oa":1,"project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"}],"quality_controlled":"1","publist_id":"4724","file_date_updated":"2020-07-14T12:45:34Z","author":[{"full_name":"Blanc, Régis","last_name":"Blanc","first_name":"Régis"},{"full_name":"Gupta, Ashutosh","last_name":"Gupta","first_name":"Ashutosh","id":"335E5684-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kovács, Laura","last_name":"Kovács","first_name":"Laura"},{"id":"320FC952-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7745-9117","first_name":"Bernhard","last_name":"Kragl","full_name":"Kragl, Bernhard"}],"volume":8312,"date_created":"2018-12-11T11:56:29Z","date_updated":"2020-08-11T10:09:42Z","year":"2013","publisher":"Springer","department":[{"_id":"ToHe"}],"publication_status":"published","article_processing_charge":"No","has_accepted_license":"1","day":"14","scopus_import":1,"series_title":"Lecture Notes in Computer Science","date_published":"2013-01-14T00:00:00Z","citation":{"mla":"Blanc, Régis, et al. Tree Interpolation in Vampire. Vol. 8312, Springer, 2013, pp. 173–81, doi:10.1007/978-3-642-45221-5_13.","short":"R. Blanc, A. Gupta, L. Kovács, B. Kragl, 8312 (2013) 173–181.","chicago":"Blanc, Régis, Ashutosh Gupta, Laura Kovács, and Bernhard Kragl. “Tree Interpolation in Vampire.” Lecture Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-45221-5_13.","ama":"Blanc R, Gupta A, Kovács L, Kragl B. Tree interpolation in Vampire. 2013;8312:173-181. doi:10.1007/978-3-642-45221-5_13","ista":"Blanc R, Gupta A, Kovács L, Kragl B. 2013. Tree interpolation in Vampire. 8312, 173–181.","apa":"Blanc, R., Gupta, A., Kovács, L., & Kragl, B. (2013). Tree interpolation in Vampire. Presented at the LPAR: Logic for Programming, Artificial Intelligence, and Reasoning, Stellenbosch, South Africa: Springer. https://doi.org/10.1007/978-3-642-45221-5_13","ieee":"R. Blanc, A. Gupta, L. Kovács, and B. Kragl, “Tree interpolation in Vampire,” vol. 8312. Springer, pp. 173–181, 2013."},"page":"173 - 181","abstract":[{"lang":"eng","text":"We describe new extensions of the Vampire theorem prover for computing tree interpolants. These extensions generalize Craig interpolation in Vampire, and can also be used to derive sequence interpolants. We evaluated our implementation on a large number of examples over the theory of linear integer arithmetic and integer-indexed arrays, with and without quantifiers. When compared to other methods, our experiments show that some examples could only be solved by our implementation."}],"type":"conference","alternative_title":["LNCS"],"oa_version":"Submitted Version","file":[{"relation":"main_file","file_id":"7858","date_updated":"2020-07-14T12:45:34Z","date_created":"2020-05-15T11:10:40Z","checksum":"9cebaafca032e6769d273f393305c705","file_name":"2013_LPAR_Blanc.pdf","access_level":"open_access","content_type":"application/pdf","file_size":279206,"creator":"dernst"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2237","intvolume":" 8312","status":"public","ddc":["000"],"title":"Tree interpolation in Vampire"},{"month":"12","project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"}],"quality_controlled":"1","doi":"10.1007/978-3-642-45221-5_17","conference":{"start_date":"2013-12-14","location":"Stellenbosch, South Africa","end_date":"2013-12-19","name":"LPAR: Logic for Programming, Artificial Intelligence, and Reasoning"},"language":[{"iso":"eng"}],"publist_id":"4723","ec_funded":1,"year":"2013","department":[{"_id":"KrCh"}],"publisher":"Springer","publication_status":"published","author":[{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"first_name":"Vojtěch","last_name":"Forejt","full_name":"Forejt, Vojtěch"},{"full_name":"Wojtczak, Dominik","first_name":"Dominik","last_name":"Wojtczak"}],"volume":8312,"date_created":"2018-12-11T11:56:30Z","date_updated":"2020-08-11T10:09:42Z","scopus_import":1,"series_title":"Lecture Notes in Computer Science","day":"01","citation":{"ama":"Chatterjee K, Forejt V, Wojtczak D. Multi-objective discounted reward verification in graphs and MDPs. 2013;8312:228-242. doi:10.1007/978-3-642-45221-5_17","apa":"Chatterjee, K., Forejt, V., & Wojtczak, D. (2013). Multi-objective discounted reward verification in graphs and MDPs. Presented at the LPAR: Logic for Programming, Artificial Intelligence, and Reasoning, Stellenbosch, South Africa: Springer. https://doi.org/10.1007/978-3-642-45221-5_17","ieee":"K. Chatterjee, V. Forejt, and D. Wojtczak, “Multi-objective discounted reward verification in graphs and MDPs,” vol. 8312. Springer, pp. 228–242, 2013.","ista":"Chatterjee K, Forejt V, Wojtczak D. 2013. Multi-objective discounted reward verification in graphs and MDPs. 8312, 228–242.","short":"K. Chatterjee, V. Forejt, D. Wojtczak, 8312 (2013) 228–242.","mla":"Chatterjee, Krishnendu, et al. Multi-Objective Discounted Reward Verification in Graphs and MDPs. Vol. 8312, Springer, 2013, pp. 228–42, doi:10.1007/978-3-642-45221-5_17.","chicago":"Chatterjee, Krishnendu, Vojtěch Forejt, and Dominik Wojtczak. “Multi-Objective Discounted Reward Verification in Graphs and MDPs.” Lecture Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-45221-5_17."},"page":"228 - 242","date_published":"2013-12-01T00:00:00Z","type":"conference","alternative_title":["LNCS"],"abstract":[{"text":"We study the problem of achieving a given value in Markov decision processes (MDPs) with several independent discounted reward objectives. We consider a generalised version of discounted reward objectives, in which the amount of discounting depends on the states visited and on the objective. This definition extends the usual definition of discounted reward, and allows to capture the systems in which the value of different commodities diminish at different and variable rates.\r\n\r\nWe establish results for two prominent subclasses of the problem, namely state-discount models where the discount factors are only dependent on the state of the MDP (and independent of the objective), and reward-discount models where they are only dependent on the objective (but not on the state of the MDP). For the state-discount models we use a straightforward reduction to expected total reward and show that the problem whether a value is achievable can be solved in polynomial time. For the reward-discount model we show that memory and randomisation of the strategies are required, but nevertheless that the problem is decidable and it is sufficient to consider strategies which after a certain number of steps behave in a memoryless way.\r\n\r\nFor the general case, we show that when restricted to graphs (i.e. MDPs with no randomisation), pure strategies and discount factors of the form 1/n where n is an integer, the problem is in PSPACE and finite memory suffices for achieving a given value. We also show that when the discount factors are not of the form 1/n, the memory required by a strategy can be infinite.\r\n","lang":"eng"}],"_id":"2238","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 8312","status":"public","title":"Multi-objective discounted reward verification in graphs and MDPs","oa_version":"None"},{"pubrep_id":"136","oa_version":"Published Version","file":[{"date_created":"2018-12-12T10:12:11Z","date_updated":"2020-07-14T12:45:34Z","checksum":"e0732e73a8b1e39483df7717d53e3e35","file_id":"4929","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":454915,"file_name":"IST-2016-136-v1+2_39.pdf","access_level":"open_access"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2243","ddc":["000","004"],"title":"Elementary modal logics over transitive structures","status":"public","intvolume":" 23","abstract":[{"text":"We show that modal logic over universally first-order definable classes of transitive frames is decidable. More precisely, let K be an arbitrary class of transitive Kripke frames definable by a universal first-order sentence. We show that the global and finite global satisfiability problems of modal logic over K are decidable in NP, regardless of choice of K. We also show that the local satisfiability and the finite local satisfiability problems of modal logic over K are decidable in NEXPTIME.","lang":"eng"}],"type":"conference","alternative_title":["LIPIcs"],"date_published":"2013-09-01T00:00:00Z","citation":{"mla":"Michaliszyn, Jakub, and Jan Otop. Elementary Modal Logics over Transitive Structures. Vol. 23, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2013, pp. 563–77, doi:10.4230/LIPIcs.CSL.2013.563.","short":"J. Michaliszyn, J. Otop, 23 (2013) 563–577.","chicago":"Michaliszyn, Jakub, and Jan Otop. “Elementary Modal Logics over Transitive Structures.” Leibniz International Proceedings in Informatics. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2013. https://doi.org/10.4230/LIPIcs.CSL.2013.563.","ama":"Michaliszyn J, Otop J. Elementary modal logics over transitive structures. 2013;23:563-577. doi:10.4230/LIPIcs.CSL.2013.563","ista":"Michaliszyn J, Otop J. 2013. Elementary modal logics over transitive structures. 23, 563–577.","apa":"Michaliszyn, J., & Otop, J. (2013). Elementary modal logics over transitive structures. Presented at the CSL: Computer Science Logic, Torino, Italy: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CSL.2013.563","ieee":"J. Michaliszyn and J. Otop, “Elementary modal logics over transitive structures,” vol. 23. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, pp. 563–577, 2013."},"page":"563 - 577","day":"01","has_accepted_license":"1","scopus_import":1,"series_title":"Leibniz International Proceedings in Informatics","author":[{"first_name":"Jakub","last_name":"Michaliszyn","full_name":"Michaliszyn, Jakub"},{"full_name":"Otop, Jan","last_name":"Otop","first_name":"Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2018-12-11T11:56:32Z","date_updated":"2020-08-11T10:09:42Z","volume":23,"year":"2013","publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","file_date_updated":"2020-07-14T12:45:34Z","ec_funded":1,"publist_id":"4708","license":"https://creativecommons.org/licenses/by/4.0/","conference":{"name":"CSL: Computer Science Logic","start_date":"2013-09-02","location":"Torino, Italy","end_date":"2013-09-05"},"doi":"10.4230/LIPIcs.CSL.2013.563","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Reactive Modeling","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"}],"month":"09"},{"day":"01","scopus_import":1,"series_title":"Lecture Notes in Computer Science","date_published":"2013-09-01T00:00:00Z","citation":{"ama":"Matoušek J, Sedgwick E, Tancer M, Wagner U. Untangling two systems of noncrossing curves. 2013;8242:472-483. doi:10.1007/978-3-319-03841-4_41","ista":"Matoušek J, Sedgwick E, Tancer M, Wagner U. 2013. Untangling two systems of noncrossing curves. 8242, 472–483.","apa":"Matoušek, J., Sedgwick, E., Tancer, M., & Wagner, U. (2013). Untangling two systems of noncrossing curves. Presented at the GD: Graph Drawing and Network Visualization, Bordeaux, France: Springer. https://doi.org/10.1007/978-3-319-03841-4_41","ieee":"J. Matoušek, E. Sedgwick, M. Tancer, and U. Wagner, “Untangling two systems of noncrossing curves,” vol. 8242. Springer, pp. 472–483, 2013.","mla":"Matoušek, Jiří, et al. Untangling Two Systems of Noncrossing Curves. Vol. 8242, Springer, 2013, pp. 472–83, doi:10.1007/978-3-319-03841-4_41.","short":"J. Matoušek, E. Sedgwick, M. Tancer, U. Wagner, 8242 (2013) 472–483.","chicago":"Matoušek, Jiří, Eric Sedgwick, Martin Tancer, and Uli Wagner. “Untangling Two Systems of Noncrossing Curves.” Lecture Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-319-03841-4_41."},"page":"472 - 483","abstract":[{"text":"We consider two systems (α1,...,αm) and (β1,...,βn) of curves drawn on a compact two-dimensional surface ℳ with boundary. Each αi and each βj is either an arc meeting the boundary of ℳ at its two endpoints, or a closed curve. The αi are pairwise disjoint except for possibly sharing endpoints, and similarly for the βj. We want to "untangle" the βj from the αi by a self-homeomorphism of ℳ; more precisely, we seek an homeomorphism φ: ℳ → ℳ fixing the boundary of ℳ pointwise such that the total number of crossings of the αi with the φ(βj) is as small as possible. This problem is motivated by an application in the algorithmic theory of embeddings and 3-manifolds. We prove that if ℳ is planar, i.e., a sphere with h ≥ 0 boundary components ("holes"), then O(mn) crossings can be achieved (independently of h), which is asymptotically tight, as an easy lower bound shows. In general, for an arbitrary (orientable or nonorientable) surface ℳ with h holes and of (orientable or nonorientable) genus g ≥ 0, we obtain an O((m + n)4) upper bound, again independent of h and g. ","lang":"eng"}],"type":"conference","alternative_title":["LNCS"],"oa_version":"Preprint","_id":"2244","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Untangling two systems of noncrossing curves","status":"public","intvolume":" 8242","month":"09","conference":{"name":"GD: Graph Drawing and Network Visualization","end_date":"2013-09-25","start_date":"2013-09-23","location":"Bordeaux, France"},"doi":"10.1007/978-3-319-03841-4_41","language":[{"iso":"eng"}],"external_id":{"arxiv":["1302.6475"]},"oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1302.6475","open_access":"1"}],"quality_controlled":"1","project":[{"grant_number":"PP00P2_138948","_id":"25FA3206-B435-11E9-9278-68D0E5697425","name":"Embeddings in Higher Dimensions: Algorithms and Combinatorics"}],"publist_id":"4707","author":[{"last_name":"Matoušek","first_name":"Jiří","full_name":"Matoušek, Jiří"},{"full_name":"Sedgwick, Eric","last_name":"Sedgwick","first_name":"Eric"},{"last_name":"Tancer","first_name":"Martin","orcid":"0000-0002-1191-6714","id":"38AC689C-F248-11E8-B48F-1D18A9856A87","full_name":"Tancer, Martin"},{"full_name":"Wagner, Uli","last_name":"Wagner","first_name":"Uli","orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"status":"public","relation":"later_version","id":"1411"}]},"date_created":"2018-12-11T11:56:32Z","date_updated":"2023-02-21T17:03:07Z","volume":8242,"acknowledgement":"We would like to thank the authors of [GHR13] for mak- ing a draft of their paper available to us, and, in particular, T. Huynh for an e-mail correspondence.","year":"2013","publication_status":"published","publisher":"Springer","department":[{"_id":"UlWa"}]},{"type":"conference","alternative_title":["LNCS"],"abstract":[{"text":"The learning with rounding (LWR) problem, introduced by Banerjee, Peikert and Rosen at EUROCRYPT ’12, is a variant of learning with errors (LWE), where one replaces random errors with deterministic rounding. The LWR problem was shown to be as hard as LWE for a setting of parameters where the modulus and modulus-to-error ratio are super-polynomial. In this work we resolve the main open problem and give a new reduction that works for a larger range of parameters, allowing for a polynomial modulus and modulus-to-error ratio. In particular, a smaller modulus gives us greater efficiency, and a smaller modulus-to-error ratio gives us greater security, which now follows from the worst-case hardness of GapSVP with polynomial (rather than super-polynomial) approximation factors.\r\n\r\nAs a tool in the reduction, we show that there is a “lossy mode” for the LWR problem, in which LWR samples only reveal partial information about the secret. This property gives us several interesting new applications, including a proof that LWR remains secure with weakly random secrets of sufficient min-entropy, and very simple constructions of deterministic encryption, lossy trapdoor functions and reusable extractors.\r\n\r\nOur approach is inspired by a technique of Goldwasser et al. from ICS ’10, which implicitly showed the existence of a “lossy mode” for LWE. By refining this technique, we also improve on the parameters of that work to only requiring a polynomial (instead of super-polynomial) modulus and modulus-to-error ratio.\r\n","lang":"eng"}],"issue":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2259","ddc":["000","004"],"title":"Learning with rounding, revisited: New reduction properties and applications","status":"public","intvolume":" 8042","pubrep_id":"684","file":[{"access_level":"open_access","file_name":"IST-2016-684-v1+1_098.pdf","content_type":"application/pdf","file_size":587898,"creator":"system","relation":"main_file","file_id":"4912","checksum":"16d428408a806b8e49eecc607deab115","date_created":"2018-12-12T10:11:55Z","date_updated":"2020-07-14T12:45:35Z"}],"oa_version":"Published Version","scopus_import":1,"series_title":"Lecture Notes in Computer Science","day":"01","has_accepted_license":"1","citation":{"apa":"Alwen, J. F., Krenn, S., Pietrzak, K. Z., & Wichs, D. (2013). Learning with rounding, revisited: New reduction properties and applications. Presented at the CRYPTO: International Cryptology Conference, Santa Barbara, CA, United States: Springer. https://doi.org/10.1007/978-3-642-40041-4_4","ieee":"J. F. Alwen, S. Krenn, K. Z. Pietrzak, and D. Wichs, “Learning with rounding, revisited: New reduction properties and applications,” vol. 8042, no. 1. Springer, pp. 57–74, 2013.","ista":"Alwen JF, Krenn S, Pietrzak KZ, Wichs D. 2013. Learning with rounding, revisited: New reduction properties and applications. 8042(1), 57–74.","ama":"Alwen JF, Krenn S, Pietrzak KZ, Wichs D. Learning with rounding, revisited: New reduction properties and applications. 2013;8042(1):57-74. doi:10.1007/978-3-642-40041-4_4","chicago":"Alwen, Joel F, Stephan Krenn, Krzysztof Z Pietrzak, and Daniel Wichs. “Learning with Rounding, Revisited: New Reduction Properties and Applications.” Lecture Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-40041-4_4.","short":"J.F. Alwen, S. Krenn, K.Z. Pietrzak, D. Wichs, 8042 (2013) 57–74.","mla":"Alwen, Joel F., et al. Learning with Rounding, Revisited: New Reduction Properties and Applications. Vol. 8042, no. 1, Springer, 2013, pp. 57–74, doi:10.1007/978-3-642-40041-4_4."},"page":"57 - 74","date_published":"2013-01-01T00:00:00Z","file_date_updated":"2020-07-14T12:45:35Z","publist_id":"4687","ec_funded":1,"year":"2013","publication_status":"published","publisher":"Springer","department":[{"_id":"KrPi"}],"author":[{"id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","first_name":"Joel F","last_name":"Alwen","full_name":"Alwen, Joel F"},{"full_name":"Krenn, Stephan","last_name":"Krenn","first_name":"Stephan","orcid":"0000-0003-2835-9093","id":"329FCCF0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pietrzak, Krzysztof Z","first_name":"Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654"},{"full_name":"Wichs, Daniel","last_name":"Wichs","first_name":"Daniel"}],"date_updated":"2021-01-12T06:56:21Z","date_created":"2018-12-11T11:56:37Z","volume":8042,"month":"01","oa":1,"quality_controlled":"1","project":[{"grant_number":"259668","_id":"258C570E-B435-11E9-9278-68D0E5697425","name":"Provable Security for Physical Cryptography","call_identifier":"FP7"}],"conference":{"end_date":"2013-08-22","start_date":"2013-08-18","location":"Santa Barbara, CA, United States","name":"CRYPTO: International Cryptology Conference"},"doi":"10.1007/978-3-642-40041-4_4","language":[{"iso":"eng"}]},{"month":"01","language":[{"iso":"eng"}],"doi":"10.1007/978-3-642-40041-4_31","conference":{"end_date":"2013-08-22","location":"Santa Barbara, CA, United States","start_date":"2013-08-18","name":"CRYPTO: International Cryptology Conference"},"project":[{"call_identifier":"FP7","name":"Provable Security for Physical Cryptography","_id":"258C570E-B435-11E9-9278-68D0E5697425","grant_number":"259668"}],"quality_controlled":"1","oa":1,"ec_funded":1,"publist_id":"4688","file_date_updated":"2020-07-14T12:45:35Z","volume":8042,"date_created":"2018-12-11T11:56:37Z","date_updated":"2021-01-12T06:56:21Z","author":[{"first_name":"Eike","last_name":"Kiltz","full_name":"Kiltz, Eike"},{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z"},{"last_name":"Szegedy","first_name":"Mario","full_name":"Szegedy, Mario"}],"publisher":"Springer","department":[{"_id":"KrPi"}],"publication_status":"published","year":"2013","has_accepted_license":"1","day":"01","series_title":"Lecture Notes in Computer Science","scopus_import":1,"date_published":"2013-01-01T00:00:00Z","page":"571 - 588","citation":{"chicago":"Kiltz, Eike, Krzysztof Z Pietrzak, and Mario Szegedy. “Digital Signatures with Minimal Overhead from Indifferentiable Random Invertible Functions.” Lecture Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-40041-4_31.","short":"E. Kiltz, K.Z. Pietrzak, M. Szegedy, 8042 (2013) 571–588.","mla":"Kiltz, Eike, et al. Digital Signatures with Minimal Overhead from Indifferentiable Random Invertible Functions. Vol. 8042, Springer, 2013, pp. 571–88, doi:10.1007/978-3-642-40041-4_31.","apa":"Kiltz, E., Pietrzak, K. Z., & Szegedy, M. (2013). Digital signatures with minimal overhead from indifferentiable random invertible functions. Presented at the CRYPTO: International Cryptology Conference, Santa Barbara, CA, United States: Springer. https://doi.org/10.1007/978-3-642-40041-4_31","ieee":"E. Kiltz, K. Z. Pietrzak, and M. Szegedy, “Digital signatures with minimal overhead from indifferentiable random invertible functions,” vol. 8042. Springer, pp. 571–588, 2013.","ista":"Kiltz E, Pietrzak KZ, Szegedy M. 2013. Digital signatures with minimal overhead from indifferentiable random invertible functions. 8042, 571–588.","ama":"Kiltz E, Pietrzak KZ, Szegedy M. Digital signatures with minimal overhead from indifferentiable random invertible functions. 2013;8042:571-588. doi:10.1007/978-3-642-40041-4_31"},"abstract":[{"text":"In a digital signature scheme with message recovery, rather than transmitting the message m and its signature σ, a single enhanced signature τ is transmitted. The verifier is able to recover m from τ and at the same time verify its authenticity. The two most important parameters of such a scheme are its security and overhead |τ| − |m|. A simple argument shows that for any scheme with “n bits security” |τ| − |m| ≥ n, i.e., the overhead is lower bounded by the security parameter n. Currently, the best known constructions in the random oracle model are far from this lower bound requiring an overhead of n + logq h , where q h is the number of queries to the random oracle. In this paper we give a construction which basically matches the n bit lower bound. We propose a simple digital signature scheme with n + o(logq h ) bits overhead, where q h denotes the number of random oracle queries.\r\n\r\nOur construction works in two steps. First, we propose a signature scheme with message recovery having optimal overhead in a new ideal model, the random invertible function model. Second, we show that a four-round Feistel network with random oracles as round functions is tightly “public-indifferentiable” from a random invertible function. At the core of our indifferentiability proof is an almost tight upper bound for the expected number of edges of the densest “small” subgraph of a random Cayley graph, which may be of independent interest.\r\n","lang":"eng"}],"alternative_title":["LNCS"],"type":"conference","oa_version":"Submitted Version","file":[{"checksum":"18a3f602cb41de184dc0e16a0e907633","date_updated":"2020-07-14T12:45:35Z","date_created":"2018-12-12T10:09:20Z","file_id":"4744","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":493175,"access_level":"open_access","file_name":"IST-2016-685-v1+1_658.pdf"}],"pubrep_id":"685","intvolume":" 8042","title":"Digital signatures with minimal overhead from indifferentiable random invertible functions","status":"public","ddc":["000","004"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2258"},{"day":"01","has_accepted_license":"1","date_published":"2013-12-01T00:00:00Z","publication":"VÖB Mitteilungen","citation":{"short":"P. Danowski, D. Goldfarb, V. Schaffner, W. Seidler, VÖB Mitteilungen 66 (2013) 559–587.","mla":"Danowski, Patrick, et al. “Linked (Open) Data - Bibliographische Daten Im Semantic Web.” VÖB Mitteilungen, vol. 66, no. 3/4, Verein Österreichischer Bibliothekarinnen und Bibliothekare, 2013, pp. 559–87.","chicago":"Danowski, Patrick, Doron Goldfarb, Verena Schaffner, and Wolfram Seidler. “Linked (Open) Data - Bibliographische Daten Im Semantic Web.” VÖB Mitteilungen. Verein Österreichischer Bibliothekarinnen und Bibliothekare, 2013.","ama":"Danowski P, Goldfarb D, Schaffner V, Seidler W. Linked (Open) Data - Bibliographische Daten im Semantic Web. VÖB Mitteilungen. 2013;66(3/4):559-587.","apa":"Danowski, P., Goldfarb, D., Schaffner, V., & Seidler, W. (2013). Linked (Open) Data - Bibliographische Daten im Semantic Web. VÖB Mitteilungen. Verein Österreichischer Bibliothekarinnen und Bibliothekare.","ieee":"P. Danowski, D. Goldfarb, V. Schaffner, and W. Seidler, “Linked (Open) Data - Bibliographische Daten im Semantic Web,” VÖB Mitteilungen, vol. 66, no. 3/4. Verein Österreichischer Bibliothekarinnen und Bibliothekare, pp. 559–587, 2013.","ista":"Danowski P, Goldfarb D, Schaffner V, Seidler W. 2013. Linked (Open) Data - Bibliographische Daten im Semantic Web. VÖB Mitteilungen. 66(3/4), 559–587."},"page":"559 - 587","abstract":[{"text":"Linked (Open) Data - bibliographic data on the Semantic Web. Report of the Working Group on Linked Data to the plenary assembly of the Austrian Library Network (translation of the title). Linked Data stands for a certain approach to publishing data on the Web. The underlying idea is to harmonise heterogeneous data sources of different origin in order to improve their accessibility and interoperability, effectively making them queryable as a big distributed database. This report summarises relevant developments in Europe as well as the Linked Data Working Group‘s strategic and technical considerations regarding the publishing of the Austrian Library Network’s (OBV’s) bibliographic datasets. It concludes with the mutual agreement that the implementation of Linked Data principles within the OBV can only be taken into consideration accompanied by a discussion about the provision of the datasets under a free license.","lang":"eng"},{"lang":"ger","text":"Linked Data steht für eine bestimmte Form der Veröffentlichung von Daten via Internet. Die zu Grunde liegende Idee ist es, Daten verschiedenster Provenienz, die derzeit teilweise gar nicht oder nur schwer zugänglich sind, in möglichst \r\neinheitlicher Form miteinander zu verknüpfen und dadurch in ihrer Gesamtheit abfragbar zu machen.\r\nDieser Bericht fasst die Entwicklungen im europäischen Raum, sowie strategische und technische Überlegungen der AG Linked Data hinsichtlich der Veröffentlichung von bibliothekarischen Daten des Österreichischen Bibliothekenverbundes (OBV) zusammen und schließt mit der gemeinsamen Übereinkunft, dass die Umsetzung von Linked Data-Prinzipien im OBV nur in Zusammenhang mit einer Diskussion über die damit einhergehende Veröffentlichung der Daten unter einer freien Lizenz angedacht werden sollte."}],"issue":"3/4","type":"journal_article","popular_science":"1","pubrep_id":"719","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":881545,"creator":"system","access_level":"open_access","file_name":"IST-2016-719-v1+1_Patrick_Danowski__Doron_Goldfarb__Verena_Schaffner__Wolfram_Seidler_Linked__Open__Data_Bibliographische_Daten_im_Semantic_Web.pdf","checksum":"ae57ffcee3720adcc27b0f2767a1e04b","date_created":"2018-12-12T10:08:09Z","date_updated":"2020-07-14T12:45:35Z","relation":"main_file","file_id":"4669"}],"_id":"2256","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Linked (Open) Data - Bibliographische Daten im Semantic Web","status":"public","ddc":["020"],"intvolume":" 66","month":"12","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"file_date_updated":"2020-07-14T12:45:35Z","publist_id":"4690","author":[{"last_name":"Danowski","first_name":"Patrick","orcid":"0000-0002-6026-4409","id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","full_name":"Danowski, Patrick"},{"first_name":"Doron","last_name":"Goldfarb","full_name":"Goldfarb, Doron"},{"first_name":"Verena","last_name":"Schaffner","full_name":"Schaffner, Verena"},{"first_name":"Wolfram","last_name":"Seidler","full_name":"Seidler, Wolfram"}],"date_updated":"2021-01-12T06:56:20Z","date_created":"2018-12-11T11:56:36Z","volume":66,"year":"2013","publication_status":"published","department":[{"_id":"E-Lib"}],"publisher":"Verein Österreichischer Bibliothekarinnen und Bibliothekare"},{"date_published":"2013-06-01T00:00:00Z","page":"518 - 533","citation":{"apa":"Bernhard, D., Fuchsbauer, G., & Ghadafi, E. (2013). Efficient signatures of knowledge and DAA in the standard model. Presented at the ACNS: Applied Cryptography and Network Security, Banff, AB, Canada: Springer. https://doi.org/10.1007/978-3-642-38980-1_33","ieee":"D. Bernhard, G. Fuchsbauer, and E. Ghadafi, “Efficient signatures of knowledge and DAA in the standard model,” vol. 7954. Springer, pp. 518–533, 2013.","ista":"Bernhard D, Fuchsbauer G, Ghadafi E. 2013. Efficient signatures of knowledge and DAA in the standard model. 7954, 518–533.","ama":"Bernhard D, Fuchsbauer G, Ghadafi E. Efficient signatures of knowledge and DAA in the standard model. 2013;7954:518-533. doi:10.1007/978-3-642-38980-1_33","chicago":"Bernhard, David, Georg Fuchsbauer, and Essam Ghadafi. “Efficient Signatures of Knowledge and DAA in the Standard Model.” Lecture Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-38980-1_33.","short":"D. Bernhard, G. Fuchsbauer, E. Ghadafi, 7954 (2013) 518–533.","mla":"Bernhard, David, et al. Efficient Signatures of Knowledge and DAA in the Standard Model. Vol. 7954, Springer, 2013, pp. 518–33, doi:10.1007/978-3-642-38980-1_33."},"day":"01","series_title":"Lecture Notes in Computer Science","scopus_import":1,"oa_version":"Submitted Version","title":"Efficient signatures of knowledge and DAA in the standard model","status":"public","intvolume":" 7954","_id":"2260","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Direct Anonymous Attestation (DAA) is one of the most complex cryptographic protocols deployed in practice. It allows an embedded secure processor known as a Trusted Platform Module (TPM) to attest to the configuration of its host computer without violating the owner’s privacy. DAA has been standardized by the Trusted Computing Group and ISO/IEC.\r\n\r\nThe security of the DAA standard and all existing schemes is analyzed in the random-oracle model. We provide the first constructions of DAA in the standard model, that is, without relying on random oracles. Our constructions use new building blocks, including the first efficient signatures of knowledge in the standard model, which have many applications beyond DAA.\r\n"}],"alternative_title":["LNCS"],"type":"conference","language":[{"iso":"eng"}],"conference":{"location":"Banff, AB, Canada","start_date":"2013-06-25","end_date":"2013-06-28","name":"ACNS: Applied Cryptography and Network Security"},"doi":"10.1007/978-3-642-38980-1_33","quality_controlled":"1","oa":1,"main_file_link":[{"url":"http://eprint.iacr.org/2012/475","open_access":"1"}],"month":"06","date_updated":"2020-08-11T10:09:44Z","date_created":"2018-12-11T11:56:37Z","volume":7954,"author":[{"full_name":"Bernhard, David","first_name":"David","last_name":"Bernhard"},{"last_name":"Fuchsbauer","first_name":"Georg","id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","full_name":"Fuchsbauer, Georg"},{"full_name":"Ghadafi, Essam","first_name":"Essam","last_name":"Ghadafi"}],"publication_status":"published","department":[{"_id":"KrPi"}],"publisher":"Springer","year":"2013","publist_id":"4686"},{"department":[{"_id":"SiHi"}],"publisher":"Company of Biologists","publication_status":"published","pmid":1,"year":"2013","volume":140,"date_created":"2018-12-11T11:56:39Z","date_updated":"2021-01-12T06:56:23Z","author":[{"full_name":"Liang, Huixuan","first_name":"Huixuan","last_name":"Liang"},{"full_name":"Xiao, Guanxi","last_name":"Xiao","first_name":"Guanxi"},{"full_name":"Yin, Haifeng","last_name":"Yin","first_name":"Haifeng"},{"full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","first_name":"Simon","last_name":"Hippenmeyer"},{"first_name":"Jonathan","last_name":"Horowitz","full_name":"Horowitz, Jonathan"},{"full_name":"Ghashghaei, Troy","last_name":"Ghashghaei","first_name":"Troy"}],"publist_id":"4681","quality_controlled":"1","external_id":{"pmid":["23293287"]},"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3561788/"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1242/dev.085621","month":"02","intvolume":" 140","status":"public","title":"Neural development is dependent on the function of specificity protein 2 in cell cycle progression","_id":"2264","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","type":"journal_article","issue":"3","abstract":[{"text":"Faithful progression through the cell cycle is crucial to the maintenance and developmental potential of stem cells. Here, we demonstrate that neural stem cells (NSCs) and intermediate neural progenitor cells (NPCs) employ a zinc-finger transcription factor specificity protein 2 (Sp2) as a cell cycle regulator in two temporally and spatially distinct progenitor domains. Differential conditional deletion of Sp2 in early embryonic cerebral cortical progenitors, and perinatal olfactory bulb progenitors disrupted transitions through G1, G2 and M phases, whereas DNA synthesis appeared intact. Cell-autonomous function of Sp2 was identified by deletion of Sp2 using mosaic analysis with double markers, which clearly established that conditional Sp2-null NSCs and NPCs are M phase arrested in vivo. Importantly, conditional deletion of Sp2 led to a decline in the generation of NPCs and neurons in the developing and postnatal brains. Our findings implicate Sp2-dependent mechanisms as novel regulators of cell cycle progression, the absence of which disrupts neurogenesis in the embryonic and postnatal brain.","lang":"eng"}],"page":"552 - 561","citation":{"chicago":"Liang, Huixuan, Guanxi Xiao, Haifeng Yin, Simon Hippenmeyer, Jonathan Horowitz, and Troy Ghashghaei. “Neural Development Is Dependent on the Function of Specificity Protein 2 in Cell Cycle Progression.” Development. Company of Biologists, 2013. https://doi.org/10.1242/dev.085621.","short":"H. Liang, G. Xiao, H. Yin, S. Hippenmeyer, J. Horowitz, T. Ghashghaei, Development 140 (2013) 552–561.","mla":"Liang, Huixuan, et al. “Neural Development Is Dependent on the Function of Specificity Protein 2 in Cell Cycle Progression.” Development, vol. 140, no. 3, Company of Biologists, 2013, pp. 552–61, doi:10.1242/dev.085621.","apa":"Liang, H., Xiao, G., Yin, H., Hippenmeyer, S., Horowitz, J., & Ghashghaei, T. (2013). Neural development is dependent on the function of specificity protein 2 in cell cycle progression. Development. Company of Biologists. https://doi.org/10.1242/dev.085621","ieee":"H. Liang, G. Xiao, H. Yin, S. Hippenmeyer, J. Horowitz, and T. Ghashghaei, “Neural development is dependent on the function of specificity protein 2 in cell cycle progression,” Development, vol. 140, no. 3. Company of Biologists, pp. 552–561, 2013.","ista":"Liang H, Xiao G, Yin H, Hippenmeyer S, Horowitz J, Ghashghaei T. 2013. Neural development is dependent on the function of specificity protein 2 in cell cycle progression. Development. 140(3), 552–561.","ama":"Liang H, Xiao G, Yin H, Hippenmeyer S, Horowitz J, Ghashghaei T. Neural development is dependent on the function of specificity protein 2 in cell cycle progression. Development. 2013;140(3):552-561. doi:10.1242/dev.085621"},"publication":"Development","date_published":"2013-02-01T00:00:00Z","scopus_import":1,"article_processing_charge":"No","day":"01"},{"type":"journal_article","extern":1,"abstract":[{"lang":"eng","text":"This paper presents a parallel, implementation-friendly analytic visibility method for triangular meshes. Together with an analytic filter convolution, it allows for a fully analytic solution to anti-aliased 3D mesh rendering on parallel hardware. Building on recent works in computational geometry, we present a new edge-triangle intersection algorithm and a novel method to complete the boundaries of all visible triangle regions after a hidden line elimination step. All stages of the method are embarrassingly parallel and easily implementable on parallel hardware. A GPU implementation is discussed and performance characteristics of the method are shown and compared to traditional sampling-based rendering methods."}],"publist_id":"4675","issue":124,"status":"public","publication_status":"published","title":"Analytic Visibility on the GPU","intvolume":" 32","publisher":"Wiley-Blackwell","_id":"2269","year":"2013","acknowledgement":"Funding was provided by the FWF grant P20768-N13.\nWe want to thank the reviewers for their insightful and helpful remarks and Gernot Ziegler for providing help with CUDA. ","date_updated":"2021-01-12T06:56:25Z","date_created":"2018-12-11T11:56:40Z","volume":32,"author":[{"last_name":"Auzinger","first_name":"Thomas","orcid":"0000-0002-1546-3265","id":"4718F954-F248-11E8-B48F-1D18A9856A87","full_name":"Thomas Auzinger"},{"full_name":"Wimmer, Michael","last_name":"Wimmer","first_name":"Michael"},{"first_name":"Stefan","last_name":"Jeschke","id":"44D6411A-F248-11E8-B48F-1D18A9856A87","full_name":"Stefan Jeschke"}],"month":"05","day":"06","quality_controlled":0,"page":"409 - 418","publication":"Computer Graphics Forum","citation":{"ama":"Auzinger T, Wimmer M, Jeschke S. Analytic Visibility on the GPU. Computer Graphics Forum. 2013;32(124):409-418. doi:DOI: 10.1111/cgf.12061","ieee":"T. Auzinger, M. Wimmer, and S. Jeschke, “Analytic Visibility on the GPU,” Computer Graphics Forum, vol. 32, no. 124. Wiley-Blackwell, pp. 409–418, 2013.","apa":"Auzinger, T., Wimmer, M., & Jeschke, S. (2013). Analytic Visibility on the GPU. Computer Graphics Forum. Wiley-Blackwell. https://doi.org/DOI: 10.1111/cgf.12061","ista":"Auzinger T, Wimmer M, Jeschke S. 2013. Analytic Visibility on the GPU. Computer Graphics Forum. 32(124), 409–418.","short":"T. Auzinger, M. Wimmer, S. Jeschke, Computer Graphics Forum 32 (2013) 409–418.","mla":"Auzinger, Thomas, et al. “Analytic Visibility on the GPU.” Computer Graphics Forum, vol. 32, no. 124, Wiley-Blackwell, 2013, pp. 409–18, doi:DOI: 10.1111/cgf.12061.","chicago":"Auzinger, Thomas, Michael Wimmer, and Stefan Jeschke. “Analytic Visibility on the GPU.” Computer Graphics Forum. Wiley-Blackwell, 2013. https://doi.org/DOI: 10.1111/cgf.12061."},"doi":"DOI: 10.1111/cgf.12061","date_published":"2013-05-06T00:00:00Z"},{"publist_id":"4674","abstract":[{"text":"Representation languages for coalitional games are a key research area in algorithmic game theory. There is an inher-\r\nent tradeoff between how general a language is, allowing it to capture more elaborate games, and how hard it is computationally to optimize and solve such games. One prominent such language is the simple yet expressive\r\nWeighted Graph Games (WGGs) representation (Deng and Papadimitriou 1994), which maintains knowledge about synergies between agents in the form of an edge weighted graph. We consider the problem of finding the optimal coalition structure in WGGs. The agents in such games are vertices in a graph, and the value of a coalition is the sum of the weights of the edges present between coalition members. The optimal coalition structure is a partition of the agents to coalitions, that maximizes the sum of utilities obtained by the coalitions. We show that finding the optimal coalition structure is not only hard for general graphs, but is also intractable for restricted families such as planar graphs which are amenable for many other combinatorial problems. We then provide algorithms with constant factor approximations for planar, minorfree and bounded degree graphs.","lang":"eng"}],"type":"conference","author":[{"full_name":"Bachrach, Yoram","last_name":"Bachrach","first_name":"Yoram"},{"full_name":"Kohli, Pushmeet","first_name":"Pushmeet","last_name":"Kohli"},{"full_name":"Kolmogorov, Vladimir","first_name":"Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Morteza","last_name":"Zadimoghaddam","full_name":"Zadimoghaddam, Morteza"}],"oa_version":"None","date_updated":"2021-01-12T06:56:25Z","date_created":"2018-12-11T11:56:41Z","_id":"2270","year":"2013","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"VlKo"}],"publisher":"AAAI Press","title":"Optimal Coalition Structures in Cooperative Graph Games","publication_status":"published","status":"public","month":"12","day":"31","date_published":"2013-12-31T00:00:00Z","conference":{"location":"Bellevue, WA, United States","start_date":"2013-07-14","end_date":"2013-07-18","name":"AAAI: Conference on Artificial Intelligence"},"language":[{"iso":"eng"}],"external_id":{"arxiv":["1108.5248"]},"oa":1,"citation":{"chicago":"Bachrach, Yoram, Pushmeet Kohli, Vladimir Kolmogorov, and Morteza Zadimoghaddam. “Optimal Coalition Structures in Cooperative Graph Games,” 81–87. AAAI Press, 2013.","mla":"Bachrach, Yoram, et al. Optimal Coalition Structures in Cooperative Graph Games. AAAI Press, 2013, pp. 81–87.","short":"Y. Bachrach, P. Kohli, V. Kolmogorov, M. Zadimoghaddam, in:, AAAI Press, 2013, pp. 81–87.","ista":"Bachrach Y, Kohli P, Kolmogorov V, Zadimoghaddam M. 2013. Optimal Coalition Structures in Cooperative Graph Games. AAAI: Conference on Artificial Intelligence, 81–87.","apa":"Bachrach, Y., Kohli, P., Kolmogorov, V., & Zadimoghaddam, M. (2013). Optimal Coalition Structures in Cooperative Graph Games (pp. 81–87). Presented at the AAAI: Conference on Artificial Intelligence, Bellevue, WA, United States: AAAI Press.","ieee":"Y. Bachrach, P. Kohli, V. Kolmogorov, and M. Zadimoghaddam, “Optimal Coalition Structures in Cooperative Graph Games,” presented at the AAAI: Conference on Artificial Intelligence, Bellevue, WA, United States, 2013, pp. 81–87.","ama":"Bachrach Y, Kohli P, Kolmogorov V, Zadimoghaddam M. Optimal Coalition Structures in Cooperative Graph Games. In: AAAI Press; 2013:81-87."},"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1108.5248"}],"page":"81-87","quality_controlled":"1"},{"abstract":[{"lang":"eng","text":"We propose a new family of message passing techniques for MAP estimation in graphical models which we call Sequential Reweighted Message Passing (SRMP). Special cases include well-known techniques such as Min-Sum Diusion (MSD) and a faster Sequential Tree-Reweighted Message Passing (TRW-S). Importantly, our derivation is simpler than the original derivation of TRW-S, and does not involve a decomposition into trees. This allows easy generalizations. We present such a generalization for the case of higher-order graphical models, and test it on several real-world problems with promising results."}],"publist_id":"4671","extern":0,"type":"report","author":[{"last_name":"Kolmogorov","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Vladimir Kolmogorov"}],"date_created":"2018-12-11T11:56:42Z","date_updated":"2019-01-24T13:07:32Z","year":"2013","_id":"2273","title":"Reweighted message passing revisited","status":"public","publication_status":"published","publisher":"IST Austria","department":[{"_id":"VlKo"}],"day":"22","month":"09","date_published":"2013-09-22T00:00:00Z","main_file_link":[{"url":"http://arxiv.org/abs/1309.5655","open_access":"1"}],"citation":{"mla":"Kolmogorov, Vladimir. Reweighted Message Passing Revisited. IST Austria, 2013.","short":"V. Kolmogorov, Reweighted Message Passing Revisited, IST Austria, 2013.","chicago":"Kolmogorov, Vladimir. Reweighted Message Passing Revisited. IST Austria, 2013.","ama":"Kolmogorov V. Reweighted Message Passing Revisited. IST Austria; 2013.","ista":"Kolmogorov V. 2013. Reweighted message passing revisited, IST Austria,p.","apa":"Kolmogorov, V. (2013). Reweighted message passing revisited. IST Austria.","ieee":"V. Kolmogorov, Reweighted message passing revisited. IST Austria, 2013."},"oa":1,"quality_controlled":0},{"year":"2013","_id":"2278","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"A serrate-notch-canoe complex mediates essential interactions between glia and neuroepithelial cells during Drosophila optic lobe development","publication_status":"published","status":"public","intvolume":" 126","publisher":"Company of Biologists","department":[{"_id":"CaHe"}],"author":[{"full_name":"Pérez Gómez, Raquel","first_name":"Raquel","last_name":"Pérez Gómez"},{"last_name":"Slovakova","first_name":"Jana","id":"30F3F2F0-F248-11E8-B48F-1D18A9856A87","full_name":"Slovakova, Jana"},{"full_name":"Rives Quinto, Noemí","last_name":"Rives Quinto","first_name":"Noemí"},{"full_name":"Krejčí, Alena","first_name":"Alena","last_name":"Krejčí"},{"first_name":"Ana","last_name":"Carmena","full_name":"Carmena, Ana"}],"date_updated":"2021-01-12T06:56:29Z","date_created":"2018-12-11T11:56:43Z","volume":126,"oa_version":"None","type":"journal_article","abstract":[{"text":"It is firmly established that interactions between neurons and glia are fundamental across species for the correct establishment of a functional brain. Here, we found that the glia of the Drosophila larval brain display an essential non-autonomous role during the development of the optic lobe. The optic lobe develops from neuroepithelial cells that proliferate by dividing symmetrically until they switch to asymmetric/differentiative divisions that generate neuroblasts. The proneural gene lethal of scute (l9sc) is transiently activated by the epidermal growth factor receptor (EGFR)-Ras signal transduction pathway at the leading edge of a proneural wave that sweeps from medial to lateral neuroepithelium, promoting this switch. This process is tightly regulated by the tissue-autonomous function within the neuroepithelium of multiple signaling pathways, including EGFR-Ras and Notch. This study shows that the Notch ligand Serrate (Ser) is expressed in the glia and it forms a complex in vivo with Notch and Canoe, which colocalize at the adherens junctions of neuroepithelial cells. This complex is crucial for interactions between glia and neuroepithelial cells during optic lobe development. Ser is tissue-autonomously required in the glia where it activates Notch to regulate its proliferation, and non-autonomously in the neuroepithelium where Ser induces Notch signaling to avoid the premature activation of the EGFR-Ras pathway and hence of L9sc. Interestingly, different Notch activity reporters showed very different expression patterns in the glia and in the neuroepithelium, suggesting the existence of tissue-specific factors that promote the expression of particular Notch target genes or/and a reporter response dependent on different thresholds of Notch signaling.","lang":"eng"}],"publist_id":"4658","issue":"21","publication":"Journal of Cell Science","citation":{"chicago":"Pérez Gómez, Raquel, Jana Slovakova, Noemí Rives Quinto, Alena Krejčí, and Ana Carmena. “A Serrate-Notch-Canoe Complex Mediates Essential Interactions between Glia and Neuroepithelial Cells during Drosophila Optic Lobe Development.” Journal of Cell Science. Company of Biologists, 2013. https://doi.org/10.1242/jcs.125617.","short":"R. Pérez Gómez, J. Slovakova, N. Rives Quinto, A. Krejčí, A. Carmena, Journal of Cell Science 126 (2013) 4873–4884.","mla":"Pérez Gómez, Raquel, et al. “A Serrate-Notch-Canoe Complex Mediates Essential Interactions between Glia and Neuroepithelial Cells during Drosophila Optic Lobe Development.” Journal of Cell Science, vol. 126, no. 21, Company of Biologists, 2013, pp. 4873–84, doi:10.1242/jcs.125617.","ieee":"R. Pérez Gómez, J. Slovakova, N. Rives Quinto, A. Krejčí, and A. Carmena, “A serrate-notch-canoe complex mediates essential interactions between glia and neuroepithelial cells during Drosophila optic lobe development,” Journal of Cell Science, vol. 126, no. 21. Company of Biologists, pp. 4873–4884, 2013.","apa":"Pérez Gómez, R., Slovakova, J., Rives Quinto, N., Krejčí, A., & Carmena, A. (2013). A serrate-notch-canoe complex mediates essential interactions between glia and neuroepithelial cells during Drosophila optic lobe development. Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.125617","ista":"Pérez Gómez R, Slovakova J, Rives Quinto N, Krejčí A, Carmena A. 2013. A serrate-notch-canoe complex mediates essential interactions between glia and neuroepithelial cells during Drosophila optic lobe development. Journal of Cell Science. 126(21), 4873–4884.","ama":"Pérez Gómez R, Slovakova J, Rives Quinto N, Krejčí A, Carmena A. A serrate-notch-canoe complex mediates essential interactions between glia and neuroepithelial cells during Drosophila optic lobe development. Journal of Cell Science. 2013;126(21):4873-4884. doi:10.1242/jcs.125617"},"quality_controlled":"1","page":"4873 - 4884","doi":"10.1242/jcs.125617","date_published":"2013-11-01T00:00:00Z","language":[{"iso":"eng"}],"scopus_import":1,"day":"01","month":"11"},{"publisher":"IEEE","department":[{"_id":"JoCs"},{"_id":"VlKo"}],"publication_status":"published","status":"public","title":"Potts model, parametric maxflow and k-submodular functions","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2276","year":"2013","oa_version":"Preprint","date_created":"2018-12-11T11:56:43Z","date_updated":"2021-01-12T06:56:28Z","author":[{"id":"4B60654C-F248-11E8-B48F-1D18A9856A87","first_name":"Igor","last_name":"Gridchyn","full_name":"Gridchyn, Igor"},{"full_name":"Kolmogorov, Vladimir","last_name":"Kolmogorov","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"}],"type":"conference","publist_id":"4668","abstract":[{"text":"The problem of minimizing the Potts energy function frequently occurs in computer vision applications. One way to tackle this NP-hard problem was proposed by Kovtun [19, 20]. It identifies a part of an optimal solution by running k maxflow computations, where k is the number of labels. The number of “labeled” pixels can be significant in some applications, e.g. 50-93% in our tests for stereo. We show how to reduce the runtime to O (log k) maxflow computations (or one parametric maxflow computation). Furthermore, the output of our algorithm allows to speed-up the subsequent alpha expansion for the unlabeled part, or can be used as it is for time-critical applications. To derive our technique, we generalize the algorithm of Felzenszwalb et al. [7] for Tree Metrics . We also show a connection to k-submodular functions from combinatorial optimization, and discuss k-submodular relaxations for general energy functions.","lang":"eng"}],"page":"2320 - 2327","quality_controlled":"1","oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1310.1771","open_access":"1"}],"citation":{"ama":"Gridchyn I, Kolmogorov V. Potts model, parametric maxflow and k-submodular functions. In: IEEE; 2013:2320-2327. doi:10.1109/ICCV.2013.288","ista":"Gridchyn I, Kolmogorov V. 2013. Potts model, parametric maxflow and k-submodular functions. ICCV: International Conference on Computer Vision, 2320–2327.","ieee":"I. Gridchyn and V. Kolmogorov, “Potts model, parametric maxflow and k-submodular functions,” presented at the ICCV: International Conference on Computer Vision, Sydney, Australia, 2013, pp. 2320–2327.","apa":"Gridchyn, I., & Kolmogorov, V. (2013). Potts model, parametric maxflow and k-submodular functions (pp. 2320–2327). Presented at the ICCV: International Conference on Computer Vision, Sydney, Australia: IEEE. https://doi.org/10.1109/ICCV.2013.288","mla":"Gridchyn, Igor, and Vladimir Kolmogorov. Potts Model, Parametric Maxflow and k-Submodular Functions. IEEE, 2013, pp. 2320–27, doi:10.1109/ICCV.2013.288.","short":"I. Gridchyn, V. Kolmogorov, in:, IEEE, 2013, pp. 2320–2327.","chicago":"Gridchyn, Igor, and Vladimir Kolmogorov. “Potts Model, Parametric Maxflow and k-Submodular Functions,” 2320–27. IEEE, 2013. https://doi.org/10.1109/ICCV.2013.288."},"external_id":{"arxiv":["1310.1771"]},"language":[{"iso":"eng"}],"doi":"10.1109/ICCV.2013.288","date_published":"2013-12-01T00:00:00Z","conference":{"start_date":"2013-12-01","location":"Sydney, Australia","end_date":"2013-12-08","name":"ICCV: International Conference on Computer Vision"},"day":"01","month":"12"},{"page":"671 - 706","publication":"SIAM Review","citation":{"chicago":"Uhler, Caroline, and Stephen Wright. “Packing Ellipsoids with Overlap.” SIAM Review. Society for Industrial and Applied Mathematics , 2013. https://doi.org/10.1137/120872309.","short":"C. Uhler, S. Wright, SIAM Review 55 (2013) 671–706.","mla":"Uhler, Caroline, and Stephen Wright. “Packing Ellipsoids with Overlap.” SIAM Review, vol. 55, no. 4, Society for Industrial and Applied Mathematics , 2013, pp. 671–706, doi:10.1137/120872309.","apa":"Uhler, C., & Wright, S. (2013). Packing ellipsoids with overlap. SIAM Review. Society for Industrial and Applied Mathematics . https://doi.org/10.1137/120872309","ieee":"C. Uhler and S. Wright, “Packing ellipsoids with overlap,” SIAM Review, vol. 55, no. 4. Society for Industrial and Applied Mathematics , pp. 671–706, 2013.","ista":"Uhler C, Wright S. 2013. Packing ellipsoids with overlap. SIAM Review. 55(4), 671–706.","ama":"Uhler C, Wright S. Packing ellipsoids with overlap. SIAM Review. 2013;55(4):671-706. doi:10.1137/120872309"},"date_published":"2013-11-07T00:00:00Z","scopus_import":1,"day":"07","status":"public","title":"Packing ellipsoids with overlap","intvolume":" 55","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2280","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"The problem of packing ellipsoids of different sizes and shapes into an ellipsoidal container so as to minimize a measure of overlap between ellipsoids is considered. A bilevel optimization formulation is given, together with an algorithm for the general case and a simpler algorithm for the special case in which all ellipsoids are in fact spheres. Convergence results are proved and computational experience is described and illustrated. The motivating application-chromosome organization in the human cell nucleus-is discussed briefly, and some illustrative results are presented.","lang":"eng"}],"issue":"4","quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1204.0235"}],"external_id":{"arxiv":["1204.0235"]},"language":[{"iso":"eng"}],"doi":"10.1137/120872309","month":"11","publication_status":"published","department":[{"_id":"CaUh"}],"publisher":"Society for Industrial and Applied Mathematics ","year":"2013","date_created":"2018-12-11T11:56:44Z","date_updated":"2021-01-12T06:56:30Z","volume":55,"author":[{"last_name":"Uhler","first_name":"Caroline","orcid":"0000-0002-7008-0216","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","full_name":"Uhler, Caroline"},{"full_name":"Wright, Stephen","first_name":"Stephen","last_name":"Wright"}],"publist_id":"4655"},{"month":"03","language":[{"iso":"eng"}],"doi":"10.1002/ece3.465","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"file_date_updated":"2020-07-14T12:45:37Z","publist_id":"4644","date_updated":"2021-01-12T06:56:32Z","date_created":"2018-12-11T11:56:47Z","volume":3,"author":[{"orcid":"0000-0001-6118-0541","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","last_name":"Pickup","first_name":"Melinda","full_name":"Pickup, Melinda"},{"full_name":"Barrett, Spencer","first_name":"Spencer","last_name":"Barrett"}],"publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Wiley-Blackwell","year":"2013","day":"01","has_accepted_license":"1","scopus_import":1,"date_published":"2013-03-01T00:00:00Z","page":"629 - 639","publication":"Ecology and Evolution","citation":{"apa":"Pickup, M., & Barrett, S. (2013). The influence of demography and local mating environment on sex ratios in a wind-pollinated dioecious plant. Ecology and Evolution. Wiley-Blackwell. https://doi.org/10.1002/ece3.465","ieee":"M. Pickup and S. Barrett, “The influence of demography and local mating environment on sex ratios in a wind-pollinated dioecious plant,” Ecology and Evolution, vol. 3, no. 3. Wiley-Blackwell, pp. 629–639, 2013.","ista":"Pickup M, Barrett S. 2013. The influence of demography and local mating environment on sex ratios in a wind-pollinated dioecious plant. Ecology and Evolution. 3(3), 629–639.","ama":"Pickup M, Barrett S. The influence of demography and local mating environment on sex ratios in a wind-pollinated dioecious plant. Ecology and Evolution. 2013;3(3):629-639. doi:10.1002/ece3.465","chicago":"Pickup, Melinda, and Spencer Barrett. “The Influence of Demography and Local Mating Environment on Sex Ratios in a Wind-Pollinated Dioecious Plant.” Ecology and Evolution. Wiley-Blackwell, 2013. https://doi.org/10.1002/ece3.465.","short":"M. Pickup, S. Barrett, Ecology and Evolution 3 (2013) 629–639.","mla":"Pickup, Melinda, and Spencer Barrett. “The Influence of Demography and Local Mating Environment on Sex Ratios in a Wind-Pollinated Dioecious Plant.” Ecology and Evolution, vol. 3, no. 3, Wiley-Blackwell, 2013, pp. 629–39, doi:10.1002/ece3.465."},"abstract":[{"text":"Negative frequency-dependent selection should result in equal sex ratios in large populations of dioecious flowering plants, but deviations from equality are commonly reported. A variety of ecological and genetic factors can explain biased sex ratios, although the mechanisms involved are not well understood. Most dioecious species are long-lived and/or clonal complicating efforts to identify stages during the life cycle when biases develop. We investigated the demographic correlates of sex-ratio variation in two chromosome races of Rumex hastatulus, an annual, wind-pollinated colonizer of open habitats from the southern USA. We examined sex ratios in 46 populations and evaluated the hypothesis that the proximity of males in the local mating environment, through its influence on gametophytic selection, is the primary cause of female-biased sex ratios. Female-biased sex ratios characterized most populations of R. hastatulus (mean sex ratio = 0.62), with significant female bias in 89% of populations. Large, high-density populations had the highest proportion of females, whereas smaller, low-density populations had sex ratios closer to equality. Progeny sex ratios were more female biased when males were in closer proximity to females, a result consistent with the gametophytic selection hypothesis. Our results suggest that interactions between demographic and genetic factors are probably the main cause of female-biased sex ratios in R. hastatulus. The annual life cycle of this species may limit the scope for selection against males and may account for the weaker degree of bias in comparison with perennial Rumex species.","lang":"eng"}],"issue":"3","type":"journal_article","file":[{"checksum":"b5531bab4c0dec396bf5c8497fe178bf","date_created":"2018-12-12T10:17:35Z","date_updated":"2020-07-14T12:45:37Z","file_id":"5290","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":626949,"access_level":"open_access","file_name":"IST-2016-416-v1+1_Pickup_et_al-2013-Ecology_and_Evolution.pdf"}],"oa_version":"Published Version","pubrep_id":"416","status":"public","ddc":["576"],"title":"The influence of demography and local mating environment on sex ratios in a wind-pollinated dioecious plant","intvolume":" 3","_id":"2287","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"date_published":"2013-11-10T00:00:00Z","page":"1405 - 1414","publication":"Nature Cell Biology","citation":{"apa":"Campinho, P., Behrndt, M., Ranft, J., Risler, T., Minc, N., & Heisenberg, C.-P. J. (2013). Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading during zebrafish epiboly. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb2869","ieee":"P. Campinho, M. Behrndt, J. Ranft, T. Risler, N. Minc, and C.-P. J. Heisenberg, “Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading during zebrafish epiboly,” Nature Cell Biology, vol. 15. Nature Publishing Group, pp. 1405–1414, 2013.","ista":"Campinho P, Behrndt M, Ranft J, Risler T, Minc N, Heisenberg C-PJ. 2013. Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading during zebrafish epiboly. Nature Cell Biology. 15, 1405–1414.","ama":"Campinho P, Behrndt M, Ranft J, Risler T, Minc N, Heisenberg C-PJ. Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading during zebrafish epiboly. Nature Cell Biology. 2013;15:1405-1414. doi:10.1038/ncb2869","chicago":"Campinho, Pedro, Martin Behrndt, Jonas Ranft, Thomas Risler, Nicolas Minc, and Carl-Philipp J Heisenberg. “Tension-Oriented Cell Divisions Limit Anisotropic Tissue Tension in Epithelial Spreading during Zebrafish Epiboly.” Nature Cell Biology. Nature Publishing Group, 2013. https://doi.org/10.1038/ncb2869.","short":"P. Campinho, M. Behrndt, J. Ranft, T. Risler, N. Minc, C.-P.J. Heisenberg, Nature Cell Biology 15 (2013) 1405–1414.","mla":"Campinho, Pedro, et al. “Tension-Oriented Cell Divisions Limit Anisotropic Tissue Tension in Epithelial Spreading during Zebrafish Epiboly.” Nature Cell Biology, vol. 15, Nature Publishing Group, 2013, pp. 1405–14, doi:10.1038/ncb2869."},"day":"10","scopus_import":1,"oa_version":"Submitted Version","status":"public","title":"Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading during zebrafish epiboly","intvolume":" 15","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2282","abstract":[{"lang":"eng","text":"Epithelial spreading is a common and fundamental aspect of various developmental and disease-related processes such as epithelial closure and wound healing. A key challenge for epithelial tissues undergoing spreading is to increase their surface area without disrupting epithelial integrity. Here we show that orienting cell divisions by tension constitutes an efficient mechanism by which the enveloping cell layer (EVL) releases anisotropic tension while undergoing spreading during zebrafish epiboly. The control of EVL cell-division orientation by tension involves cell elongation and requires myosin II activity to align the mitotic spindle with the main tension axis. We also found that in the absence of tension-oriented cell divisions and in the presence of increased tissue tension, EVL cells undergo ectopic fusions, suggesting that the reduction of tension anisotropy by oriented cell divisions is required to prevent EVL cells from fusing. We conclude that cell-division orientation by tension constitutes a key mechanism for limiting tension anisotropy and thus promoting tissue spreading during EVL epiboly."}],"type":"journal_article","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"}],"language":[{"iso":"eng"}],"doi":"10.1038/ncb2869","quality_controlled":"1","project":[{"grant_number":"I 930-B20","_id":"252ABD0A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Control of Epithelial Cell Layer Spreading in Zebrafish"}],"oa":1,"main_file_link":[{"url":"http://hal.upmc.fr/hal-00983313/","open_access":"1"}],"month":"11","date_created":"2018-12-11T11:56:45Z","date_updated":"2023-02-21T17:02:44Z","volume":15,"author":[{"full_name":"Campinho, Pedro","orcid":"0000-0002-8526-5416","id":"3AFBBC42-F248-11E8-B48F-1D18A9856A87","last_name":"Campinho","first_name":"Pedro"},{"full_name":"Behrndt, Martin","first_name":"Martin","last_name":"Behrndt","id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jonas","last_name":"Ranft","full_name":"Ranft, Jonas"},{"last_name":"Risler","first_name":"Thomas","full_name":"Risler, Thomas"},{"first_name":"Nicolas","last_name":"Minc","full_name":"Minc, Nicolas"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"1403"}]},"publication_status":"published","department":[{"_id":"CaHe"}],"publisher":"Nature Publishing Group","acknowledgement":"This work was supported by the IST Austria and MPI-CBG ","year":"2013","publist_id":"4652"},{"scopus_import":1,"month":"11","day":"14","quality_controlled":"1","page":"1125 - 1136","publication":"Naturwissenschaften","citation":{"ista":"Pull C, Hughes W, Brown M. 2013. Tolerating an infection: an indirect benefit of co-founding queen associations in the ant Lasius niger . Naturwissenschaften. 100(12), 1125–1136.","apa":"Pull, C., Hughes, W., & Brown, M. (2013). Tolerating an infection: an indirect benefit of co-founding queen associations in the ant Lasius niger . Naturwissenschaften. Springer. https://doi.org/10.1007/s00114-013-1115-5","ieee":"C. Pull, W. Hughes, and M. Brown, “Tolerating an infection: an indirect benefit of co-founding queen associations in the ant Lasius niger ,” Naturwissenschaften, vol. 100, no. 12. Springer, pp. 1125–1136, 2013.","ama":"Pull C, Hughes W, Brown M. Tolerating an infection: an indirect benefit of co-founding queen associations in the ant Lasius niger . Naturwissenschaften. 2013;100(12):1125-1136. doi:10.1007/s00114-013-1115-5","chicago":"Pull, Christopher, William Hughes, and Markus Brown. “Tolerating an Infection: An Indirect Benefit of Co-Founding Queen Associations in the Ant Lasius Niger .” Naturwissenschaften. Springer, 2013. https://doi.org/10.1007/s00114-013-1115-5.","mla":"Pull, Christopher, et al. “Tolerating an Infection: An Indirect Benefit of Co-Founding Queen Associations in the Ant Lasius Niger .” Naturwissenschaften, vol. 100, no. 12, Springer, 2013, pp. 1125–36, doi:10.1007/s00114-013-1115-5.","short":"C. Pull, W. Hughes, M. Brown, Naturwissenschaften 100 (2013) 1125–1136."},"language":[{"iso":"eng"}],"doi":"10.1007/s00114-013-1115-5","date_published":"2013-11-14T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Pathogens exert a strong selection pressure on organisms to evolve effective immune defences. In addition to individual immunity, social organisms can act cooperatively to produce collective defences. In many ant species, queens have the option to found a colony alone or in groups with other, often unrelated, conspecifics. These associations are transient, usually lasting only as long as each queen benefits from the presence of others. In fact, once the first workers emerge, queens fight to the death for dominance. One potential advantage of co-founding may be that queens benefit from collective disease defences, such as mutual grooming, that act against common soil pathogens. We test this hypothesis by exposing single and co-founding queens to a fungal parasite, in order to assess whether queens in co-founding associations have improved survival. Surprisingly, co-foundresses exposed to the entomopathogenic fungus Metarhizium did not engage in cooperative disease defences, and consequently, we find no direct benefit of multiple queens on survival. However, an indirect benefit was observed, with parasite-exposed queens producing more brood when they co-founded, than when they were alone. We suggest this is due to a trade-off between reproduction and immunity. Additionally, we report an extraordinary ability of the queens to tolerate an infection for long periods after parasite exposure. Our study suggests that there are no social immunity benefits for co-founding ant queens, but that in parasite-rich environments, the presence of additional queens may nevertheless improve the chances of colony founding success."}],"issue":"12","publist_id":"4649","title":"Tolerating an infection: an indirect benefit of co-founding queen associations in the ant Lasius niger ","status":"public","publication_status":"published","intvolume":" 100","department":[{"_id":"SyCr"}],"publisher":"Springer","_id":"2283","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2013","date_updated":"2021-01-12T06:56:31Z","date_created":"2018-12-11T11:56:45Z","oa_version":"None","volume":100,"author":[{"full_name":"Pull, Christopher","id":"3C7F4840-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1122-3982","first_name":"Christopher","last_name":"Pull"},{"full_name":"Hughes, William","last_name":"Hughes","first_name":"William"},{"full_name":"Brown, Markus","id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87","first_name":"Markus","last_name":"Brown"}]},{"issue":"21","abstract":[{"lang":"eng","text":"The spatiotemporal control of cell divisions is a key factor in epithelial morphogenesis and patterning. Mao et al (2013) now describe how differential rates of proliferation within the Drosophila wing disc epithelium give rise to anisotropic tissue tension in peripheral/proximal regions of the disc. Such global tissue tension anisotropy in turn determines the orientation of cell divisions by controlling epithelial cell elongation."}],"type":"journal_article","oa_version":"Submitted Version","_id":"2286","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 32","status":"public","title":"The force and effect of cell proliferation","day":"04","scopus_import":1,"date_published":"2013-10-04T00:00:00Z","citation":{"mla":"Campinho, Pedro, and Carl-Philipp J. Heisenberg. “The Force and Effect of Cell Proliferation.” EMBO Journal, vol. 32, no. 21, Wiley-Blackwell, 2013, pp. 2783–84, doi:10.1038/emboj.2013.225.","short":"P. Campinho, C.-P.J. Heisenberg, EMBO Journal 32 (2013) 2783–2784.","chicago":"Campinho, Pedro, and Carl-Philipp J Heisenberg. “The Force and Effect of Cell Proliferation.” EMBO Journal. Wiley-Blackwell, 2013. https://doi.org/10.1038/emboj.2013.225.","ama":"Campinho P, Heisenberg C-PJ. The force and effect of cell proliferation. EMBO Journal. 2013;32(21):2783-2784. doi:10.1038/emboj.2013.225","ista":"Campinho P, Heisenberg C-PJ. 2013. The force and effect of cell proliferation. EMBO Journal. 32(21), 2783–2784.","apa":"Campinho, P., & Heisenberg, C.-P. J. (2013). The force and effect of cell proliferation. EMBO Journal. Wiley-Blackwell. https://doi.org/10.1038/emboj.2013.225","ieee":"P. Campinho and C.-P. J. Heisenberg, “The force and effect of cell proliferation,” EMBO Journal, vol. 32, no. 21. Wiley-Blackwell, pp. 2783–2784, 2013."},"publication":"EMBO Journal","page":"2783 - 2784","publist_id":"4645","author":[{"first_name":"Pedro","last_name":"Campinho","id":"3AFBBC42-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8526-5416","full_name":"Campinho, Pedro"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J"}],"volume":32,"date_updated":"2021-01-12T06:56:32Z","date_created":"2018-12-11T11:56:46Z","pmid":1,"year":"2013","publisher":"Wiley-Blackwell","department":[{"_id":"CaHe"}],"publication_status":"published","month":"10","doi":"10.1038/emboj.2013.225","language":[{"iso":"eng"}],"oa":1,"external_id":{"pmid":["24097062"]},"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3817470/"}],"quality_controlled":"1"},{"has_accepted_license":"1","day":"05","scopus_import":1,"date_published":"2013-10-05T00:00:00Z","citation":{"ieee":"T. A. Henzinger, “Quantitative reactive modeling and verification,” Computer Science Research and Development, vol. 28, no. 4. Springer, pp. 331–344, 2013.","apa":"Henzinger, T. A. (2013). Quantitative reactive modeling and verification. Computer Science Research and Development. Springer. https://doi.org/10.1007/s00450-013-0251-7","ista":"Henzinger TA. 2013. Quantitative reactive modeling and verification. Computer Science Research and Development. 28(4), 331–344.","ama":"Henzinger TA. Quantitative reactive modeling and verification. Computer Science Research and Development. 2013;28(4):331-344. doi:10.1007/s00450-013-0251-7","chicago":"Henzinger, Thomas A. “Quantitative Reactive Modeling and Verification.” Computer Science Research and Development. Springer, 2013. https://doi.org/10.1007/s00450-013-0251-7.","short":"T.A. Henzinger, Computer Science Research and Development 28 (2013) 331–344.","mla":"Henzinger, Thomas A. “Quantitative Reactive Modeling and Verification.” Computer Science Research and Development, vol. 28, no. 4, Springer, 2013, pp. 331–44, doi:10.1007/s00450-013-0251-7."},"publication":"Computer Science Research and Development","page":"331 - 344","issue":"4","abstract":[{"lang":"eng","text":"Formal verification aims to improve the quality of software by detecting errors before they do harm. At the basis of formal verification is the logical notion of correctness, which purports to capture whether or not a program behaves as desired. We suggest that the boolean partition of software into correct and incorrect programs falls short of the practical need to assess the behavior of software in a more nuanced fashion against multiple criteria. We therefore propose to introduce quantitative fitness measures for programs, specifically for measuring the function, performance, and robustness of reactive programs such as concurrent processes. This article describes the goals of the ERC Advanced Investigator Project QUAREM. The project aims to build and evaluate a theory of quantitative fitness measures for reactive models. Such a theory must strive to obtain quantitative generalizations of the paradigms that have been success stories in qualitative reactive modeling, such as compositionality, property-preserving abstraction and abstraction refinement, model checking, and synthesis. The theory will be evaluated not only in the context of software and hardware engineering, but also in the context of systems biology. In particular, we will use the quantitative reactive models and fitness measures developed in this project for testing hypotheses about the mechanisms behind data from biological experiments."}],"type":"journal_article","pubrep_id":"626","file":[{"file_size":570361,"content_type":"application/pdf","creator":"system","file_name":"IST-2016-626-v1+1_s00450-013-0251-7.pdf","access_level":"open_access","date_created":"2018-12-12T10:17:51Z","date_updated":"2020-07-14T12:45:37Z","checksum":"f117a00f9f046165bfa95595681e08a0","relation":"main_file","file_id":"5308"}],"oa_version":"Published Version","_id":"2289","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 28","title":"Quantitative reactive modeling and verification","status":"public","ddc":["000"],"month":"10","doi":"10.1007/s00450-013-0251-7","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"project":[{"grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","call_identifier":"FP7"}],"quality_controlled":"1","ec_funded":1,"publist_id":"4642","file_date_updated":"2020-07-14T12:45:37Z","author":[{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"volume":28,"date_updated":"2021-01-12T06:56:33Z","date_created":"2018-12-11T11:56:47Z","year":"2013","publisher":"Springer","department":[{"_id":"ToHe"}],"publication_status":"published"},{"publist_id":"4639","year":"2013","pmid":1,"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"National Academy of Sciences","author":[{"first_name":"Yohann","last_name":"Boutté","full_name":"Boutté, Yohann"},{"first_name":"Kristoffer","last_name":"Jonsson","full_name":"Jonsson, Kristoffer"},{"last_name":"Mcfarlane","first_name":"Heather","full_name":"Mcfarlane, Heather"},{"full_name":"Johnson, Errin","first_name":"Errin","last_name":"Johnson"},{"first_name":"Delphine","last_name":"Gendre","full_name":"Gendre, Delphine"},{"first_name":"Ranjan","last_name":"Swarup","full_name":"Swarup, Ranjan"},{"full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml"},{"full_name":"Samuels, Lacey","last_name":"Samuels","first_name":"Lacey"},{"full_name":"Robert, Stéphanie","last_name":"Robert","first_name":"Stéphanie"},{"first_name":"Rishikesh","last_name":"Bhalerao","full_name":"Bhalerao, Rishikesh"}],"date_updated":"2021-01-12T06:56:33Z","date_created":"2018-12-11T11:56:48Z","volume":110,"month":"10","oa":1,"external_id":{"pmid":["24043780"]},"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3791722/","open_access":"1"}],"quality_controlled":"1","doi":"10.1073/pnas.1309057110","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"lang":"eng","text":"The plant hormone indole-acetic acid (auxin) is essential for many aspects of plant development. Auxin-mediated growth regulation typically involves the establishment of an auxin concentration gradient mediated by polarly localized auxin transporters. The localization of auxin carriers and their amount at the plasma membrane are controlled by membrane trafficking processes such as secretion, endocytosis, and recycling. In contrast to endocytosis or recycling, how the secretory pathway mediates the localization of auxin carriers is not well understood. In this study we have used the differential cell elongation process during apical hook development to elucidate the mechanisms underlying the post-Golgi trafficking of auxin carriers in Arabidopsis. We show that differential cell elongation during apical hook development is defective in Arabidopsis mutant echidna (ech). ECH protein is required for the trans-Golgi network (TGN)-mediated trafficking of the auxin influx carrier AUX1 to the plasma membrane. In contrast, ech mutation only marginally perturbs the trafficking of the highly related auxin influx carrier LIKE-AUX1-3 or the auxin efflux carrier PIN-FORMED-3, both also involved in hook development. Electron tomography reveals that the trafficking defects in ech mutant are associated with the perturbation of secretory vesicle genesis from the TGN. Our results identify differential mechanisms for the post-Golgi trafficking of de novo-synthesized auxin carriers to plasma membrane from the TGN and reveal how trafficking of auxin influx carriers mediates the control of differential cell elongation in apical hook development."}],"issue":"40","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2290","title":"ECHIDNA mediated post Golgi trafficking of auxin carriers for differential cell elongation","status":"public","intvolume":" 110","oa_version":"Submitted Version","scopus_import":1,"day":"01","publication":"PNAS","citation":{"ieee":"Y. Boutté et al., “ECHIDNA mediated post Golgi trafficking of auxin carriers for differential cell elongation,” PNAS, vol. 110, no. 40. National Academy of Sciences, pp. 16259–16264, 2013.","apa":"Boutté, Y., Jonsson, K., Mcfarlane, H., Johnson, E., Gendre, D., Swarup, R., … Bhalerao, R. (2013). ECHIDNA mediated post Golgi trafficking of auxin carriers for differential cell elongation. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1309057110","ista":"Boutté Y, Jonsson K, Mcfarlane H, Johnson E, Gendre D, Swarup R, Friml J, Samuels L, Robert S, Bhalerao R. 2013. ECHIDNA mediated post Golgi trafficking of auxin carriers for differential cell elongation. PNAS. 110(40), 16259–16264.","ama":"Boutté Y, Jonsson K, Mcfarlane H, et al. ECHIDNA mediated post Golgi trafficking of auxin carriers for differential cell elongation. PNAS. 2013;110(40):16259-16264. doi:10.1073/pnas.1309057110","chicago":"Boutté, Yohann, Kristoffer Jonsson, Heather Mcfarlane, Errin Johnson, Delphine Gendre, Ranjan Swarup, Jiří Friml, Lacey Samuels, Stéphanie Robert, and Rishikesh Bhalerao. “ECHIDNA Mediated Post Golgi Trafficking of Auxin Carriers for Differential Cell Elongation.” PNAS. National Academy of Sciences, 2013. https://doi.org/10.1073/pnas.1309057110.","short":"Y. Boutté, K. Jonsson, H. Mcfarlane, E. Johnson, D. Gendre, R. Swarup, J. Friml, L. Samuels, S. Robert, R. Bhalerao, PNAS 110 (2013) 16259–16264.","mla":"Boutté, Yohann, et al. “ECHIDNA Mediated Post Golgi Trafficking of Auxin Carriers for Differential Cell Elongation.” PNAS, vol. 110, no. 40, National Academy of Sciences, 2013, pp. 16259–64, doi:10.1073/pnas.1309057110."},"page":"16259 - 16264","date_published":"2013-10-01T00:00:00Z"},{"publisher":"IEEE","department":[{"_id":"ChLa"}],"publication_status":"published","status":"public","title":"Drosophila Embryo Stage Annotation using Label Propagation","_id":"2294","year":"2013","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","date_updated":"2021-01-12T06:56:35Z","date_created":"2018-12-11T11:56:49Z","author":[{"first_name":"Tomas","last_name":"Kazmar","full_name":"Kazmar, Tomas"},{"full_name":"Kvon, Evgeny","first_name":"Evgeny","last_name":"Kvon"},{"first_name":"Alexander","last_name":"Stark","full_name":"Stark, Alexander"},{"full_name":"Lampert, Christoph","last_name":"Lampert","first_name":"Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"type":"conference","publist_id":"4634","ec_funded":1,"abstract":[{"text":"In this work we propose a system for automatic classification of Drosophila embryos into developmental stages.\r\nWhile the system is designed to solve an actual problem in biological research, we believe that the principle underly-\r\ning it is interesting not only for biologists, but also for researchers in computer vision. The main idea is to combine two orthogonal sources of information: one is a classifier trained on strongly invariant features, which makes it applicable to images of very different conditions, but also leads to rather noisy predictions. The other is a label propagation step based on a more powerful similarity measure that however is only consistent within specific subsets of the data at a time.\r\nIn our biological setup, the information sources are the shape and the staining patterns of embryo images. We show\r\nexperimentally that while neither of the methods can be used by itself to achieve satisfactory results, their combina-\r\ntion achieves prediction quality comparable to human performance.","lang":"eng"}],"project":[{"grant_number":"308036","_id":"2532554C-B435-11E9-9278-68D0E5697425","name":"Lifelong Learning of Visual Scene Understanding","call_identifier":"FP7"}],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"http://www.cv-foundation.org/openaccess/ICCV2013.py"}],"oa":1,"citation":{"chicago":"Kazmar, Tomas, Evgeny Kvon, Alexander Stark, and Christoph Lampert. “Drosophila Embryo Stage Annotation Using Label Propagation.” IEEE, 2013. https://doi.org/10.1109/ICCV.2013.139.","short":"T. Kazmar, E. Kvon, A. Stark, C. Lampert, in:, IEEE, 2013.","mla":"Kazmar, Tomas, et al. Drosophila Embryo Stage Annotation Using Label Propagation. IEEE, 2013, doi:10.1109/ICCV.2013.139.","ieee":"T. Kazmar, E. Kvon, A. Stark, and C. Lampert, “Drosophila Embryo Stage Annotation using Label Propagation,” presented at the ICCV: International Conference on Computer Vision, Sydney, Australia, 2013.","apa":"Kazmar, T., Kvon, E., Stark, A., & Lampert, C. (2013). Drosophila Embryo Stage Annotation using Label Propagation. Presented at the ICCV: International Conference on Computer Vision, Sydney, Australia: IEEE. https://doi.org/10.1109/ICCV.2013.139","ista":"Kazmar T, Kvon E, Stark A, Lampert C. 2013. Drosophila Embryo Stage Annotation using Label Propagation. ICCV: International Conference on Computer Vision.","ama":"Kazmar T, Kvon E, Stark A, Lampert C. Drosophila Embryo Stage Annotation using Label Propagation. In: IEEE; 2013. doi:10.1109/ICCV.2013.139"},"language":[{"iso":"eng"}],"date_published":"2013-12-01T00:00:00Z","doi":"10.1109/ICCV.2013.139","conference":{"start_date":"2013-12-01","location":"Sydney, Australia","end_date":"2013-12-08","name":"ICCV: International Conference on Computer Vision"},"scopus_import":1,"month":"12","day":"01"},{"page":"VI - 854","quality_controlled":"1","citation":{"ieee":"K. Chatterjee and J. Sgall, Eds., Mathematical Foundations of Computer Science 2013, vol. 8087. Springer, 2013, p. VI-854.","apa":"Chatterjee, K., & Sgall, J. (Eds.). (2013). Mathematical Foundations of Computer Science 2013 (Vol. 8087, p. VI-854). Presented at the MFCS: Mathematical Foundations of Computer Science, Klosterneuburg, Austria: Springer. https://doi.org/10.1007/978-3-642-40313-2","ista":"Chatterjee K, Sgall J eds. 2013. Mathematical Foundations of Computer Science 2013, Springer,p.","ama":"Chatterjee K, Sgall J, eds. Mathematical Foundations of Computer Science 2013. Vol 8087. Springer; 2013:VI-854. doi:10.1007/978-3-642-40313-2","chicago":"Chatterjee, Krishnendu, and Jiri Sgall, eds. Mathematical Foundations of Computer Science 2013. Vol. 8087. Lecture Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-40313-2.","short":"K. Chatterjee, J. Sgall, eds., Mathematical Foundations of Computer Science 2013, Springer, 2013.","mla":"Chatterjee, Krishnendu, and Jiri Sgall, editors. Mathematical Foundations of Computer Science 2013. Vol. 8087, Springer, 2013, p. VI-854, doi:10.1007/978-3-642-40313-2."},"language":[{"iso":"eng"}],"date_published":"2013-08-08T00:00:00Z","doi":"10.1007/978-3-642-40313-2","conference":{"location":"Klosterneuburg, Austria","start_date":"2013-08-26","end_date":"2013-08-30","name":"MFCS: Mathematical Foundations of Computer Science"},"series_title":"Lecture Notes in Computer Science","scopus_import":1,"publication_identifier":{"isbn":["978-3-642-40312-5"]},"month":"08","day":"08","intvolume":" 8087","department":[{"_id":"KrCh"}],"editor":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"full_name":"Sgall, Jiri","last_name":"Sgall","first_name":"Jiri"}],"publisher":"Springer","publication_status":"published","status":"public","title":"Mathematical Foundations of Computer Science 2013","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2292","year":"2013","volume":8087,"oa_version":"None","date_created":"2018-12-11T11:56:48Z","date_updated":"2020-08-11T10:09:45Z","alternative_title":["LNCS"],"type":"conference_editor","publist_id":"4636","abstract":[{"lang":"eng","text":"This book constitutes the thoroughly refereed conference proceedings of the 38th International Symposium on Mathematical Foundations of Computer Science, MFCS 2013, held in Klosterneuburg, Austria, in August 2013. The 67 revised full papers presented together with six invited talks were carefully selected from 191 submissions. Topics covered include algorithmic game theory, algorithmic learning theory, algorithms and data structures, automata, formal languages, bioinformatics, complexity, computational geometry, computer-assisted reasoning, concurrency theory, databases and knowledge-based systems, foundations of computing, logic in computer science, models of computation, semantics and verification of programs, and theoretical issues in artificial intelligence."}]},{"scopus_import":1,"day":"01","month":"12","quality_controlled":"1","page":"825 - 832","project":[{"call_identifier":"FP7","name":"Lifelong Learning of Visual Scene Understanding","grant_number":"308036","_id":"2532554C-B435-11E9-9278-68D0E5697425"}],"main_file_link":[{"open_access":"1","url":"www.cv-foundation.org/openaccess/content_iccv_2013/papers/Sharmanska_Learning_to_Rank_2013_ICCV_paper.pdf"}],"oa":1,"citation":{"ieee":"V. Sharmanska, N. Quadrianto, and C. Lampert, “Learning to rank using privileged information,” presented at the ICCV: International Conference on Computer Vision, Sydney, Australia, 2013, pp. 825–832.","apa":"Sharmanska, V., Quadrianto, N., & Lampert, C. (2013). Learning to rank using privileged information (pp. 825–832). Presented at the ICCV: International Conference on Computer Vision, Sydney, Australia: IEEE. https://doi.org/10.1109/ICCV.2013.107","ista":"Sharmanska V, Quadrianto N, Lampert C. 2013. Learning to rank using privileged information. ICCV: International Conference on Computer Vision, 825–832.","ama":"Sharmanska V, Quadrianto N, Lampert C. Learning to rank using privileged information. In: IEEE; 2013:825-832. doi:10.1109/ICCV.2013.107","chicago":"Sharmanska, Viktoriia, Novi Quadrianto, and Christoph Lampert. “Learning to Rank Using Privileged Information,” 825–32. IEEE, 2013. https://doi.org/10.1109/ICCV.2013.107.","short":"V. Sharmanska, N. Quadrianto, C. Lampert, in:, IEEE, 2013, pp. 825–832.","mla":"Sharmanska, Viktoriia, et al. Learning to Rank Using Privileged Information. IEEE, 2013, pp. 825–32, doi:10.1109/ICCV.2013.107."},"language":[{"iso":"eng"}],"conference":{"name":"ICCV: International Conference on Computer Vision","end_date":"2013-12-08","start_date":"2013-12-01","location":"Sydney, Australia"},"date_published":"2013-12-01T00:00:00Z","doi":"10.1109/ICCV.2013.107","type":"conference","abstract":[{"lang":"eng","text":"Many computer vision problems have an asymmetric distribution of information between training and test time. In this work, we study the case where we are given additional information about the training data, which however will not be available at test time. This situation is called learning using privileged information (LUPI). We introduce two maximum-margin techniques that are able to make use of this additional source of information, and we show that the framework is applicable to several scenarios that have been studied in computer vision before. Experiments with attributes, bounding boxes, image tags and rationales as additional information in object classification show promising results."}],"ec_funded":1,"publist_id":"4635","publication_status":"published","status":"public","title":"Learning to rank using privileged information","department":[{"_id":"ChLa"}],"publisher":"IEEE","_id":"2293","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2013","date_created":"2018-12-11T11:56:49Z","date_updated":"2023-02-23T10:36:41Z","oa_version":"Submitted Version","author":[{"full_name":"Sharmanska, Viktoriia","first_name":"Viktoriia","last_name":"Sharmanska","id":"2EA6D09E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0192-9308"},{"first_name":"Novi","last_name":"Quadrianto","full_name":"Quadrianto, Novi"},{"full_name":"Lampert, Christoph","first_name":"Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887"}]},{"month":"09","day":"01","scopus_import":1,"date_published":"2013-09-01T00:00:00Z","doi":"10.1109/CSF.2013.15","conference":{"location":"New Orleans, LA, United States","start_date":"2013-09-26","end_date":"2013-09-28","name":"CSF: Computer Security Foundations"},"language":[{"iso":"eng"}],"main_file_link":[{"url":"http://eprint.iacr.org/2013/492","open_access":"1"}],"oa":1,"citation":{"chicago":"Ferrara, Anna, Georg Fuchsbauer, and Bogdan Warinschi. “Cryptographically Enforced RBAC,” 115–29. IEEE, 2013. https://doi.org/10.1109/CSF.2013.15.","mla":"Ferrara, Anna, et al. Cryptographically Enforced RBAC. IEEE, 2013, pp. 115–29, doi:10.1109/CSF.2013.15.","short":"A. Ferrara, G. Fuchsbauer, B. Warinschi, in:, IEEE, 2013, pp. 115–129.","ista":"Ferrara A, Fuchsbauer G, Warinschi B. 2013. Cryptographically enforced RBAC. CSF: Computer Security Foundations, 115–129.","ieee":"A. Ferrara, G. Fuchsbauer, and B. Warinschi, “Cryptographically enforced RBAC,” presented at the CSF: Computer Security Foundations, New Orleans, LA, United States, 2013, pp. 115–129.","apa":"Ferrara, A., Fuchsbauer, G., & Warinschi, B. (2013). Cryptographically enforced RBAC (pp. 115–129). Presented at the CSF: Computer Security Foundations, New Orleans, LA, United States: IEEE. https://doi.org/10.1109/CSF.2013.15","ama":"Ferrara A, Fuchsbauer G, Warinschi B. Cryptographically enforced RBAC. In: IEEE; 2013:115-129. doi:10.1109/CSF.2013.15"},"page":"115 - 129","quality_controlled":"1","publist_id":"4637","abstract":[{"text":"Cryptographic access control promises to offer easily distributed trust and broader applicability, while reducing reliance on low-level online monitors. Traditional implementations of cryptographic access control rely on simple cryptographic primitives whereas recent endeavors employ primitives with richer functionality and security guarantees. Worryingly, few of the existing cryptographic access-control schemes come with precise guarantees, the gap between the policy specification and the implementation being analyzed only informally, if at all. In this paper we begin addressing this shortcoming. Unlike prior work that targeted ad-hoc policy specification, we look at the well-established Role-Based Access Control (RBAC) model, as used in a typical file system. In short, we provide a precise syntax for a computational version of RBAC, offer rigorous definitions for cryptographic policy enforcement of a large class of RBAC security policies, and demonstrate that an implementation based on attribute-based encryption meets our security notions. We view our main contribution as being at the conceptual level. Although we work with RBAC for concreteness, our general methodology could guide future research for uses of cryptography in other access-control models. \r\n","lang":"eng"}],"type":"conference","author":[{"full_name":"Ferrara, Anna","first_name":"Anna","last_name":"Ferrara"},{"full_name":"Fuchsbauer, Georg","first_name":"Georg","last_name":"Fuchsbauer","id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Bogdan","last_name":"Warinschi","full_name":"Warinschi, Bogdan"}],"oa_version":"Submitted Version","date_updated":"2021-01-12T06:56:34Z","date_created":"2018-12-11T11:56:48Z","year":"2013","_id":"2291","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"KrPi"}],"publisher":"IEEE","title":"Cryptographically enforced RBAC","publication_status":"published","status":"public"},{"publist_id":"4643","abstract":[{"text":"This book constitutes the proceedings of the 11th International Conference on Computational Methods in Systems Biology, CMSB 2013, held in Klosterneuburg, Austria, in September 2013. The 15 regular papers included in this volume were carefully reviewed and selected from 27 submissions. They deal with computational models for all levels, from molecular and cellular, to organs and entire organisms.","lang":"eng"}],"type":"conference_editor","alternative_title":["LNCS"],"volume":8130,"oa_version":"None","date_updated":"2019-08-02T12:37:44Z","date_created":"2018-12-11T11:56:47Z","year":"2013","_id":"2288","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 8130","publisher":"Springer","department":[{"_id":"ToHe"}],"editor":[{"full_name":"Gupta, Ashutosh","id":"335E5684-F248-11E8-B48F-1D18A9856A87","first_name":"Ashutosh","last_name":"Gupta"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger"}],"status":"public","title":"Computational Methods in Systems Biology","publication_status":"published","publication_identifier":{"isbn":["978-3-642-40707-9"]},"day":"01","month":"07","date_published":"2013-07-01T00:00:00Z","doi":"10.1007/978-3-642-40708-6","conference":{"end_date":"2013-09-24","location":"Klosterneuburg, Austria","start_date":"2013-09-22","name":"CMSB: Computational Methods in Systems Biology"},"language":[{"iso":"eng"}],"citation":{"ama":"Gupta A, Henzinger TA, eds. Computational Methods in Systems Biology. Vol 8130. Springer; 2013. doi:10.1007/978-3-642-40708-6","ista":"Gupta A, Henzinger TA eds. 2013. Computational Methods in Systems Biology, Springer,p.","ieee":"A. Gupta and T. A. Henzinger, Eds., Computational Methods in Systems Biology, vol. 8130. Springer, 2013.","apa":"Gupta, A., & Henzinger, T. A. (Eds.). (2013). Computational Methods in Systems Biology (Vol. 8130). Presented at the CMSB: Computational Methods in Systems Biology, Klosterneuburg, Austria: Springer. https://doi.org/10.1007/978-3-642-40708-6","mla":"Gupta, Ashutosh, and Thomas A. Henzinger, editors. Computational Methods in Systems Biology. Vol. 8130, Springer, 2013, doi:10.1007/978-3-642-40708-6.","short":"A. Gupta, T.A. Henzinger, eds., Computational Methods in Systems Biology, Springer, 2013.","chicago":"Gupta, Ashutosh, and Thomas A Henzinger, eds. Computational Methods in Systems Biology. Vol. 8130. Springer, 2013. https://doi.org/10.1007/978-3-642-40708-6."},"quality_controlled":"1"},{"scopus_import":1,"has_accepted_license":"1","day":"01","page":"150 - 171","citation":{"ista":"Dragoi C, Enea C, Sighireanu M. 2013. Local shape analysis for overlaid data structures. SAS: Static Analysis Symposium, LNCS, vol. 7935, 150–171.","ieee":"C. Dragoi, C. Enea, and M. Sighireanu, “Local shape analysis for overlaid data structures,” presented at the SAS: Static Analysis Symposium, Seattle, WA, United States, 2013, vol. 7935, pp. 150–171.","apa":"Dragoi, C., Enea, C., & Sighireanu, M. (2013). Local shape analysis for overlaid data structures (Vol. 7935, pp. 150–171). Presented at the SAS: Static Analysis Symposium, Seattle, WA, United States: Springer. https://doi.org/10.1007/978-3-642-38856-9_10","ama":"Dragoi C, Enea C, Sighireanu M. Local shape analysis for overlaid data structures. In: Vol 7935. Springer; 2013:150-171. doi:10.1007/978-3-642-38856-9_10","chicago":"Dragoi, Cezara, Constantin Enea, and Mihaela Sighireanu. “Local Shape Analysis for Overlaid Data Structures,” 7935:150–71. Springer, 2013. https://doi.org/10.1007/978-3-642-38856-9_10.","mla":"Dragoi, Cezara, et al. Local Shape Analysis for Overlaid Data Structures. Vol. 7935, Springer, 2013, pp. 150–71, doi:10.1007/978-3-642-38856-9_10.","short":"C. Dragoi, C. Enea, M. Sighireanu, in:, Springer, 2013, pp. 150–171."},"date_published":"2013-01-01T00:00:00Z","alternative_title":["LNCS"],"type":"conference","abstract":[{"lang":"eng","text":"We present a shape analysis for programs that manipulate overlaid data structures which share sets of objects. The abstract domain contains Separation Logic formulas that (1) combine a per-object separating conjunction with a per-field separating conjunction and (2) constrain a set of variables interpreted as sets of objects. The definition of the abstract domain operators is based on a notion of homomorphism between formulas, viewed as graphs, used recently to define optimal decision procedures for fragments of the Separation Logic. Based on a Frame Rule that supports the two versions of the separating conjunction, the analysis is able to reason in a modular manner about non-overlaid data structures and then, compose information only at a few program points, e.g., procedure returns. 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Our contributions are as follows: (a) We present detailed formal specifications for the AHB Arbiter incorporating the missing details, and obtain significant improvements in the synthesis results (both with respect to the number of gates in the synthesized circuit and with respect to the time taken to synthesize the circuit), and (b) we present formal specifications to generate compact circuits for the remaining two main components of AMBA AHB, namely, AHB Master and AHB Slave. 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The language also provides default liveness checks that an event cannot be potentially deferred forever. P was used to implement and verify the core of the USB device driver stack that ships with Microsoft Windows 8. The resulting driver is more reliable and performs better than its prior incarnation (which did not use P); we have more confidence in the robustness of its design due to the language abstractions and verification provided by P."}],"publisher":"ACM","department":[{"_id":"ToHe"}],"status":"public","publication_status":"published","title":"P: Safe asynchronous event-driven programming","year":"2013","_id":"2301","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","date_created":"2018-12-11T11:56:52Z","date_updated":"2021-01-12T06:56:38Z","author":[{"last_name":"Desai","first_name":"Ankush","full_name":"Desai, Ankush"},{"last_name":"Gupta","first_name":"Vivek","full_name":"Gupta, Vivek"},{"first_name":"Ethan","last_name":"Jackson","full_name":"Jackson, Ethan"},{"first_name":"Shaz","last_name":"Qadeer","full_name":"Qadeer, Shaz"},{"first_name":"Sriram","last_name":"Rajamani","full_name":"Rajamani, Sriram"},{"full_name":"Zufferey, Damien","orcid":"0000-0002-3197-8736","id":"4397AC76-F248-11E8-B48F-1D18A9856A87","last_name":"Zufferey","first_name":"Damien"}]},{"scopus_import":1,"day":"01","citation":{"ama":"Giuliani A, Lieb É, Seiringer R. Realization of stripes and slabs in two and three dimensions. Physical Review B. 2013;88(6). doi:10.1103/PhysRevB.88.064401","ista":"Giuliani A, Lieb É, Seiringer R. 2013. Realization of stripes and slabs in two and three dimensions. Physical Review B. 88(6), 064401.","apa":"Giuliani, A., Lieb, É., & Seiringer, R. (2013). Realization of stripes and slabs in two and three dimensions. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.88.064401","ieee":"A. Giuliani, É. Lieb, and R. Seiringer, “Realization of stripes and slabs in two and three dimensions,” Physical Review B, vol. 88, no. 6. American Physical Society, 2013.","mla":"Giuliani, Alessandro, et al. “Realization of Stripes and Slabs in Two and Three Dimensions.” Physical Review B, vol. 88, no. 6, 064401, American Physical Society, 2013, doi:10.1103/PhysRevB.88.064401.","short":"A. Giuliani, É. Lieb, R. Seiringer, Physical Review B 88 (2013).","chicago":"Giuliani, Alessandro, Élliott Lieb, and Robert Seiringer. “Realization of Stripes and Slabs in Two and Three Dimensions.” Physical Review B. American Physical Society, 2013. https://doi.org/10.1103/PhysRevB.88.064401."},"publication":"Physical Review B","date_published":"2013-08-01T00:00:00Z","type":"journal_article","issue":"6","abstract":[{"text":"We consider Ising models in two and three dimensions with nearest neighbor ferromagnetic interactions and long-range, power law decaying, antiferromagnetic interactions. If the strength of the ferromagnetic coupling J is larger than a critical value Jc, then the ground state is homogeneous and ferromagnetic. As the critical value is approached from smaller values of J, it is believed that the ground state consists of a periodic array of stripes (d=2) or slabs (d=3), all of the same size and alternating magnetization. Here we prove rigorously that the ground state energy per site converges to that of the optimal periodic striped or slabbed state, in the limit that J tends to the ferromagnetic transition point. While this theorem does not prove rigorously that the ground state is precisely striped or slabbed, it does prove that in any suitably large box the ground state is striped or slabbed with high probability.","lang":"eng"}],"intvolume":" 88","title":"Realization of stripes and slabs in two and three dimensions","status":"public","_id":"2300","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","month":"08","quality_controlled":"1","oa":1,"external_id":{"arxiv":["1305.5323"]},"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1305.5323"}],"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevB.88.064401","article_number":"064401","publist_id":"4627","department":[{"_id":"RoSe"}],"publisher":"American Physical Society","publication_status":"published","year":"2013","volume":88,"date_updated":"2021-01-12T06:56:38Z","date_created":"2018-12-11T11:56:51Z","author":[{"full_name":"Giuliani, Alessandro","first_name":"Alessandro","last_name":"Giuliani"},{"first_name":"Élliott","last_name":"Lieb","full_name":"Lieb, Élliott"},{"full_name":"Seiringer, Robert","first_name":"Robert","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521"}]},{"article_type":"review","quality_controlled":"1","page":"557 - 568","publication":"Frontiers in Biology","citation":{"chicago":"Hippenmeyer, Simon. “Dissection of Gene Function at Clonal Level Using Mosaic Analysis with Double Markers.” Frontiers in Biology. Springer, 2013. https://doi.org/10.1007/s11515-013-1279-6.","mla":"Hippenmeyer, Simon. “Dissection of Gene Function at Clonal Level Using Mosaic Analysis with Double Markers.” Frontiers in Biology, vol. 8, no. 6, Springer, 2013, pp. 557–68, doi:10.1007/s11515-013-1279-6.","short":"S. Hippenmeyer, Frontiers in Biology 8 (2013) 557–568.","ista":"Hippenmeyer S. 2013. Dissection of gene function at clonal level using mosaic analysis with double markers. Frontiers in Biology. 8(6), 557–568.","ieee":"S. Hippenmeyer, “Dissection of gene function at clonal level using mosaic analysis with double markers,” Frontiers in Biology, vol. 8, no. 6. Springer, pp. 557–568, 2013.","apa":"Hippenmeyer, S. (2013). Dissection of gene function at clonal level using mosaic analysis with double markers. Frontiers in Biology. Springer. https://doi.org/10.1007/s11515-013-1279-6","ama":"Hippenmeyer S. Dissection of gene function at clonal level using mosaic analysis with double markers. Frontiers in Biology. 2013;8(6):557-568. doi:10.1007/s11515-013-1279-6"},"language":[{"iso":"eng"}],"doi":"10.1007/s11515-013-1279-6","date_published":"2013-09-03T00:00:00Z","scopus_import":1,"month":"09","day":"03","title":"Dissection of gene function at clonal level using mosaic analysis with double markers","status":"public","publication_status":"published","department":[{"_id":"SiHi"}],"publisher":"Springer","intvolume":" 8","_id":"2303","year":"2013","acknowledgement":"This work was supported by IST Austria institutional funds.","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:56:52Z","date_updated":"2021-01-12T06:56:39Z","volume":8,"oa_version":"None","author":[{"full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","first_name":"Simon","last_name":"Hippenmeyer"}],"type":"journal_article","abstract":[{"lang":"eng","text":"MADM (Mosaic Analysis with Double Markers) technology offers a genetic approach in mice to visualize and concomitantly manipulate genetically defined cells at clonal level and single cell resolution. MADM employs Cre recombinase/loxP-dependent interchromosomal mitotic recombination to reconstitute two split marker genes—green GFP and red tdTomato—and can label sparse clones of homozygous mutant cells in one color and wild-type cells in the other color in an otherwise unlabeled background. At present, major MADM applications include lineage tracing, single cell labeling, conditional knockouts in small populations of cells and induction of uniparental chromosome disomy to assess effects of genomic imprinting. MADM can be applied universally in the mouse with the sole limitation being the specificity of the promoter controlling Cre recombinase expression. Here I review recent developments and extensions of the MADM technique and give an overview of the major discoveries and progresses enabled by the implementation of the novel genetic MADM tools."}],"publist_id":"4624","issue":"6"},{"date_updated":"2021-01-12T06:56:39Z","date_created":"2018-12-11T11:56:53Z","volume":43,"oa_version":"None","author":[{"id":"2A77D7A2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8379-3768","first_name":"Florian","last_name":"Pausinger","full_name":"Pausinger, Florian"}],"status":"public","publication_status":"published","title":"Van der Corput sequences and linear permutations","intvolume":" 43","department":[{"_id":"HeEd"}],"publisher":"Elsevier","acknowledgement":"This research is supported by the Graduate school of IST Austria (Institute of Science and Technology Austria).","_id":"2304","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2013","abstract":[{"lang":"eng","text":"This extended abstract is concerned with the irregularities of distribution of one-dimensional permuted van der Corput sequences that are generated from linear permutations. We show how to obtain upper bounds for the discrepancy and diaphony of these sequences, by relating them to Kronecker sequences and applying earlier results of Faure and Niederreiter."}],"publist_id":"4623","type":"journal_article","language":[{"iso":"eng"}],"date_published":"2013-09-05T00:00:00Z","doi":"10.1016/j.endm.2013.07.008","quality_controlled":"1","page":"43 - 50","publication":"Electronic Notes in Discrete Mathematics","citation":{"ista":"Pausinger F. 2013. Van der Corput sequences and linear permutations. Electronic Notes in Discrete Mathematics. 43, 43–50.","ieee":"F. Pausinger, “Van der Corput sequences and linear permutations,” Electronic Notes in Discrete Mathematics, vol. 43. Elsevier, pp. 43–50, 2013.","apa":"Pausinger, F. (2013). Van der Corput sequences and linear permutations. Electronic Notes in Discrete Mathematics. Elsevier. https://doi.org/10.1016/j.endm.2013.07.008","ama":"Pausinger F. Van der Corput sequences and linear permutations. Electronic Notes in Discrete Mathematics. 2013;43:43-50. doi:10.1016/j.endm.2013.07.008","chicago":"Pausinger, Florian. “Van Der Corput Sequences and Linear Permutations.” Electronic Notes in Discrete Mathematics. Elsevier, 2013. https://doi.org/10.1016/j.endm.2013.07.008.","mla":"Pausinger, Florian. “Van Der Corput Sequences and Linear Permutations.” Electronic Notes in Discrete Mathematics, vol. 43, Elsevier, 2013, pp. 43–50, doi:10.1016/j.endm.2013.07.008.","short":"F. Pausinger, Electronic Notes in Discrete Mathematics 43 (2013) 43–50."},"day":"05","month":"09","scopus_import":1},{"article_processing_charge":"No","language":[{"iso":"eng"}],"conference":{"name":"ICMP: International Congress on Mathematical Physics"},"doi":"10.1142/9789814449243_0063","date_published":"2013-01-01T00:00:00Z","page":"610-619","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1209.4046"}],"external_id":{"arxiv":["1209.4046"]},"citation":{"ista":"Seiringer R, Yngvason J, Zagrebnov V. 2013. Disordered Bose-Einstein condensates with interaction. ICMP: International Congress on Mathematical Physics, 610–619.","ieee":"R. Seiringer, J. Yngvason, and V. Zagrebnov, “Disordered Bose-Einstein condensates with interaction,” presented at the ICMP: International Congress on Mathematical Physics, 2013, pp. 610–619.","apa":"Seiringer, R., Yngvason, J., & Zagrebnov, V. (2013). Disordered Bose-Einstein condensates with interaction (pp. 610–619). Presented at the ICMP: International Congress on Mathematical Physics, World Scientific Publishing. https://doi.org/10.1142/9789814449243_0063","ama":"Seiringer R, Yngvason J, Zagrebnov V. Disordered Bose-Einstein condensates with interaction. In: World Scientific Publishing; 2013:610-619. doi:10.1142/9789814449243_0063","chicago":"Seiringer, Robert, Jakob Yngvason, and Valentin Zagrebnov. “Disordered Bose-Einstein Condensates with Interaction,” 610–19. World Scientific Publishing, 2013. https://doi.org/10.1142/9789814449243_0063.","mla":"Seiringer, Robert, et al. Disordered Bose-Einstein Condensates with Interaction. World Scientific Publishing, 2013, pp. 610–19, doi:10.1142/9789814449243_0063.","short":"R. Seiringer, J. Yngvason, V. Zagrebnov, in:, World Scientific Publishing, 2013, pp. 610–619."},"oa":1,"extern":"1","abstract":[{"text":" We study the effects of random scatterers on the ground state of the one-dimensional Lieb-Liniger model of interacting bosons on the unit interval in the Gross-Pitaevskii regime. We prove that Bose Einstein condensation survives even a strong random potential with a high density of scatterers. The character of the wave function of the condensate, however, depends in an essential way on the interplay between randomness and the strength of the two-body interaction. For low density of scatterers or strong interactions the wave function extends over the whole interval. High density of scatterers and weak interaction, on the other hand, leads to localization of the wave function in a fragmented subset of the interval. ","lang":"eng"}],"publist_id":"4612","type":"conference","date_created":"2018-12-11T11:56:57Z","date_updated":"2021-01-12T06:56:43Z","oa_version":"None","author":[{"full_name":"Seiringer, Robert","last_name":"Seiringer","first_name":"Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Yngvason, Jakob","first_name":"Jakob","last_name":"Yngvason"},{"first_name":"Valentin","last_name":"Zagrebnov","full_name":"Zagrebnov, Valentin"}],"title":"Disordered Bose-Einstein condensates with interaction","status":"public","publication_status":"published","publisher":"World Scientific Publishing","_id":"2315","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2013"},{"type":"conference","abstract":[{"lang":"eng","text":"In a recent paper [7] we give the first rigorous derivation of the celebrated Ginzburg-Landau (GL)theory, starting from the microscopic Bardeen- Cooper-Schrieffer (BCS)model. Here we present our results in the simplified case of a one-dimensional system of particles interacting via a δ-potential."}],"publist_id":"4608","extern":1,"_id":"2319","year":"2013","status":"public","publication_status":"published","title":" Derivation of Ginzburg-Landau theory for a one-dimensional system with contact interaction","publisher":"Springer","author":[{"full_name":"Frank, Rupert L","last_name":"Frank","first_name":"Rupert"},{"full_name":"Hainzl, Christian","last_name":"Hainzl","first_name":"Christian"},{"full_name":"Robert Seiringer","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","first_name":"Robert"},{"full_name":"Solovej, Jan P","last_name":"Solovej","first_name":"Jan"}],"date_updated":"2021-01-12T06:56:45Z","date_created":"2018-12-11T11:56:58Z","day":"01","month":"01","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1103.1866"}],"oa":1,"citation":{"ama":"Frank R, Hainzl C, Seiringer R, Solovej J. Derivation of Ginzburg-Landau theory for a one-dimensional system with contact interaction. In: Springer; 2013:57-88. doi:10.1007/978-3-0348-0531-5_3","ista":"Frank R, Hainzl C, Seiringer R, Solovej J. 2013. Derivation of Ginzburg-Landau theory for a one-dimensional system with contact interaction. OTAMP: Operator Theory, Analysis and Mathematical Physics, 57–88.","apa":"Frank, R., Hainzl, C., Seiringer, R., & Solovej, J. (2013). Derivation of Ginzburg-Landau theory for a one-dimensional system with contact interaction (pp. 57–88). Presented at the OTAMP: Operator Theory, Analysis and Mathematical Physics, Springer. https://doi.org/10.1007/978-3-0348-0531-5_3","ieee":"R. Frank, C. Hainzl, R. Seiringer, and J. Solovej, “ Derivation of Ginzburg-Landau theory for a one-dimensional system with contact interaction,” presented at the OTAMP: Operator Theory, Analysis and Mathematical Physics, 2013, pp. 57–88.","mla":"Frank, Rupert, et al. Derivation of Ginzburg-Landau Theory for a One-Dimensional System with Contact Interaction. Springer, 2013, pp. 57–88, doi:10.1007/978-3-0348-0531-5_3.","short":"R. Frank, C. Hainzl, R. Seiringer, J. Solovej, in:, Springer, 2013, pp. 57–88.","chicago":"Frank, Rupert, Christian Hainzl, Robert Seiringer, and Jan Solovej. “ Derivation of Ginzburg-Landau Theory for a One-Dimensional System with Contact Interaction,” 57–88. Springer, 2013. https://doi.org/10.1007/978-3-0348-0531-5_3."},"quality_controlled":0,"page":"57 - 88","conference":{"name":"OTAMP: Operator Theory, Analysis and Mathematical Physics"},"date_published":"2013-01-01T00:00:00Z","doi":"10.1007/978-3-0348-0531-5_3"},{"month":"08","oa":1,"quality_controlled":"1","project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425"}],"conference":{"name":"CONCUR: Concurrency Theory","start_date":"2013-08-27","location":"Buenos Aires, Argentina","end_date":"2013-08-30"},"doi":"10.1007/978-3-642-40184-8_18","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:45:39Z","ec_funded":1,"publist_id":"4598","year":"2013","publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","author":[{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A"},{"id":"4C7638DA-F248-11E8-B48F-1D18A9856A87","last_name":"Sezgin","first_name":"Ali","full_name":"Sezgin, Ali"},{"full_name":"Vafeiadis, Viktor","first_name":"Viktor","last_name":"Vafeiadis"}],"related_material":{"record":[{"status":"public","relation":"later_version","id":"1832"}]},"date_updated":"2023-02-23T10:16:27Z","date_created":"2018-12-11T11:57:01Z","volume":8052,"scopus_import":1,"series_title":"Lecture Notes in Computer Science","day":"01","has_accepted_license":"1","citation":{"ista":"Henzinger TA, Sezgin A, Vafeiadis V. 2013. Aspect-oriented linearizability proofs. 8052, 242–256.","ieee":"T. A. Henzinger, A. Sezgin, and V. Vafeiadis, “Aspect-oriented linearizability proofs,” vol. 8052. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, pp. 242–256, 2013.","apa":"Henzinger, T. A., Sezgin, A., & Vafeiadis, V. (2013). Aspect-oriented linearizability proofs. Presented at the CONCUR: Concurrency Theory, Buenos Aires, Argentina: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.1007/978-3-642-40184-8_18","ama":"Henzinger TA, Sezgin A, Vafeiadis V. Aspect-oriented linearizability proofs. 2013;8052:242-256. doi:10.1007/978-3-642-40184-8_18","chicago":"Henzinger, Thomas A, Ali Sezgin, and Viktor Vafeiadis. “Aspect-Oriented Linearizability Proofs.” Lecture Notes in Computer Science. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2013. https://doi.org/10.1007/978-3-642-40184-8_18.","mla":"Henzinger, Thomas A., et al. Aspect-Oriented Linearizability Proofs. Vol. 8052, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2013, pp. 242–56, doi:10.1007/978-3-642-40184-8_18.","short":"T.A. Henzinger, A. Sezgin, V. Vafeiadis, 8052 (2013) 242–256."},"page":"242 - 256","date_published":"2013-08-01T00:00:00Z","type":"conference","alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"Linearizability of concurrent data structures is usually proved by monolithic simulation arguments relying on identifying the so-called linearization points. Regrettably, such proofs, whether manual or automatic, are often complicated and scale poorly to advanced non-blocking concurrency patterns, such as helping and optimistic updates.\r\nIn response, we propose a more modular way of checking linearizability of concurrent queue algorithms that does not involve identifying linearization points. We reduce the task of proving linearizability with respect to the queue specification to establishing four basic properties, each of which can be proved independently by simpler arguments. As a demonstration of our approach, we verify the Herlihy and Wing queue, an algorithm that is challenging to verify by a simulation proof."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2328","ddc":["000","004"],"title":"Aspect-oriented linearizability proofs","status":"public","intvolume":" 8052","pubrep_id":"197","oa_version":"Submitted Version","file":[{"access_level":"open_access","file_name":"IST-2014-197-v1+1_main-queue-verification.pdf","creator":"system","file_size":337059,"content_type":"application/pdf","file_id":"4721","relation":"main_file","checksum":"bdbb520de91751fe0136309ad4ef67e4","date_updated":"2020-07-14T12:45:39Z","date_created":"2018-12-12T10:08:58Z"}]},{"day":"01","month":"02","doi":"10.1215/00127094-2019477","date_published":"2013-02-01T00:00:00Z","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1108.4246"}],"citation":{"short":"R. Frank, M. Lewin, É. Lieb, R. Seiringer, Duke Mathematical Journal 162 (2013) 435–495.","mla":"Frank, Rupert, et al. “A Positive Density Analogue of the Lieb-Thirring Inequality.” Duke Mathematical Journal, vol. 162, no. 3, Duke University Press, 2013, pp. 435–95, doi:10.1215/00127094-2019477.","chicago":"Frank, Rupert, Mathieu Lewin, Élliott Lieb, and Robert Seiringer. “A Positive Density Analogue of the Lieb-Thirring Inequality.” Duke Mathematical Journal. Duke University Press, 2013. https://doi.org/10.1215/00127094-2019477.","ama":"Frank R, Lewin M, Lieb É, Seiringer R. A positive density analogue of the Lieb-Thirring inequality. Duke Mathematical Journal. 2013;162(3):435-495. doi:10.1215/00127094-2019477","ieee":"R. Frank, M. Lewin, É. Lieb, and R. Seiringer, “A positive density analogue of the Lieb-Thirring inequality,” Duke Mathematical Journal, vol. 162, no. 3. Duke University Press, pp. 435–495, 2013.","apa":"Frank, R., Lewin, M., Lieb, É., & Seiringer, R. (2013). A positive density analogue of the Lieb-Thirring inequality. Duke Mathematical Journal. Duke University Press. https://doi.org/10.1215/00127094-2019477","ista":"Frank R, Lewin M, Lieb É, Seiringer R. 2013. A positive density analogue of the Lieb-Thirring inequality. Duke Mathematical Journal. 162(3), 435–495."},"oa":1,"publication":"Duke Mathematical Journal","page":"435 - 495","quality_controlled":0,"publist_id":"4521","issue":"3","abstract":[{"lang":"eng","text":"The Lieb-Thirring inequalities give a bound on the negative eigenvalues of a Schrödinger operator in terms of an Lp-norm of the potential. These are dual to bounds on the H1-norms of a system of orthonormal functions. Here we extend these bounds to analogous inequalities for perturbations of the Fermi sea of noninteracting particles (i.e., for perturbations of the continuous spectrum of the Laplacian by local potentials)."}],"extern":1,"type":"journal_article","author":[{"full_name":"Frank, Rupert L","first_name":"Rupert","last_name":"Frank"},{"full_name":"Lewin, Mathieu","last_name":"Lewin","first_name":"Mathieu"},{"first_name":"Élliott","last_name":"Lieb","full_name":"Lieb, Élliott H"},{"full_name":"Robert Seiringer","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","first_name":"Robert"}],"volume":162,"date_updated":"2021-01-12T06:57:17Z","date_created":"2018-12-11T11:57:28Z","_id":"2404","year":"2013","publisher":"Duke University Press","intvolume":" 162","status":"public","publication_status":"published","title":"A positive density analogue of the Lieb-Thirring inequality"},{"issue":"1","publist_id":"4520","abstract":[{"text":"We study the effects of random scatterers on the ground state of the one-dimensional Lieb-Liniger model of interacting bosons on the unit interval. We prove that, in the Gross-Pitaevskii limit, Bose Einstein condensation takes place in the whole parameter range considered. The character of the wave function of the condensate, however, depends in an essential way on the interplay between randomness and the strength of the two-body interaction. For low density of scatterers or strong interactions the wave function extends over the whole interval. High density of scatterers and weak interaction, on the other hand, leads to localization of the wave function in a fragmented subset of the unit interval.","lang":"eng"}],"extern":1,"type":"journal_article","author":[{"first_name":"Robert","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","full_name":"Robert Seiringer"},{"full_name":"Yngvason, Jakob","last_name":"Yngvason","first_name":"Jakob"},{"full_name":"Zagrebnov, Valentin A","last_name":"Zagrebnov","first_name":"Valentin"}],"volume":217,"date_updated":"2021-01-12T06:57:17Z","date_created":"2018-12-11T11:57:29Z","year":"2013","_id":"2406","publisher":"Springer","intvolume":" 217","title":"Condensation of interacting bosons in a random potential","status":"public","publication_status":"published","day":"01","month":"02","date_published":"2013-02-01T00:00:00Z","doi":"10.1140/epjst/e2013-01759-5","citation":{"chicago":"Seiringer, Robert, Jakob Yngvason, and Valentin Zagrebnov. “Condensation of Interacting Bosons in a Random Potential.” European Physical Journal: Special Topics. Springer, 2013. https://doi.org/10.1140/epjst/e2013-01759-5.","short":"R. Seiringer, J. Yngvason, V. Zagrebnov, European Physical Journal: Special Topics 217 (2013) 103–107.","mla":"Seiringer, Robert, et al. “Condensation of Interacting Bosons in a Random Potential.” European Physical Journal: Special Topics, vol. 217, no. 1, Springer, 2013, pp. 103–07, doi:10.1140/epjst/e2013-01759-5.","ieee":"R. Seiringer, J. Yngvason, and V. Zagrebnov, “Condensation of interacting bosons in a random potential,” European Physical Journal: Special Topics, vol. 217, no. 1. Springer, pp. 103–107, 2013.","apa":"Seiringer, R., Yngvason, J., & Zagrebnov, V. (2013). Condensation of interacting bosons in a random potential. European Physical Journal: Special Topics. Springer. https://doi.org/10.1140/epjst/e2013-01759-5","ista":"Seiringer R, Yngvason J, Zagrebnov V. 2013. Condensation of interacting bosons in a random potential. European Physical Journal: Special Topics. 217(1), 103–107.","ama":"Seiringer R, Yngvason J, Zagrebnov V. Condensation of interacting bosons in a random potential. European Physical Journal: Special Topics. 2013;217(1):103-107. doi:10.1140/epjst/e2013-01759-5"},"publication":"European Physical Journal: Special Topics","page":"103 - 107","quality_controlled":0},{"day":"01","month":"04","publication":"Communications in Mathematical Physics","citation":{"ieee":"R. Frank, É. Lieb, and R. Seiringer, “Symmetry of bipolaron bound states for small Coulomb repulsion,” Communications in Mathematical Physics, vol. 319, no. 2. Springer, pp. 557–573, 2013.","apa":"Frank, R., Lieb, É., & Seiringer, R. (2013). Symmetry of bipolaron bound states for small Coulomb repulsion. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-012-1604-y","ista":"Frank R, Lieb É, Seiringer R. 2013. Symmetry of bipolaron bound states for small Coulomb repulsion. Communications in Mathematical Physics. 319(2), 557–573.","ama":"Frank R, Lieb É, Seiringer R. Symmetry of bipolaron bound states for small Coulomb repulsion. Communications in Mathematical Physics. 2013;319(2):557-573. doi:10.1007/s00220-012-1604-y","chicago":"Frank, Rupert, Élliott Lieb, and Robert Seiringer. “Symmetry of Bipolaron Bound States for Small Coulomb Repulsion.” Communications in Mathematical Physics. Springer, 2013. https://doi.org/10.1007/s00220-012-1604-y.","short":"R. Frank, É. Lieb, R. Seiringer, Communications in Mathematical Physics 319 (2013) 557–573.","mla":"Frank, Rupert, et al. “Symmetry of Bipolaron Bound States for Small Coulomb Repulsion.” Communications in Mathematical Physics, vol. 319, no. 2, Springer, 2013, pp. 557–73, doi:10.1007/s00220-012-1604-y."},"main_file_link":[{"url":"http://arxiv.org/abs/1201.3954","open_access":"1"}],"oa":1,"quality_controlled":0,"page":"557 - 573","date_published":"2013-04-01T00:00:00Z","doi":"10.1007/s00220-012-1604-y","type":"journal_article","abstract":[{"text":"We consider the bipolaron in the Pekar-Tomasevich approximation and address the question whether the ground state is spherically symmetric or not. Numerical analysis has, so far, not completely settled the question. Our contribution is to prove rigorously that the ground state remains spherical for small values of the electron-electron Coulomb repulsion.","lang":"eng"}],"publist_id":"4522","issue":"2","extern":1,"year":"2013","_id":"2405","publication_status":"published","status":"public","title":"Symmetry of bipolaron bound states for small Coulomb repulsion","intvolume":" 319","publisher":"Springer","author":[{"full_name":"Frank, Rupert L","last_name":"Frank","first_name":"Rupert"},{"full_name":"Lieb, Élliott H","first_name":"Élliott","last_name":"Lieb"},{"orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","first_name":"Robert","full_name":"Robert Seiringer"}],"date_updated":"2021-01-12T06:57:17Z","date_created":"2018-12-11T11:57:28Z","volume":319},{"month":"09","day":"01","doi":"10.1007/s00220-013-1736-8","date_published":"2013-09-01T00:00:00Z","page":"559 - 591","quality_controlled":0,"main_file_link":[{"url":"http://arxiv.org/abs/1205.5259","open_access":"1"}],"citation":{"ama":"Grech P, Seiringer R. The excitation spectrum for weakly interacting Bosons in a trap. Communications in Mathematical Physics. 2013;322(2):559-591. doi:10.1007/s00220-013-1736-8","ista":"Grech P, Seiringer R. 2013. The excitation spectrum for weakly interacting Bosons in a trap. Communications in Mathematical Physics. 322(2), 559–591.","apa":"Grech, P., & Seiringer, R. (2013). The excitation spectrum for weakly interacting Bosons in a trap. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-013-1736-8","ieee":"P. Grech and R. Seiringer, “The excitation spectrum for weakly interacting Bosons in a trap,” Communications in Mathematical Physics, vol. 322, no. 2. Springer, pp. 559–591, 2013.","mla":"Grech, Philip, and Robert Seiringer. “The Excitation Spectrum for Weakly Interacting Bosons in a Trap.” Communications in Mathematical Physics, vol. 322, no. 2, Springer, 2013, pp. 559–91, doi:10.1007/s00220-013-1736-8.","short":"P. Grech, R. Seiringer, Communications in Mathematical Physics 322 (2013) 559–591.","chicago":"Grech, Philip, and Robert Seiringer. “The Excitation Spectrum for Weakly Interacting Bosons in a Trap.” Communications in Mathematical Physics. Springer, 2013. https://doi.org/10.1007/s00220-013-1736-8."},"oa":1,"publication":"Communications in Mathematical Physics","extern":1,"issue":"2","publist_id":"4518","abstract":[{"text":"We investigate the low-energy excitation spectrum of a Bose gas confined in a trap, with weak long-range repulsive interactions. In particular, we prove that the spectrum can be described in terms of the eigenvalues of an effective one-particle operator, as predicted by the Bogoliubov approximation.","lang":"eng"}],"type":"journal_article","volume":322,"date_updated":"2021-01-12T06:57:18Z","date_created":"2018-12-11T11:57:29Z","author":[{"full_name":"Grech, Philip","first_name":"Philip","last_name":"Grech"},{"full_name":"Robert Seiringer","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","first_name":"Robert"}],"intvolume":" 322","publisher":"Springer","title":"The excitation spectrum for weakly interacting Bosons in a trap","publication_status":"published","status":"public","_id":"2408","year":"2013"},{"author":[{"full_name":"Kupczok, Anne","last_name":"Kupczok","first_name":"Anne","id":"2BB22BC2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Bollback, Jonathan P","last_name":"Bollback","first_name":"Jonathan P","orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87"}],"volume":13,"date_created":"2018-12-11T11:57:31Z","date_updated":"2021-01-12T06:57:20Z","year":"2013","publisher":"BioMed Central","department":[{"_id":"JoBo"}],"publication_status":"published","publist_id":"4514","file_date_updated":"2020-07-14T12:45:40Z","doi":"10.1186/1471-2148-13-54","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","month":"02","pubrep_id":"397","oa_version":"Published Version","file":[{"file_name":"IST-2015-397-v1+1_1471-2148-13-54.pdf","access_level":"open_access","file_size":518729,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"5268","date_created":"2018-12-12T10:17:15Z","date_updated":"2020-07-14T12:45:40Z","checksum":"029c7e0b198c19312b66ecce3cabb22f"}],"_id":"2412","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 13","status":"public","ddc":["576"],"title":"Probabilistic models for CRISPR spacer content evolution ","issue":"1","abstract":[{"text":"Background: The CRISPR/Cas system is known to act as an adaptive and heritable immune system in Eubacteria and Archaea. Immunity is encoded in an array of spacer sequences. Each spacer can provide specific immunity to invasive elements that carry the same or a similar sequence. Even in closely related strains, spacer content is very dynamic and evolves quickly. Standard models of nucleotide evolutioncannot be applied to quantify its rate of change since processes other than single nucleotide changes determine its evolution.Methods We present probabilistic models that are specific for spacer content evolution. They account for the different processes of insertion and deletion. Insertions can be constrained to occur on one end only or are allowed to occur throughout the array. One deletion event can affect one spacer or a whole fragment of adjacent spacers. Parameters of the underlying models are estimated for a pair of arrays by maximum likelihood using explicit ancestor enumeration.Results Simulations show that parameters are well estimated on average under the models presented here. There is a bias in the rate estimation when including fragment deletions. The models also estimate times between pairs of strains. But with increasing time, spacer overlap goes to zero, and thus there is an upper bound on the distance that can be estimated. Spacer content similarities are displayed in a distance based phylogeny using the estimated times.We use the presented models to analyze different Yersinia pestis data sets and find that the results among them are largely congruent. The models also capture the variation in diversity of spacers among the data sets. A comparison of spacer-based phylogenies and Cas gene phylogenies shows that they resolve very different time scales for this data set.Conclusions The simulations and data analyses show that the presented models are useful for quantifying spacer content evolution and for displaying spacer content similarities of closely related strains in a phylogeny. This allows for comparisons of different CRISPR arrays or for comparisons between CRISPR arrays and nucleotide substitution rates.","lang":"eng"}],"type":"journal_article","date_published":"2013-02-26T00:00:00Z","citation":{"chicago":"Kupczok, Anne, and Jonathan P Bollback. “Probabilistic Models for CRISPR Spacer Content Evolution .” BMC Evolutionary Biology. BioMed Central, 2013. https://doi.org/10.1186/1471-2148-13-54.","short":"A. Kupczok, J.P. Bollback, BMC Evolutionary Biology 13 (2013) 54–54.","mla":"Kupczok, Anne, and Jonathan P. Bollback. “Probabilistic Models for CRISPR Spacer Content Evolution .” BMC Evolutionary Biology, vol. 13, no. 1, BioMed Central, 2013, pp. 54–54, doi:10.1186/1471-2148-13-54.","ieee":"A. Kupczok and J. P. Bollback, “Probabilistic models for CRISPR spacer content evolution ,” BMC Evolutionary Biology, vol. 13, no. 1. BioMed Central, pp. 54–54, 2013.","apa":"Kupczok, A., & Bollback, J. P. (2013). Probabilistic models for CRISPR spacer content evolution . BMC Evolutionary Biology. BioMed Central. https://doi.org/10.1186/1471-2148-13-54","ista":"Kupczok A, Bollback JP. 2013. Probabilistic models for CRISPR spacer content evolution . BMC Evolutionary Biology. 13(1), 54–54.","ama":"Kupczok A, Bollback JP. Probabilistic models for CRISPR spacer content evolution . BMC Evolutionary Biology. 2013;13(1):54-54. doi:10.1186/1471-2148-13-54"},"publication":"BMC Evolutionary Biology","page":"54 - 54","has_accepted_license":"1","day":"26","scopus_import":1},{"abstract":[{"lang":"eng","text":"Progress in understanding the global brain dynamics has remained slow to date in large part because of the highly multiscale nature of brain activity. Indeed, normal brain dynamics is characterized by complex interactions between multiple levels: from the microscopic scale of single neurons to the mesoscopic level of local groups of neurons, and finally to the macroscopic level of the whole brain. Among the most difficult tasks are those of identifying which scales are significant for a given particular function and describing how the scales affect each other. It is important to realize that the scales of time and space are linked together, or even intertwined, and that causal inference is far more ambiguous between than within levels. We approach this problem from the perspective of our recent work on simultaneous recording from micro- and macroelectrodes in the human brain. We propose a physiological description of these multilevel interactions, based on phase–amplitude coupling of neuronal oscillations that operate at multiple frequencies and on different spatial scales. Specifically, the amplitude of the oscillations on a particular spatial scale is modulated by phasic variations in neuronal excitability induced by lower frequency oscillations that emerge on a larger spatial scale. Following this general principle, it is possible to scale up or scale down the multiscale brain dynamics. It is expected that large-scale network oscillations in the low-frequency range, mediating downward effects, may play an important role in attention and consciousness."}],"publist_id":"4513","alternative_title":["Reviews of Nonlinear Dynamics and Complexity"],"type":"book_chapter","date_created":"2018-12-11T11:57:31Z","date_updated":"2021-01-12T06:57:20Z","oa_version":"None","author":[{"full_name":"Valderrama, Mario","first_name":"Mario","last_name":"Valderrama"},{"orcid":"0000-0002-8790-1914","id":"421234E8-F248-11E8-B48F-1D18A9856A87","last_name":"Botella Soler","first_name":"Vicente","full_name":"Botella Soler, Vicente"},{"full_name":"Le Van Quyen, Michel","last_name":"Le Van Quyen","first_name":"Michel"}],"status":"public","publication_status":"published","title":"Neuronal oscillations scale up and scale down the brain dynamics ","publisher":"Wiley-VCH","editor":[{"first_name":"Misha","last_name":"Meyer","full_name":"Meyer, Misha"},{"last_name":"Pesenson","first_name":"Z.","full_name":"Pesenson, Z."}],"department":[{"_id":"GaTk"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"2413","year":"2013","month":"08","day":"01","publication_identifier":{"eisbn":["9783527671632"],"isbn":["9783527411986 "]},"scopus_import":1,"language":[{"iso":"eng"}],"doi":"10.1002/9783527671632.ch08","date_published":"2013-08-01T00:00:00Z","quality_controlled":"1","publication":"Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain","citation":{"mla":"Valderrama, Mario, et al. “Neuronal Oscillations Scale up and Scale down the Brain Dynamics .” Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain, edited by Misha Meyer and Z. Pesenson, Wiley-VCH, 2013, doi:10.1002/9783527671632.ch08.","short":"M. Valderrama, V. Botella Soler, M. Le Van Quyen, in:, M. Meyer, Z. Pesenson (Eds.), Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain, Wiley-VCH, 2013.","chicago":"Valderrama, Mario, Vicente Botella Soler, and Michel Le Van Quyen. “Neuronal Oscillations Scale up and Scale down the Brain Dynamics .” In Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain, edited by Misha Meyer and Z. Pesenson. Wiley-VCH, 2013. https://doi.org/10.1002/9783527671632.ch08.","ama":"Valderrama M, Botella Soler V, Le Van Quyen M. Neuronal oscillations scale up and scale down the brain dynamics . In: Meyer M, Pesenson Z, eds. Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain. Wiley-VCH; 2013. doi:10.1002/9783527671632.ch08","ista":"Valderrama M, Botella Soler V, Le Van Quyen M. 2013.Neuronal oscillations scale up and scale down the brain dynamics . In: Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain. Reviews of Nonlinear Dynamics and Complexity, .","ieee":"M. Valderrama, V. Botella Soler, and M. Le Van Quyen, “Neuronal oscillations scale up and scale down the brain dynamics ,” in Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain, M. Meyer and Z. Pesenson, Eds. Wiley-VCH, 2013.","apa":"Valderrama, M., Botella Soler, V., & Le Van Quyen, M. (2013). Neuronal oscillations scale up and scale down the brain dynamics . In M. Meyer & Z. Pesenson (Eds.), Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain. Wiley-VCH. https://doi.org/10.1002/9783527671632.ch08"}},{"abstract":[{"text":"Here, we describe a novel virulent bacteriophage that infects Bacillus weihenstephanensis, isolated from soil in Austria. It is the first phage to be discovered that infects this species. Here, we present the complete genome sequence of this podovirus. ","lang":"eng"}],"issue":"3","type":"journal_article","oa_version":"Published Version","file":[{"file_id":"5291","relation":"main_file","checksum":"0751ec74b695567e0cdf02aaf9c26829","date_created":"2018-12-12T10:17:36Z","date_updated":"2020-07-14T12:45:40Z","access_level":"open_access","file_name":"IST-2015-398-v1+1_Genome_Announc.-2013-Redondo-.pdf","creator":"system","content_type":"application/pdf","file_size":130026}],"pubrep_id":"398","title":"Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis","status":"public","ddc":["576"],"intvolume":" 1","_id":"2410","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"13","has_accepted_license":"1","scopus_import":1,"date_published":"2013-06-13T00:00:00Z","publication":"Genome Announcements","citation":{"chicago":"Fernandes Redondo, Rodrigo A, Anne Kupczok, Gertraud Stift, and Jonathan P Bollback. “Complete Genome Sequence of the Novel Phage MG-B1 Infecting Bacillus Weihenstephanensis.” Genome Announcements. American Society for Microbiology, 2013. https://doi.org/10.1128/genomeA.00216-13.","short":"R.A. Fernandes Redondo, A. Kupczok, G. Stift, J.P. Bollback, Genome Announcements 1 (2013).","mla":"Fernandes Redondo, Rodrigo A., et al. “Complete Genome Sequence of the Novel Phage MG-B1 Infecting Bacillus Weihenstephanensis.” Genome Announcements, vol. 1, no. 3, American Society for Microbiology, 2013, doi:10.1128/genomeA.00216-13.","ieee":"R. A. Fernandes Redondo, A. Kupczok, G. Stift, and J. P. Bollback, “Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis,” Genome Announcements, vol. 1, no. 3. American Society for Microbiology, 2013.","apa":"Fernandes Redondo, R. A., Kupczok, A., Stift, G., & Bollback, J. P. (2013). Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis. Genome Announcements. American Society for Microbiology. https://doi.org/10.1128/genomeA.00216-13","ista":"Fernandes Redondo RA, Kupczok A, Stift G, Bollback JP. 2013. Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis. Genome Announcements. 1(3).","ama":"Fernandes Redondo RA, Kupczok A, Stift G, Bollback JP. Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis. Genome Announcements. 2013;1(3). doi:10.1128/genomeA.00216-13"},"file_date_updated":"2020-07-14T12:45:40Z","publist_id":"4516","date_updated":"2021-01-12T06:57:19Z","date_created":"2018-12-11T11:57:30Z","volume":1,"author":[{"orcid":"0000-0002-5837-2793","id":"409D5C96-F248-11E8-B48F-1D18A9856A87","last_name":"Fernandes Redondo","first_name":"Rodrigo A","full_name":"Fernandes Redondo, Rodrigo A"},{"full_name":"Kupczok, Anne","id":"2BB22BC2-F248-11E8-B48F-1D18A9856A87","last_name":"Kupczok","first_name":"Anne"},{"full_name":"Stift, Gertraud","id":"2DB195CA-F248-11E8-B48F-1D18A9856A87","last_name":"Stift","first_name":"Gertraud"},{"last_name":"Bollback","first_name":"Jonathan P","orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","full_name":"Bollback, Jonathan P"}],"publication_status":"published","department":[{"_id":"JoBo"},{"_id":"LifeSc"}],"publisher":"American Society for Microbiology","year":"2013","month":"06","language":[{"iso":"eng"}],"doi":"10.1128/genomeA.00216-13","quality_controlled":"1","oa":1},{"month":"07","language":[{"iso":"eng"}],"doi":"10.1007/978-3-642-39799-8_54","conference":{"name":"CAV: Computer Aided Verification","location":"St. Petersburg, Russia","start_date":"2013-07-13","end_date":"2013-07-19"},"quality_controlled":"1","oa":1,"publist_id":"4456","file_date_updated":"2020-07-14T12:45:41Z","volume":8044,"date_created":"2018-12-11T11:57:43Z","date_updated":"2020-08-11T10:09:47Z","author":[{"first_name":"Ruzica","last_name":"Piskac","full_name":"Piskac, Ruzica"},{"full_name":"Wies, Thomas","last_name":"Wies","first_name":"Thomas","id":"447BFB88-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Damien","last_name":"Zufferey","id":"4397AC76-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3197-8736","full_name":"Zufferey, Damien"}],"department":[{"_id":"ToHe"}],"publisher":"Springer","publication_status":"published","year":"2013","has_accepted_license":"1","article_processing_charge":"No","day":"01","series_title":"Lecture Notes in Computer Science","scopus_import":1,"date_published":"2013-07-01T00:00:00Z","page":"773 - 789","citation":{"ista":"Piskac R, Wies T, Zufferey D. 2013. Automating separation logic using SMT. 8044, 773–789.","apa":"Piskac, R., Wies, T., & Zufferey, D. (2013). Automating separation logic using SMT. Presented at the CAV: Computer Aided Verification, St. Petersburg, Russia: Springer. https://doi.org/10.1007/978-3-642-39799-8_54","ieee":"R. Piskac, T. Wies, and D. Zufferey, “Automating separation logic using SMT,” vol. 8044. Springer, pp. 773–789, 2013.","ama":"Piskac R, Wies T, Zufferey D. Automating separation logic using SMT. 2013;8044:773-789. doi:10.1007/978-3-642-39799-8_54","chicago":"Piskac, Ruzica, Thomas Wies, and Damien Zufferey. “Automating Separation Logic Using SMT.” Lecture Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-39799-8_54.","mla":"Piskac, Ruzica, et al. Automating Separation Logic Using SMT. Vol. 8044, Springer, 2013, pp. 773–89, doi:10.1007/978-3-642-39799-8_54.","short":"R. Piskac, T. Wies, D. Zufferey, 8044 (2013) 773–789."},"abstract":[{"text":"Separation logic (SL) has gained widespread popularity because of its ability to succinctly express complex invariants of a program’s heap configurations. Several specialized provers have been developed for decidable SL fragments. However, these provers cannot be easily extended or combined with solvers for other theories that are important in program verification, e.g., linear arithmetic. In this paper, we present a reduction of decidable SL fragments to a decidable first-order theory that fits well into the satisfiability modulo theories (SMT) framework. We show how to use this reduction to automate satisfiability, entailment, frame inference, and abduction problems for separation logic using SMT solvers. Our approach provides a simple method of integrating separation logic into existing verification tools that provide SMT backends, and an elegant way of combining SL fragments with other decidable first-order theories. We implemented this approach in a verification tool and applied it to heap-manipulating programs whose verification involves reasoning in theory combinations.\r\n","lang":"eng"}],"alternative_title":["LNCS"],"type":"conference","file":[{"content_type":"application/pdf","file_size":309182,"creator":"dernst","access_level":"open_access","file_name":"2013_CAV_Piskac.pdf","checksum":"2e866932ab688f47ecd504acb4d5c7d4","date_updated":"2020-07-14T12:45:41Z","date_created":"2020-05-15T11:13:01Z","relation":"main_file","file_id":"7859"}],"oa_version":"Submitted Version","intvolume":" 8044","ddc":["000"],"status":"public","title":"Automating separation logic using SMT","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2447"},{"project":[{"name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://doi.org/10.1111/nph.12437","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1111/nph.12437","month":"12","department":[{"_id":"JiFr"}],"publisher":"Wiley","publication_status":"published","year":"2013","acknowledgement":"The authors thank Dr Christian Luschnig (University of Natural Resources and Life Sciences (BOKU), Vienna, Austria) for the anti-PIN2 antibody, Professor Mark Estelle (University of California, San Diego, CA, USA) for tir1-1 mutant seeds and, last but not least, to Dr David Morris for critical reading of the manuscript. We also thank Markéta Pařezová and Jana Stýblová for excellent technical assistance. This work was supported by the Grant Agency of the Czech Republic (P305/11/0797 to E.Z. and 13-40637S to J.F.), the Central European Institute of Technology project CZ.1.05/1.1.00/02.0068 from the European Regional Development Fund and by a European Research Council starting independent research grant ERC-2011-StG-20101109-PSDP (to J.F.).","volume":200,"date_updated":"2022-06-07T08:57:52Z","date_created":"2018-12-11T11:57:41Z","author":[{"first_name":"Sibu","last_name":"Simon","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1998-6741","full_name":"Simon, Sibu"},{"last_name":"Kubeš","first_name":"Martin","full_name":"Kubeš, Martin"},{"full_name":"Baster, Pawel","id":"3028BD74-F248-11E8-B48F-1D18A9856A87","last_name":"Baster","first_name":"Pawel"},{"full_name":"Robert, Stéphanie","first_name":"Stéphanie","last_name":"Robert"},{"full_name":"Dobrev, Petre","first_name":"Petre","last_name":"Dobrev"},{"last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí"},{"full_name":"Petrášek, Jan","first_name":"Jan","last_name":"Petrášek"},{"first_name":"Eva","last_name":"Zažímalová","full_name":"Zažímalová, Eva"}],"ec_funded":1,"publist_id":"4460","page":"1034 - 1048","article_type":"original","citation":{"chicago":"Simon, Sibu, Martin Kubeš, Pawel Baster, Stéphanie Robert, Petre Dobrev, Jiří Friml, Jan Petrášek, and Eva Zažímalová. “Defining the Selectivity of Processes along the Auxin Response Chain: A Study Using Auxin Analogues.” New Phytologist. Wiley, 2013. https://doi.org/10.1111/nph.12437.","short":"S. Simon, M. Kubeš, P. Baster, S. Robert, P. Dobrev, J. Friml, J. Petrášek, E. Zažímalová, New Phytologist 200 (2013) 1034–1048.","mla":"Simon, Sibu, et al. “Defining the Selectivity of Processes along the Auxin Response Chain: A Study Using Auxin Analogues.” New Phytologist, vol. 200, no. 4, Wiley, 2013, pp. 1034–48, doi:10.1111/nph.12437.","apa":"Simon, S., Kubeš, M., Baster, P., Robert, S., Dobrev, P., Friml, J., … Zažímalová, E. (2013). Defining the selectivity of processes along the auxin response chain: A study using auxin analogues. New Phytologist. Wiley. https://doi.org/10.1111/nph.12437","ieee":"S. Simon et al., “Defining the selectivity of processes along the auxin response chain: A study using auxin analogues,” New Phytologist, vol. 200, no. 4. Wiley, pp. 1034–1048, 2013.","ista":"Simon S, Kubeš M, Baster P, Robert S, Dobrev P, Friml J, Petrášek J, Zažímalová E. 2013. Defining the selectivity of processes along the auxin response chain: A study using auxin analogues. New Phytologist. 200(4), 1034–1048.","ama":"Simon S, Kubeš M, Baster P, et al. Defining the selectivity of processes along the auxin response chain: A study using auxin analogues. New Phytologist. 2013;200(4):1034-1048. doi:10.1111/nph.12437"},"publication":"New Phytologist","date_published":"2013-12-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01","intvolume":" 200","title":"Defining the selectivity of processes along the auxin response chain: A study using auxin analogues","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2443","oa_version":"Published Version","type":"journal_article","issue":"4","abstract":[{"lang":"eng","text":"The mode of action of auxin is based on its non-uniform distribution within tissues and organs. Despite the wide use of several auxin analogues in research and agriculture, little is known about the specificity of different auxin-related transport and signalling processes towards these compounds. Using seedlings of Arabidopsis thaliana and suspension-cultured cells of Nicotiana tabacum (BY-2), the physiological activity of several auxin analogues was investigated, together with their capacity to induce auxin-dependent gene expression, to inhibit endocytosis and to be transported across the plasma membrane. This study shows that the specificity criteria for different auxin-related processes vary widely. Notably, the special behaviour of some synthetic auxin analogues suggests that they might be useful tools in investigations of the molecular mechanism of auxin action. Thus, due to their differential stimulatory effects on DR5 expression, indole-3-propionic (IPA) and 2,4,5-trichlorophenoxy acetic (2,4,5-T) acids can serve in studies of TRANSPORT INHIBITOR RESPONSE 1/AUXIN SIGNALLING F-BOX (TIR1/AFB)-mediated auxin signalling, and 5-fluoroindole-3-acetic acid (5-F-IAA) can help to discriminate between transcriptional and non-transcriptional pathways of auxin signalling. The results demonstrate that the major determinants for the auxin-like physiological potential of a particular compound are very complex and involve its chemical and metabolic stability, its ability to distribute in tissues in a polar manner and its activity towards auxin signalling machinery."}]},{"status":"public","title":"Automata with generalized Rabin pairs for probabilistic model checking and LTL synthesis","intvolume":" 8044","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2446","oa_version":"Preprint","alternative_title":["LNCS"],"type":"conference","abstract":[{"lang":"eng","text":"The model-checking problem for probabilistic systems crucially relies on the translation of LTL to deterministic Rabin automata (DRW). Our recent Safraless translation [KE12, GKE12] for the LTL(F,G) fragment produces smaller automata as compared to the traditional approach. In this work, instead of DRW we consider deterministic automata with acceptance condition given as disjunction of generalized Rabin pairs (DGRW). The Safraless translation of LTL(F,G) formulas to DGRW results in smaller automata as compared to DRW. We present algorithms for probabilistic model-checking as well as game solving for DGRW conditions. Our new algorithms lead to improvement both in terms of theoretical bounds as well as practical evaluation. We compare PRISM with and without our new translation, and show that the new translation leads to significant improvements."}],"page":"559 - 575","citation":{"ieee":"K. Chatterjee, A. Gaiser, and J. Kretinsky, “Automata with generalized Rabin pairs for probabilistic model checking and LTL synthesis,” vol. 8044. Springer, pp. 559–575, 2013.","apa":"Chatterjee, K., Gaiser, A., & Kretinsky, J. (2013). Automata with generalized Rabin pairs for probabilistic model checking and LTL synthesis. Presented at the CAV: Computer Aided Verification, St. Petersburg, Russia: Springer. https://doi.org/10.1007/978-3-642-39799-8_37","ista":"Chatterjee K, Gaiser A, Kretinsky J. 2013. Automata with generalized Rabin pairs for probabilistic model checking and LTL synthesis. 8044, 559–575.","ama":"Chatterjee K, Gaiser A, Kretinsky J. Automata with generalized Rabin pairs for probabilistic model checking and LTL synthesis. 2013;8044:559-575. doi:10.1007/978-3-642-39799-8_37","chicago":"Chatterjee, Krishnendu, Andreas Gaiser, and Jan Kretinsky. “Automata with Generalized Rabin Pairs for Probabilistic Model Checking and LTL Synthesis.” Lecture Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-39799-8_37.","short":"K. Chatterjee, A. Gaiser, J. Kretinsky, 8044 (2013) 559–575.","mla":"Chatterjee, Krishnendu, et al. Automata with Generalized Rabin Pairs for Probabilistic Model Checking and LTL Synthesis. Vol. 8044, Springer, 2013, pp. 559–75, doi:10.1007/978-3-642-39799-8_37."},"date_published":"2013-07-01T00:00:00Z","series_title":"Lecture Notes in Computer Science","scopus_import":1,"day":"01","publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"Springer","year":"2013","date_updated":"2020-08-11T10:09:47Z","date_created":"2018-12-11T11:57:42Z","volume":8044,"author":[{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"full_name":"Gaiser, Andreas","last_name":"Gaiser","first_name":"Andreas"},{"first_name":"Jan","last_name":"Kretinsky","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8122-2881","full_name":"Kretinsky, Jan"}],"publist_id":"4457","ec_funded":1,"quality_controlled":"1","project":[{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"name":"Game Theory","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1304.5281"}],"oa":1,"external_id":{"arxiv":["1304.5281"]},"language":[{"iso":"eng"}],"conference":{"name":"CAV: Computer Aided Verification","location":"St. Petersburg, Russia","start_date":"2013-07-13","end_date":"2013-07-19"},"doi":"10.1007/978-3-642-39799-8_37","month":"07"},{"publication_status":"published","publisher":"Springer","department":[{"_id":"KrCh"}],"year":"2013","date_created":"2018-12-11T11:57:42Z","date_updated":"2020-08-11T10:09:47Z","volume":8044,"author":[{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"first_name":"Jakub","last_name":"Ła̧Cki","full_name":"Ła̧Cki, Jakub"}],"ec_funded":1,"publist_id":"4459","quality_controlled":"1","project":[{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1304.0084","open_access":"1"}],"external_id":{"arxiv":["1304.0084"]},"language":[{"iso":"eng"}],"conference":{"start_date":"2013-07-13","location":"St. Petersburg, Russia","end_date":"2013-07-19","name":"CAV: Computer Aided Verification"},"doi":"10.1007/978-3-642-39799-8_36","month":"07","status":"public","title":"Faster algorithms for Markov decision processes with low treewidth","intvolume":" 8044","_id":"2444","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","alternative_title":["LNCS"],"type":"conference","abstract":[{"text":"We consider two core algorithmic problems for probabilistic verification: the maximal end-component decomposition and the almost-sure reachability set computation for Markov decision processes (MDPs). For MDPs with treewidth k, we present two improved static algorithms for both the problems that run in time O(n·k 2.38·2k ) and O(m·logn· k), respectively, where n is the number of states and m is the number of edges, significantly improving the previous known O(n·k·√n· k) bound for low treewidth. We also present decremental algorithms for both problems for MDPs with constant treewidth that run in amortized logarithmic time, which is a huge improvement over the previously known algorithms that require amortized linear time.","lang":"eng"}],"page":"543 - 558","citation":{"mla":"Chatterjee, Krishnendu, and Jakub Ła̧Cki. Faster Algorithms for Markov Decision Processes with Low Treewidth. Vol. 8044, Springer, 2013, pp. 543–58, doi:10.1007/978-3-642-39799-8_36.","short":"K. Chatterjee, J. Ła̧Cki, 8044 (2013) 543–558.","chicago":"Chatterjee, Krishnendu, and Jakub Ła̧Cki. “Faster Algorithms for Markov Decision Processes with Low Treewidth.” Lecture Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-39799-8_36.","ama":"Chatterjee K, Ła̧Cki J. Faster algorithms for Markov decision processes with low treewidth. 2013;8044:543-558. doi:10.1007/978-3-642-39799-8_36","ista":"Chatterjee K, Ła̧Cki J. 2013. Faster algorithms for Markov decision processes with low treewidth. 8044, 543–558.","ieee":"K. Chatterjee and J. Ła̧Cki, “Faster algorithms for Markov decision processes with low treewidth,” vol. 8044. Springer, pp. 543–558, 2013.","apa":"Chatterjee, K., & Ła̧Cki, J. (2013). Faster algorithms for Markov decision processes with low treewidth. Presented at the CAV: Computer Aided Verification, St. Petersburg, Russia: Springer. https://doi.org/10.1007/978-3-642-39799-8_36"},"date_published":"2013-07-01T00:00:00Z","series_title":"Lecture Notes in Computer Science","scopus_import":1,"day":"01"},{"type":"journal_article","issue":"6","publist_id":"4454","abstract":[{"text":"Intracellular protein routing is mediated by vesicular transport which is tightly regulated in eukaryotes. The protein and lipid homeostasis depends on coordinated delivery of de novo synthesized or recycled cargoes to the plasma membrane by exocytosis and their subsequent removal by rerouting them for recycling or degradation. Here, we report the characterization of protein affected trafficking 3 (pat3) mutant that we identified by an epifluorescence-based forward genetic screen for mutants defective in subcellular distribution of Arabidopsis auxin transporter PIN1–GFP. While pat3 displays largely normal plant morphology and development in nutrient-rich conditions, it shows strong ectopic intracellular accumulations of different plasma membrane cargoes in structures that resemble prevacuolar compartments (PVC) with an aberrant morphology. Genetic mapping revealed that pat3 is defective in vacuolar protein sorting 35A (VPS35A), a putative subunit of the retromer complex that mediates retrograde trafficking between the PVC and trans-Golgi network. Similarly, a mutant defective in another retromer subunit, vps29, shows comparable subcellular defects in PVC morphology and protein accumulation. Thus, our data provide evidence that the retromer components VPS35A and VPS29 are essential for normal PVC morphology and normal trafficking of plasma membrane proteins in plants. In addition, we show that, out of the three VPS35 retromer subunits present in Arabidopsis thaliana genome, the VPS35 homolog A plays a prevailing role in trafficking to the lytic vacuole, presenting another level of complexity in the retromer-dependent vacuolar sorting. ","lang":"eng"}],"publisher":"Cell Press","intvolume":" 6","department":[{"_id":"JiFr"}],"title":"Retromer subunits VPS35A and VPS29 mediate prevacuolar compartment (PVC) function in Arabidopsis","publication_status":"published","status":"public","_id":"2449","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2013","volume":6,"oa_version":"None","date_created":"2018-12-11T11:57:44Z","date_updated":"2021-01-12T06:57:33Z","author":[{"full_name":"Nodzyński, Tomasz","last_name":"Nodzyński","first_name":"Tomasz"},{"last_name":"Feraru","first_name":"Murguel","full_name":"Feraru, Murguel"},{"full_name":"Hirsch, Sibylle","first_name":"Sibylle","last_name":"Hirsch"},{"full_name":"De Rycke, Riet","last_name":"De Rycke","first_name":"Riet"},{"last_name":"Nicuales","first_name":"Claudiu","full_name":"Nicuales, Claudiu"},{"last_name":"Van Leene","first_name":"Jelle","full_name":"Van Leene, Jelle"},{"last_name":"De Jaeger","first_name":"Geert","full_name":"De Jaeger, Geert"},{"first_name":"Steffen","last_name":"Vanneste","full_name":"Vanneste, Steffen"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí"}],"scopus_import":1,"day":"01","month":"11","page":"1849 - 1862","quality_controlled":"1","citation":{"ama":"Nodzyński T, Feraru M, Hirsch S, et al. Retromer subunits VPS35A and VPS29 mediate prevacuolar compartment (PVC) function in Arabidopsis. Molecular Plant. 2013;6(6):1849-1862. doi:10.1093/mp/sst044","ieee":"T. Nodzyński et al., “Retromer subunits VPS35A and VPS29 mediate prevacuolar compartment (PVC) function in Arabidopsis,” Molecular Plant, vol. 6, no. 6. Cell Press, pp. 1849–1862, 2013.","apa":"Nodzyński, T., Feraru, M., Hirsch, S., De Rycke, R., Nicuales, C., Van Leene, J., … Friml, J. (2013). Retromer subunits VPS35A and VPS29 mediate prevacuolar compartment (PVC) function in Arabidopsis. Molecular Plant. Cell Press. https://doi.org/10.1093/mp/sst044","ista":"Nodzyński T, Feraru M, Hirsch S, De Rycke R, Nicuales C, Van Leene J, De Jaeger G, Vanneste S, Friml J. 2013. Retromer subunits VPS35A and VPS29 mediate prevacuolar compartment (PVC) function in Arabidopsis. Molecular Plant. 6(6), 1849–1862.","short":"T. Nodzyński, M. Feraru, S. Hirsch, R. De Rycke, C. Nicuales, J. Van Leene, G. De Jaeger, S. Vanneste, J. Friml, Molecular Plant 6 (2013) 1849–1862.","mla":"Nodzyński, Tomasz, et al. “Retromer Subunits VPS35A and VPS29 Mediate Prevacuolar Compartment (PVC) Function in Arabidopsis.” Molecular Plant, vol. 6, no. 6, Cell Press, 2013, pp. 1849–62, doi:10.1093/mp/sst044.","chicago":"Nodzyński, Tomasz, Murguel Feraru, Sibylle Hirsch, Riet De Rycke, Claudiu Nicuales, Jelle Van Leene, Geert De Jaeger, Steffen Vanneste, and Jiří Friml. “Retromer Subunits VPS35A and VPS29 Mediate Prevacuolar Compartment (PVC) Function in Arabidopsis.” Molecular Plant. Cell Press, 2013. https://doi.org/10.1093/mp/sst044."},"publication":"Molecular Plant","language":[{"iso":"eng"}],"doi":"10.1093/mp/sst044","date_published":"2013-11-01T00:00:00Z"},{"type":"journal_article","abstract":[{"lang":"eng","text":"Background: Abundance and distribution of the plant hormone auxin play important roles in plant development. Besides other metabolic processes, various auxin carriers control the cellular level of active auxin and, hence, are major regulators of cellular auxin homeostasis. Despite the developmental importance of auxin transporters, a simple medium-to-high throughput approach to assess carrier activities is still missing. Here we show that carrier driven depletion of cellular auxin correlates with reduced nuclear auxin signaling in tobacco Bright Yellow-2 (BY-2) cell cultures.Results: We developed an easy to use transient single-cell-based system to detect carrier activity. We use the relative changes in signaling output of the auxin responsive promoter element DR5 to indirectly visualize auxin carrier activity. The feasibility of the transient approach was demonstrated by pharmacological and genetic interference with auxin signaling and transport. As a proof of concept, we provide visual evidence that the prominent auxin transport proteins PIN-FORMED (PIN)2 and PIN5 regulate cellular auxin homeostasis at the plasma membrane and endoplasmic reticulum (ER), respectively. Our data suggest that PIN2 and PIN5 have different sensitivities to the auxin transport inhibitor 1-naphthylphthalamic acid (NPA). Also the putative PIN-LIKES (PILS) auxin carrier activity at the ER is insensitive to NPA in our system, indicating that NPA blocks intercellular, but not intracellular auxin transport.Conclusions: This single-cell-based system is a useful tool by which the activity of putative auxin carriers, such as PINs, PILS and WALLS ARE THIN1 (WAT1), can be indirectly visualized in a medium-to-high throughput manner. Moreover, our single cell system might be useful to investigate also other hormonal signaling pathways, such as cytokinin."}],"publist_id":"4451","issue":"1","extern":1,"_id":"2452","year":"2013","title":"Single-cell-based system to monitor carrier driven cellular auxin homeostasis","status":"public","publication_status":"published","publisher":"BioMed Central","intvolume":" 13","author":[{"full_name":"Barbez, Elke","last_name":"Barbez","first_name":"Elke"},{"full_name":"Laňková, Martina","first_name":"Martina","last_name":"Laňková"},{"full_name":"Pařezová, Markéta","first_name":"Markéta","last_name":"Pařezová"},{"first_name":"Alexis","last_name":"Maizel","full_name":"Maizel, Alexis"},{"full_name":"Zažímalová, Eva","first_name":"Eva","last_name":"Zažímalová"},{"first_name":"Jan","last_name":"Petrášek","full_name":"Petrášek, Jan"},{"full_name":"Jirí Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml"},{"first_name":"Jürgen","last_name":"Kleine Vehn","full_name":"Kleine-Vehn, Jürgen"}],"date_updated":"2021-01-12T06:57:34Z","date_created":"2018-12-11T11:57:45Z","volume":13,"month":"02","day":"01","publication":"BMC Plant Biology","citation":{"ama":"Barbez E, Laňková M, Pařezová M, et al. Single-cell-based system to monitor carrier driven cellular auxin homeostasis. BMC Plant Biology. 2013;13(1). doi:10.1186/1471-2229-13-20","ista":"Barbez E, Laňková M, Pařezová M, Maizel A, Zažímalová E, Petrášek J, Friml J, Kleine Vehn J. 2013. Single-cell-based system to monitor carrier driven cellular auxin homeostasis. BMC Plant Biology. 13(1).","ieee":"E. Barbez et al., “Single-cell-based system to monitor carrier driven cellular auxin homeostasis,” BMC Plant Biology, vol. 13, no. 1. BioMed Central, 2013.","apa":"Barbez, E., Laňková, M., Pařezová, M., Maizel, A., Zažímalová, E., Petrášek, J., … Kleine Vehn, J. (2013). Single-cell-based system to monitor carrier driven cellular auxin homeostasis. BMC Plant Biology. BioMed Central. https://doi.org/10.1186/1471-2229-13-20","mla":"Barbez, Elke, et al. “Single-Cell-Based System to Monitor Carrier Driven Cellular Auxin Homeostasis.” BMC Plant Biology, vol. 13, no. 1, BioMed Central, 2013, doi:10.1186/1471-2229-13-20.","short":"E. Barbez, M. Laňková, M. Pařezová, A. Maizel, E. Zažímalová, J. Petrášek, J. Friml, J. Kleine Vehn, BMC Plant Biology 13 (2013).","chicago":"Barbez, Elke, Martina Laňková, Markéta Pařezová, Alexis Maizel, Eva Zažímalová, Jan Petrášek, Jiří Friml, and Jürgen Kleine Vehn. “Single-Cell-Based System to Monitor Carrier Driven Cellular Auxin Homeostasis.” BMC Plant Biology. BioMed Central, 2013. https://doi.org/10.1186/1471-2229-13-20."},"quality_controlled":0,"doi":"10.1186/1471-2229-13-20","date_published":"2013-02-01T00:00:00Z"},{"publisher":"Frontiers Research Foundation","intvolume":" 4","status":"public","publication_status":"published","title":"Interaction of PLS and PIN and hormonal crosstalk in Arabidopsis root development","_id":"2450","year":"2013","volume":4,"date_updated":"2021-01-12T06:57:34Z","date_created":"2018-12-11T11:57:44Z","author":[{"last_name":"Liu","first_name":"Junli","full_name":"Liu, Junli"},{"last_name":"Menhi","first_name":"Saher","full_name":"Menhi, Saher"},{"last_name":"Topping","first_name":"Jennifer","full_name":"Topping, Jennifer"},{"full_name":"Jirí Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí"},{"last_name":"Lindsey","first_name":"Keith","full_name":"Lindsey, Keith"}],"type":"journal_article","extern":1,"publist_id":"4453","issue":"75","abstract":[{"lang":"eng","text":"Understanding how hormones and genes interact to coordinate plant growth is a major challenge in developmental biology. The activities of auxin, ethylene, and cytokinin depend on cellular context and exhibit either synergistic or antagonistic interactions. Here we use experimentation and network construction to elucidate the role of the interaction of the POLARIS peptide (PLS) and the auxin efflux carrier PIN proteins in the crosstalk of three hormones (auxin, ethylene, and cytokinin) in Arabidopsis root development. In ethylene hypersignaling mutants such as polaris (pls), we show experimentally that expression of both PIN1 and PIN2 significantly increases. This relationship is analyzed in the context of the crosstalk between auxin, ethylene, and cytokinin: in pls, endogenous auxin, ethylene and cytokinin concentration decreases, approximately remains unchanged and increases, respectively. Experimental data are integrated into a hormonal crosstalk network through combination with information in literature. Network construction reveals that the regulation of both PIN1 and PIN2 is predominantly via ethylene signaling. In addition, it is deduced that the relationship between cytokinin and PIN1 and PIN2 levels implies a regulatory role of cytokinin in addition to its regulation to auxin, ethylene, and PLS levels. We discuss how the network of hormones and genes coordinates plant growth by simultaneously regulating the activities of auxin, ethylene, and cytokinin signaling pathways.hormonal crosstalk, root development, auxin flux, PIN proteins, PLS protein, signaling network"}],"quality_controlled":0,"citation":{"short":"J. Liu, S. Menhi, J. Topping, J. Friml, K. Lindsey, Frontiers in Plant Science 4 (2013).","mla":"Liu, Junli, et al. “Interaction of PLS and PIN and Hormonal Crosstalk in Arabidopsis Root Development.” Frontiers in Plant Science, vol. 4, no. 75, Frontiers Research Foundation, 2013, doi:10.3389/fpls.2013.00075.","chicago":"Liu, Junli, Saher Menhi, Jennifer Topping, Jiří Friml, and Keith Lindsey. “Interaction of PLS and PIN and Hormonal Crosstalk in Arabidopsis Root Development.” Frontiers in Plant Science. Frontiers Research Foundation, 2013. https://doi.org/10.3389/fpls.2013.00075.","ama":"Liu J, Menhi S, Topping J, Friml J, Lindsey K. Interaction of PLS and PIN and hormonal crosstalk in Arabidopsis root development. Frontiers in Plant Science. 2013;4(75). doi:10.3389/fpls.2013.00075","ieee":"J. Liu, S. Menhi, J. Topping, J. Friml, and K. Lindsey, “Interaction of PLS and PIN and hormonal crosstalk in Arabidopsis root development,” Frontiers in Plant Science, vol. 4, no. 75. Frontiers Research Foundation, 2013.","apa":"Liu, J., Menhi, S., Topping, J., Friml, J., & Lindsey, K. (2013). Interaction of PLS and PIN and hormonal crosstalk in Arabidopsis root development. Frontiers in Plant Science. Frontiers Research Foundation. https://doi.org/10.3389/fpls.2013.00075","ista":"Liu J, Menhi S, Topping J, Friml J, Lindsey K. 2013. Interaction of PLS and PIN and hormonal crosstalk in Arabidopsis root development. Frontiers in Plant Science. 4(75)."},"publication":"Frontiers in Plant Science","doi":"10.3389/fpls.2013.00075","date_published":"2013-04-01T00:00:00Z","month":"04","day":"01"},{"extern":1,"publist_id":"7659","issue":"680","abstract":[{"lang":"eng","text":"For given non-zero integers a, b, q we investigate the density of solutions (x; y) ∈ ℤ2 to the binary cubic congruence ax2 + by3 ≡ 0 mod q, and use it to establish the Manin conjecture for a singular del Pezzo surface of degree 2 defined over ℚ."}],"type":"journal_article","date_created":"2018-12-11T11:45:24Z","date_updated":"2021-01-12T06:57:33Z","author":[{"first_name":"Stephan","last_name":"Baier","full_name":"Baier, Stephan"},{"full_name":"Timothy Browning","first_name":"Timothy D","last_name":"Browning","id":"35827D50-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8314-0177"}],"publisher":"Walter de Gruyter","title":"Inhomogeneous cubic congruences and rational points on del Pezzo surfaces","status":"public","publication_status":"published","_id":"245","year":"2013","day":"01","month":"07","date_published":"2013-07-01T00:00:00Z","doi":"10.1515/crelle.2012.039","page":"69 - 151","quality_controlled":0,"oa":1,"citation":{"ama":"Baier S, Browning TD. Inhomogeneous cubic congruences and rational points on del Pezzo surfaces. Journal fur die Reine und Angewandte Mathematik. 2013;(680):69-151. doi:10.1515/crelle.2012.039","ista":"Baier S, Browning TD. 2013. Inhomogeneous cubic congruences and rational points on del Pezzo surfaces. Journal fur die Reine und Angewandte Mathematik. (680), 69–151.","ieee":"S. Baier and T. D. Browning, “Inhomogeneous cubic congruences and rational points on del Pezzo surfaces,” Journal fur die Reine und Angewandte Mathematik, no. 680. Walter de Gruyter, pp. 69–151, 2013.","apa":"Baier, S., & Browning, T. D. (2013). Inhomogeneous cubic congruences and rational points on del Pezzo surfaces. Journal Fur Die Reine Und Angewandte Mathematik. Walter de Gruyter. https://doi.org/10.1515/crelle.2012.039","mla":"Baier, Stephan, and Timothy D. Browning. “Inhomogeneous Cubic Congruences and Rational Points on Del Pezzo Surfaces.” Journal Fur Die Reine Und Angewandte Mathematik, no. 680, Walter de Gruyter, 2013, pp. 69–151, doi:10.1515/crelle.2012.039.","short":"S. Baier, T.D. Browning, Journal Fur Die Reine Und Angewandte Mathematik (2013) 69–151.","chicago":"Baier, Stephan, and Timothy D Browning. “Inhomogeneous Cubic Congruences and Rational Points on Del Pezzo Surfaces.” Journal Fur Die Reine Und Angewandte Mathematik. Walter de Gruyter, 2013. https://doi.org/10.1515/crelle.2012.039."},"main_file_link":[{"url":"https://arxiv.org/abs/1011.3434","open_access":"1"}],"publication":"Journal fur die Reine und Angewandte Mathematik"},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"2457","year":"2013","title":"Origin and evolution of PIN auxin transporters in the green lineage","status":"public","publication_status":"published","intvolume":" 18","publisher":"Cell Press","author":[{"full_name":"Viaene, Tom","last_name":"Viaene","first_name":"Tom"},{"first_name":"Charles","last_name":"Delwiche","full_name":"Delwiche, Charles"},{"full_name":"Rensing, Stefan","first_name":"Stefan","last_name":"Rensing"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml","full_name":"Friml, Jirí"}],"date_updated":"2021-01-12T06:57:36Z","date_created":"2018-12-11T11:57:46Z","oa_version":"None","volume":18,"type":"journal_article","publist_id":"4446","issue":"1","extern":"1","publication":"Trends in Plant Science","citation":{"ista":"Viaene T, Delwiche C, Rensing S, Friml J. 2013. Origin and evolution of PIN auxin transporters in the green lineage. Trends in Plant Science. 18(1), 5–10.","apa":"Viaene, T., Delwiche, C., Rensing, S., & Friml, J. (2013). Origin and evolution of PIN auxin transporters in the green lineage. Trends in Plant Science. Cell Press. https://doi.org/10.1016/j.tplants.2012.08.009","ieee":"T. Viaene, C. Delwiche, S. Rensing, and J. Friml, “Origin and evolution of PIN auxin transporters in the green lineage,” Trends in Plant Science, vol. 18, no. 1. Cell Press, pp. 5–10, 2013.","ama":"Viaene T, Delwiche C, Rensing S, Friml J. Origin and evolution of PIN auxin transporters in the green lineage. Trends in Plant Science. 2013;18(1):5-10. doi:10.1016/j.tplants.2012.08.009","chicago":"Viaene, Tom, Charles Delwiche, Stefan Rensing, and Jiří Friml. “Origin and Evolution of PIN Auxin Transporters in the Green Lineage.” Trends in Plant Science. Cell Press, 2013. https://doi.org/10.1016/j.tplants.2012.08.009.","mla":"Viaene, Tom, et al. “Origin and Evolution of PIN Auxin Transporters in the Green Lineage.” Trends in Plant Science, vol. 18, no. 1, Cell Press, 2013, pp. 5–10, doi:10.1016/j.tplants.2012.08.009.","short":"T. Viaene, C. Delwiche, S. Rensing, J. Friml, Trends in Plant Science 18 (2013) 5–10."},"quality_controlled":"1","page":"5 - 10","date_published":"2013-01-01T00:00:00Z","doi":"10.1016/j.tplants.2012.08.009","language":[{"iso":"eng"}],"day":"01","month":"01"},{"abstract":[{"lang":"eng","text":"Given an intersection of two quadrics X Pm1, with m > 9, the quantitative arithmetic of the set X(Q) is investigated under the assumption that the singular locus of X consists of a pair of conjugate singular points defined over Q(i)."}],"publist_id":"7658","issue":"9","extern":1,"type":"journal_article","author":[{"full_name":"Timothy Browning","id":"35827D50-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8314-0177","first_name":"Timothy D","last_name":"Browning"},{"full_name":"Munshi, Ritabrata","last_name":"Munshi","first_name":"Ritabrata"}],"date_updated":"2021-01-12T06:57:37Z","date_created":"2018-12-11T11:45:25Z","volume":149,"year":"2013","_id":"246","acknowledgement":"EP/E053262/1\tEngineering and Physical Sciences Research Council","title":"Rational points on singular intersections of quadrics","publication_status":"published","status":"public","publisher":"Cambridge University Press","intvolume":" 149","day":"01","month":"09","doi":"10.1112/S0010437X13007185","date_published":"2013-09-01T00:00:00Z","publication":"Compositio Mathematica","citation":{"ama":"Browning TD, Munshi R. Rational points on singular intersections of quadrics. Compositio Mathematica. 2013;149(9):1457-1494. doi:10.1112/S0010437X13007185","ista":"Browning TD, Munshi R. 2013. Rational points on singular intersections of quadrics. Compositio Mathematica. 149(9), 1457–1494.","apa":"Browning, T. D., & Munshi, R. (2013). Rational points on singular intersections of quadrics. Compositio Mathematica. Cambridge University Press. https://doi.org/10.1112/S0010437X13007185","ieee":"T. D. Browning and R. Munshi, “Rational points on singular intersections of quadrics,” Compositio Mathematica, vol. 149, no. 9. Cambridge University Press, pp. 1457–1494, 2013.","mla":"Browning, Timothy D., and Ritabrata Munshi. “Rational Points on Singular Intersections of Quadrics.” Compositio Mathematica, vol. 149, no. 9, Cambridge University Press, 2013, pp. 1457–94, doi:10.1112/S0010437X13007185.","short":"T.D. Browning, R. Munshi, Compositio Mathematica 149 (2013) 1457–1494.","chicago":"Browning, Timothy D, and Ritabrata Munshi. “Rational Points on Singular Intersections of Quadrics.” Compositio Mathematica. Cambridge University Press, 2013. https://doi.org/10.1112/S0010437X13007185."},"quality_controlled":0,"page":"1457 - 1494"},{"_id":"2471","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 8","title":"Mechanism of protein kinetic stabilization by engineered disulfide crosslinks","status":"public","ddc":["570"],"pubrep_id":"414","oa_version":"Published Version","file":[{"date_created":"2018-12-12T10:15:07Z","date_updated":"2020-07-14T12:45:41Z","checksum":"c0c96cc76ed7ef0d036a31a7e33c9a37","relation":"main_file","file_id":"5124","file_size":1323666,"content_type":"application/pdf","creator":"system","file_name":"IST-2016-414-v1+1_journal.pone.0070013.pdf","access_level":"open_access"}],"type":"journal_article","issue":"7","abstract":[{"lang":"eng","text":"The impact of disulfide bonds on protein stability goes beyond simple equilibrium thermodynamics effects associated with the conformational entropy of the unfolded state. Indeed, disulfide crosslinks may play a role in the prevention of dysfunctional association and strongly affect the rates of irreversible enzyme inactivation, highly relevant in biotechnological applications. While these kinetic-stability effects remain poorly understood, by analogy with proposed mechanisms for processes of protein aggregation and fibrillogenesis, we propose that they may be determined by the properties of sparsely-populated, partially-unfolded intermediates. Here we report the successful design, on the basis of high temperature molecular-dynamics simulations, of six thermodynamically and kinetically stabilized variants of phytase from Citrobacter braakii (a biotechnologically important enzyme) with one, two or three engineered disulfides. Activity measurements and 3D crystal structure determination demonstrate that the engineered crosslinks do not cause dramatic alterations in the native structure. The inactivation kinetics for all the variants displays a strongly non-Arrhenius temperature dependence, with the time-scale for the irreversible denaturation process reaching a minimum at a given temperature within the range of the denaturation transition. We show this striking feature to be a signature of a key role played by a partially unfolded, intermediate state/ensemble. Energetic and mutational analyses confirm that the intermediate is highly unfolded (akin to a proposed critical intermediate in the misfolding of the prion protein), a result that explains the observed kinetic stabilization. Our results provide a rationale for the kinetic-stability consequences of disulfide-crosslink engineering and an experimental methodology to arrive at energetic/structural descriptions of the sparsely populated and elusive intermediates that play key roles in irreversible protein denaturation."}],"citation":{"apa":"Sanchez-Romero, I., Ariza, A., Wilson, K., Skjøt, M., Vind, J., De Maria, L., … Sánchez Ruiz, J. (2013). Mechanism of protein kinetic stabilization by engineered disulfide crosslinks. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0070013","ieee":"I. Sanchez-Romero et al., “Mechanism of protein kinetic stabilization by engineered disulfide crosslinks,” PLoS One, vol. 8, no. 7. Public Library of Science, 2013.","ista":"Sanchez-Romero I, Ariza A, Wilson K, Skjøt M, Vind J, De Maria L, Skov L, Sánchez Ruiz J. 2013. Mechanism of protein kinetic stabilization by engineered disulfide crosslinks. PLoS One. 8(7), e70013.","ama":"Sanchez-Romero I, Ariza A, Wilson K, et al. Mechanism of protein kinetic stabilization by engineered disulfide crosslinks. PLoS One. 2013;8(7). doi:10.1371/journal.pone.0070013","chicago":"Sanchez-Romero, Inmaculada, Antonio Ariza, Keith Wilson, Michael Skjøt, Jesper Vind, Leonardo De Maria, Lars Skov, and Jose Sánchez Ruiz. “Mechanism of Protein Kinetic Stabilization by Engineered Disulfide Crosslinks.” PLoS One. Public Library of Science, 2013. https://doi.org/10.1371/journal.pone.0070013.","short":"I. Sanchez-Romero, A. Ariza, K. Wilson, M. Skjøt, J. Vind, L. De Maria, L. Skov, J. Sánchez Ruiz, PLoS One 8 (2013).","mla":"Sanchez-Romero, Inmaculada, et al. “Mechanism of Protein Kinetic Stabilization by Engineered Disulfide Crosslinks.” PLoS One, vol. 8, no. 7, e70013, Public Library of Science, 2013, doi:10.1371/journal.pone.0070013."},"publication":"PLoS One","date_published":"2013-07-30T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"30","year":"2013","department":[{"_id":"HaJa"}],"publisher":"Public Library of Science","publication_status":"published","author":[{"id":"3D9C5D30-F248-11E8-B48F-1D18A9856A87","first_name":"Inmaculada","last_name":"Sanchez Romero","full_name":"Sanchez Romero, Inmaculada"},{"full_name":"Ariza, Antonio","first_name":"Antonio","last_name":"Ariza"},{"first_name":"Keith","last_name":"Wilson","full_name":"Wilson, Keith"},{"full_name":"Skjøt, Michael","last_name":"Skjøt","first_name":"Michael"},{"last_name":"Vind","first_name":"Jesper","full_name":"Vind, Jesper"},{"first_name":"Leonardo","last_name":"De Maria","full_name":"De Maria, Leonardo"},{"full_name":"Skov, Lars","first_name":"Lars","last_name":"Skov"},{"full_name":"Sánchez Ruiz, Jose","first_name":"Jose","last_name":"Sánchez Ruiz"}],"volume":8,"date_created":"2018-12-11T11:57:51Z","date_updated":"2021-01-12T06:57:41Z","article_number":"e70013","publist_id":"4430","file_date_updated":"2020-07-14T12:45:41Z","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","doi":"10.1371/journal.pone.0070013","language":[{"iso":"eng"}],"month":"07"},{"has_accepted_license":"1","day":"29","scopus_import":1,"date_published":"2013-07-29T00:00:00Z","citation":{"ama":"Cazzonelli C, Vanstraelen M, Simon S, et al. Role of the Arabidopsis PIN6 auxin transporter in auxin homeostasis and auxin-mediated development. PLoS One. 2013;8(7). doi:10.1371/journal.pone.0070069","ista":"Cazzonelli C, Vanstraelen M, Simon S, Yin K, Carron Arthur A, Nisar N, Tarle G, Cuttriss A, Searle I, Benková E, Mathesius U, Masle J, Friml J, Pogson B. 2013. Role of the Arabidopsis PIN6 auxin transporter in auxin homeostasis and auxin-mediated development. PLoS One. 8(7), e70069.","ieee":"C. Cazzonelli et al., “Role of the Arabidopsis PIN6 auxin transporter in auxin homeostasis and auxin-mediated development,” PLoS One, vol. 8, no. 7. Public Library of Science, 2013.","apa":"Cazzonelli, C., Vanstraelen, M., Simon, S., Yin, K., Carron Arthur, A., Nisar, N., … Pogson, B. (2013). Role of the Arabidopsis PIN6 auxin transporter in auxin homeostasis and auxin-mediated development. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0070069","mla":"Cazzonelli, Christopher, et al. “Role of the Arabidopsis PIN6 Auxin Transporter in Auxin Homeostasis and Auxin-Mediated Development.” PLoS One, vol. 8, no. 7, e70069, Public Library of Science, 2013, doi:10.1371/journal.pone.0070069.","short":"C. Cazzonelli, M. Vanstraelen, S. Simon, K. Yin, A. Carron Arthur, N. Nisar, G. Tarle, A. Cuttriss, I. Searle, E. Benková, U. Mathesius, J. Masle, J. Friml, B. Pogson, PLoS One 8 (2013).","chicago":"Cazzonelli, Christopher, Marleen Vanstraelen, Sibu Simon, Kuide Yin, Ashley Carron Arthur, Nazia Nisar, Gauri Tarle, et al. “Role of the Arabidopsis PIN6 Auxin Transporter in Auxin Homeostasis and Auxin-Mediated Development.” PLoS One. Public Library of Science, 2013. https://doi.org/10.1371/journal.pone.0070069."},"publication":"PLoS One","issue":"7","abstract":[{"text":"Plant-specific PIN-formed (PIN) efflux transporters for the plant hormone auxin are required for tissue-specific directional auxin transport and cellular auxin homeostasis. The Arabidopsis PIN protein family has been shown to play important roles in developmental processes such as embryogenesis, organogenesis, vascular tissue differentiation, root meristem patterning and tropic growth. Here we analyzed roles of the less characterised Arabidopsis PIN6 auxin transporter. PIN6 is auxin-inducible and is expressed during multiple auxin-regulated developmental processes. Loss of pin6 function interfered with primary root growth and lateral root development. Misexpression of PIN6 affected auxin transport and interfered with auxin homeostasis in other growth processes such as shoot apical dominance, lateral root primordia development, adventitious root formation, root hair outgrowth and root waving. These changes in auxin-regulated growth correlated with a reduction in total auxin transport as well as with an altered activity of DR5-GUS auxin response reporter. Overall, the data indicate that PIN6 regulates auxin homeostasis during plant development.","lang":"eng"}],"type":"journal_article","pubrep_id":"393","file":[{"content_type":"application/pdf","file_size":9003465,"creator":"system","file_name":"IST-2015-393-v1+1_journal.pone.0070069.pdf","access_level":"open_access","date_updated":"2020-07-14T12:45:41Z","date_created":"2018-12-12T10:16:34Z","checksum":"3be71828b6c2ba9c90eb7056e3f7f57a","relation":"main_file","file_id":"5222"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2472","intvolume":" 8","status":"public","ddc":["580","570"],"title":"Role of the Arabidopsis PIN6 auxin transporter in auxin homeostasis and auxin-mediated development","month":"07","doi":"10.1371/journal.pone.0070069","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"project":[{"_id":"253FCA6A-B435-11E9-9278-68D0E5697425","grant_number":"207362","call_identifier":"FP7","name":"Hormonal cross-talk in plant organogenesis"},{"name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","publist_id":"4431","ec_funded":1,"file_date_updated":"2020-07-14T12:45:41Z","article_number":"e70069","author":[{"first_name":"Christopher","last_name":"Cazzonelli","full_name":"Cazzonelli, Christopher"},{"first_name":"Marleen","last_name":"Vanstraelen","full_name":"Vanstraelen, Marleen"},{"full_name":"Simon, Sibu","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1998-6741","first_name":"Sibu","last_name":"Simon"},{"first_name":"Kuide","last_name":"Yin","full_name":"Yin, Kuide"},{"last_name":"Carron Arthur","first_name":"Ashley","full_name":"Carron Arthur, Ashley"},{"full_name":"Nisar, Nazia","first_name":"Nazia","last_name":"Nisar"},{"first_name":"Gauri","last_name":"Tarle","full_name":"Tarle, Gauri"},{"full_name":"Cuttriss, Abby","last_name":"Cuttriss","first_name":"Abby"},{"last_name":"Searle","first_name":"Iain","full_name":"Searle, Iain"},{"last_name":"Benková","first_name":"Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva"},{"last_name":"Mathesius","first_name":"Ulrike","full_name":"Mathesius, Ulrike"},{"last_name":"Masle","first_name":"Josette","full_name":"Masle, Josette"},{"full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml"},{"first_name":"Barry","last_name":"Pogson","full_name":"Pogson, Barry"}],"volume":8,"date_created":"2018-12-11T11:57:52Z","date_updated":"2021-01-12T06:57:41Z","year":"2013","publisher":"Public Library of Science","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"publication_status":"published"},{"publist_id":"4432","file_date_updated":"2020-07-14T12:45:41Z","article_number":"e70050","volume":8,"date_created":"2018-12-11T11:57:51Z","date_updated":"2021-01-12T06:57:40Z","author":[{"full_name":"Čovanová, Milada","first_name":"Milada","last_name":"Čovanová"},{"full_name":"Sauer, Michael","last_name":"Sauer","first_name":"Michael"},{"first_name":"Jan","last_name":"Rychtář","full_name":"Rychtář, Jan"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí"},{"full_name":"Petrášek, Jan","last_name":"Petrášek","first_name":"Jan"},{"full_name":"Zažímalová, Eva","first_name":"Eva","last_name":"Zažímalová"}],"department":[{"_id":"JiFr"}],"publisher":"Public Library of Science","publication_status":"published","year":"2013","month":"07","language":[{"iso":"eng"}],"doi":"10.1371/journal.pone.0070050","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"issue":"7","abstract":[{"lang":"eng","text":"Background:Auxin binding protein 1 (ABP1) is a putative auxin receptor and its function is indispensable for plant growth and development. ABP1 has been shown to be involved in auxin-dependent regulation of cell division and expansion, in plasma-membrane-related processes such as changes in transmembrane potential, and in the regulation of clathrin-dependent endocytosis. However, the ABP1-regulated downstream pathway remains elusive.Methodology/Principal Findings:Using auxin transport assays and quantitative analysis of cellular morphology we show that ABP1 regulates auxin efflux from tobacco BY-2 cells. The overexpression of ABP1can counterbalance increased auxin efflux and auxin starvation phenotypes caused by the overexpression of PIN auxin efflux carrier. Relevant mechanism involves the ABP1-controlled vesicle trafficking processes, including positive regulation of endocytosis of PIN auxin efflux carriers, as indicated by fluorescence recovery after photobleaching (FRAP) and pharmacological manipulations.Conclusions/Significance:The findings indicate the involvement of ABP1 in control of rate of auxin transport across plasma membrane emphasizing the role of ABP1 in regulation of PIN activity at the plasma membrane, and highlighting the relevance of ABP1 for the formation of developmentally important, PIN-dependent auxin gradients."}],"type":"journal_article","oa_version":"Published Version","file":[{"file_id":"4681","relation":"main_file","checksum":"2d47ef47616ef4de1d517d146548184e","date_created":"2018-12-12T10:08:21Z","date_updated":"2020-07-14T12:45:41Z","access_level":"open_access","file_name":"IST-2016-413-v1+1_journal.pone.0070050.pdf","creator":"system","content_type":"application/pdf","file_size":2294955}],"pubrep_id":"413","intvolume":" 8","title":"Overexpression of the auxin binding PROTEIN1 modulates PIN-dependent auxin transport in tobacco cells","ddc":["570"],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2470","has_accepted_license":"1","day":"23","scopus_import":1,"date_published":"2013-07-23T00:00:00Z","citation":{"mla":"Čovanová, Milada, et al. “Overexpression of the Auxin Binding PROTEIN1 Modulates PIN-Dependent Auxin Transport in Tobacco Cells.” PLoS One, vol. 8, no. 7, e70050, Public Library of Science, 2013, doi:10.1371/journal.pone.0070050.","short":"M. Čovanová, M. Sauer, J. Rychtář, J. Friml, J. Petrášek, E. Zažímalová, PLoS One 8 (2013).","chicago":"Čovanová, Milada, Michael Sauer, Jan Rychtář, Jiří Friml, Jan Petrášek, and Eva Zažímalová. “Overexpression of the Auxin Binding PROTEIN1 Modulates PIN-Dependent Auxin Transport in Tobacco Cells.” PLoS One. Public Library of Science, 2013. https://doi.org/10.1371/journal.pone.0070050.","ama":"Čovanová M, Sauer M, Rychtář J, Friml J, Petrášek J, Zažímalová E. Overexpression of the auxin binding PROTEIN1 modulates PIN-dependent auxin transport in tobacco cells. PLoS One. 2013;8(7). doi:10.1371/journal.pone.0070050","ista":"Čovanová M, Sauer M, Rychtář J, Friml J, Petrášek J, Zažímalová E. 2013. Overexpression of the auxin binding PROTEIN1 modulates PIN-dependent auxin transport in tobacco cells. PLoS One. 8(7), e70050.","apa":"Čovanová, M., Sauer, M., Rychtář, J., Friml, J., Petrášek, J., & Zažímalová, E. (2013). Overexpression of the auxin binding PROTEIN1 modulates PIN-dependent auxin transport in tobacco cells. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0070050","ieee":"M. Čovanová, M. Sauer, J. Rychtář, J. Friml, J. Petrášek, and E. Zažímalová, “Overexpression of the auxin binding PROTEIN1 modulates PIN-dependent auxin transport in tobacco cells,” PLoS One, vol. 8, no. 7. Public Library of Science, 2013."},"publication":"PLoS One"},{"pubrep_id":"605","oa_version":"Submitted Version","file":[{"creator":"system","content_type":"application/pdf","file_size":8601561,"file_name":"IST-2016-605-v1+1_tetflip_fixed.pdf","access_level":"open_access","date_updated":"2020-07-14T12:45:41Z","date_created":"2018-12-12T10:17:25Z","checksum":"aeea6b0ff2b27c695aeb8408c7d2fc50","file_id":"5279","relation":"main_file"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2466","intvolume":" 32","ddc":["000"],"title":"Highly adaptive liquid simulations on tetrahedral meshes","status":"public","issue":"4","abstract":[{"lang":"eng","text":"We introduce a new method for efficiently simulating liquid with extreme amounts of spatial adaptivity. Our method combines several key components to drastically speed up the simulation of large-scale fluid phenomena: We leverage an alternative Eulerian tetrahedral mesh discretization to significantly reduce the complexity of the pressure solve while increasing the robustness with respect to element quality and removing the possibility of locking. Next, we enable subtle free-surface phenomena by deriving novel second-order boundary conditions consistent with our discretization. We couple this discretization with a spatially adaptive Fluid-Implicit Particle (FLIP) method, enabling efficient, robust, minimally-dissipative simulations that can undergo sharp changes in spatial resolution while minimizing artifacts. Along the way, we provide a new method for generating a smooth and detailed surface from a set of particles with variable sizes. Finally, we explore several new sizing functions for determining spatially adaptive simulation resolutions, and we show how to couple them to our simulator. We combine each of these elements to produce a simulation algorithm that is capable of creating animations at high maximum resolutions while avoiding common pitfalls like inaccurate boundary conditions and inefficient computation."}],"type":"journal_article","date_published":"2013-07-01T00:00:00Z","citation":{"chicago":"Ando, Ryoichi, Nils Thuerey, and Chris Wojtan. “Highly Adaptive Liquid Simulations on Tetrahedral Meshes.” ACM Transactions on Graphics. ACM, 2013. https://doi.org/10.1145/2461912.2461982.","short":"R. Ando, N. Thuerey, C. Wojtan, ACM Transactions on Graphics 32 (2013).","mla":"Ando, Ryoichi, et al. “Highly Adaptive Liquid Simulations on Tetrahedral Meshes.” ACM Transactions on Graphics, vol. 32, no. 4, 103, ACM, 2013, doi:10.1145/2461912.2461982.","apa":"Ando, R., Thuerey, N., & Wojtan, C. (2013). Highly adaptive liquid simulations on tetrahedral meshes. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/2461912.2461982","ieee":"R. Ando, N. Thuerey, and C. Wojtan, “Highly adaptive liquid simulations on tetrahedral meshes,” ACM Transactions on Graphics, vol. 32, no. 4. ACM, 2013.","ista":"Ando R, Thuerey N, Wojtan C. 2013. Highly adaptive liquid simulations on tetrahedral meshes. ACM Transactions on Graphics. 32(4), 103.","ama":"Ando R, Thuerey N, Wojtan C. Highly adaptive liquid simulations on tetrahedral meshes. ACM Transactions on Graphics. 2013;32(4). doi:10.1145/2461912.2461982"},"publication":"ACM Transactions on Graphics","has_accepted_license":"1","day":"01","scopus_import":1,"author":[{"first_name":"Ryoichi","last_name":"Ando","full_name":"Ando, Ryoichi"},{"full_name":"Thuerey, Nils","last_name":"Thuerey","first_name":"Nils"},{"full_name":"Wojtan, Christopher J","last_name":"Wojtan","first_name":"Christopher J","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"}],"volume":32,"date_created":"2018-12-11T11:57:50Z","date_updated":"2023-02-23T10:44:14Z","year":"2013","department":[{"_id":"ChWo"}],"publisher":"ACM","publication_status":"published","publist_id":"4436","file_date_updated":"2020-07-14T12:45:41Z","article_number":"103","doi":"10.1145/2461912.2461982","language":[{"iso":"eng"}],"oa":1,"quality_controlled":"1","month":"07"},{"doi":"10.1145/2461912.2462027","language":[{"iso":"eng"}],"oa":1,"quality_controlled":"1","month":"07","author":[{"last_name":"Bernstein","first_name":"Gilbert","full_name":"Bernstein, Gilbert"},{"last_name":"Wojtan","first_name":"Christopher J","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","full_name":"Wojtan, Christopher J"}],"date_created":"2018-12-11T11:57:50Z","date_updated":"2023-02-23T10:44:16Z","volume":32,"year":"2013","publication_status":"published","department":[{"_id":"ChWo"}],"publisher":"ACM","file_date_updated":"2020-07-14T12:45:41Z","publist_id":"4435","article_number":"34","date_published":"2013-07-01T00:00:00Z","publication":"ACM Transactions on Graphics","citation":{"ista":"Bernstein G, Wojtan C. 2013. Putting holes in holey geometry: Topology change for arbitrary surfaces. ACM Transactions on Graphics. 32(4), 34.","apa":"Bernstein, G., & Wojtan, C. (2013). Putting holes in holey geometry: Topology change for arbitrary surfaces. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/2461912.2462027","ieee":"G. Bernstein and C. Wojtan, “Putting holes in holey geometry: Topology change for arbitrary surfaces,” ACM Transactions on Graphics, vol. 32, no. 4. ACM, 2013.","ama":"Bernstein G, Wojtan C. Putting holes in holey geometry: Topology change for arbitrary surfaces. ACM Transactions on Graphics. 2013;32(4). doi:10.1145/2461912.2462027","chicago":"Bernstein, Gilbert, and Chris Wojtan. “Putting Holes in Holey Geometry: Topology Change for Arbitrary Surfaces.” ACM Transactions on Graphics. ACM, 2013. https://doi.org/10.1145/2461912.2462027.","mla":"Bernstein, Gilbert, and Chris Wojtan. “Putting Holes in Holey Geometry: Topology Change for Arbitrary Surfaces.” ACM Transactions on Graphics, vol. 32, no. 4, 34, ACM, 2013, doi:10.1145/2461912.2462027.","short":"G. Bernstein, C. Wojtan, ACM Transactions on Graphics 32 (2013)."},"day":"01","has_accepted_license":"1","scopus_import":1,"pubrep_id":"604","file":[{"file_size":3514674,"content_type":"application/pdf","creator":"system","access_level":"open_access","file_name":"IST-2016-604-v1+1_toptop2013.pdf","checksum":"9c8425d62246996ca632c5a01870515b","date_created":"2018-12-12T10:09:43Z","date_updated":"2020-07-14T12:45:41Z","relation":"main_file","file_id":"4768"}],"oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2467","title":"Putting holes in holey geometry: Topology change for arbitrary surfaces","ddc":["000"],"status":"public","intvolume":" 32","abstract":[{"lang":"eng","text":"This paper presents a method for computing topology changes for triangle meshes in an interactive geometric modeling environment. Most triangle meshes in practice do not exhibit desirable geometric properties, so we develop a solution that is independent of standard assumptions and robust to geometric errors. Specifically, we provide the first method for topology change applicable to arbitrary non-solid, non-manifold, non-closed, self-intersecting surfaces. We prove that this new method for topology change produces the expected conventional results when applied to solid (closed, manifold, non-self-intersecting) surfaces---that is, we prove a backwards-compatibility property relative to prior work. Beyond solid surfaces, we present empirical evidence that our method remains tolerant to a variety of surface aberrations through the incorporation of a novel error correction scheme. Finally, we demonstrate how topology change applied to non-solid objects enables wholly new and useful behaviors."}],"issue":"4","type":"journal_article"},{"status":"public","ddc":["000"],"title":"Liquid surface tracking with error compensation","intvolume":" 32","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2468","file":[{"checksum":"53d905e0180e23ef3e813b969ffed4e1","date_created":"2018-12-12T10:09:37Z","date_updated":"2020-07-14T12:45:41Z","file_id":"4761","relation":"main_file","creator":"system","file_size":5813685,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2016-603-v1+1_liquidError_web.pdf"}],"oa_version":"Submitted Version","pubrep_id":"603","type":"journal_article","abstract":[{"text":"Our work concerns the combination of an Eulerian liquid simulation with a high-resolution surface tracker (e.g. the level set method or a Lagrangian triangle mesh). The naive application of a high-resolution surface tracker to a low-resolution velocity field can produce many visually disturbing physical and topological artifacts that limit their use in practice. We address these problems by defining an error function which compares the current state of the surface tracker to the set of physically valid surface states. By reducing this error with a gradient descent technique, we introduce a novel physics-based surface fairing method. Similarly, by treating this error function as a potential energy, we derive a new surface correction force that mimics the vortex sheet equations. We demonstrate our results with both level set and mesh-based surface trackers.","lang":"eng"}],"issue":"4","publication":"ACM Transactions on Graphics","citation":{"ama":"Bojsen-Hansen M, Wojtan C. Liquid surface tracking with error compensation. ACM Transactions on Graphics. 2013;32(4). doi:10.1145/2461912.2461991","apa":"Bojsen-Hansen, M., & Wojtan, C. (2013). Liquid surface tracking with error compensation. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/2461912.2461991","ieee":"M. Bojsen-Hansen and C. Wojtan, “Liquid surface tracking with error compensation,” ACM Transactions on Graphics, vol. 32, no. 4. ACM, 2013.","ista":"Bojsen-Hansen M, Wojtan C. 2013. Liquid surface tracking with error compensation. ACM Transactions on Graphics. 32(4), 68.","short":"M. Bojsen-Hansen, C. Wojtan, ACM Transactions on Graphics 32 (2013).","mla":"Bojsen-Hansen, Morten, and Chris Wojtan. “Liquid Surface Tracking with Error Compensation.” ACM Transactions on Graphics, vol. 32, no. 4, 68, ACM, 2013, doi:10.1145/2461912.2461991.","chicago":"Bojsen-Hansen, Morten, and Chris Wojtan. “Liquid Surface Tracking with Error Compensation.” ACM Transactions on Graphics. ACM, 2013. https://doi.org/10.1145/2461912.2461991."},"date_published":"2013-07-01T00:00:00Z","scopus_import":1,"day":"01","has_accepted_license":"1","publication_status":"published","department":[{"_id":"ChWo"}],"publisher":"ACM","year":"2013","date_created":"2018-12-11T11:57:50Z","date_updated":"2023-02-23T10:44:18Z","volume":32,"author":[{"full_name":"Bojsen-Hansen, Morten","orcid":"0000-0002-4417-3224","id":"439F0C8C-F248-11E8-B48F-1D18A9856A87","last_name":"Bojsen-Hansen","first_name":"Morten"},{"full_name":"Wojtan, Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546","first_name":"Christopher J","last_name":"Wojtan"}],"article_number":"68","file_date_updated":"2020-07-14T12:45:41Z","publist_id":"4434","quality_controlled":"1","oa":1,"language":[{"iso":"eng"}],"doi":"10.1145/2461912.2461991","month":"07"},{"scopus_import":1,"has_accepted_license":"1","day":"22","citation":{"ama":"Maître J-L, Heisenberg C-PJ. Three functions of cadherins in cell adhesion. Current Biology. 2013;23(14):R626-R633. doi:10.1016/j.cub.2013.06.019","ista":"Maître J-L, Heisenberg C-PJ. 2013. Three functions of cadherins in cell adhesion. Current Biology. 23(14), R626–R633.","ieee":"J.-L. Maître and C.-P. J. Heisenberg, “Three functions of cadherins in cell adhesion,” Current Biology, vol. 23, no. 14. Cell Press, pp. R626–R633, 2013.","apa":"Maître, J.-L., & Heisenberg, C.-P. J. (2013). Three functions of cadherins in cell adhesion. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2013.06.019","mla":"Maître, Jean-Léon, and Carl-Philipp J. Heisenberg. “Three Functions of Cadherins in Cell Adhesion.” Current Biology, vol. 23, no. 14, Cell Press, 2013, pp. R626–33, doi:10.1016/j.cub.2013.06.019.","short":"J.-L. Maître, C.-P.J. Heisenberg, Current Biology 23 (2013) R626–R633.","chicago":"Maître, Jean-Léon, and Carl-Philipp J Heisenberg. “Three Functions of Cadherins in Cell Adhesion.” Current Biology. Cell Press, 2013. https://doi.org/10.1016/j.cub.2013.06.019."},"publication":"Current Biology","page":"R626 - R633","date_published":"2013-07-22T00:00:00Z","type":"journal_article","issue":"14","abstract":[{"text":"Cadherins are transmembrane proteins that mediate cell–cell adhesion in animals. By regulating contact formation and stability, cadherins play a crucial role in tissue morphogenesis and homeostasis. Here, we review the three major unctions of cadherins in cell–cell contact formation and stability. Two of those functions lead to a decrease in interfacial ension at the forming cell–cell contact, thereby promoting contact expansion — first, by providing adhesion tension that lowers interfacial tension at the cell–cell contact, and second, by signaling to the actomyosin cytoskeleton in order to reduce cortex tension and thus interfacial tension at the contact. The third function of cadherins in cell–cell contact formation is to stabilize the contact by resisting mechanical forces that pull on the contact.","lang":"eng"}],"_id":"2469","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 23","title":"Three functions of cadherins in cell adhesion","status":"public","ddc":["570"],"oa_version":"Published Version","file":[{"file_name":"2013_CurrentBiology_Maitre.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":247320,"file_id":"5881","relation":"main_file","date_updated":"2020-07-14T12:45:41Z","date_created":"2019-01-24T15:40:22Z","checksum":"6a424b2f007b41d4955a9135793b2162"}],"month":"07","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["23885883"]},"quality_controlled":"1","doi":"10.1016/j.cub.2013.06.019","language":[{"iso":"eng"}],"publist_id":"4433","file_date_updated":"2020-07-14T12:45:41Z","pmid":1,"year":"2013","publisher":"Cell Press","department":[{"_id":"CaHe"}],"publication_status":"published","author":[{"orcid":"0000-0002-3688-1474","id":"48F1E0D8-F248-11E8-B48F-1D18A9856A87","last_name":"Maître","first_name":"Jean-Léon","full_name":"Maître, Jean-Léon"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J"}],"volume":23,"date_updated":"2021-01-12T06:57:40Z","date_created":"2018-12-11T11:57:51Z"},{"acknowledgement":"EP/E053262/1\tEngineering and Physical Sciences Research Council","_id":"247","year":"2013","intvolume":" 56","publisher":"Unknown","title":"The Lang-Weil estimate for cubic hypersurfaces","publication_status":"published","status":"public","author":[{"full_name":"Timothy Browning","last_name":"Browning","first_name":"Timothy D","orcid":"0000-0002-8314-0177","id":"35827D50-F248-11E8-B48F-1D18A9856A87"}],"volume":56,"date_updated":"2021-01-12T06:57:40Z","date_created":"2018-12-11T11:45:25Z","type":"journal_article","issue":"3","publist_id":"7657","abstract":[{"lang":"eng","text":"An improved estimate is provided for the number of Fq-rational points on a geometrically irreducible, projective, cubic hypersurface that is not equal to a cone."}],"extern":1,"citation":{"short":"T.D. Browning, Canadian Mathematical Bulletin 56 (2013) 500–502.","mla":"Browning, Timothy D. “The Lang-Weil Estimate for Cubic Hypersurfaces.” Canadian Mathematical Bulletin, vol. 56, no. 3, Unknown, 2013, pp. 500–02, doi:10.4153/CMB-2011-177-4.","chicago":"Browning, Timothy D. “The Lang-Weil Estimate for Cubic Hypersurfaces.” Canadian Mathematical Bulletin. Unknown, 2013. https://doi.org/10.4153/CMB-2011-177-4.","ama":"Browning TD. The Lang-Weil estimate for cubic hypersurfaces. Canadian Mathematical Bulletin. 2013;56(3):500-502. doi:10.4153/CMB-2011-177-4","ieee":"T. D. Browning, “The Lang-Weil estimate for cubic hypersurfaces,” Canadian Mathematical Bulletin, vol. 56, no. 3. Unknown, pp. 500–502, 2013.","apa":"Browning, T. D. (2013). The Lang-Weil estimate for cubic hypersurfaces. Canadian Mathematical Bulletin. Unknown. https://doi.org/10.4153/CMB-2011-177-4","ista":"Browning TD. 2013. The Lang-Weil estimate for cubic hypersurfaces. Canadian Mathematical Bulletin. 56(3), 500–502."},"publication":"Canadian Mathematical Bulletin","page":"500 - 502","quality_controlled":0,"date_published":"2013-08-31T00:00:00Z","doi":"10.4153/CMB-2011-177-4","day":"31","month":"08"},{"abstract":[{"lang":"eng","text":"When a mutation with selective advantage s spreads through a panmictic population, it may cause two lineages at a linked locus to coalesce; the probability of coalescence is exp(−2rT), where T∼log(2Ns)/s is the time to fixation, N is the number of haploid individuals, and r is the recombination rate. Population structure delays fixation, and so weakens the effect of a selective sweep. However, favourable alleles spread through a spatially continuous population behind a narrow wavefront; ancestral lineages are confined at the tip of this front, and so coalesce rapidly. In extremely dense populations, coalescence is dominated by rare fluctuations ahead of the front. However, we show that for moderate densities, a simple quasi-deterministic approximation applies: the rate of coalescence within the front is λ∼2g(η)/(ρℓ), where ρ is the population density and is the characteristic scale of the wavefront; g(η) depends only on the strength of random drift, . The net effect of a sweep on coalescence also depends crucially on whether two lineages are ever both within the wavefront at the same time: even in the extreme case when coalescence within the front is instantaneous, the net rate of coalescence may be lower than in a single panmictic population. Sweeps can also have a substantial impact on the rate of gene flow. A single lineage will jump to a new location when it is hit by a sweep, with mean square displacement ; this can be substantial if the species’ range, L, is large, even if the species-wide rate of sweeps per map length, Λ/R, is small. This effect is half as strong in two dimensions. In contrast, the rate of coalescence between lineages, at random locations in space and on the genetic map, is proportional to (c/L)(Λ/R), where c is the wavespeed: thus, on average, one-dimensional structure is likely to reduce coalescence due to sweeps, relative to panmixis. In two dimensions, genes must move along the front before they can coalesce; this process is rapid, being dominated by rare fluctuations. This leads to a dramatically higher rate of coalescence within the wavefront than if lineages simply diffused along the front. Nevertheless, the net rate of coalescence due to a sweep through a two-dimensional population is likely to be lower than it would be with panmixis."}],"issue":"8","type":"journal_article","pubrep_id":"118","file":[{"access_level":"open_access","file_name":"IST-2013-118-v1+1_bartonetalRevision.pdf","content_type":"application/pdf","file_size":1706282,"creator":"system","relation":"main_file","file_id":"5376","checksum":"4274ec1f433b838a7d5b941cc9684ca7","date_created":"2018-12-12T10:18:54Z","date_updated":"2020-07-14T12:45:41Z"}],"oa_version":"Submitted Version","_id":"2473","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Genetic hitch-hiking in spatially extended populations","status":"public","ddc":["570"],"intvolume":" 87","day":"03","has_accepted_license":"1","scopus_import":1,"date_published":"2013-01-03T00:00:00Z","publication":"Theoretical Population Biology","citation":{"chicago":"Barton, Nicholas H, Alison Etheridge, Jerome Kelleher, and Amandine Véber. “Genetic Hitch-Hiking in Spatially Extended Populations.” Theoretical Population Biology. Elsevier, 2013. https://doi.org/10.1016/j.tpb.2012.12.001.","short":"N.H. Barton, A. Etheridge, J. Kelleher, A. Véber, Theoretical Population Biology 87 (2013) 75–89.","mla":"Barton, Nicholas H., et al. “Genetic Hitch-Hiking in Spatially Extended Populations.” Theoretical Population Biology, vol. 87, no. 8, Elsevier, 2013, pp. 75–89, doi:10.1016/j.tpb.2012.12.001.","ieee":"N. H. Barton, A. Etheridge, J. Kelleher, and A. Véber, “Genetic hitch-hiking in spatially extended populations,” Theoretical Population Biology, vol. 87, no. 8. Elsevier, pp. 75–89, 2013.","apa":"Barton, N. H., Etheridge, A., Kelleher, J., & Véber, A. (2013). Genetic hitch-hiking in spatially extended populations. Theoretical Population Biology. Elsevier. https://doi.org/10.1016/j.tpb.2012.12.001","ista":"Barton NH, Etheridge A, Kelleher J, Véber A. 2013. Genetic hitch-hiking in spatially extended populations. Theoretical Population Biology. 87(8), 75–89.","ama":"Barton NH, Etheridge A, Kelleher J, Véber A. Genetic hitch-hiking in spatially extended populations. Theoretical Population Biology. 2013;87(8):75-89. doi:10.1016/j.tpb.2012.12.001"},"page":"75 - 89","file_date_updated":"2020-07-14T12:45:41Z","ec_funded":1,"publist_id":"4428","author":[{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"},{"full_name":"Etheridge, Alison","first_name":"Alison","last_name":"Etheridge"},{"full_name":"Kelleher, Jerome","first_name":"Jerome","last_name":"Kelleher"},{"full_name":"Véber, Amandine","first_name":"Amandine","last_name":"Véber"}],"date_created":"2018-12-11T11:57:52Z","date_updated":"2021-01-12T06:57:42Z","volume":87,"year":"2013","publication_status":"published","publisher":"Elsevier","department":[{"_id":"NiBa"}],"month":"01","doi":"10.1016/j.tpb.2012.12.001","language":[{"iso":"eng"}],"oa":1,"quality_controlled":"1","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation"}]},{"extern":1,"abstract":[{"text":"Despite the pivotal functions of the NMDA receptor (NMDAR) for neural circuit development and synaptic plasticity, the molecular mechanisms underlying the dynamics of NMDAR trafficking are poorly understood. The cell adhesion molecule neuroligin-1 (NL1) modifies NMDAR-dependent synaptic transmission and synaptic plasticity, but it is unclear whether NL1 controls synaptic accumulation or function of the receptors. Here, we provide evidence that NL1 regulates the abundance of NMDARs at postsynaptic sites. This function relies on extracellular, NL1 isoform-specific sequences that facilitate biochemical interactions between NL1 and the NMDAR GluN1 subunit. Our work uncovers NL1 isoform-specific cisinteractions with ionotropic glutamate receptors as a key mechanism for controlling synaptic properties.","lang":"eng"}],"publist_id":"4423","issue":"2","type":"journal_article","date_created":"2018-12-11T11:57:54Z","date_updated":"2021-01-12T06:57:43Z","volume":110,"author":[{"full_name":"Budreck, Elaine C","first_name":"Elaine","last_name":"Budreck"},{"full_name":"Kwon, Oh-Bin","last_name":"Kwon","first_name":"Oh"},{"full_name":"Jung, Jung-Hoon","last_name":"Jung","first_name":"Jung"},{"last_name":"Baudouin","first_name":"Stéphane","full_name":"Baudouin, Stéphane J"},{"first_name":"Albert","last_name":"Thommen","full_name":"Thommen, Albert"},{"first_name":"Hye","last_name":"Kim","full_name":"Kim, Hye-Sun"},{"full_name":"Fukazawa, Yugo","last_name":"Fukazawa","first_name":"Yugo"},{"full_name":"Harumi Harada","first_name":"Harumi","last_name":"Harada","id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7429-7896"},{"full_name":"Tabuchi, Katsuhiko","last_name":"Tabuchi","first_name":"Katsuhiko"},{"first_name":"Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","full_name":"Ryuichi Shigemoto"},{"full_name":"Scheiffele, Peter","first_name":"Peter","last_name":"Scheiffele"},{"full_name":"Kim, Joung-Hun","last_name":"Kim","first_name":"Joung"}],"status":"public","publication_status":"published","title":"Neuroligin-1 controls synaptic abundance of NMDA-type glutamate receptors through extracellular coupling","publisher":"National Academy of Sciences","intvolume":" 110","_id":"2478","year":"2013","day":"08","month":"01","doi":"10.1073/pnas.1214718110","date_published":"2013-01-08T00:00:00Z","quality_controlled":0,"page":"725 - 730","publication":"PNAS","citation":{"ista":"Budreck E, Kwon O, Jung J, Baudouin S, Thommen A, Kim H, Fukazawa Y, Harada H, Tabuchi K, Shigemoto R, Scheiffele P, Kim J. 2013. Neuroligin-1 controls synaptic abundance of NMDA-type glutamate receptors through extracellular coupling. PNAS. 110(2), 725–730.","apa":"Budreck, E., Kwon, O., Jung, J., Baudouin, S., Thommen, A., Kim, H., … Kim, J. (2013). Neuroligin-1 controls synaptic abundance of NMDA-type glutamate receptors through extracellular coupling. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1214718110","ieee":"E. Budreck et al., “Neuroligin-1 controls synaptic abundance of NMDA-type glutamate receptors through extracellular coupling,” PNAS, vol. 110, no. 2. National Academy of Sciences, pp. 725–730, 2013.","ama":"Budreck E, Kwon O, Jung J, et al. Neuroligin-1 controls synaptic abundance of NMDA-type glutamate receptors through extracellular coupling. PNAS. 2013;110(2):725-730. doi:10.1073/pnas.1214718110","chicago":"Budreck, Elaine, Oh Kwon, Jung Jung, Stéphane Baudouin, Albert Thommen, Hye Kim, Yugo Fukazawa, et al. “Neuroligin-1 Controls Synaptic Abundance of NMDA-Type Glutamate Receptors through Extracellular Coupling.” PNAS. National Academy of Sciences, 2013. https://doi.org/10.1073/pnas.1214718110.","mla":"Budreck, Elaine, et al. “Neuroligin-1 Controls Synaptic Abundance of NMDA-Type Glutamate Receptors through Extracellular Coupling.” PNAS, vol. 110, no. 2, National Academy of Sciences, 2013, pp. 725–30, doi:10.1073/pnas.1214718110.","short":"E. Budreck, O. Kwon, J. Jung, S. Baudouin, A. Thommen, H. Kim, Y. Fukazawa, H. Harada, K. Tabuchi, R. Shigemoto, P. Scheiffele, J. Kim, PNAS 110 (2013) 725–730."}},{"month":"11","day":"29","doi":"10.1112/plms/pdt060","date_published":"2013-11-29T00:00:00Z","oa":1,"citation":{"short":"R. De La Bretèche, T.D. Browning, Proceedings of the London Mathematical Society 108 (2013) 1030–1078.","mla":"De La Bretèche, Régis, and Timothy D. Browning. “Density of Châtelet Surfaces Failing the Hasse Principle.” Proceedings of the London Mathematical Society, vol. 108, no. 4, Oxford University Press, 2013, pp. 1030–78, doi:10.1112/plms/pdt060.","chicago":"De La Bretèche, Régis, and Timothy D Browning. “Density of Châtelet Surfaces Failing the Hasse Principle.” Proceedings of the London Mathematical Society. Oxford University Press, 2013. https://doi.org/10.1112/plms/pdt060.","ama":"De La Bretèche R, Browning TD. Density of Châtelet surfaces failing the Hasse principle. Proceedings of the London Mathematical Society. 2013;108(4):1030-1078. doi:10.1112/plms/pdt060","ieee":"R. De La Bretèche and T. D. Browning, “Density of Châtelet surfaces failing the Hasse principle,” Proceedings of the London Mathematical Society, vol. 108, no. 4. Oxford University Press, pp. 1030–1078, 2013.","apa":"De La Bretèche, R., & Browning, T. D. (2013). Density of Châtelet surfaces failing the Hasse principle. Proceedings of the London Mathematical Society. Oxford University Press. https://doi.org/10.1112/plms/pdt060","ista":"De La Bretèche R, Browning TD. 2013. Density of Châtelet surfaces failing the Hasse principle. Proceedings of the London Mathematical Society. 108(4), 1030–1078."},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1210.4010"}],"publication":"Proceedings of the London Mathematical Society","page":"1030 - 1078","quality_controlled":0,"issue":"4","publist_id":"7652","abstract":[{"lang":"eng","text":"Châtelet surfaces provide a rich source of geometrically rational surfaces that do not always satisfy the Hasse principle. Restricting attention to a special class of Châtelet surfaces, we investigate the frequency that such counter-examples arise over the rational numbers."}],"extern":1,"type":"journal_article","author":[{"last_name":"De La Bretèche","first_name":"Régis","full_name":"de la Bretèche, Régis"},{"full_name":"Timothy Browning","orcid":"0000-0002-8314-0177","id":"35827D50-F248-11E8-B48F-1D18A9856A87","last_name":"Browning","first_name":"Timothy D"}],"volume":108,"date_created":"2018-12-11T11:45:26Z","date_updated":"2021-01-12T06:57:51Z","_id":"250","acknowledgement":"While working on this paper, the first author was supported by an IUF Junior and ANR while the second author was supported by ERC grant 306457.","year":"2013","intvolume":" 108","publisher":"Oxford University Press","publication_status":"published","status":"public","title":"Density of Châtelet surfaces failing the Hasse principle"},{"day":"14","month":"05","date_published":"2013-05-14T00:00:00Z","doi":"10.5802/jtnb.857","quality_controlled":0,"page":"25 - 44","publication":"Journal de Theorie des Nombres de Bordeaux","citation":{"short":"R. De La Bretèche, T.D. Browning, Journal de Theorie Des Nombres de Bordeaux 26 (2013) 25–44.","mla":"De La Bretèche, Régis, and Timothy D. Browning. “Counter Examples to the Hasse Principle among Certain Coflasque Tori.” Journal de Theorie Des Nombres de Bordeaux, vol. 26, no. 1, Universite de Bordeaux I, 2013, pp. 25–44, doi:10.5802/jtnb.857.","chicago":"De La Bretèche, Régis, and Timothy D Browning. “Counter Examples to the Hasse Principle among Certain Coflasque Tori.” Journal de Theorie Des Nombres de Bordeaux. Universite de Bordeaux I, 2013. https://doi.org/10.5802/jtnb.857.","ama":"De La Bretèche R, Browning TD. Counter examples to the Hasse principle among certain coflasque tori. Journal de Theorie des Nombres de Bordeaux. 2013;26(1):25-44. doi:10.5802/jtnb.857","apa":"De La Bretèche, R., & Browning, T. D. (2013). Counter examples to the Hasse principle among certain coflasque tori. Journal de Theorie Des Nombres de Bordeaux. Universite de Bordeaux I. https://doi.org/10.5802/jtnb.857","ieee":"R. De La Bretèche and T. D. Browning, “Counter examples to the Hasse principle among certain coflasque tori,” Journal de Theorie des Nombres de Bordeaux, vol. 26, no. 1. Universite de Bordeaux I, pp. 25–44, 2013.","ista":"De La Bretèche R, Browning TD. 2013. Counter examples to the Hasse principle among certain coflasque tori. Journal de Theorie des Nombres de Bordeaux. 26(1), 25–44."},"extern":1,"abstract":[{"text":"We study the density of varieties in a certain family which do not satisfy the Hasse principle. This work relies on results recently obtained by Colliot-Thélène [3].","lang":"eng"}],"publist_id":"7651","issue":"1","type":"journal_article","date_updated":"2021-01-12T06:57:55Z","date_created":"2018-12-11T11:45:26Z","volume":26,"author":[{"full_name":"de la Bretèche, Régis","first_name":"Régis","last_name":"De La Bretèche"},{"last_name":"Browning","first_name":"Timothy D","orcid":"0000-0002-8314-0177","id":"35827D50-F248-11E8-B48F-1D18A9856A87","full_name":"Timothy Browning"}],"publication_status":"published","status":"public","title":"Counter examples to the Hasse principle among certain coflasque tori","publisher":"Universite de Bordeaux I","intvolume":" 26","year":"2013","_id":"251"},{"publist_id":"4384","ec_funded":1,"file_date_updated":"2020-07-14T12:45:42Z","department":[{"_id":"ToHe"}],"publisher":"Springer","publication_status":"published","acknowledgement":"ERC Grant QUALITY. ","year":"2013","volume":7966,"date_updated":"2020-08-11T10:09:47Z","date_created":"2018-12-11T11:58:08Z","author":[{"full_name":"Almagor, Shaull","first_name":"Shaull","last_name":"Almagor"},{"first_name":"Udi","last_name":"Boker","id":"31E297B6-F248-11E8-B48F-1D18A9856A87","full_name":"Boker, Udi"},{"last_name":"Kupferman","first_name":"Orna","full_name":"Kupferman, Orna"}],"month":"07","project":[{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"name":"Quantitative Reactive Modeling","call_identifier":"FP7","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/978-3-642-39212-2_3","conference":{"name":"ICALP: Automata, Languages and Programming","end_date":"2013-07-12","location":"Riga, Latvia","start_date":"2013-07-08"},"alternative_title":["LNCS"],"type":"conference","issue":"Part 2","abstract":[{"text":"Traditional formal methods are based on a Boolean satisfaction notion: a reactive system satisfies, or not, a given specification. We generalize formal methods to also address the quality of systems. As an adequate specification formalism we introduce the linear temporal logic LTL[F]. The satisfaction value of an LTL[F] formula is a number between 0 and 1, describing the quality of the satisfaction. The logic generalizes traditional LTL by augmenting it with a (parameterized) set F of arbitrary functions over the interval [0,1]. For example, F may contain the maximum or minimum between the satisfaction values of subformulas, their product, and their average. The classical decision problems in formal methods, such as satisfiability, model checking, and synthesis, are generalized to search and optimization problems in the quantitative setting. For example, model checking asks for the quality in which a specification is satisfied, and synthesis returns a system satisfying the specification with the highest quality. Reasoning about quality gives rise to other natural questions, like the distance between specifications. We formalize these basic questions and study them for LTL[F]. By extending the automata-theoretic approach for LTL to a setting that takes quality into an account, we are able to solve the above problems and show that reasoning about LTL[F] has roughly the same complexity as reasoning about traditional LTL.","lang":"eng"}],"intvolume":" 7966","ddc":["000"],"title":"Formalizing and reasoning about quality","status":"public","_id":"2517","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","file":[{"file_name":"2013_ICALP_Almagor.pdf","access_level":"open_access","content_type":"application/pdf","file_size":363031,"creator":"dernst","relation":"main_file","file_id":"7860","date_created":"2020-05-15T11:16:12Z","date_updated":"2020-07-14T12:45:42Z","checksum":"85afbf6c18a2c7e377c52c9410e2d824"}],"series_title":"Lecture Notes in Computer Science","scopus_import":1,"article_processing_charge":"No","has_accepted_license":"1","day":"01","page":"15 - 27","citation":{"apa":"Almagor, S., Boker, U., & Kupferman, O. (2013). Formalizing and reasoning about quality. Presented at the ICALP: Automata, Languages and Programming, Riga, Latvia: Springer. https://doi.org/10.1007/978-3-642-39212-2_3","ieee":"S. Almagor, U. Boker, and O. Kupferman, “Formalizing and reasoning about quality,” vol. 7966, no. Part 2. Springer, pp. 15–27, 2013.","ista":"Almagor S, Boker U, Kupferman O. 2013. Formalizing and reasoning about quality. 7966(Part 2), 15–27.","ama":"Almagor S, Boker U, Kupferman O. Formalizing and reasoning about quality. 2013;7966(Part 2):15-27. doi:10.1007/978-3-642-39212-2_3","chicago":"Almagor, Shaull, Udi Boker, and Orna Kupferman. “Formalizing and Reasoning about Quality.” Lecture Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-39212-2_3.","short":"S. Almagor, U. Boker, O. Kupferman, 7966 (2013) 15–27.","mla":"Almagor, Shaull, et al. Formalizing and Reasoning about Quality. Vol. 7966, no. Part 2, Springer, 2013, pp. 15–27, doi:10.1007/978-3-642-39212-2_3."},"date_published":"2013-07-01T00:00:00Z"},{"oa_version":"Preprint","status":"public","title":"The power of linear programming for finite-valued CSPs: A constructive characterization","intvolume":" 7965","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"2518","abstract":[{"text":"A class of valued constraint satisfaction problems (VCSPs) is characterised by a valued constraint language, a fixed set of cost functions on a finite domain. An instance of the problem is specified by a sum of cost functions from the language with the goal to minimise the sum. We study which classes of finite-valued languages can be solved exactly by the basic linear programming relaxation (BLP). Thapper and Živný showed [20] that if BLP solves the language then the language admits a binary commutative fractional polymorphism. We prove that the converse is also true. This leads to a necessary and a sufficient condition which can be checked in polynomial time for a given language. In contrast, the previous necessary and sufficient condition due to [20] involved infinitely many inequalities. More recently, Thapper and Živný [21] showed (using, in particular, a technique introduced in this paper) that core languages that do not satisfy our condition are NP-hard. Taken together, these results imply that a finite-valued language can either be solved using Linear Programming or is NP-hard.","lang":"eng"}],"issue":"1","alternative_title":["LNCS"],"type":"conference","date_published":"2013-07-01T00:00:00Z","page":"625 - 636","citation":{"ama":"Kolmogorov V. The power of linear programming for finite-valued CSPs: A constructive characterization. In: Vol 7965. Springer; 2013:625-636. doi:10.1007/978-3-642-39206-1_53","ieee":"V. Kolmogorov, “The power of linear programming for finite-valued CSPs: A constructive characterization,” presented at the ICALP: Automata, Languages and Programming, Riga, Latvia, 2013, vol. 7965, no. 1, pp. 625–636.","apa":"Kolmogorov, V. (2013). The power of linear programming for finite-valued CSPs: A constructive characterization (Vol. 7965, pp. 625–636). Presented at the ICALP: Automata, Languages and Programming, Riga, Latvia: Springer. https://doi.org/10.1007/978-3-642-39206-1_53","ista":"Kolmogorov V. 2013. The power of linear programming for finite-valued CSPs: A constructive characterization. ICALP: Automata, Languages and Programming, LNCS, vol. 7965, 625–636.","short":"V. Kolmogorov, in:, Springer, 2013, pp. 625–636.","mla":"Kolmogorov, Vladimir. The Power of Linear Programming for Finite-Valued CSPs: A Constructive Characterization. Vol. 7965, no. 1, Springer, 2013, pp. 625–36, doi:10.1007/978-3-642-39206-1_53.","chicago":"Kolmogorov, Vladimir. “The Power of Linear Programming for Finite-Valued CSPs: A Constructive Characterization,” 7965:625–36. Springer, 2013. https://doi.org/10.1007/978-3-642-39206-1_53."},"day":"01","scopus_import":1,"date_created":"2018-12-11T11:58:08Z","date_updated":"2023-02-23T10:35:42Z","volume":7965,"author":[{"full_name":"Kolmogorov, Vladimir","first_name":"Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"status":"public","relation":"later_version","id":"2271"}]},"publication_status":"published","department":[{"_id":"VlKo"}],"publisher":"Springer","year":"2013","publist_id":"4383","language":[{"iso":"eng"}],"conference":{"start_date":"2013-07-08","location":"Riga, Latvia","end_date":"2013-07-12","name":"ICALP: Automata, Languages and Programming"},"doi":"10.1007/978-3-642-39206-1_53","quality_controlled":"1","oa":1,"external_id":{"arxiv":["1207.7213"]},"main_file_link":[{"url":"http://arxiv.org/abs/1207.7213","open_access":"1"}],"month":"07"},{"publist_id":"4385","issue":"3","abstract":[{"lang":"eng","text":"We study the problem of object recognition for categories for which we have no training examples, a task also called zero-data or zero-shot learning. This situation has hardly been studied in computer vision research, even though it occurs frequently: the world contains tens of thousands of different object classes and for only few of them image collections have been formed and suitably annotated. To tackle the problem we introduce attribute-based classification: objects are identified based on a high-level description that is phrased in terms of semantic attributes, such as the object's color or shape. Because the identification of each such property transcends the specific learning task at hand, the attribute classifiers can be pre-learned independently, e.g. from existing image datasets unrelated to the current task. Afterwards, new classes can be detected based on their attribute representation, without the need for a new training phase. In this paper we also introduce a new dataset, Animals with Attributes, of over 30,000 images of 50 animal classes, annotated with 85 semantic attributes. Extensive experiments on this and two more datasets show that attribute-based classification indeed is able to categorize images without access to any training images of the target classes."}],"type":"journal_article","oa_version":"None","volume":36,"date_created":"2018-12-11T11:58:08Z","date_updated":"2021-01-12T06:57:58Z","author":[{"full_name":"Lampert, Christoph","last_name":"Lampert","first_name":"Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Hannes","last_name":"Nickisch","full_name":"Nickisch, Hannes"},{"last_name":"Harmeling","first_name":"Stefan","full_name":"Harmeling, Stefan"}],"intvolume":" 36","department":[{"_id":"ChLa"}],"publisher":"IEEE","title":"Attribute-based classification for zero-shot learning of object categories","publication_status":"published","status":"public","year":"2013","_id":"2516","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"07","day":"30","scopus_import":1,"language":[{"iso":"eng"}],"doi":"10.1109/TPAMI.2013.140","date_published":"2013-07-30T00:00:00Z","page":"453 - 465","quality_controlled":"1","citation":{"chicago":"Lampert, Christoph, Hannes Nickisch, and Stefan Harmeling. “Attribute-Based Classification for Zero-Shot Learning of Object Categories.” IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE, 2013. https://doi.org/10.1109/TPAMI.2013.140.","short":"C. Lampert, H. Nickisch, S. Harmeling, IEEE Transactions on Pattern Analysis and Machine Intelligence 36 (2013) 453–465.","mla":"Lampert, Christoph, et al. “Attribute-Based Classification for Zero-Shot Learning of Object Categories.” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 36, no. 3, IEEE, 2013, pp. 453–65, doi:10.1109/TPAMI.2013.140.","ieee":"C. Lampert, H. Nickisch, and S. Harmeling, “Attribute-based classification for zero-shot learning of object categories,” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 36, no. 3. IEEE, pp. 453–465, 2013.","apa":"Lampert, C., Nickisch, H., & Harmeling, S. (2013). Attribute-based classification for zero-shot learning of object categories. IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE. https://doi.org/10.1109/TPAMI.2013.140","ista":"Lampert C, Nickisch H, Harmeling S. 2013. Attribute-based classification for zero-shot learning of object categories. IEEE Transactions on Pattern Analysis and Machine Intelligence. 36(3), 453–465.","ama":"Lampert C, Nickisch H, Harmeling S. Attribute-based classification for zero-shot learning of object categories. IEEE Transactions on Pattern Analysis and Machine Intelligence. 2013;36(3):453-465. doi:10.1109/TPAMI.2013.140"},"publication":"IEEE Transactions on Pattern Analysis and Machine Intelligence"},{"pubrep_id":"137","oa_version":"Submitted Version","file":[{"file_id":"5134","relation":"main_file","date_created":"2018-12-12T10:15:16Z","date_updated":"2020-07-14T12:45:42Z","checksum":"325f20c4b926bd74d39006b97df572bd","file_name":"IST-2013-137-v1+1_QuaShaKnoGha13.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":1117100}],"_id":"2520","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"The supervised IBP: Neighbourhood preserving infinite latent feature models","ddc":["000"],"abstract":[{"lang":"eng","text":"We propose a probabilistic model to infer supervised latent variables in\r\nthe Hamming space from observed data. Our model allows simultaneous\r\ninference of the number of binary latent variables, and their values. The\r\nlatent variables preserve neighbourhood structure of the data in a sense\r\nthat objects in the same semantic concept have similar latent values, and\r\nobjects in different concepts have dissimilar latent values. We formulate\r\nthe supervised infinite latent variable problem based on an intuitive\r\nprinciple of pulling objects together if they are of the same type, and\r\npushing them apart if they are not. We then combine this principle with a\r\nflexible Indian Buffet Process prior on the latent variables. We show that\r\nthe inferred supervised latent variables can be directly used to perform a\r\nnearest neighbour search for the purpose of retrieval. We introduce a new\r\napplication of dynamically extending hash codes, and show how to\r\neffectively couple the structure of the hash codes with continuously\r\ngrowing structure of the neighbourhood preserving infinite latent feature\r\nspace."}],"type":"conference","date_published":"2013-07-11T00:00:00Z","citation":{"ista":"Quadrianto N, Sharmanska V, Knowles D, Ghahramani Z. 2013. The supervised IBP: Neighbourhood preserving infinite latent feature models. Proceedings of the 29th conference uncertainty in Artificial Intelligence. UAI: Uncertainty in Artificial Intelligence, 527–536.","ieee":"N. Quadrianto, V. Sharmanska, D. Knowles, and Z. Ghahramani, “The supervised IBP: Neighbourhood preserving infinite latent feature models,” in Proceedings of the 29th conference uncertainty in Artificial Intelligence, Bellevue, WA, United States, 2013, pp. 527–536.","apa":"Quadrianto, N., Sharmanska, V., Knowles, D., & Ghahramani, Z. (2013). The supervised IBP: Neighbourhood preserving infinite latent feature models. In Proceedings of the 29th conference uncertainty in Artificial Intelligence (pp. 527–536). Bellevue, WA, United States: AUAI Press.","ama":"Quadrianto N, Sharmanska V, Knowles D, Ghahramani Z. The supervised IBP: Neighbourhood preserving infinite latent feature models. In: Proceedings of the 29th Conference Uncertainty in Artificial Intelligence. AUAI Press; 2013:527-536.","chicago":"Quadrianto, Novi, Viktoriia Sharmanska, David Knowles, and Zoubin Ghahramani. “The Supervised IBP: Neighbourhood Preserving Infinite Latent Feature Models.” In Proceedings of the 29th Conference Uncertainty in Artificial Intelligence, 527–36. AUAI Press, 2013.","mla":"Quadrianto, Novi, et al. “The Supervised IBP: Neighbourhood Preserving Infinite Latent Feature Models.” Proceedings of the 29th Conference Uncertainty in Artificial Intelligence, AUAI Press, 2013, pp. 527–36.","short":"N. Quadrianto, V. Sharmanska, D. Knowles, Z. Ghahramani, in:, Proceedings of the 29th Conference Uncertainty in Artificial Intelligence, AUAI Press, 2013, pp. 527–536."},"publication":"Proceedings of the 29th conference uncertainty in Artificial Intelligence","page":"527 - 536","has_accepted_license":"1","day":"11","scopus_import":1,"author":[{"full_name":"Quadrianto, Novi","first_name":"Novi","last_name":"Quadrianto"},{"orcid":"0000-0003-0192-9308","id":"2EA6D09E-F248-11E8-B48F-1D18A9856A87","last_name":"Sharmanska","first_name":"Viktoriia","full_name":"Sharmanska, Viktoriia"},{"last_name":"Knowles","first_name":"David","full_name":"Knowles, David"},{"full_name":"Ghahramani, Zoubin","first_name":"Zoubin","last_name":"Ghahramani"}],"date_updated":"2023-02-23T10:46:36Z","date_created":"2018-12-11T11:58:09Z","year":"2013","publisher":"AUAI Press","department":[{"_id":"ChLa"}],"publication_status":"published","publist_id":"4381","file_date_updated":"2020-07-14T12:45:42Z","conference":{"name":"UAI: Uncertainty in Artificial Intelligence","location":"Bellevue, WA, United States","start_date":"2013-07-11","end_date":"2013-07-15"},"language":[{"iso":"eng"}],"oa":1,"quality_controlled":"1","publication_identifier":{"isbn":["9780974903996"]},"month":"07"},{"day":"06","month":"09","doi":"10.1112/S0025579313000132","date_published":"2013-09-06T00:00:00Z","quality_controlled":0,"page":"101 - 107","publication":"Mathematika","citation":{"ama":"Browning TD. Counting rational points on cubic hypersurfaces: Corrigendum. Mathematika. 2013;60(1):101-107. doi:10.1112/S0025579313000132","ista":"Browning TD. 2013. Counting rational points on cubic hypersurfaces: Corrigendum. Mathematika. 60(1), 101–107.","ieee":"T. D. Browning, “Counting rational points on cubic hypersurfaces: Corrigendum,” Mathematika, vol. 60, no. 1. Unknown, pp. 101–107, 2013.","apa":"Browning, T. D. (2013). Counting rational points on cubic hypersurfaces: Corrigendum. Mathematika. Unknown. https://doi.org/10.1112/S0025579313000132","mla":"Browning, Timothy D. “Counting Rational Points on Cubic Hypersurfaces: Corrigendum.” Mathematika, vol. 60, no. 1, Unknown, 2013, pp. 101–07, doi:10.1112/S0025579313000132.","short":"T.D. Browning, Mathematika 60 (2013) 101–107.","chicago":"Browning, Timothy D. “Counting Rational Points on Cubic Hypersurfaces: Corrigendum.” Mathematika. Unknown, 2013. https://doi.org/10.1112/S0025579313000132."},"extern":1,"publist_id":"7649","issue":"1","type":"journal_article","date_created":"2018-12-11T11:45:27Z","date_updated":"2021-01-12T06:58:03Z","volume":60,"author":[{"full_name":"Timothy Browning","id":"35827D50-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8314-0177","first_name":"Timothy D","last_name":"Browning"}],"status":"public","title":"Counting rational points on cubic hypersurfaces: Corrigendum","publication_status":"published","publisher":"Unknown","intvolume":" 60","year":"2013","_id":"253"},{"author":[{"full_name":"Dobi, Alice","last_name":"Dobi","first_name":"Alice"},{"first_name":"Simone","last_name":"Sartori","full_name":"Sartori, Simone B"},{"full_name":"Busti, Daniela","first_name":"Daniela","last_name":"Busti"},{"full_name":"Van Der Putten, Herman V","first_name":"Herman","last_name":"Van Der Putten"},{"full_name":"Singewald, Nicolas","last_name":"Singewald","first_name":"Nicolas"},{"last_name":"Shigemoto","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Ryuichi Shigemoto"},{"first_name":"Francesco","last_name":"Ferraguti","full_name":"Ferraguti, Francesco"}],"date_updated":"2021-01-12T06:59:05Z","date_created":"2018-12-11T11:59:06Z","volume":66,"year":"2013","_id":"2692","status":"public","publication_status":"published","title":"Neural substrates for the distinct effects of presynaptic group III metabotropic glutamate receptors on extinction of contextual fear conditioning in mice","publisher":"Elsevier","intvolume":" 66","abstract":[{"lang":"eng","text":"The group III metabotropic glutamate (mGlu) receptors mGlu7 and mGlu8 are receiving increased attention as potential novel therapeutic targets for anxiety disorders. The effects mediated by these receptors appear to result from a complex interplay of facilitatory and inhibitory actions at different brain sites in the anxiety/fear circuits. To better understand the effect of mGlu7 and mGlu8 receptors on extinction of contextual fear and their critical sites of action in the fear networks, we focused on the amygdala. Direct injection into the basolateral complex of the amygdala of the mGlu7 receptor agonist AMN082 facilitated extinction, whereas the mGlu8 receptor agonist (S)-3,4-DCPG sustained freezing during the extinction acquisition trial. We also determined at the ultrastructural level the synaptic distribution of these receptors in the basal nucleus (BA) and intercalated cell clusters (ITCs) of the amygdala. Both areas are thought to exert key roles in fear extinction. We demonstrate that mGlu7 and mGlu8 receptors are located in different presynaptic terminals forming both asymmetric and symmetric synapses, and that they preferentially target neurons expressing mGlu1α receptors mostly located around ITCs. In addition we show that mGlu7 and mGlu8 receptors were segregated to different inputs to a significant extent. In particular, mGlu7a receptors were primarily onto glutamatergic afferents arising from the BA or midline thalamic nuclei, but not the medial prefrontal cortex (mPFC), as revealed by combined anterograde tracing and pre-embedding electron microscopy. On the other hand, mGlu8a showed a more restricted distribution in the BA and appeared absent from thalamic, mPFC and intrinsic inputs. This segregation of mGlu7 and mGlu8 receptors in different neuronal pathways of the fear circuit might explain the distinct effects on fear extinction training observed with mGlu7 and mGlu8 receptor agonists."}],"publist_id":"4205","extern":1,"type":"journal_article","doi":"10.1016/j.neuropharm.2012.05.025","date_published":"2013-03-01T00:00:00Z","publication":"Neuropharmacology","citation":{"ama":"Dobi A, Sartori S, Busti D, et al. Neural substrates for the distinct effects of presynaptic group III metabotropic glutamate receptors on extinction of contextual fear conditioning in mice. Neuropharmacology. 2013;66:274-289. doi:10.1016/j.neuropharm.2012.05.025","ista":"Dobi A, Sartori S, Busti D, Van Der Putten H, Singewald N, Shigemoto R, Ferraguti F. 2013. Neural substrates for the distinct effects of presynaptic group III metabotropic glutamate receptors on extinction of contextual fear conditioning in mice. Neuropharmacology. 66, 274–289.","ieee":"A. Dobi et al., “Neural substrates for the distinct effects of presynaptic group III metabotropic glutamate receptors on extinction of contextual fear conditioning in mice,” Neuropharmacology, vol. 66. Elsevier, pp. 274–289, 2013.","apa":"Dobi, A., Sartori, S., Busti, D., Van Der Putten, H., Singewald, N., Shigemoto, R., & Ferraguti, F. (2013). Neural substrates for the distinct effects of presynaptic group III metabotropic glutamate receptors on extinction of contextual fear conditioning in mice. Neuropharmacology. Elsevier. https://doi.org/10.1016/j.neuropharm.2012.05.025","mla":"Dobi, Alice, et al. “Neural Substrates for the Distinct Effects of Presynaptic Group III Metabotropic Glutamate Receptors on Extinction of Contextual Fear Conditioning in Mice.” Neuropharmacology, vol. 66, Elsevier, 2013, pp. 274–89, doi:10.1016/j.neuropharm.2012.05.025.","short":"A. Dobi, S. Sartori, D. Busti, H. Van Der Putten, N. Singewald, R. Shigemoto, F. Ferraguti, Neuropharmacology 66 (2013) 274–289.","chicago":"Dobi, Alice, Simone Sartori, Daniela Busti, Herman Van Der Putten, Nicolas Singewald, Ryuichi Shigemoto, and Francesco Ferraguti. “Neural Substrates for the Distinct Effects of Presynaptic Group III Metabotropic Glutamate Receptors on Extinction of Contextual Fear Conditioning in Mice.” Neuropharmacology. Elsevier, 2013. https://doi.org/10.1016/j.neuropharm.2012.05.025."},"quality_controlled":0,"page":"274 - 289","day":"01","month":"03"},{"day":"20","month":"02","page":"3668 - 3678","quality_controlled":0,"citation":{"ista":"Indriati D, Kamasawa N, Matsui K, Meredith A, Watanabe M, Shigemoto R. 2013. Quantitative localization of Cav2.1 (P/Q-Type) voltage-dependent calcium channels in Purkinje cells: Somatodendritic gradient and distinct somatic coclustering with calcium-activated potassium channels. Journal of Neuroscience. 33(8), 3668–3678.","apa":"Indriati, D., Kamasawa, N., Matsui, K., Meredith, A., Watanabe, M., & Shigemoto, R. (2013). Quantitative localization of Cav2.1 (P/Q-Type) voltage-dependent calcium channels in Purkinje cells: Somatodendritic gradient and distinct somatic coclustering with calcium-activated potassium channels. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.2921-12.2013","ieee":"D. Indriati, N. Kamasawa, K. Matsui, A. Meredith, M. Watanabe, and R. Shigemoto, “Quantitative localization of Cav2.1 (P/Q-Type) voltage-dependent calcium channels in Purkinje cells: Somatodendritic gradient and distinct somatic coclustering with calcium-activated potassium channels,” Journal of Neuroscience, vol. 33, no. 8. Society for Neuroscience, pp. 3668–3678, 2013.","ama":"Indriati D, Kamasawa N, Matsui K, Meredith A, Watanabe M, Shigemoto R. Quantitative localization of Cav2.1 (P/Q-Type) voltage-dependent calcium channels in Purkinje cells: Somatodendritic gradient and distinct somatic coclustering with calcium-activated potassium channels. Journal of Neuroscience. 2013;33(8):3668-3678. doi:10.1523/JNEUROSCI.2921-12.2013","chicago":"Indriati, Dwi, Naomi Kamasawa, Ko Matsui, Andrea Meredith, Masahiko Watanabe, and Ryuichi Shigemoto. “Quantitative Localization of Cav2.1 (P/Q-Type) Voltage-Dependent Calcium Channels in Purkinje Cells: Somatodendritic Gradient and Distinct Somatic Coclustering with Calcium-Activated Potassium Channels.” Journal of Neuroscience. Society for Neuroscience, 2013. https://doi.org/10.1523/JNEUROSCI.2921-12.2013.","mla":"Indriati, Dwi, et al. “Quantitative Localization of Cav2.1 (P/Q-Type) Voltage-Dependent Calcium Channels in Purkinje Cells: Somatodendritic Gradient and Distinct Somatic Coclustering with Calcium-Activated Potassium Channels.” Journal of Neuroscience, vol. 33, no. 8, Society for Neuroscience, 2013, pp. 3668–78, doi:10.1523/JNEUROSCI.2921-12.2013.","short":"D. Indriati, N. Kamasawa, K. Matsui, A. Meredith, M. Watanabe, R. Shigemoto, Journal of Neuroscience 33 (2013) 3668–3678."},"publication":"Journal of Neuroscience","date_published":"2013-02-20T00:00:00Z","doi":"10.1523/JNEUROSCI.2921-12.2013","type":"journal_article","extern":1,"publist_id":"4206","issue":"8","abstract":[{"lang":"eng","text":"P/Q-type voltage-dependent calcium channels play key roles in transmitter release, integration of dendritic signals, generation of dendritic spikes, and gene expression. High intracellular calcium concentration transient produced by these channels is restricted to tens to hundreds of nanometers from the channels. Therefore, precise localization of these channels along the plasma membrane was long sought to decipher how each neuronal cell function is controlled. Here, we analyzed the distribution of Cav2.1 subunit of the P/Q-type channel using highly sensitive SDS-digested freeze-fracture replica labeling in the rat cerebellar Purkinje cells. The labeling efficiency was such that the number of immunogold particles in each parallel fiber active zone was comparable to that of functional channels calculated from previous reports. Two distinct patterns of Cav2.1 distribution, scattered and clustered, were found in Purkinje cells. The scattered Cav2.1 had a somatodendritic gradient with the density of immunogold particles increasing 2.5-fold from soma to distal dendrites. The other population with 74-fold higher density than the scattered particles was found within clusters of intramembrane particles on the P-face of soma and primary dendrites. Both populations of Cav2.1 were found as early as P3 and increased in the second postnatal week to a mature level. Using double immunogold labeling, we found that virtually all of the Cav2.1 clusters were colocalized with two types of calcium-activated potassium channels, BK and SK2, with the nearest neighbor distance of 40∼nm. Calcium nanodomain created by the opening of Cav2.1 channels likely activates the two channels that limit the extent of depolarization."}],"publisher":"Society for Neuroscience","intvolume":" 33","publication_status":"published","title":"Quantitative localization of Cav2.1 (P/Q-Type) voltage-dependent calcium channels in Purkinje cells: Somatodendritic gradient and distinct somatic coclustering with calcium-activated potassium channels","status":"public","year":"2013","_id":"2691","volume":33,"date_created":"2018-12-11T11:59:05Z","date_updated":"2021-01-12T06:59:05Z","author":[{"full_name":"Indriati, Dwi Wahyu","first_name":"Dwi","last_name":"Indriati"},{"full_name":"Kamasawa, Naomi","last_name":"Kamasawa","first_name":"Naomi"},{"full_name":"Matsui, Ko","first_name":"Ko","last_name":"Matsui"},{"full_name":"Meredith, Andrea L","first_name":"Andrea","last_name":"Meredith"},{"full_name":"Watanabe, Masahiko","first_name":"Masahiko","last_name":"Watanabe"},{"full_name":"Ryuichi Shigemoto","first_name":"Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444"}]},{"doi":"10.1113/jphysiol.2012.241398","date_published":"2013-01-01T00:00:00Z","page":"219 - 239","quality_controlled":0,"citation":{"chicago":"Budisantoso, Timotheus, Harumi Harada, Naomi Kamasawa, Yugo Fukazawa, Ryuichi Shigemoto, and Ko Matsui. “Evaluation of Glutamate Concentration Transient in the Synaptic Cleft of the Rat Calyx of Held.” Journal of Physiology. Wiley-Blackwell, 2013. https://doi.org/10.1113/jphysiol.2012.241398.","mla":"Budisantoso, Timotheus, et al. “Evaluation of Glutamate Concentration Transient in the Synaptic Cleft of the Rat Calyx of Held.” Journal of Physiology, vol. 591, no. 1, Wiley-Blackwell, 2013, pp. 219–39, doi:10.1113/jphysiol.2012.241398.","short":"T. Budisantoso, H. Harada, N. Kamasawa, Y. Fukazawa, R. Shigemoto, K. Matsui, Journal of Physiology 591 (2013) 219–239.","ista":"Budisantoso T, Harada H, Kamasawa N, Fukazawa Y, Shigemoto R, Matsui K. 2013. Evaluation of glutamate concentration transient in the synaptic cleft of the rat calyx of Held. Journal of Physiology. 591(1), 219–239.","apa":"Budisantoso, T., Harada, H., Kamasawa, N., Fukazawa, Y., Shigemoto, R., & Matsui, K. (2013). Evaluation of glutamate concentration transient in the synaptic cleft of the rat calyx of Held. Journal of Physiology. Wiley-Blackwell. https://doi.org/10.1113/jphysiol.2012.241398","ieee":"T. Budisantoso, H. Harada, N. Kamasawa, Y. Fukazawa, R. Shigemoto, and K. Matsui, “Evaluation of glutamate concentration transient in the synaptic cleft of the rat calyx of Held,” Journal of Physiology, vol. 591, no. 1. Wiley-Blackwell, pp. 219–239, 2013.","ama":"Budisantoso T, Harada H, Kamasawa N, Fukazawa Y, Shigemoto R, Matsui K. Evaluation of glutamate concentration transient in the synaptic cleft of the rat calyx of Held. Journal of Physiology. 2013;591(1):219-239. doi:10.1113/jphysiol.2012.241398"},"publication":"Journal of Physiology","month":"01","day":"01","volume":591,"date_created":"2018-12-11T11:59:05Z","date_updated":"2021-01-12T06:59:04Z","author":[{"first_name":"Timotheus","last_name":"Budisantoso","full_name":"Budisantoso, Timotheus"},{"full_name":"Harumi Harada","last_name":"Harada","first_name":"Harumi","orcid":"0000-0001-7429-7896","id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kamasawa, Naomi","first_name":"Naomi","last_name":"Kamasawa"},{"full_name":"Fukazawa, Yugo","first_name":"Yugo","last_name":"Fukazawa"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","first_name":"Ryuichi","last_name":"Shigemoto","full_name":"Ryuichi Shigemoto"},{"full_name":"Matsui, Ko","last_name":"Matsui","first_name":"Ko"}],"intvolume":" 591","publisher":"Wiley-Blackwell","publication_status":"published","title":"Evaluation of glutamate concentration transient in the synaptic cleft of the rat calyx of Held","status":"public","year":"2013","_id":"2690","extern":1,"issue":"1","publist_id":"4207","abstract":[{"lang":"eng","text":"Establishing the spatiotemporal concentration profile of neurotransmitter following synaptic vesicular release is essential for our understanding of inter-neuronal communication. Such profile is a determinant of synaptic strength, short-term plasticity and inter-synaptic crosstalk. Synaptically released glutamate has been suggested to reach a few millimolar in concentration and last for <1 ms. The synaptic cleft is often conceived as a single concentration compartment, whereas a huge gradient likely exists. Modelling studies have attempted to describe this gradient, but two key parameters, the number of glutamate in a vesicle (NGlu) and its diffusion coefficient (DGlu) in the extracellular space, remained unresolved. To determine this profile, the rat calyx of Held synapse at postnatal day 12-16 was studied where diffusion of glutamate occurs two-dimensionally and where quantification of AMPA receptor distribution on individual postsynaptic specialization on medial nucleus of the trapezoid body principal cells is possible using SDS-digested freeze-fracture replica labelling. To assess the performance of these receptors as glutamate sensors, a kinetic model of the receptors was constructed from outside-out patch recordings. From here, we simulated synaptic responses and compared them with the EPSC recordings. Combinations of NGlu and DGlu with an optimum of 7000 and 0.3 μm2 ms-1 reproduced the data, suggesting slow diffusion. Further simulations showed that a single vesicle does not saturate the synaptic receptors, and that glutamate spillover does not affect the conductance amplitude at this synapse. Using the estimated profile, we also evaluated how the number of multiple vesicle releases at individual active zones affects the amplitude of postsynaptic signals."}],"type":"journal_article"},{"issue":"18","publist_id":"4204","abstract":[{"lang":"eng","text":"Inhibitory parvalbumin-containing interneurons (PVIs) control neuronal discharge and support the generation of theta- and gammafrequency oscillations in cortical networks. Fast GABAergic input onto PVIs is crucial for their synchronization and oscillatory entrainment, but the role of metabotropic GABAB receptors (GABABRs) in mediating slow presynaptic and postsynaptic inhibition remains unknown. In this study, we have combined high-resolution immunoelectron microscopy, whole-cell patch-clamp recording, and computational modeling to investigate the subcellular distribution and effects of GABABRs and their postsynaptic effector Kir3 channels in rat hippocampal PVIs. Pre-embedding immunogold labeling revealed that the receptors and channels localize at high levels to the extrasynaptic membrane of parvalbumin-immunoreactive dendrites. Immunoreactivity forGABABRs was also present at lower levels on PVI axon terminals. Whole-cell recordings further showed that synaptically released GABA in response to extracellular stimulation evokes large GABABR-mediated slow IPSCs in perisomatic-targeting (PT) PVIs, but only small or no currents in dendrite-targeting (DT) PVIs. In contrast, paired recordings demonstrated that GABABR activation results in presynaptic inhibition at the output synapses of both PT and DT PVIs, but more strongly in the latter. Finally, computational analysis indicated that GABAB IPSCs can phasically modulate the discharge of PT interneurons at theta frequencies. In summary, our results show that GABABRs differentially mediate slow presynaptic and postsynaptic inhibition in PVIs and can contribute to the dynamic modulation of their activity during oscillations. Furthermore, these data provide evidence for a compartment-specific molecular divergence of hippocampal PVI subtypes, suggesting that activation of GABABRs may shift the balance between perisomatic and dendritic inhibition."}],"extern":1,"type":"journal_article","author":[{"full_name":"Booker, Sam A","last_name":"Booker","first_name":"Sam"},{"last_name":"Gross","first_name":"Anna","full_name":"Gross, Anna"},{"first_name":"Daniel","last_name":"Althof","full_name":"Althof, Daniel"},{"full_name":"Ryuichi Shigemoto","last_name":"Shigemoto","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Bernhard","last_name":"Bettler","full_name":"Bettler, Bernhard"},{"last_name":"Frotscher","first_name":"Michael","full_name":"Frotscher, Michael"},{"first_name":"Matthew","last_name":"Hearing","full_name":"Hearing, Matthew C"},{"last_name":"Wickman","first_name":"Kevin","full_name":"Wickman, Kevin D"},{"full_name":"Watanabe, Masahiko","first_name":"Masahiko","last_name":"Watanabe"},{"last_name":"Kulik","first_name":"Ákos","full_name":"Kulik, Ákos"},{"full_name":"Vida, Imre","first_name":"Imre","last_name":"Vida"}],"volume":33,"date_updated":"2021-01-12T06:59:05Z","date_created":"2018-12-11T11:59:06Z","year":"2013","_id":"2693","intvolume":" 33","publisher":"Society for Neuroscience","title":"Differential GABAB-receptor-mediated effects in perisomatic- and dendrite-targeting parvalbumin interneurons","publication_status":"published","status":"public","day":"01","month":"05","doi":"10.1523/JNEUROSCI.1186-12.2013","date_published":"2013-05-01T00:00:00Z","citation":{"ista":"Booker S, Gross A, Althof D, Shigemoto R, Bettler B, Frotscher M, Hearing M, Wickman K, Watanabe M, Kulik Á, Vida I. 2013. Differential GABAB-receptor-mediated effects in perisomatic- and dendrite-targeting parvalbumin interneurons. Journal of Neuroscience. 33(18), 7961–7974.","ieee":"S. Booker et al., “Differential GABAB-receptor-mediated effects in perisomatic- and dendrite-targeting parvalbumin interneurons,” Journal of Neuroscience, vol. 33, no. 18. Society for Neuroscience, pp. 7961–7974, 2013.","apa":"Booker, S., Gross, A., Althof, D., Shigemoto, R., Bettler, B., Frotscher, M., … Vida, I. (2013). Differential GABAB-receptor-mediated effects in perisomatic- and dendrite-targeting parvalbumin interneurons. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.1186-12.2013","ama":"Booker S, Gross A, Althof D, et al. Differential GABAB-receptor-mediated effects in perisomatic- and dendrite-targeting parvalbumin interneurons. Journal of Neuroscience. 2013;33(18):7961-7974. doi:10.1523/JNEUROSCI.1186-12.2013","chicago":"Booker, Sam, Anna Gross, Daniel Althof, Ryuichi Shigemoto, Bernhard Bettler, Michael Frotscher, Matthew Hearing, et al. “Differential GABAB-Receptor-Mediated Effects in Perisomatic- and Dendrite-Targeting Parvalbumin Interneurons.” Journal of Neuroscience. Society for Neuroscience, 2013. https://doi.org/10.1523/JNEUROSCI.1186-12.2013.","mla":"Booker, Sam, et al. “Differential GABAB-Receptor-Mediated Effects in Perisomatic- and Dendrite-Targeting Parvalbumin Interneurons.” Journal of Neuroscience, vol. 33, no. 18, Society for Neuroscience, 2013, pp. 7961–74, doi:10.1523/JNEUROSCI.1186-12.2013.","short":"S. Booker, A. Gross, D. Althof, R. Shigemoto, B. Bettler, M. Frotscher, M. Hearing, K. Wickman, M. Watanabe, Á. Kulik, I. Vida, Journal of Neuroscience 33 (2013) 7961–7974."},"publication":"Journal of Neuroscience","page":"7961 - 7974","quality_controlled":0},{"year":"2013","_id":"2698","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Stability and semiclassics in self-generated fields","publication_status":"published","status":"public","intvolume":" 15","department":[{"_id":"LaEr"}],"publisher":"European Mathematical Society","author":[{"last_name":"Erdös","first_name":"László","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","full_name":"Erdös, László"},{"full_name":"Fournais, Søren","first_name":"Søren","last_name":"Fournais"},{"full_name":"Solovej, Jan","last_name":"Solovej","first_name":"Jan"}],"date_created":"2018-12-11T11:59:07Z","date_updated":"2021-01-12T06:59:07Z","volume":15,"oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"We consider non-interacting particles subject to a fixed external potential V and a self-generated magnetic field B. The total energy includes the field energy β∫B2 and we minimize over all particle states and magnetic fields. In the case of spin-1/2 particles this minimization leads to the coupled Maxwell-Pauli system. The parameter β tunes the coupling strength between the field and the particles and it effectively determines the strength of the field. We investigate the stability and the semiclassical asymptotics, h→0, of the total ground state energy E(β,h,V). The relevant parameter measuring the field strength in the semiclassical limit is κ=βh. We are not able to give the exact leading order semiclassical asymptotics uniformly in κ or even for fixed κ. We do however give upper and lower bounds on E with almost matching dependence on κ. In the simultaneous limit h→0 and κ→∞ we show that the standard non-magnetic Weyl asymptotics holds. The same result also holds for the spinless case, i.e. where the Pauli operator is replaced by the Schrödinger operator."}],"issue":"6","publist_id":"4198","publication":"Journal of the European Mathematical Society","citation":{"chicago":"Erdös, László, Søren Fournais, and Jan Solovej. “Stability and Semiclassics in Self-Generated Fields.” Journal of the European Mathematical Society. European Mathematical Society, 2013. https://doi.org/10.4171/JEMS/416.","mla":"Erdös, László, et al. “Stability and Semiclassics in Self-Generated Fields.” Journal of the European Mathematical Society, vol. 15, no. 6, European Mathematical Society, 2013, pp. 2093–113, doi:10.4171/JEMS/416.","short":"L. Erdös, S. Fournais, J. Solovej, Journal of the European Mathematical Society 15 (2013) 2093–2113.","ista":"Erdös L, Fournais S, Solovej J. 2013. Stability and semiclassics in self-generated fields. Journal of the European Mathematical Society. 15(6), 2093–2113.","ieee":"L. Erdös, S. Fournais, and J. Solovej, “Stability and semiclassics in self-generated fields,” Journal of the European Mathematical Society, vol. 15, no. 6. European Mathematical Society, pp. 2093–2113, 2013.","apa":"Erdös, L., Fournais, S., & Solovej, J. (2013). Stability and semiclassics in self-generated fields. Journal of the European Mathematical Society. European Mathematical Society. https://doi.org/10.4171/JEMS/416","ama":"Erdös L, Fournais S, Solovej J. Stability and semiclassics in self-generated fields. Journal of the European Mathematical Society. 2013;15(6):2093-2113. doi:10.4171/JEMS/416"},"main_file_link":[{"url":"http://arxiv.org/abs/1105.0506","open_access":"1"}],"oa":1,"external_id":{"arxiv":["1105.0506"]},"quality_controlled":"1","page":"2093 - 2113","date_published":"2013-10-16T00:00:00Z","doi":"10.4171/JEMS/416","language":[{"iso":"eng"}],"month":"10","day":"16"},{"page":"367 - 416","quality_controlled":0,"oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1205.5669","open_access":"1"}],"citation":{"short":"L. Erdös, A. Knowles, H. Yau, J. Yin, Communications in Mathematical Physics 323 (2013) 367–416.","mla":"Erdös, László, et al. “Delocalization and Diffusion Profile for Random Band Matrices.” Communications in Mathematical Physics, vol. 323, no. 1, Springer, 2013, pp. 367–416, doi:10.1007/s00220-013-1773-3.","chicago":"Erdös, László, Antti Knowles, Horng Yau, and Jun Yin. “Delocalization and Diffusion Profile for Random Band Matrices.” Communications in Mathematical Physics. Springer, 2013. https://doi.org/10.1007/s00220-013-1773-3.","ama":"Erdös L, Knowles A, Yau H, Yin J. Delocalization and diffusion profile for random band matrices. Communications in Mathematical Physics. 2013;323(1):367-416. doi:10.1007/s00220-013-1773-3","apa":"Erdös, L., Knowles, A., Yau, H., & Yin, J. (2013). Delocalization and diffusion profile for random band matrices. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-013-1773-3","ieee":"L. Erdös, A. Knowles, H. Yau, and J. Yin, “Delocalization and diffusion profile for random band matrices,” Communications in Mathematical Physics, vol. 323, no. 1. Springer, pp. 367–416, 2013.","ista":"Erdös L, Knowles A, Yau H, Yin J. 2013. Delocalization and diffusion profile for random band matrices. Communications in Mathematical Physics. 323(1), 367–416."},"publication":"Communications in Mathematical Physics","date_published":"2013-10-01T00:00:00Z","doi":"10.1007/s00220-013-1773-3","day":"01","month":"10","intvolume":" 323","publisher":"Springer","publication_status":"published","title":"Delocalization and diffusion profile for random band matrices","status":"public","year":"2013","_id":"2697","volume":323,"date_created":"2018-12-11T11:59:07Z","date_updated":"2021-01-12T06:59:07Z","author":[{"full_name":"László Erdös","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","first_name":"László"},{"first_name":"Antti","last_name":"Knowles","full_name":"Knowles, Antti"},{"first_name":"Horng","last_name":"Yau","full_name":"Yau, Horng-Tzer"},{"first_name":"Jun","last_name":"Yin","full_name":"Yin, Jun"}],"type":"journal_article","extern":1,"publist_id":"4199","issue":"1","abstract":[{"text":"We consider Hermitian and symmetric random band matrices H = (h xy ) in d⩾1 d ⩾ 1 dimensions. The matrix entries h xy , indexed by x,y∈(Z/LZ)d x , y ∈ ( Z / L Z ) d , are independent, centred random variables with variances sxy=E|hxy|2 s x y = E | h x y | 2 . We assume that s xy is negligible if |x − y| exceeds the band width W. In one dimension we prove that the eigenvectors of H are delocalized if W≫L4/5 W ≫ L 4 / 5 . We also show that the magnitude of the matrix entries |Gxy|2 | G x y | 2 of the resolvent G=G(z)=(H−z)−1 G = G ( z ) = ( H - z ) - 1 is self-averaging and we compute E|Gxy|2 E | G x y | 2 . We show that, as L→∞ L → ∞ and W≫L4/5 W ≫ L 4 / 5 , the behaviour of E|Gxy|2 E | G x y | 2 is governed by a diffusion operator whose diffusion constant we compute. Similar results are obtained in higher dimensions.","lang":"eng"}]},{"oa":1,"quality_controlled":"1","project":[{"name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152"}],"conference":{"location":"Amsterdam, Netherlands","start_date":"2013-07-06","end_date":"2013-07-10","name":"GECCO: Genetic and evolutionary computation conference"},"doi":"10.1145/2463372.2463568","language":[{"iso":"eng"}],"month":"07","year":"2013","publication_status":"published","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"publisher":"ACM","author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H"},{"first_name":"Tiago","last_name":"Paixao","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953","full_name":"Paixao, Tiago"}],"date_updated":"2021-01-12T06:59:15Z","date_created":"2018-12-11T11:59:14Z","file_date_updated":"2020-07-14T12:45:45Z","publist_id":"4174","ec_funded":1,"publication":"Proceedings of the 15th annual conference on Genetic and evolutionary computation","citation":{"mla":"Barton, Nicholas H., and Tiago Paixao. “Can Quantitative and Population Genetics Help Us Understand Evolutionary Computation?” Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation, ACM, 2013, pp. 1573–80, doi:10.1145/2463372.2463568.","short":"N.H. Barton, T. Paixao, in:, Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation, ACM, 2013, pp. 1573–1580.","chicago":"Barton, Nicholas H, and Tiago Paixao. “Can Quantitative and Population Genetics Help Us Understand Evolutionary Computation?” In Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation, 1573–80. ACM, 2013. https://doi.org/10.1145/2463372.2463568.","ama":"Barton NH, Paixao T. Can quantitative and population genetics help us understand evolutionary computation? In: Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation. ACM; 2013:1573-1580. doi:10.1145/2463372.2463568","ista":"Barton NH, Paixao T. 2013. Can quantitative and population genetics help us understand evolutionary computation? Proceedings of the 15th annual conference on Genetic and evolutionary computation. GECCO: Genetic and evolutionary computation conference, 1573–1580.","ieee":"N. H. Barton and T. Paixao, “Can quantitative and population genetics help us understand evolutionary computation?,” in Proceedings of the 15th annual conference on Genetic and evolutionary computation, Amsterdam, Netherlands, 2013, pp. 1573–1580.","apa":"Barton, N. H., & Paixao, T. (2013). Can quantitative and population genetics help us understand evolutionary computation? In Proceedings of the 15th annual conference on Genetic and evolutionary computation (pp. 1573–1580). Amsterdam, Netherlands: ACM. https://doi.org/10.1145/2463372.2463568"},"page":"1573 - 1580","date_published":"2013-07-01T00:00:00Z","scopus_import":1,"day":"01","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2718","ddc":["570"],"status":"public","title":"Can quantitative and population genetics help us understand evolutionary computation?","pubrep_id":"564","oa_version":"Submitted Version","file":[{"content_type":"application/pdf","file_size":475844,"creator":"system","file_name":"IST-2016-564-v1+1_NickGECCO_2013_1_-1.pdf","access_level":"open_access","date_created":"2018-12-12T10:15:38Z","date_updated":"2020-07-14T12:45:45Z","checksum":"9d9be9090ce5c20766e0eb076ace5b98","relation":"main_file","file_id":"5159"}],"type":"conference","abstract":[{"text":"Even though both population and quantitative genetics, and evolutionary computation, deal with the same questions, they have developed largely independently of each other. I review key results from each field, emphasising those that apply independently of the (usually unknown) relation between genotype and phenotype. The infinitesimal model provides a simple framework for predicting the response of complex traits to selection, which in biology has proved remarkably successful. This allows one to choose the schedule of population sizes and selection intensities that will maximise the response to selection, given that the total number of individuals realised, C = ∑t Nt, is constrained. This argument shows that for an additive trait (i.e., determined by the sum of effects of the genes), the optimum population size and the maximum possible response (i.e., the total change in trait mean) are both proportional to √C.","lang":"eng"}]},{"scopus_import":1,"article_processing_charge":"No","day":"01","citation":{"ama":"Long H, Paixao T, Azevedo R, Zufall R. Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila. Genetics. 2013;195(2):527-540. doi:10.1534/genetics.113.153536","ieee":"H. Long, T. Paixao, R. Azevedo, and R. Zufall, “Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila,” Genetics, vol. 195, no. 2. Genetics Society of America, pp. 527–540, 2013.","apa":"Long, H., Paixao, T., Azevedo, R., & Zufall, R. (2013). Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.113.153536","ista":"Long H, Paixao T, Azevedo R, Zufall R. 2013. Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila. Genetics. 195(2), 527–540.","short":"H. Long, T. Paixao, R. Azevedo, R. Zufall, Genetics 195 (2013) 527–540.","mla":"Long, Hongan, et al. “Accumulation of Spontaneous Mutations in the Ciliate Tetrahymena Thermophila.” Genetics, vol. 195, no. 2, Genetics Society of America, 2013, pp. 527–40, doi:10.1534/genetics.113.153536.","chicago":"Long, Hongan, Tiago Paixao, Ricardo Azevedo, and Rebecca Zufall. “Accumulation of Spontaneous Mutations in the Ciliate Tetrahymena Thermophila.” Genetics. Genetics Society of America, 2013. https://doi.org/10.1534/genetics.113.153536."},"publication":"Genetics","page":"527-540","date_published":"2013-10-01T00:00:00Z","type":"journal_article","issue":"2","abstract":[{"text":"Knowledge of the rate and fitness effects of mutations is essential for understanding the process of evolution. Mutations are inherently difficult to study because they are rare and are frequently eliminated by natural selection. In the ciliate Tetrahymena thermophila, mutations can accumulate in the germline genome without being exposed to selection. We have conducted a mutation accumulation (MA) experiment in this species. Assuming that all mutations are deleterious and have the same effect, we estimate that the deleterious mutation rate per haploid germline genome per generation is U = 0.0047 (95% credible interval: 0.0015, 0.0125), and that germline mutations decrease fitness by s = 11% when expressed in a homozygous state (95% CI: 4.4%, 27%). We also estimate that deleterious mutations are partially recessive on average (h = 0.26; 95% CI: –0.022, 0.62) and that the rate of lethal mutations is <10% of the deleterious mutation rate. Comparisons between the observed evolutionary responses in the germline and somatic genomes and the results from individual-based simulations of MA suggest that the two genomes have similar mutational parameters. These are the first estimates of the deleterious mutation rate and fitness effects from the eukaryotic supergroup Chromalveolata and are within the range of those of other eukaryotes.","lang":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"2720","intvolume":" 195","title":"Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila","status":"public","oa_version":"Submitted Version","month":"10","external_id":{"pmid":["23934880"]},"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3781978/"}],"oa":1,"project":[{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152"}],"quality_controlled":"1","doi":"10.1534/genetics.113.153536","language":[{"iso":"eng"}],"ec_funded":1,"publist_id":"4172","pmid":1,"year":"2013","publisher":"Genetics Society of America","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"publication_status":"published","author":[{"first_name":"Hongan","last_name":"Long","full_name":"Long, Hongan"},{"last_name":"Paixao","first_name":"Tiago","orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","full_name":"Paixao, Tiago"},{"last_name":"Azevedo","first_name":"Ricardo","full_name":"Azevedo, Ricardo"},{"last_name":"Zufall","first_name":"Rebecca","full_name":"Zufall, Rebecca"}],"volume":195,"date_updated":"2021-01-12T06:59:16Z","date_created":"2018-12-11T11:59:15Z"},{"quality_controlled":"1","project":[{"name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"page":"845 - 852","publication":"Proceedings of the 15th annual conference on Genetic and evolutionary computation","citation":{"chicago":"Paixao, Tiago, and Nicholas H Barton. “A Variance Decomposition Approach to the Analysis of Genetic Algorithms.” In Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation, 845–52. ACM, 2013. https://doi.org/10.1145/2463372.2463470.","short":"T. Paixao, N.H. Barton, in:, Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation, ACM, 2013, pp. 845–852.","mla":"Paixao, Tiago, and Nicholas H. Barton. “A Variance Decomposition Approach to the Analysis of Genetic Algorithms.” Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation, ACM, 2013, pp. 845–52, doi:10.1145/2463372.2463470.","ieee":"T. Paixao and N. H. Barton, “A variance decomposition approach to the analysis of genetic algorithms,” in Proceedings of the 15th annual conference on Genetic and evolutionary computation, Amsterdam, Netherlands, 2013, pp. 845–852.","apa":"Paixao, T., & Barton, N. H. (2013). A variance decomposition approach to the analysis of genetic algorithms. In Proceedings of the 15th annual conference on Genetic and evolutionary computation (pp. 845–852). Amsterdam, Netherlands: ACM. https://doi.org/10.1145/2463372.2463470","ista":"Paixao T, Barton NH. 2013. A variance decomposition approach to the analysis of genetic algorithms. Proceedings of the 15th annual conference on Genetic and evolutionary computation. GECCO: Genetic and evolutionary computation conference, 845–852.","ama":"Paixao T, Barton NH. A variance decomposition approach to the analysis of genetic algorithms. In: Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation. ACM; 2013:845-852. doi:10.1145/2463372.2463470"},"language":[{"iso":"eng"}],"conference":{"start_date":"2013-07-06","location":"Amsterdam, Netherlands","end_date":"2013-07-10","name":"GECCO: Genetic and evolutionary computation conference"},"date_published":"2013-07-01T00:00:00Z","doi":"10.1145/2463372.2463470","scopus_import":1,"month":"07","day":"01","title":"A variance decomposition approach to the analysis of genetic algorithms","publication_status":"published","status":"public","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"publisher":"ACM","_id":"2719","year":"2013","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:59:15Z","date_updated":"2021-01-12T06:59:15Z","oa_version":"None","author":[{"id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953","first_name":"Tiago","last_name":"Paixao","full_name":"Paixao, Tiago"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H"}],"type":"conference","abstract":[{"lang":"eng","text":"Prediction of the evolutionary process is a long standing problem both in the theory of evolutionary biology and evolutionary computation (EC). It has long been realized that heritable variation is crucial to both the response to selection and the success of genetic algorithms. However, not all variation contributes in the same way to the response. Quantitative genetics has developed a large body of work trying to estimate and understand how different components of the variance in fitness in the population contribute to the response to selection. We illustrate how to apply some concepts of quantitative genetics to the analysis of genetic algorithms. In particular, we derive estimates for the short term prediction of the response to selection and we use variance decomposition to gain insight on local aspects of the landscape. Finally, we propose a new population based genetic algorithm that uses these methods to improve its operation."}],"publist_id":"4173","ec_funded":1},{"publist_id":"4107","year":"2013","department":[{"_id":"LaEr"}],"publisher":"Springer","publication_status":"published","author":[{"full_name":"Erdös, László","last_name":"Erdös","first_name":"László","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Brendan","last_name":"Farrell","full_name":"Farrell, Brendan"}],"volume":152,"date_created":"2018-12-11T11:59:34Z","date_updated":"2021-01-12T06:59:41Z","month":"07","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1207.0031"}],"oa":1,"external_id":{"arxiv":["1207.0031"]},"quality_controlled":"1","doi":"10.1007/s10955-013-0807-8","language":[{"iso":"eng"}],"type":"journal_article","issue":"6","abstract":[{"lang":"eng","text":"We consider random n×n matrices of the form (XX*+YY*)^{-1/2}YY*(XX*+YY*)^{-1/2}, where X and Y have independent entries with zero mean and variance one. These matrices are the natural generalization of the Gaussian case, which are known as MANOVA matrices and which have joint eigenvalue density given by the third classical ensemble, the Jacobi ensemble. We show that, away from the spectral edge, the eigenvalue density converges to the limiting density of the Jacobi ensemble even on the shortest possible scales of order 1/n (up to log n factors). This result is the analogue of the local Wigner semicircle law and the local Marchenko-Pastur law for general MANOVA matrices."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2782","intvolume":" 152","status":"public","title":"Local eigenvalue density for general MANOVA matrices","oa_version":"Preprint","scopus_import":1,"day":"18","citation":{"mla":"Erdös, László, and Brendan Farrell. “Local Eigenvalue Density for General MANOVA Matrices.” Journal of Statistical Physics, vol. 152, no. 6, Springer, 2013, pp. 1003–32, doi:10.1007/s10955-013-0807-8.","short":"L. Erdös, B. Farrell, Journal of Statistical Physics 152 (2013) 1003–1032.","chicago":"Erdös, László, and Brendan Farrell. “Local Eigenvalue Density for General MANOVA Matrices.” Journal of Statistical Physics. Springer, 2013. https://doi.org/10.1007/s10955-013-0807-8.","ama":"Erdös L, Farrell B. Local eigenvalue density for general MANOVA matrices. Journal of Statistical Physics. 2013;152(6):1003-1032. doi:10.1007/s10955-013-0807-8","ista":"Erdös L, Farrell B. 2013. Local eigenvalue density for general MANOVA matrices. Journal of Statistical Physics. 152(6), 1003–1032.","ieee":"L. Erdös and B. Farrell, “Local eigenvalue density for general MANOVA matrices,” Journal of Statistical Physics, vol. 152, no. 6. Springer, pp. 1003–1032, 2013.","apa":"Erdös, L., & Farrell, B. (2013). Local eigenvalue density for general MANOVA matrices. Journal of Statistical Physics. Springer. https://doi.org/10.1007/s10955-013-0807-8"},"publication":"Journal of Statistical Physics","page":"1003 - 1032","date_published":"2013-07-18T00:00:00Z"},{"type":"journal_article","publist_id":"4109","issue":"3 B","abstract":[{"text":"We consider the ensemble of adjacency matrices of Erdős-Rényi random graphs, that is, graphs on N vertices where every edge is chosen independently and with probability p = p(N). We rescale the matrix so that its bulk eigenvalues are of order one. We prove that, as long as pN→∞(with a speed at least logarithmic in N), the density of eigenvalues of the Erdős-Rényi ensemble is given by the Wigner semicircle law for spectral windows of length larger than N-1 (up to logarithmic corrections). As a consequence, all eigenvectors are proved to be completely delocalized in the sense that the ℓ∞-norms of the ℓ2-normalized eigenvectors are at most of order N-1/2 with a very high probability. The estimates in this paper will be used in the companion paper [Spectral statistics of Erdős-Rényi graphs II: Eigenvalue spacing and the extreme eigenvalues (2011) Preprint] to prove the universality of eigenvalue distributions both in the bulk and at the spectral edges under the further restriction that pN »N2/3.","lang":"eng"}],"extern":1,"year":"2013","_id":"2781","intvolume":" 41","publisher":"Institute of Mathematical Statistics","title":"Spectral statistics of Erdős-Rényi graphs I: Local semicircle law","publication_status":"published","status":"public","author":[{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","first_name":"László","last_name":"Erdös","full_name":"László Erdös"},{"full_name":"Knowles, Antti","last_name":"Knowles","first_name":"Antti"},{"full_name":"Yau, Horng-Tzer","last_name":"Yau","first_name":"Horng"},{"full_name":"Yin, Jun","first_name":"Jun","last_name":"Yin"}],"volume":41,"date_created":"2018-12-11T11:59:34Z","date_updated":"2021-01-12T06:59:41Z","day":"01","month":"05","citation":{"mla":"Erdös, László, et al. “Spectral Statistics of Erdős-Rényi Graphs I: Local Semicircle Law.” Annals of Probability, vol. 41, no. 3 B, Institute of Mathematical Statistics, 2013, pp. 2279–375, doi:10.1214/11-AOP734.","short":"L. Erdös, A. Knowles, H. Yau, J. Yin, Annals of Probability 41 (2013) 2279–2375.","chicago":"Erdös, László, Antti Knowles, Horng Yau, and Jun Yin. “Spectral Statistics of Erdős-Rényi Graphs I: Local Semicircle Law.” Annals of Probability. Institute of Mathematical Statistics, 2013. https://doi.org/10.1214/11-AOP734.","ama":"Erdös L, Knowles A, Yau H, Yin J. Spectral statistics of Erdős-Rényi graphs I: Local semicircle law. Annals of Probability. 2013;41(3 B):2279-2375. doi:10.1214/11-AOP734","ista":"Erdös L, Knowles A, Yau H, Yin J. 2013. Spectral statistics of Erdős-Rényi graphs I: Local semicircle law. Annals of Probability. 41(3 B), 2279–2375.","apa":"Erdös, L., Knowles, A., Yau, H., & Yin, J. (2013). Spectral statistics of Erdős-Rényi graphs I: Local semicircle law. Annals of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/11-AOP734","ieee":"L. Erdös, A. Knowles, H. Yau, and J. Yin, “Spectral statistics of Erdős-Rényi graphs I: Local semicircle law,” Annals of Probability, vol. 41, no. 3 B. Institute of Mathematical Statistics, pp. 2279–2375, 2013."},"main_file_link":[{"url":"http://arxiv.org/abs/1103.1919","open_access":"1"}],"oa":1,"publication":"Annals of Probability","page":"2279 - 2375","quality_controlled":0,"date_published":"2013-05-01T00:00:00Z","doi":"10.1214/11-AOP734"},{"day":"01","month":"12","doi":"10.1007/s00023-013-0235-y","date_published":"2013-12-01T00:00:00Z","page":"1837 - 1926","quality_controlled":0,"citation":{"ama":"Erdös L, Knowles A, Yau H. Averaging fluctuations in resolvents of random band matrices. Annales Henri Poincare. 2013;14(8):1837-1926. doi:10.1007/s00023-013-0235-y","ieee":"L. Erdös, A. Knowles, and H. Yau, “Averaging fluctuations in resolvents of random band matrices,” Annales Henri Poincare, vol. 14, no. 8. Birkhäuser, pp. 1837–1926, 2013.","apa":"Erdös, L., Knowles, A., & Yau, H. (2013). Averaging fluctuations in resolvents of random band matrices. Annales Henri Poincare. Birkhäuser. https://doi.org/10.1007/s00023-013-0235-y","ista":"Erdös L, Knowles A, Yau H. 2013. Averaging fluctuations in resolvents of random band matrices. Annales Henri Poincare. 14(8), 1837–1926.","short":"L. Erdös, A. Knowles, H. Yau, Annales Henri Poincare 14 (2013) 1837–1926.","mla":"Erdös, László, et al. “Averaging Fluctuations in Resolvents of Random Band Matrices.” Annales Henri Poincare, vol. 14, no. 8, Birkhäuser, 2013, pp. 1837–926, doi:10.1007/s00023-013-0235-y.","chicago":"Erdös, László, Antti Knowles, and Horng Yau. “Averaging Fluctuations in Resolvents of Random Band Matrices.” Annales Henri Poincare. Birkhäuser, 2013. https://doi.org/10.1007/s00023-013-0235-y."},"oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1205.5664"}],"publication":"Annales Henri Poincare","extern":1,"publist_id":"4110","issue":"8","abstract":[{"text":"We consider a general class of random matrices whose entries are centred random variables, independent up to a symmetry constraint. We establish precise high-probability bounds on the averages of arbitrary monomials in the resolvent matrix entries. Our results generalize the previous results of Erdős et al. (Ann Probab, arXiv:1103.1919, 2013; Commun Math Phys, arXiv:1103.3869, 2013; J Combin 1(2):15-85, 2011) which constituted a key step in the proof of the local semicircle law with optimal error bound in mean-field random matrix models. Our bounds apply to random band matrices and improve previous estimates from order 2 to order 4 in the cases relevant to applications. In particular, they lead to a proof of the diffusion approximation for the magnitude of the resolvent of random band matrices. This, in turn, implies new delocalization bounds on the eigenvectors. The applications are presented in a separate paper (Erdős et al., arXiv:1205.5669, 2013).","lang":"eng"}],"type":"journal_article","volume":14,"date_created":"2018-12-11T11:59:33Z","date_updated":"2021-01-12T06:59:40Z","author":[{"full_name":"László Erdös","first_name":"László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603"},{"last_name":"Knowles","first_name":"Antti","full_name":"Knowles, Antti"},{"first_name":"Horng","last_name":"Yau","full_name":"Yau, Horng-Tzer"}],"publisher":"Birkhäuser","intvolume":" 14","title":"Averaging fluctuations in resolvents of random band matrices","publication_status":"published","status":"public","_id":"2780","year":"2013"},{"has_accepted_license":"1","day":"01","scopus_import":1,"date_published":"2013-06-01T00:00:00Z","citation":{"short":"M. Čadek, M. Krcál, J. Matoušek, L. Vokřínek, U. Wagner, in:, 45th Annual ACM Symposium on Theory of Computing, ACM, 2013, pp. 595–604.","mla":"Čadek, Martin, et al. “Extending Continuous Maps: Polynomiality and Undecidability.” 45th Annual ACM Symposium on Theory of Computing, ACM, 2013, pp. 595–604, doi:10.1145/2488608.2488683.","chicago":"Čadek, Martin, Marek Krcál, Jiří Matoušek, Lukáš Vokřínek, and Uli Wagner. “Extending Continuous Maps: Polynomiality and Undecidability.” In 45th Annual ACM Symposium on Theory of Computing, 595–604. ACM, 2013. https://doi.org/10.1145/2488608.2488683.","ama":"Čadek M, Krcál M, Matoušek J, Vokřínek L, Wagner U. Extending continuous maps: Polynomiality and undecidability. In: 45th Annual ACM Symposium on Theory of Computing. ACM; 2013:595-604. doi:10.1145/2488608.2488683","apa":"Čadek, M., Krcál, M., Matoušek, J., Vokřínek, L., & Wagner, U. (2013). Extending continuous maps: Polynomiality and undecidability. In 45th Annual ACM Symposium on theory of computing (pp. 595–604). Palo Alto, CA, United States: ACM. https://doi.org/10.1145/2488608.2488683","ieee":"M. Čadek, M. Krcál, J. Matoušek, L. Vokřínek, and U. Wagner, “Extending continuous maps: Polynomiality and undecidability,” in 45th Annual ACM Symposium on theory of computing, Palo Alto, CA, United States, 2013, pp. 595–604.","ista":"Čadek M, Krcál M, Matoušek J, Vokřínek L, Wagner U. 2013. Extending continuous maps: Polynomiality and undecidability. 45th Annual ACM Symposium on theory of computing. STOC: Symposium on the Theory of Computing, 595–604."},"publication":"45th Annual ACM Symposium on theory of computing","page":"595 - 604","abstract":[{"text":"We consider several basic problems of algebraic topology, with connections to combinatorial and geometric questions, from the point of view of computational complexity. The extension problem asks, given topological spaces X; Y , a subspace A ⊆ X, and a (continuous) map f : A → Y , whether f can be extended to a map X → Y . For computational purposes, we assume that X and Y are represented as finite simplicial complexes, A is a subcomplex of X, and f is given as a simplicial map. In this generality the problem is undecidable, as follows from Novikov's result from the 1950s on uncomputability of the fundamental group π1(Y ). We thus study the problem under the assumption that, for some k ≥ 2, Y is (k - 1)-connected; informally, this means that Y has \\no holes up to dimension k-1" (a basic example of such a Y is the sphere Sk). We prove that, on the one hand, this problem is still undecidable for dimX = 2k. On the other hand, for every fixed k ≥ 2, we obtain an algorithm that solves the extension problem in polynomial time assuming Y (k - 1)-connected and dimX ≤ 2k - 1. For dimX ≤ 2k - 2, the algorithm also provides a classification of all extensions up to homotopy (continuous deformation). This relies on results of our SODA 2012 paper, and the main new ingredient is a machinery of objects with polynomial-time homology, which is a polynomial-time analog of objects with effective homology developed earlier by Sergeraert et al. We also consider the computation of the higher homotopy groups πk(Y ), k ≥ 2, for a 1-connected Y . Their computability was established by Brown in 1957; we show that πk(Y ) can be computed in polynomial time for every fixed k ≥ 2. On the other hand, Anick proved in 1989 that computing πk(Y ) is #P-hard if k is a part of input, where Y is a cell complex with certain rather compact encoding. We strengthen his result to #P-hardness for Y given as a simplicial complex. ","lang":"eng"}],"type":"conference","pubrep_id":"533","oa_version":"Submitted Version","file":[{"file_id":"5081","relation":"main_file","date_created":"2018-12-12T10:14:29Z","date_updated":"2020-07-14T12:45:48Z","checksum":"06c2ce5c1135fbc1f71ca15eeb242dcf","file_name":"IST-2016-533-v1+1_Extending_continuous_maps_polynomiality_and_undecidability.pdf","access_level":"open_access","creator":"system","file_size":447945,"content_type":"application/pdf"}],"_id":"2807","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","ddc":["510"],"title":"Extending continuous maps: Polynomiality and undecidability","month":"06","doi":"10.1145/2488608.2488683","conference":{"name":"STOC: Symposium on the Theory of Computing","start_date":"2013-06-01","location":"Palo Alto, CA, United States","end_date":"2013-06-04"},"language":[{"iso":"eng"}],"oa":1,"quality_controlled":"1","publist_id":"4078","file_date_updated":"2020-07-14T12:45:48Z","author":[{"full_name":"Čadek, Martin","last_name":"Čadek","first_name":"Martin"},{"id":"33E21118-F248-11E8-B48F-1D18A9856A87","first_name":"Marek","last_name":"Krcál","full_name":"Krcál, Marek"},{"full_name":"Matoušek, Jiří","last_name":"Matoušek","first_name":"Jiří"},{"first_name":"Lukáš","last_name":"Vokřínek","full_name":"Vokřínek, Lukáš"},{"orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","last_name":"Wagner","first_name":"Uli","full_name":"Wagner, Uli"}],"date_created":"2018-12-11T11:59:42Z","date_updated":"2021-01-12T06:59:51Z","year":"2013","department":[{"_id":"UlWa"},{"_id":"HeEd"}],"publisher":"ACM","publication_status":"published"},{"type":"journal_article","issue":"3","abstract":[{"lang":"eng","text":"In order to establish a reference for analysis of the function of auxin and the auxin biosynthesis regulators SHORT INTERNODE/ STYLISH (SHI/STY) during Physcomitrella patens reproductive development, we have described male (antheridial) and female (archegonial) development in detail, including temporal and positional information of organ initiation. This has allowed us to define discrete stages of organ morphogenesis and to show that reproductive organ development in P. patens is highly organized and that organ phyllotaxis differs between vegetative and reproductive development. Using the PpSHI1 and PpSHI2 reporter and knockout lines, the auxin reporters GmGH3pro:GUS and PpPINApro:GFP-GUS, and the auxin-conjugating transgene PpSHI2pro:IAAL, we could show that the PpSHI genes, and by inference also auxin, play important roles for reproductive organ development in moss. The PpSHI genes are required for the apical opening of the reproductive organs, the final differentiation of the egg cell, and the progression of canal cells into a cell death program. The apical cells of the archegonium, the canal cells, and the egg cell are also sites of auxin responsiveness and are affected by reduced levels of active auxin, suggesting that auxin mediates PpSHI function in the reproductive organs."}],"intvolume":" 162","status":"public","title":"The moss physcomitrella patens reproductive organ development is highly organized, affected by the two SHI/STY genes and by the level of active auxin in the SHI/STY expression domain","_id":"2808","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","scopus_import":1,"day":"03","page":"1406 - 1419","citation":{"apa":"Landberg, K., Pederson, E., Viaene, T., Bozorg, B., Friml, J., Jönsson, H., … Sundberg, E. (2013). The moss physcomitrella patens reproductive organ development is highly organized, affected by the two SHI/STY genes and by the level of active auxin in the SHI/STY expression domain. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1104/pp.113.214023","ieee":"K. Landberg et al., “The moss physcomitrella patens reproductive organ development is highly organized, affected by the two SHI/STY genes and by the level of active auxin in the SHI/STY expression domain,” Plant Physiology, vol. 162, no. 3. American Society of Plant Biologists, pp. 1406–1419, 2013.","ista":"Landberg K, Pederson E, Viaene T, Bozorg B, Friml J, Jönsson H, Thelander M, Sundberg E. 2013. The moss physcomitrella patens reproductive organ development is highly organized, affected by the two SHI/STY genes and by the level of active auxin in the SHI/STY expression domain. Plant Physiology. 162(3), 1406–1419.","ama":"Landberg K, Pederson E, Viaene T, et al. The moss physcomitrella patens reproductive organ development is highly organized, affected by the two SHI/STY genes and by the level of active auxin in the SHI/STY expression domain. Plant Physiology. 2013;162(3):1406-1419. doi:10.1104/pp.113.214023","chicago":"Landberg, Katarina, Eric Pederson, Tom Viaene, Behruz Bozorg, Jiří Friml, Henrik Jönsson, Mattias Thelander, and Eva Sundberg. “The Moss Physcomitrella Patens Reproductive Organ Development Is Highly Organized, Affected by the Two SHI/STY Genes and by the Level of Active Auxin in the SHI/STY Expression Domain.” Plant Physiology. American Society of Plant Biologists, 2013. https://doi.org/10.1104/pp.113.214023.","short":"K. Landberg, E. Pederson, T. Viaene, B. Bozorg, J. Friml, H. Jönsson, M. Thelander, E. Sundberg, Plant Physiology 162 (2013) 1406–1419.","mla":"Landberg, Katarina, et al. “The Moss Physcomitrella Patens Reproductive Organ Development Is Highly Organized, Affected by the Two SHI/STY Genes and by the Level of Active Auxin in the SHI/STY Expression Domain.” Plant Physiology, vol. 162, no. 3, American Society of Plant Biologists, 2013, pp. 1406–19, doi:10.1104/pp.113.214023."},"publication":"Plant Physiology","date_published":"2013-07-03T00:00:00Z","publist_id":"4079","publisher":"American Society of Plant Biologists","department":[{"_id":"JiFr"}],"publication_status":"published","pmid":1,"year":"2013","volume":162,"date_updated":"2021-01-12T06:59:51Z","date_created":"2018-12-11T11:59:42Z","author":[{"full_name":"Landberg, Katarina","first_name":"Katarina","last_name":"Landberg"},{"full_name":"Pederson, Eric","last_name":"Pederson","first_name":"Eric"},{"last_name":"Viaene","first_name":"Tom","full_name":"Viaene, Tom"},{"last_name":"Bozorg","first_name":"Behruz","full_name":"Bozorg, Behruz"},{"first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"},{"last_name":"Jönsson","first_name":"Henrik","full_name":"Jönsson, Henrik"},{"full_name":"Thelander, Mattias","first_name":"Mattias","last_name":"Thelander"},{"first_name":"Eva","last_name":"Sundberg","full_name":"Sundberg, Eva"}],"month":"07","quality_controlled":"1","external_id":{"pmid":["23669745"]},"oa":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3707547/"}],"language":[{"iso":"eng"}],"doi":"10.1104/pp.113.214023"},{"month":"06","day":"06","scopus_import":1,"date_published":"2013-06-06T00:00:00Z","doi":"10.1063/1.4807704","language":[{"iso":"eng"}],"citation":{"ama":"Avila K, Hof B. High-precision Taylor-Couette experiment to study subcritical transitions and the role of boundary conditions and size effects. Review of Scientific Instruments. 2013;84(6). doi:10.1063/1.4807704","apa":"Avila, K., & Hof, B. (2013). High-precision Taylor-Couette experiment to study subcritical transitions and the role of boundary conditions and size effects. Review of Scientific Instruments. American Institute of Physics. https://doi.org/10.1063/1.4807704","ieee":"K. Avila and B. Hof, “High-precision Taylor-Couette experiment to study subcritical transitions and the role of boundary conditions and size effects,” Review of Scientific Instruments, vol. 84, no. 6. American Institute of Physics, 2013.","ista":"Avila K, Hof B. 2013. High-precision Taylor-Couette experiment to study subcritical transitions and the role of boundary conditions and size effects. Review of Scientific Instruments. 84(6), 065106.","short":"K. Avila, B. Hof, Review of Scientific Instruments 84 (2013).","mla":"Avila, Kerstin, and Björn Hof. “High-Precision Taylor-Couette Experiment to Study Subcritical Transitions and the Role of Boundary Conditions and Size Effects.” Review of Scientific Instruments, vol. 84, no. 6, 065106, American Institute of Physics, 2013, doi:10.1063/1.4807704.","chicago":"Avila, Kerstin, and Björn Hof. “High-Precision Taylor-Couette Experiment to Study Subcritical Transitions and the Role of Boundary Conditions and Size Effects.” Review of Scientific Instruments. American Institute of Physics, 2013. https://doi.org/10.1063/1.4807704."},"publication":"Review of Scientific Instruments","quality_controlled":"1","publist_id":"4081","issue":"6","abstract":[{"text":"A novel Taylor-Couette system has been constructed for investigations of transitional as well as high Reynolds number turbulent flows in very large aspect ratios. The flexibility of the setup enables studies of a variety of problems regarding hydrodynamic instabilities and turbulence in rotating flows. The inner and outer cylinders and the top and bottom endplates can be rotated independently with rotation rates of up to 30 Hz, thereby covering five orders of magnitude in Reynolds numbers (Re = 101-106). The radius ratio can be easily changed, the highest realized one is η = 0.98 corresponding to an aspect ratio of 260 gap width in the vertical and 300 in the azimuthal direction. For η < 0.98 the aspect ratio can be dynamically changed during measurements and complete transparency in the radial direction over the full length of the cylinders is provided by the usage of a precision glass inner cylinder. The temperatures of both cylinders are controlled independently. Overall this apparatus combines an unmatched variety in geometry, rotation rates, and temperatures, which is provided by a sophisticated high-precision bearing system. Possible applications are accurate studies of the onset of turbulence and spatio-temporal intermittent flow patterns in very large domains, transport processes of turbulence at high Re, the stability of Keplerian flows for different boundary conditions, and studies of baroclinic instabilities.","lang":"eng"}],"type":"journal_article","article_number":"065106","author":[{"first_name":"Kerstin","last_name":"Avila","full_name":"Avila, Kerstin"},{"first_name":"Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn"}],"oa_version":"None","volume":84,"date_updated":"2021-01-12T06:59:50Z","date_created":"2018-12-11T11:59:42Z","year":"2013","_id":"2806","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 84","publisher":"American Institute of Physics","department":[{"_id":"BjHo"}],"publication_status":"published","title":"High-precision Taylor-Couette experiment to study subcritical transitions and the role of boundary conditions and size effects","status":"public"},{"publisher":"Cambridge University Press","intvolume":" 723","title":"Lagrangian approach to laminar-turbulent interfaces in transitional pipe flow","publication_status":"published","status":"public","_id":"2805","year":"2013","volume":723,"date_created":"2018-12-11T11:59:41Z","date_updated":"2021-01-12T06:59:50Z","author":[{"full_name":"Holzner, Markus","last_name":"Holzner","first_name":"Markus"},{"full_name":"Song, Baofang","last_name":"Song","first_name":"Baofang"},{"full_name":"Avila, Marc","first_name":"Marc","last_name":"Avila"},{"full_name":"Björn Hof","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","first_name":"Björn"}],"type":"journal_article","extern":1,"publist_id":"4084","abstract":[{"lang":"eng","text":"Transition in shear flows is characterized by localized turbulent regions embedded in the surrounding laminar flow. These so-called turbulent spots or puffs are observed in a variety of shear flows and in certain Reynolds-number regimes, and they are advected by the flow while keeping their characteristic length. We show here for the case of pipe flow that this seemingly passive advection of turbulent puffs involves continuous entrainment and relaminarization of laminar and turbulent fluid across strongly convoluted interfaces. Surprisingly, interface areas are almost two orders of magnitude larger than the pipe cross-section, while local entrainment velocities are much smaller than the mean speed. Even though these velocities were shown to be small and proportional to the Kolmogorov velocity scale (in agreement with a prediction by Corrsin) in a flow without mean shear before, we find that, in pipe flow, local entrainment velocities are about an order of magnitude smaller than this scale. The Lagrangian method used to study the dynamics of the laminar-turbulent interfaces allows accurate determination of the leading and trailing edge speeds. However, to resolve the highly complex interface dynamics requires much higher numerical resolutions than for ordinary turbulent flows. This method also reveals that the volume flux across the leading edge has the same radial dependence but the opposite sign as that across the trailing edge, and it is this symmetry that is responsible for the puff shape remaining constant."}],"page":"140 - 162","quality_controlled":0,"citation":{"chicago":"Holzner, Markus, Baofang Song, Marc Avila, and Björn Hof. “Lagrangian Approach to Laminar-Turbulent Interfaces in Transitional Pipe Flow.” Journal of Fluid Mechanics. Cambridge University Press, 2013. https://doi.org/10.1017/jfm.2013.127.","mla":"Holzner, Markus, et al. “Lagrangian Approach to Laminar-Turbulent Interfaces in Transitional Pipe Flow.” Journal of Fluid Mechanics, vol. 723, Cambridge University Press, 2013, pp. 140–62, doi:10.1017/jfm.2013.127.","short":"M. Holzner, B. Song, M. Avila, B. Hof, Journal of Fluid Mechanics 723 (2013) 140–162.","ista":"Holzner M, Song B, Avila M, Hof B. 2013. Lagrangian approach to laminar-turbulent interfaces in transitional pipe flow. Journal of Fluid Mechanics. 723, 140–162.","ieee":"M. Holzner, B. Song, M. Avila, and B. Hof, “Lagrangian approach to laminar-turbulent interfaces in transitional pipe flow,” Journal of Fluid Mechanics, vol. 723. Cambridge University Press, pp. 140–162, 2013.","apa":"Holzner, M., Song, B., Avila, M., & Hof, B. (2013). Lagrangian approach to laminar-turbulent interfaces in transitional pipe flow. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2013.127","ama":"Holzner M, Song B, Avila M, Hof B. Lagrangian approach to laminar-turbulent interfaces in transitional pipe flow. Journal of Fluid Mechanics. 2013;723:140-162. doi:10.1017/jfm.2013.127"},"publication":"Journal of Fluid Mechanics","date_published":"2013-05-01T00:00:00Z","doi":"10.1017/jfm.2013.127","month":"05","day":"01"},{"month":"06","doi":"10.1371/journal.pgen.1003580","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","publist_id":"4075","file_date_updated":"2020-07-14T12:45:48Z","article_number":"e1003580","author":[{"last_name":"De Vos","first_name":"Marjon","id":"3111FFAC-F248-11E8-B48F-1D18A9856A87","full_name":"De Vos, Marjon"},{"last_name":"Poelwijk","first_name":"Frank","full_name":"Poelwijk, Frank"},{"first_name":"Nico","last_name":"Battich","full_name":"Battich, Nico"},{"full_name":"Ndika, Joseph","last_name":"Ndika","first_name":"Joseph"},{"full_name":"Tans, Sander","last_name":"Tans","first_name":"Sander"}],"volume":9,"date_updated":"2021-01-12T06:59:52Z","date_created":"2018-12-11T11:59:43Z","year":"2013","publisher":"Public Library of Science","department":[{"_id":"ToBo"}],"publication_status":"published","has_accepted_license":"1","day":"27","scopus_import":1,"date_published":"2013-06-27T00:00:00Z","citation":{"chicago":"Vos, Marjon de, Frank Poelwijk, Nico Battich, Joseph Ndika, and Sander Tans. “Environmental Dependence of Genetic Constraint.” PLoS Genetics. Public Library of Science, 2013. https://doi.org/10.1371/journal.pgen.1003580.","short":"M. de Vos, F. Poelwijk, N. Battich, J. Ndika, S. Tans, PLoS Genetics 9 (2013).","mla":"de Vos, Marjon, et al. “Environmental Dependence of Genetic Constraint.” PLoS Genetics, vol. 9, no. 6, e1003580, Public Library of Science, 2013, doi:10.1371/journal.pgen.1003580.","apa":"de Vos, M., Poelwijk, F., Battich, N., Ndika, J., & Tans, S. (2013). Environmental dependence of genetic constraint. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1003580","ieee":"M. de Vos, F. Poelwijk, N. Battich, J. Ndika, and S. Tans, “Environmental dependence of genetic constraint,” PLoS Genetics, vol. 9, no. 6. Public Library of Science, 2013.","ista":"de Vos M, Poelwijk F, Battich N, Ndika J, Tans S. 2013. Environmental dependence of genetic constraint. PLoS Genetics. 9(6), e1003580.","ama":"de Vos M, Poelwijk F, Battich N, Ndika J, Tans S. Environmental dependence of genetic constraint. PLoS Genetics. 2013;9(6). doi:10.1371/journal.pgen.1003580"},"publication":"PLoS Genetics","issue":"6","abstract":[{"lang":"eng","text":"The epistatic interactions that underlie evolutionary constraint have mainly been studied for constant external conditions. However, environmental changes may modulate epistasis and hence affect genetic constraints. Here we investigate genetic constraints in the adaptive evolution of a novel regulatory function in variable environments, using the lac repressor, LacI, as a model system. We have systematically reconstructed mutational trajectories from wild type LacI to three different variants that each exhibit an inverse response to the inducing ligand IPTG, and analyzed the higher-order interactions between genetic and environmental changes. We find epistasis to depend strongly on the environment. As a result, mutational steps essential to inversion but inaccessible by positive selection in one environment, become accessible in another. We present a graphical method to analyze the observed complex higher-order interactions between multiple mutations and environmental change, and show how the interactions can be explained by a combination of mutational effects on allostery and thermodynamic stability. This dependency of genetic constraint on the environment should fundamentally affect evolutionary dynamics and affects the interpretation of phylogenetic data."}],"type":"journal_article","pubrep_id":"412","file":[{"creator":"system","content_type":"application/pdf","file_size":474655,"file_name":"IST-2016-412-v1+1_journal.pgen.1003580.pdf","access_level":"open_access","date_created":"2018-12-12T10:08:51Z","date_updated":"2020-07-14T12:45:48Z","checksum":"7a4736dd80496d29ff6908b6f2329b4e","file_id":"4713","relation":"main_file"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2810","intvolume":" 9","title":"Environmental dependence of genetic constraint","status":"public","ddc":["570"]},{"year":"2013","publication_status":"published","publisher":"World Scientific Publishing","department":[{"_id":"KrCh"}],"author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"first_name":"Luca","last_name":"Alfaro","full_name":"Alfaro, Luca"},{"full_name":"Majumdar, Ritankar","first_name":"Ritankar","last_name":"Majumdar"}],"date_updated":"2021-01-12T06:59:54Z","date_created":"2018-12-11T11:59:44Z","volume":24,"ec_funded":1,"publist_id":"4070","oa":1,"external_id":{"arxiv":["0804.4525"]},"main_file_link":[{"url":"https://arxiv.org/abs/0804.4525","open_access":"1"}],"quality_controlled":"1","project":[{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","call_identifier":"FWF","name":"Game Theory"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"doi":"10.1142/S0129054113400066","language":[{"iso":"eng"}],"month":"02","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2814","title":"The complexity of coverage","status":"public","intvolume":" 24","oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"We study the problem of generating a test sequence that achieves maximal coverage for a reactive system under test. We formulate the problem as a repeated game between the tester and the system, where the system state space is partitioned according to some coverage criterion and the objective of the tester is to maximize the set of partitions (or coverage goals) visited during the game. We show the complexity of the maximal coverage problem for non-deterministic systems is PSPACE-complete, but is NP-complete for deterministic systems. For the special case of non-deterministic systems with a re-initializing "reset" action, which represent running a new test input on a re-initialized system, we show that the complexity is coNP-complete. Our proof technique for reset games uses randomized testing strategies that circumvent the exponentially large memory requirement of deterministic testing strategies. We also discuss the memory requirement for deterministic strategies and extensions of our results to other models, such as pushdown systems and timed systems."}],"issue":"2","publication":"International Journal of Foundations of Computer Science","citation":{"chicago":"Chatterjee, Krishnendu, Luca Alfaro, and Ritankar Majumdar. “The Complexity of Coverage.” International Journal of Foundations of Computer Science. World Scientific Publishing, 2013. https://doi.org/10.1142/S0129054113400066.","short":"K. Chatterjee, L. Alfaro, R. Majumdar, International Journal of Foundations of Computer Science 24 (2013) 165–185.","mla":"Chatterjee, Krishnendu, et al. “The Complexity of Coverage.” International Journal of Foundations of Computer Science, vol. 24, no. 2, World Scientific Publishing, 2013, pp. 165–85, doi:10.1142/S0129054113400066.","ieee":"K. Chatterjee, L. Alfaro, and R. Majumdar, “The complexity of coverage,” International Journal of Foundations of Computer Science, vol. 24, no. 2. World Scientific Publishing, pp. 165–185, 2013.","apa":"Chatterjee, K., Alfaro, L., & Majumdar, R. (2013). The complexity of coverage. International Journal of Foundations of Computer Science. World Scientific Publishing. https://doi.org/10.1142/S0129054113400066","ista":"Chatterjee K, Alfaro L, Majumdar R. 2013. The complexity of coverage. International Journal of Foundations of Computer Science. 24(2), 165–185.","ama":"Chatterjee K, Alfaro L, Majumdar R. The complexity of coverage. International Journal of Foundations of Computer Science. 2013;24(2):165-185. doi:10.1142/S0129054113400066"},"page":"165 - 185","date_published":"2013-02-01T00:00:00Z","scopus_import":1,"day":"01"},{"oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2811","intvolume":" 87","status":"public","title":"Nature of laminar-turbulence intermittency in shear flows","issue":"6","abstract":[{"lang":"eng","text":"In pipe, channel, and boundary layer flows turbulence first occurs intermittently in space and time: at moderate Reynolds numbers domains of disordered turbulent motion are separated by quiescent laminar regions. Based on direct numerical simulations of pipe flow we argue here that the spatial intermittency has its origin in a nearest neighbor interaction between turbulent regions. We further show that in this regime turbulent flows are intrinsically intermittent with a well-defined equilibrium turbulent fraction but without ever assuming a steady pattern. This transition scenario is analogous to that found in simple models such as coupled map lattices. The scaling observed implies that laminar intermissions of the turbulent flow will persist to arbitrarily large Reynolds numbers."}],"type":"journal_article","date_published":"2013-06-18T00:00:00Z","citation":{"ieee":"M. Avila and B. Hof, “Nature of laminar-turbulence intermittency in shear flows,” Physical Review E, vol. 87, no. 6. American Institute of Physics, 2013.","apa":"Avila, M., & Hof, B. (2013). Nature of laminar-turbulence intermittency in shear flows. Physical Review E. American Institute of Physics. https://doi.org/10.1103/PhysRevE.87.063012","ista":"Avila M, Hof B. 2013. Nature of laminar-turbulence intermittency in shear flows. Physical Review E. 87(6), 063012.","ama":"Avila M, Hof B. Nature of laminar-turbulence intermittency in shear flows. Physical Review E. 2013;87(6). doi:10.1103/PhysRevE.87.063012","chicago":"Avila, Marc, and Björn Hof. “Nature of Laminar-Turbulence Intermittency in Shear Flows.” Physical Review E. American Institute of Physics, 2013. https://doi.org/10.1103/PhysRevE.87.063012.","short":"M. Avila, B. Hof, Physical Review E 87 (2013).","mla":"Avila, Marc, and Björn Hof. “Nature of Laminar-Turbulence Intermittency in Shear Flows.” Physical Review E, vol. 87, no. 6, 063012, American Institute of Physics, 2013, doi:10.1103/PhysRevE.87.063012."},"publication":"Physical Review E","day":"18","scopus_import":1,"author":[{"full_name":"Avila, Marc","last_name":"Avila","first_name":"Marc"},{"first_name":"Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn"}],"volume":87,"date_updated":"2021-01-12T06:59:53Z","date_created":"2018-12-11T11:59:43Z","year":"2013","department":[{"_id":"BjHo"}],"publisher":"American Institute of Physics","publication_status":"published","ec_funded":1,"publist_id":"4074","article_number":"063012","doi":"10.1103/PhysRevE.87.063012","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1306.5890"}],"external_id":{"arxiv":["1306.5890"]},"project":[{"name":"Decoding the complexity of turbulence at its origin","call_identifier":"FP7","grant_number":"306589","_id":"25152F3A-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","month":"06"},{"external_id":{"pmid":["23757498"]},"oa":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3696777/"}],"quality_controlled":"1","doi":"10.1073/pnas.1219666110","language":[{"iso":"eng"}],"month":"06","pmid":1,"year":"2013","publisher":"National Academy of Sciences","department":[{"_id":"BjHo"}],"publication_status":"published","author":[{"first_name":"Devranjan","last_name":"Samanta","full_name":"Samanta, Devranjan"},{"full_name":"Dubief, Yves","first_name":"Yves","last_name":"Dubief"},{"first_name":"Markus","last_name":"Holzner","full_name":"Holzner, Markus"},{"full_name":"Schäfer, Christof","last_name":"Schäfer","first_name":"Christof"},{"last_name":"Morozov","first_name":"Alexander","full_name":"Morozov, Alexander"},{"full_name":"Wagner, Christian","last_name":"Wagner","first_name":"Christian"},{"full_name":"Hof, Björn","first_name":"Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754"}],"volume":110,"date_updated":"2021-01-12T06:59:54Z","date_created":"2018-12-11T11:59:44Z","publist_id":"4073","citation":{"chicago":"Samanta, Devranjan, Yves Dubief, Markus Holzner, Christof Schäfer, Alexander Morozov, Christian Wagner, and Björn Hof. “Elasto-Inertial Turbulence.” PNAS. National Academy of Sciences, 2013. https://doi.org/10.1073/pnas.1219666110.","mla":"Samanta, Devranjan, et al. “Elasto-Inertial Turbulence.” PNAS, vol. 110, no. 26, National Academy of Sciences, 2013, pp. 10557–62, doi:10.1073/pnas.1219666110.","short":"D. Samanta, Y. Dubief, M. Holzner, C. Schäfer, A. Morozov, C. Wagner, B. Hof, PNAS 110 (2013) 10557–10562.","ista":"Samanta D, Dubief Y, Holzner M, Schäfer C, Morozov A, Wagner C, Hof B. 2013. Elasto-inertial turbulence. PNAS. 110(26), 10557–10562.","ieee":"D. Samanta et al., “Elasto-inertial turbulence,” PNAS, vol. 110, no. 26. National Academy of Sciences, pp. 10557–10562, 2013.","apa":"Samanta, D., Dubief, Y., Holzner, M., Schäfer, C., Morozov, A., Wagner, C., & Hof, B. (2013). Elasto-inertial turbulence. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1219666110","ama":"Samanta D, Dubief Y, Holzner M, et al. Elasto-inertial turbulence. PNAS. 2013;110(26):10557-10562. doi:10.1073/pnas.1219666110"},"publication":"PNAS","page":"10557 - 10562","date_published":"2013-06-25T00:00:00Z","scopus_import":1,"day":"25","_id":"2813","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 110","title":"Elasto-inertial turbulence","status":"public","oa_version":"Submitted Version","type":"journal_article","issue":"26","abstract":[{"lang":"eng","text":"Turbulence is ubiquitous in nature, yet even for the case of ordinary Newtonian fluids like water, our understanding of this phenomenon is limited. Many liquids of practical importance are more complicated (e.g., blood, polymer melts, paints), however; they exhibit elastic as well as viscous characteristics, and the relation between stress and strain is nonlinear. We demonstrate here for a model system of such complex fluids that at high shear rates, turbulence is not simply modified as previously believed but is suppressed and replaced by a different type of disordered motion, elasto-inertial turbulence. Elasto-inertial turbulence is found to occur at much lower Reynolds numbers than Newtonian turbulence, and the dynamical properties differ significantly. The friction scaling observed coincides with the so-called "maximum drag reduction" asymptote, which is exhibited by a wide range of viscoelastic fluids."}]},{"acknowledgement":"Some of the authors were partially supported by the GIGA ANR grant (contract ANR-09-BLAN-0331-01) and the European project CG-Learning (contract 255827).","_id":"2812","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2013","publisher":"ACM","department":[{"_id":"HeEd"}],"title":"Homological reconstruction and simplification in R3","status":"public","publication_status":"published","related_material":{"record":[{"status":"public","relation":"later_version","id":"1805"}]},"author":[{"first_name":"Dominique","last_name":"Attali","full_name":"Attali, Dominique"},{"id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9683-0724","first_name":"Ulrich","last_name":"Bauer","full_name":"Bauer, Ulrich"},{"full_name":"Devillers, Olivier","first_name":"Olivier","last_name":"Devillers"},{"full_name":"Glisse, Marc","first_name":"Marc","last_name":"Glisse"},{"last_name":"Lieutier","first_name":"André","full_name":"Lieutier, André"}],"oa_version":"Submitted Version","date_updated":"2023-02-23T10:15:15Z","date_created":"2018-12-11T11:59:44Z","type":"conference","publist_id":"4072","abstract":[{"text":"We consider the problem of deciding whether the persistent homology group of a simplicial pair (K, L) can be realized as the homology H* (X) of some complex X with L ⊂ X ⊂ K. We show that this problem is NP-complete even if K is embedded in ℝ3. As a consequence, we show that it is NP-hard to simplify level and sublevel sets of scalar functions on S3 within a given tolerance constraint. This problem has relevance to the visualization of medical images by isosurfaces. We also show an implication to the theory of well groups of scalar functions: not every well group can be realized by some level set, and deciding whether a well group can be realized is NP-hard.","lang":"eng"}],"oa":1,"citation":{"ista":"Attali D, Bauer U, Devillers O, Glisse M, Lieutier A. 2013. Homological reconstruction and simplification in R3. Proceedings of the 29th annual symposium on Computational Geometry. SoCG: Symposium on Computational Geometry, 117–125.","ieee":"D. Attali, U. Bauer, O. Devillers, M. Glisse, and A. Lieutier, “Homological reconstruction and simplification in R3,” in Proceedings of the 29th annual symposium on Computational Geometry, Rio de Janeiro, Brazil, 2013, pp. 117–125.","apa":"Attali, D., Bauer, U., Devillers, O., Glisse, M., & Lieutier, A. (2013). Homological reconstruction and simplification in R3. In Proceedings of the 29th annual symposium on Computational Geometry (pp. 117–125). Rio de Janeiro, Brazil: ACM. https://doi.org/10.1145/2462356.2462373","ama":"Attali D, Bauer U, Devillers O, Glisse M, Lieutier A. Homological reconstruction and simplification in R3. In: Proceedings of the 29th Annual Symposium on Computational Geometry. ACM; 2013:117-125. doi:10.1145/2462356.2462373","chicago":"Attali, Dominique, Ulrich Bauer, Olivier Devillers, Marc Glisse, and André Lieutier. “Homological Reconstruction and Simplification in R3.” In Proceedings of the 29th Annual Symposium on Computational Geometry, 117–25. ACM, 2013. https://doi.org/10.1145/2462356.2462373.","mla":"Attali, Dominique, et al. “Homological Reconstruction and Simplification in R3.” Proceedings of the 29th Annual Symposium on Computational Geometry, ACM, 2013, pp. 117–25, doi:10.1145/2462356.2462373.","short":"D. Attali, U. Bauer, O. Devillers, M. Glisse, A. Lieutier, in:, Proceedings of the 29th Annual Symposium on Computational Geometry, ACM, 2013, pp. 117–125."},"main_file_link":[{"url":"http://hal.archives-ouvertes.fr/hal-00833791/","open_access":"1"}],"publication":"Proceedings of the 29th annual symposium on Computational Geometry","page":"117 - 125","quality_controlled":"1","date_published":"2013-06-01T00:00:00Z","doi":"10.1145/2462356.2462373","conference":{"start_date":"2013-06-17","location":"Rio de Janeiro, Brazil","end_date":"2013-06-20","name":"SoCG: Symposium on Computational Geometry"},"language":[{"iso":"eng"}],"scopus_import":1,"day":"01","month":"06"},{"status":"public","ddc":["000"],"title":"Density games","intvolume":" 334","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2817","oa_version":"Published Version","file":[{"file_size":834604,"content_type":"application/pdf","creator":"system","access_level":"open_access","file_name":"IST-2016-400-v1+1_1-s2.0-S0022519313002609-main.pdf","checksum":"3c29059ab03a4b8f97a07646b817ddbb","date_updated":"2020-07-14T12:45:49Z","date_created":"2018-12-12T10:14:54Z","relation":"main_file","file_id":"5110"}],"pubrep_id":"400","type":"journal_article","abstract":[{"lang":"eng","text":"The basic idea of evolutionary game theory is that payoff determines reproductive rate. Successful individuals have a higher payoff and produce more offspring. But in evolutionary and ecological situations there is not only reproductive rate but also carrying capacity. Individuals may differ in their exposure to density limiting effects. Here we explore an alternative approach to evolutionary game theory by assuming that the payoff from the game determines the carrying capacity of individual phenotypes. Successful strategies are less affected by density limitation (crowding) and reach higher equilibrium abundance. We demonstrate similarities and differences between our framework and the standard replicator equation. Our equation is defined on the positive orthant, instead of the simplex, but has the same equilibrium points as the replicator equation. Linear stability analysis produces the classical conditions for asymptotic stability of pure strategies, but the stability properties of internal equilibria can differ in the two frameworks. For example, in a two-strategy game with an internal equilibrium that is always stable under the replicator equation, the corresponding equilibrium can be unstable in the new framework resulting in a limit cycle."}],"page":"26 - 34","publication":"Journal of Theoretical Biology","citation":{"mla":"Novak, Sebastian, et al. “Density Games.” Journal of Theoretical Biology, vol. 334, Elsevier, 2013, pp. 26–34, doi:10.1016/j.jtbi.2013.05.029.","short":"S. Novak, K. Chatterjee, M. Nowak, Journal of Theoretical Biology 334 (2013) 26–34.","chicago":"Novak, Sebastian, Krishnendu Chatterjee, and Martin Nowak. “Density Games.” Journal of Theoretical Biology. Elsevier, 2013. https://doi.org/10.1016/j.jtbi.2013.05.029.","ama":"Novak S, Chatterjee K, Nowak M. Density games. Journal of Theoretical Biology. 2013;334:26-34. doi:10.1016/j.jtbi.2013.05.029","ista":"Novak S, Chatterjee K, Nowak M. 2013. Density games. Journal of Theoretical Biology. 334, 26–34.","ieee":"S. Novak, K. Chatterjee, and M. Nowak, “Density games,” Journal of Theoretical Biology, vol. 334. Elsevier, pp. 26–34, 2013.","apa":"Novak, S., Chatterjee, K., & Nowak, M. (2013). Density games. Journal of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2013.05.029"},"date_published":"2013-10-07T00:00:00Z","scopus_import":1,"day":"07","has_accepted_license":"1","publication_status":"published","department":[{"_id":"NiBa"},{"_id":"KrCh"}],"publisher":"Elsevier","year":"2013","date_updated":"2021-01-12T06:59:55Z","date_created":"2018-12-11T11:59:45Z","volume":334,"author":[{"full_name":"Novak, Sebastian","last_name":"Novak","first_name":"Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"full_name":"Nowak, Martin","first_name":"Martin","last_name":"Nowak"}],"file_date_updated":"2020-07-14T12:45:49Z","publist_id":"3984","ec_funded":1,"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"call_identifier":"FWF","name":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"doi":"10.1016/j.jtbi.2013.05.029","month":"10"},{"intvolume":" 1","status":"public","title":"Quantitative timed simulation functions and refinement metrics for real-time systems","_id":"2819","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","type":"conference","abstract":[{"text":"We introduce quantatitive timed refinement metrics and quantitative timed simulation functions, incorporating zenoness checks, for timed systems. These functions assign positive real numbers between zero and infinity which quantify the timing mismatches between two timed systems, amongst non-zeno runs. We quantify timing mismatches in three ways: (1) the maximum timing mismatch that can arise, (2) the "steady-state" maximum 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 functions to within any desired degree of accuracy. In order to compute the values of the quantitative simulation functions, 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 for player 1, and then use these algorithms to compute the values of the quantitative timed simulation functions. ","lang":"eng"}],"page":"273 - 282","citation":{"short":"K. Chatterjee, V. Prabhu, in:, Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control, Springer, 2013, pp. 273–282.","mla":"Chatterjee, Krishnendu, and Vinayak Prabhu. “Quantitative Timed Simulation Functions and Refinement Metrics for Real-Time Systems.” Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control, vol. 1, Springer, 2013, pp. 273–82, doi:10.1145/2461328.2461370.","chicago":"Chatterjee, Krishnendu, and Vinayak Prabhu. “Quantitative Timed Simulation Functions and Refinement Metrics for Real-Time Systems.” In Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control, 1:273–82. Springer, 2013. https://doi.org/10.1145/2461328.2461370.","ama":"Chatterjee K, Prabhu V. Quantitative timed simulation functions and refinement metrics for real-time systems. In: Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control. Vol 1. Springer; 2013:273-282. doi:10.1145/2461328.2461370","ieee":"K. Chatterjee and V. Prabhu, “Quantitative timed simulation functions and refinement metrics for real-time systems,” in Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control, Philadelphia, PA USA, 2013, vol. 1, pp. 273–282.","apa":"Chatterjee, K., & Prabhu, V. (2013). Quantitative timed simulation functions and refinement metrics for real-time systems. In Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control (Vol. 1, pp. 273–282). Philadelphia, PA USA: Springer. https://doi.org/10.1145/2461328.2461370","ista":"Chatterjee K, Prabhu V. 2013. Quantitative timed simulation functions and refinement metrics for real-time systems. Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control. HSCC: Hybrid Systems - Computation and Control vol. 1, 273–282."},"publication":"Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control","date_published":"2013-04-01T00:00:00Z","scopus_import":1,"day":"01","department":[{"_id":"KrCh"}],"publisher":"Springer","publication_status":"published","year":"2013","acknowledgement":"This work has been financially supported in part by the European Commission FP7-ICT Cognitive Systems, Interaction, and Robotics under the contract # 270180 (NOP-TILUS); by Fundacao para Ciencia e Tecnologia under project PTDC/EEA-CRO/104901/2008 (Modeling and control of Networked vehicle systems in persistent autonomous operations); by Austrian Science Fund (FWF) Grant No P 23499-N23 on Modern Graph Algorithmic Techniques in Formal Verification; FWF NFN Grant No S11407-N23 (RiSE); ERC Start grant (279307: Graph Games); and the Microsoft faculty fellows award","volume":1,"date_created":"2018-12-11T11:59:46Z","date_updated":"2021-01-12T06:59:56Z","author":[{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Prabhu","first_name":"Vinayak","full_name":"Prabhu, Vinayak"}],"ec_funded":1,"publist_id":"3982","project":[{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1212.6556"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1145/2461328.2461370","conference":{"start_date":"2013-04-08","location":"Philadelphia, PA USA","end_date":"2013-04-11","name":"HSCC: Hybrid Systems - Computation and Control"},"month":"04"},{"scopus_import":1,"day":"01","page":"1661 - 1692","publication":"Neural Computation","citation":{"ama":"Rajan K, Marre O, Tkačik G. Learning quadratic receptive fields from neural responses to natural stimuli. Neural Computation. 2013;25(7):1661-1692. doi:10.1162/NECO_a_00463","ista":"Rajan K, Marre O, Tkačik G. 2013. Learning quadratic receptive fields from neural responses to natural stimuli. Neural Computation. 25(7), 1661–1692.","apa":"Rajan, K., Marre, O., & Tkačik, G. (2013). Learning quadratic receptive fields from neural responses to natural stimuli. Neural Computation. MIT Press . https://doi.org/10.1162/NECO_a_00463","ieee":"K. Rajan, O. Marre, and G. Tkačik, “Learning quadratic receptive fields from neural responses to natural stimuli,” Neural Computation, vol. 25, no. 7. MIT Press , pp. 1661–1692, 2013.","mla":"Rajan, Kanaka, et al. “Learning Quadratic Receptive Fields from Neural Responses to Natural Stimuli.” Neural Computation, vol. 25, no. 7, MIT Press , 2013, pp. 1661–92, doi:10.1162/NECO_a_00463.","short":"K. Rajan, O. Marre, G. Tkačik, Neural Computation 25 (2013) 1661–1692.","chicago":"Rajan, Kanaka, Olivier Marre, and Gašper Tkačik. “Learning Quadratic Receptive Fields from Neural Responses to Natural Stimuli.” Neural Computation. MIT Press , 2013. https://doi.org/10.1162/NECO_a_00463."},"date_published":"2013-07-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Models of neural responses to stimuli with complex spatiotemporal correlation structure often assume that neurons are selective for only a small number of linear projections of a potentially high-dimensional input. In this review, we explore recent modeling approaches where the neural response depends on the quadratic form of the input rather than on its linear projection, that is, the neuron is sensitive to the local covariance structure of the signal preceding the spike. To infer this quadratic dependence in the presence of arbitrary (e.g., naturalistic) stimulus distribution, we review several inference methods, focusing in particular on two information theory–based approaches (maximization of stimulus energy and of noise entropy) and two likelihood-based approaches (Bayesian spike-triggered covariance and extensions of generalized linear models). We analyze the formal relationship between the likelihood-based and information-based approaches to demonstrate how they lead to consistent inference. We demonstrate the practical feasibility of these procedures by using model neurons responding to a flickering variance stimulus."}],"issue":"7","status":"public","title":"Learning quadratic receptive fields from neural responses to natural stimuli","intvolume":" 25","_id":"2818","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","month":"07","quality_controlled":"1","external_id":{"arxiv":["1209.0121"]},"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1209.0121"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1162/NECO_a_00463","publist_id":"3983","publication_status":"published","publisher":"MIT Press ","department":[{"_id":"GaTk"}],"year":"2013","date_created":"2018-12-11T11:59:45Z","date_updated":"2021-01-12T06:59:56Z","volume":25,"author":[{"last_name":"Rajan","first_name":"Kanaka","full_name":"Rajan, Kanaka"},{"first_name":"Olivier","last_name":"Marre","full_name":"Marre, Olivier"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","first_name":"Gasper","last_name":"Tkacik","full_name":"Tkacik, Gasper"}]},{"intvolume":" 92","title":"Mutations in SCO2 are associated with autosomal-dominant high-grade myopia","status":"public","_id":"2826","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","type":"journal_article","issue":"5","abstract":[{"lang":"eng","text":"Myopia, or near-sightedness, is an ocular refractive error of unfocused image quality in front of the retinal plane. Individuals with high-grade myopia (dioptric power greater than -6.00) are predisposed to ocular morbidities such as glaucoma, retinal detachment, and myopic maculopathy. Nonsyndromic, high-grade myopia is highly heritable, and to date multiple gene loci have been reported. We performed exome sequencing in 4 individuals from an 11-member family of European descent from the United States. Affected individuals had a mean dioptric spherical equivalent of -22.00 sphere. A premature stop codon mutation c.157C>T (p.Gln53*) cosegregating with disease was discovered within SCO2 that maps to chromosome 22q13.33. Subsequent analyses identified three additional mutations in three highly myopic unrelated individuals (c.341G>A, c.418G>A, and c.776C>T). To determine differential gene expression in a developmental mouse model, we induced myopia by applying a -15.00D lens over one eye. Messenger RNA levels of SCO2 were significantly downregulated in myopic mouse retinae. Immunohistochemistry in mouse eyes confirmed SCO2 protein localization in retina, retinal pigment epithelium, and sclera. SCO2 encodes for a copper homeostasis protein influential in mitochondrial cytochrome c oxidase activity. Copper deficiencies have been linked with photoreceptor loss and myopia with increased scleral wall elasticity. Retinal thinning has been reported with an SC02 variant. Human mutation identification with support from an induced myopic animal provides biological insights of myopic development."}],"page":"820 - 826","citation":{"chicago":"Tran Viet, Khanh, Caldwell Powell, Veluchamy Barathi, Thomas Klemm, Sebastian Maurer Stroh, Vachiranee Limviphuvadh, Vincent Soler, et al. “Mutations in SCO2 Are Associated with Autosomal-Dominant High-Grade Myopia.” American Journal of Human Genetics. Cell Press, 2013. https://doi.org/10.1016/j.ajhg.2013.04.005.","mla":"Tran Viet, Khanh, et al. “Mutations in SCO2 Are Associated with Autosomal-Dominant High-Grade Myopia.” American Journal of Human Genetics, vol. 92, no. 5, Cell Press, 2013, pp. 820–26, doi:10.1016/j.ajhg.2013.04.005.","short":"K. Tran Viet, C. Powell, V. Barathi, T. Klemm, S. Maurer Stroh, V. Limviphuvadh, V. Soler, C. Ho, T. Yanovitch, G. Schneider, Y. Li, E. Nading, R. Metlapally, S. Saw, L. Goh, S. Rozen, T. Young, American Journal of Human Genetics 92 (2013) 820–826.","ista":"Tran Viet K, Powell C, Barathi V, Klemm T, Maurer Stroh S, Limviphuvadh V, Soler V, Ho C, Yanovitch T, Schneider G, Li Y, Nading E, Metlapally R, Saw S, Goh L, Rozen S, Young T. 2013. Mutations in SCO2 are associated with autosomal-dominant high-grade myopia. American Journal of Human Genetics. 92(5), 820–826.","apa":"Tran Viet, K., Powell, C., Barathi, V., Klemm, T., Maurer Stroh, S., Limviphuvadh, V., … Young, T. (2013). Mutations in SCO2 are associated with autosomal-dominant high-grade myopia. American Journal of Human Genetics. Cell Press. https://doi.org/10.1016/j.ajhg.2013.04.005","ieee":"K. Tran Viet et al., “Mutations in SCO2 are associated with autosomal-dominant high-grade myopia,” American Journal of Human Genetics, vol. 92, no. 5. Cell Press, pp. 820–826, 2013.","ama":"Tran Viet K, Powell C, Barathi V, et al. Mutations in SCO2 are associated with autosomal-dominant high-grade myopia. American Journal of Human Genetics. 2013;92(5):820-826. doi:10.1016/j.ajhg.2013.04.005"},"publication":"American Journal of Human Genetics","date_published":"2013-05-02T00:00:00Z","scopus_import":1,"day":"02","publisher":"Cell Press","department":[{"_id":"MD"}],"publication_status":"published","pmid":1,"year":"2013","volume":92,"date_created":"2018-12-11T11:59:48Z","date_updated":"2021-01-12T06:59:59Z","author":[{"full_name":"Tran Viet, Khanh","first_name":"Khanh","last_name":"Tran Viet"},{"first_name":"Caldwell","last_name":"Powell","full_name":"Powell, Caldwell"},{"last_name":"Barathi","first_name":"Veluchamy","full_name":"Barathi, Veluchamy"},{"full_name":"Klemm, Thomas","last_name":"Klemm","first_name":"Thomas"},{"first_name":"Sebastian","last_name":"Maurer Stroh","full_name":"Maurer Stroh, Sebastian"},{"first_name":"Vachiranee","last_name":"Limviphuvadh","full_name":"Limviphuvadh, Vachiranee"},{"last_name":"Soler","first_name":"Vincent","full_name":"Soler, Vincent"},{"full_name":"Ho, Candice","first_name":"Candice","last_name":"Ho"},{"first_name":"Tammy","last_name":"Yanovitch","full_name":"Yanovitch, Tammy"},{"full_name":"Schneider, Georg","id":"329095A0-F248-11E8-B48F-1D18A9856A87","last_name":"Schneider","first_name":"Georg"},{"full_name":"Li, Yi","first_name":"Yi","last_name":"Li"},{"first_name":"Erica","last_name":"Nading","full_name":"Nading, Erica"},{"full_name":"Metlapally, Ravikanth","first_name":"Ravikanth","last_name":"Metlapally"},{"last_name":"Saw","first_name":"Seang","full_name":"Saw, Seang"},{"first_name":"Liang","last_name":"Goh","full_name":"Goh, Liang"},{"full_name":"Rozen, Steve","last_name":"Rozen","first_name":"Steve"},{"last_name":"Young","first_name":"Terri","full_name":"Young, Terri"}],"publist_id":"3974","quality_controlled":"1","external_id":{"pmid":["23643385"]},"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3644634/","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.ajhg.2013.04.005","month":"05"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2822","title":"3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture","status":"public","intvolume":" 110","oa_version":"Submitted Version","type":"journal_article","abstract":[{"lang":"eng","text":"Identification of genes that control root system architecture in crop plants requires innovations that enable high-throughput and accurate measurements of root system architecture through time. We demonstrate the ability of a semiautomated 3D in vivo imaging and digital phenotyping pipeline to interrogate the quantitative genetic basis of root system growth in a rice biparental mapping population, Bala x Azucena. We phenotyped >1,400 3D root models and >57,000 2D images for a suite of 25 traits that quantified the distribution, shape, extent of exploration, and the intrinsic size of root networks at days 12, 14, and 16 of growth in a gellan gum medium. From these data we identified 89 quantitative trait loci, some of which correspond to those found previously in soil-grown plants, and provide evidence for genetic tradeoffs in root growth allocations, such as between the extent and thoroughness of exploration. We also developed a multivariate method for generating and mapping central root architecture phenotypes and used it to identify five major quantitative trait loci (r2 = 24-37%), two of which were not identified by our univariate analysis. Our imaging and analytical platform provides a means to identify genes with high potential for improving root traits and agronomic qualities of crops."}],"issue":"18","publication":"PNAS","citation":{"apa":"Topp, C., Iyer Pascuzzi, A., Anderson, J., Lee, C., Zurek, P., Symonova, O., … Benfey, P. (2013). 3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1304354110","ieee":"C. Topp et al., “3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture,” PNAS, vol. 110, no. 18. National Academy of Sciences, pp. E1695–E1704, 2013.","ista":"Topp C, Iyer Pascuzzi A, Anderson J, Lee C, Zurek P, Symonova O, Zheng Y, Bucksch A, Mileyko Y, Galkovskyi T, Moore B, Harer J, Edelsbrunner H, Mitchell Olds T, Weitz J, Benfey P. 2013. 3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture. PNAS. 110(18), E1695–E1704.","ama":"Topp C, Iyer Pascuzzi A, Anderson J, et al. 3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture. PNAS. 2013;110(18):E1695-E1704. doi:10.1073/pnas.1304354110","chicago":"Topp, Christopher, Anjali Iyer Pascuzzi, Jill Anderson, Cheng Lee, Paul Zurek, Olga Symonova, Ying Zheng, et al. “3D Phenotyping and Quantitative Trait Locus Mapping Identify Core Regions of the Rice Genome Controlling Root Architecture.” PNAS. National Academy of Sciences, 2013. https://doi.org/10.1073/pnas.1304354110.","short":"C. Topp, A. Iyer Pascuzzi, J. Anderson, C. Lee, P. Zurek, O. Symonova, Y. Zheng, A. Bucksch, Y. Mileyko, T. Galkovskyi, B. Moore, J. Harer, H. Edelsbrunner, T. Mitchell Olds, J. Weitz, P. Benfey, PNAS 110 (2013) E1695–E1704.","mla":"Topp, Christopher, et al. “3D Phenotyping and Quantitative Trait Locus Mapping Identify Core Regions of the Rice Genome Controlling Root Architecture.” PNAS, vol. 110, no. 18, National Academy of Sciences, 2013, pp. E1695–704, doi:10.1073/pnas.1304354110."},"page":"E1695 - E1704","date_published":"2013-04-30T00:00:00Z","scopus_import":1,"day":"30","year":"2013","pmid":1,"publication_status":"published","department":[{"_id":"MaJö"},{"_id":"HeEd"}],"publisher":"National Academy of Sciences","author":[{"full_name":"Topp, Christopher","first_name":"Christopher","last_name":"Topp"},{"full_name":"Iyer Pascuzzi, Anjali","first_name":"Anjali","last_name":"Iyer Pascuzzi"},{"full_name":"Anderson, Jill","first_name":"Jill","last_name":"Anderson"},{"last_name":"Lee","first_name":"Cheng","full_name":"Lee, Cheng"},{"full_name":"Zurek, Paul","last_name":"Zurek","first_name":"Paul"},{"last_name":"Symonova","first_name":"Olga","id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","full_name":"Symonova, Olga"},{"full_name":"Zheng, Ying","last_name":"Zheng","first_name":"Ying"},{"full_name":"Bucksch, Alexander","last_name":"Bucksch","first_name":"Alexander"},{"last_name":"Mileyko","first_name":"Yuriy","full_name":"Mileyko, Yuriy"},{"first_name":"Taras","last_name":"Galkovskyi","full_name":"Galkovskyi, Taras"},{"full_name":"Moore, Brad","last_name":"Moore","first_name":"Brad"},{"last_name":"Harer","first_name":"John","full_name":"Harer, John"},{"full_name":"Edelsbrunner, Herbert","first_name":"Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833"},{"full_name":"Mitchell Olds, Thomas","first_name":"Thomas","last_name":"Mitchell Olds"},{"first_name":"Joshua","last_name":"Weitz","full_name":"Weitz, Joshua"},{"full_name":"Benfey, Philip","last_name":"Benfey","first_name":"Philip"}],"date_updated":"2021-01-12T06:59:58Z","date_created":"2018-12-11T11:59:47Z","volume":110,"publist_id":"3979","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4378147/"}],"external_id":{"pmid":["25673779"]},"oa":1,"quality_controlled":"1","doi":"10.1073/pnas.1304354110","language":[{"iso":"eng"}],"month":"04"},{"date_created":"2018-12-11T11:59:46Z","date_updated":"2021-01-12T06:59:57Z","volume":25,"author":[{"first_name":"Estelle","last_name":"Remy","full_name":"Remy, Estelle"},{"last_name":"Cabrito","first_name":"Tânia","full_name":"Cabrito, Tânia"},{"full_name":"Baster, Pawel","first_name":"Pawel","last_name":"Baster","id":"3028BD74-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Batista","first_name":"Rita","full_name":"Batista, Rita"},{"last_name":"Teixeira","first_name":"Miguel","full_name":"Teixeira, Miguel"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí","full_name":"Friml, Jirí"},{"last_name":"Sá Correia","first_name":"Isabel","full_name":"Sá Correia, Isabel"},{"last_name":"Duque","first_name":"Paula","full_name":"Duque, Paula"}],"publication_status":"published","publisher":"American Society of Plant Biologists","department":[{"_id":"JiFr"}],"year":"2013","pmid":1,"publist_id":"3980","language":[{"iso":"eng"}],"doi":"10.1105/tpc.113.110353","quality_controlled":"1","external_id":{"pmid":["23524662"]},"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3634696/","open_access":"1"}],"oa":1,"month":"04","oa_version":"Submitted Version","status":"public","title":"A major facilitator superfamily transporter plays a dual role in polar auxin transport and drought stress tolerance in Arabidopsis","intvolume":" 25","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2821","abstract":[{"lang":"eng","text":"Many key aspects of plant development are regulated by the polarized transport of the phytohormone auxin. Cellular auxin efflux, the rate-limiting step in this process, has been shown to rely on the coordinated action of PIN-formed (PIN) and B-type ATP binding cassette (ABCB) carriers. Here, we report that polar auxin transport in the Arabidopsis thaliana root also requires the action of a Major Facilitator Superfamily (MFS) transporter, Zinc-Induced Facilitator-Like 1 (ZIFL1). Sequencing, promoter-reporter, and fluorescent protein fusion experiments indicate that the full-length ZIFL1.1 protein and a truncated splice isoform, ZIFL1.3, localize to the tonoplast of root cells and the plasma membrane of leaf stomatal guard cells, respectively. Using reverse genetics, we show that the ZIFL1.1 transporter regulates various root auxin-related processes, while the ZIFL1.3 isoform mediates drought tolerance by regulating stomatal closure. Auxin transport and immunolocalization assays demonstrate that ZIFL1.1 indirectly modulates cellular auxin efflux during shootward auxin transport at the root tip, likely by regulating plasma membrane PIN2 abundance. Finally, heterologous expression in yeast revealed that ZIFL1.1 and ZIFL1.3 share H+-coupled K+ transport activity. Thus, by determining the subcellular and tissue distribution of two isoforms, alternative splicing dictates a dual function for the ZIFL1 transporter. We propose that this MFS carrier regulates stomatal movements and polar auxin transport by modulating potassium and proton fluxes in Arabidopsis cells."}],"issue":"3","type":"journal_article","date_published":"2013-04-24T00:00:00Z","page":"901 - 926","publication":"Plant Cell","citation":{"ama":"Remy E, Cabrito T, Baster P, et al. A major facilitator superfamily transporter plays a dual role in polar auxin transport and drought stress tolerance in Arabidopsis. Plant Cell. 2013;25(3):901-926. doi:10.1105/tpc.113.110353","apa":"Remy, E., Cabrito, T., Baster, P., Batista, R., Teixeira, M., Friml, J., … Duque, P. (2013). A major facilitator superfamily transporter plays a dual role in polar auxin transport and drought stress tolerance in Arabidopsis. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.113.110353","ieee":"E. Remy et al., “A major facilitator superfamily transporter plays a dual role in polar auxin transport and drought stress tolerance in Arabidopsis,” Plant Cell, vol. 25, no. 3. American Society of Plant Biologists, pp. 901–926, 2013.","ista":"Remy E, Cabrito T, Baster P, Batista R, Teixeira M, Friml J, Sá Correia I, Duque P. 2013. A major facilitator superfamily transporter plays a dual role in polar auxin transport and drought stress tolerance in Arabidopsis. Plant Cell. 25(3), 901–926.","short":"E. Remy, T. Cabrito, P. Baster, R. Batista, M. Teixeira, J. Friml, I. Sá Correia, P. Duque, Plant Cell 25 (2013) 901–926.","mla":"Remy, Estelle, et al. “A Major Facilitator Superfamily Transporter Plays a Dual Role in Polar Auxin Transport and Drought Stress Tolerance in Arabidopsis.” Plant Cell, vol. 25, no. 3, American Society of Plant Biologists, 2013, pp. 901–26, doi:10.1105/tpc.113.110353.","chicago":"Remy, Estelle, Tânia Cabrito, Pawel Baster, Rita Batista, Miguel Teixeira, Jiří Friml, Isabel Sá Correia, and Paula Duque. “A Major Facilitator Superfamily Transporter Plays a Dual Role in Polar Auxin Transport and Drought Stress Tolerance in Arabidopsis.” Plant Cell. American Society of Plant Biologists, 2013. https://doi.org/10.1105/tpc.113.110353."},"day":"24","scopus_import":1},{"publist_id":"3972","volume":110,"date_updated":"2021-01-12T06:59:59Z","date_created":"2018-12-11T11:59:48Z","author":[{"first_name":"Yunlong","last_name":"Du","full_name":"Du, Yunlong"},{"first_name":"Ricardo","last_name":"Tejos","full_name":"Tejos, Ricardo"},{"last_name":"Beck","first_name":"Martina","full_name":"Beck, Martina"},{"full_name":"Himschoot, Ellie","last_name":"Himschoot","first_name":"Ellie"},{"full_name":"Li, Hongjiang","last_name":"Li","first_name":"Hongjiang","orcid":"0000-0001-5039-9660","id":"33CA54A6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Silke","last_name":"Robatzek","full_name":"Robatzek, Silke"},{"first_name":"Steffen","last_name":"Vanneste","full_name":"Vanneste, Steffen"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml","full_name":"Friml, Jirí"}],"publisher":"National Academy of Sciences","department":[{"_id":"JiFr"}],"publication_status":"published","pmid":1,"year":"2013","month":"05","language":[{"iso":"eng"}],"doi":"10.1073/pnas.1220205110","project":[{"_id":"2574781E-B435-11E9-9278-68D0E5697425","name":"Koerber Prize 2010"}],"quality_controlled":"1","oa":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3651428/","open_access":"1"}],"external_id":{"pmid":["23613581"]},"issue":"19","abstract":[{"text":"Removal of cargos from the cell surface via endocytosis is an efficient mechanism to regulate activities of plasma membrane (PM)-resident proteins, such as receptors or transporters. Salicylic acid (SA) is an important plant hormone that is traditionally associated with pathogen defense. Here, we describe an unanticipated effect of SA on subcellular endocytic cycling of proteins. Both exogenous treatments and endogenously enhanced SA levels repressed endocytosis of different PM proteins. The SA effect on endocytosis did not involve transcription or known components of the SA signaling pathway for transcriptional regulation. SA likely targets an endocytic mechanism that involves the coat protein clathrin, because SA interfered with the clathrin incidence at the PM and clathrin-deficient mutants were less sensitive to the impact of SA on the auxin distribution and root bending during the gravitropic response. By contrast, SA did not affect the ligand-induced endocytosis of the FLAGELLIN SENSING2 (FLS2) receptor during pathogen responses. Our data suggest that the established SA impact on transcription in plant immunity and the nontranscriptional effect of SA on clathrin-mediated endocytosis are independent mechanisms by which SA regulates distinct aspects of plant physiology.","lang":"eng"}],"type":"journal_article","oa_version":"Submitted Version","intvolume":" 110","title":"Salicylic acid interferes with clathrin-mediated endocytic protein trafficking","status":"public","_id":"2827","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"07","scopus_import":1,"date_published":"2013-05-07T00:00:00Z","page":"7946 - 7951","citation":{"mla":"Du, Yunlong, et al. “Salicylic Acid Interferes with Clathrin-Mediated Endocytic Protein Trafficking.” PNAS, vol. 110, no. 19, National Academy of Sciences, 2013, pp. 7946–51, doi:10.1073/pnas.1220205110.","short":"Y. Du, R. Tejos, M. Beck, E. Himschoot, H. Li, S. Robatzek, S. Vanneste, J. Friml, PNAS 110 (2013) 7946–7951.","chicago":"Du, Yunlong, Ricardo Tejos, Martina Beck, Ellie Himschoot, Hongjiang Li, Silke Robatzek, Steffen Vanneste, and Jiří Friml. “Salicylic Acid Interferes with Clathrin-Mediated Endocytic Protein Trafficking.” PNAS. National Academy of Sciences, 2013. https://doi.org/10.1073/pnas.1220205110.","ama":"Du Y, Tejos R, Beck M, et al. Salicylic acid interferes with clathrin-mediated endocytic protein trafficking. PNAS. 2013;110(19):7946-7951. doi:10.1073/pnas.1220205110","ista":"Du Y, Tejos R, Beck M, Himschoot E, Li H, Robatzek S, Vanneste S, Friml J. 2013. Salicylic acid interferes with clathrin-mediated endocytic protein trafficking. PNAS. 110(19), 7946–7951.","ieee":"Y. Du et al., “Salicylic acid interferes with clathrin-mediated endocytic protein trafficking,” PNAS, vol. 110, no. 19. National Academy of Sciences, pp. 7946–7951, 2013.","apa":"Du, Y., Tejos, R., Beck, M., Himschoot, E., Li, H., Robatzek, S., … Friml, J. (2013). Salicylic acid interferes with clathrin-mediated endocytic protein trafficking. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1220205110"},"publication":"PNAS"},{"publist_id":"3978","issue":"3","abstract":[{"text":"The primary goal of restoration is to create self-sustaining ecological communities that are resilient to periodic disturbance. Currently, little is known about how restored communities respond to disturbance events such as fire and how this response compares to remnant vegetation. Following the 2003 fires in south-eastern Australia we examined the post-fire response of revegetation plantings and compared this to remnant vegetation. Ten burnt and 10 unburnt (control) sites were assessed for each of three types of vegetation (direct seeding revegetation, revegetation using nursery seedlings (tubestock) and remnant woodland). Sixty sampling sites were surveyed 6months after fire to quantify the initial survival of mid- and overstorey plant species in each type of vegetation. Three and 5years after fire all sites were resurveyed to assess vegetation structure, species diversity and vigour, as well as indicators of soil function. Overall, revegetation showed high (>60%) post-fire survival, but this varied among species depending on regeneration strategy (obligate seeder or resprouter). The native ground cover, mid- and overstorey in both types of plantings showed rapid recovery of vegetation structure and cover within 3years of fire. This recovery was similar to the burnt remnant woodlands. Non-native (exotic) ground cover initially increased after fire, but was no different in burnt and unburnt sites 5years after fire. Fire had no effect on species richness, but burnt direct seeding sites had reduced species diversity (Simpson's Diversity Index) while diversity was higher in burnt remnant woodlands. Indices of soil function in all types of vegetation had recovered to levels found in unburnt sites 5years after fire. These results indicate that even young revegetation (stands <10years old) showed substantial recovery from disturbance by fire. This suggests that revegetation can provide an important basis for restoring woodland communities in the fire-prone Australian environment.","lang":"eng"}],"type":"journal_article","volume":38,"oa_version":"None","date_updated":"2021-01-12T06:59:58Z","date_created":"2018-12-11T11:59:47Z","author":[{"id":"2C78037E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6118-0541","first_name":"Melinda","last_name":"Pickup","full_name":"Pickup, Melinda"},{"last_name":"Wilson","first_name":"Susie","full_name":"Wilson, Susie"},{"first_name":"David","last_name":"Freudenberger","full_name":"Freudenberger, David"},{"full_name":"Nicholls, Nick","first_name":"Nick","last_name":"Nicholls"},{"last_name":"Gould","first_name":"Lori","full_name":"Gould, Lori"},{"last_name":"Hnatiuk","first_name":"Sarah","full_name":"Hnatiuk, Sarah"},{"first_name":"Jeni","last_name":"Delandre","full_name":"Delandre, Jeni"}],"publisher":"Wiley-Blackwell","department":[{"_id":"NiBa"}],"intvolume":" 38","title":"Post-fire recovery of revegetated woodland communities in south-eastern Australia","publication_status":"published","status":"public","_id":"2823","year":"2013","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"05","day":"01","scopus_import":1,"language":[{"iso":"eng"}],"doi":"10.1111/j.1442-9993.2012.02404.x","date_published":"2013-05-01T00:00:00Z","page":"300 - 312","quality_controlled":"1","citation":{"ama":"Pickup M, Wilson S, Freudenberger D, et al. Post-fire recovery of revegetated woodland communities in south-eastern Australia. Austral Ecology. 2013;38(3):300-312. doi:10.1111/j.1442-9993.2012.02404.x","ista":"Pickup M, Wilson S, Freudenberger D, Nicholls N, Gould L, Hnatiuk S, Delandre J. 2013. Post-fire recovery of revegetated woodland communities in south-eastern Australia. Austral Ecology. 38(3), 300–312.","apa":"Pickup, M., Wilson, S., Freudenberger, D., Nicholls, N., Gould, L., Hnatiuk, S., & Delandre, J. (2013). Post-fire recovery of revegetated woodland communities in south-eastern Australia. Austral Ecology. Wiley-Blackwell. https://doi.org/10.1111/j.1442-9993.2012.02404.x","ieee":"M. Pickup et al., “Post-fire recovery of revegetated woodland communities in south-eastern Australia,” Austral Ecology, vol. 38, no. 3. Wiley-Blackwell, pp. 300–312, 2013.","mla":"Pickup, Melinda, et al. “Post-Fire Recovery of Revegetated Woodland Communities in South-Eastern Australia.” Austral Ecology, vol. 38, no. 3, Wiley-Blackwell, 2013, pp. 300–12, doi:10.1111/j.1442-9993.2012.02404.x.","short":"M. Pickup, S. Wilson, D. Freudenberger, N. Nicholls, L. Gould, S. Hnatiuk, J. Delandre, Austral Ecology 38 (2013) 300–312.","chicago":"Pickup, Melinda, Susie Wilson, David Freudenberger, Nick Nicholls, Lori Gould, Sarah Hnatiuk, and Jeni Delandre. “Post-Fire Recovery of Revegetated Woodland Communities in South-Eastern Australia.” Austral Ecology. Wiley-Blackwell, 2013. https://doi.org/10.1111/j.1442-9993.2012.02404.x."},"publication":"Austral Ecology"}]