[{"citation":{"ista":"Aichholzer O, Biedl T, Hackl T, Held M, Huber S, Palfrader P, Vogtenhuber B. 2015.Representing directed trees as straight skeletons. In: Graph Drawing and Network Visualization. LNCS, vol. 9411, 335–347.","chicago":"Aichholzer, Oswin, Therese Biedl, Thomas Hackl, Martin Held, Stefan Huber, Peter Palfrader, and Birgit Vogtenhuber. “Representing Directed Trees as Straight Skeletons.” In Graph Drawing and Network Visualization, 9411:335–47. Springer Nature, 2015. https://doi.org/10.1007/978-3-319-27261-0_28.","short":"O. Aichholzer, T. Biedl, T. Hackl, M. Held, S. Huber, P. Palfrader, B. Vogtenhuber, in:, Graph Drawing and Network Visualization, Springer Nature, 2015, pp. 335–347.","ieee":"O. Aichholzer et al., “Representing directed trees as straight skeletons,” in Graph Drawing and Network Visualization, vol. 9411, Springer Nature, 2015, pp. 335–347.","ama":"Aichholzer O, Biedl T, Hackl T, et al. Representing directed trees as straight skeletons. In: Graph Drawing and Network Visualization. Vol 9411. Springer Nature; 2015:335-347. doi:10.1007/978-3-319-27261-0_28","apa":"Aichholzer, O., Biedl, T., Hackl, T., Held, M., Huber, S., Palfrader, P., & Vogtenhuber, B. (2015). Representing directed trees as straight skeletons. In Graph Drawing and Network Visualization (Vol. 9411, pp. 335–347). Los Angeles, CA, United States: Springer Nature. https://doi.org/10.1007/978-3-319-27261-0_28","mla":"Aichholzer, Oswin, et al. “Representing Directed Trees as Straight Skeletons.” Graph Drawing and Network Visualization, vol. 9411, Springer Nature, 2015, pp. 335–47, doi:10.1007/978-3-319-27261-0_28."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","author":[{"first_name":"Oswin","last_name":"Aichholzer","full_name":"Aichholzer, Oswin"},{"last_name":"Biedl","full_name":"Biedl, Therese","first_name":"Therese"},{"last_name":"Hackl","full_name":"Hackl, Thomas","first_name":"Thomas"},{"full_name":"Held, Martin","last_name":"Held","first_name":"Martin"},{"id":"4700A070-F248-11E8-B48F-1D18A9856A87","first_name":"Stefan","full_name":"Huber, Stefan","orcid":"0000-0002-8871-5814","last_name":"Huber"},{"full_name":"Palfrader, Peter","last_name":"Palfrader","first_name":"Peter"},{"first_name":"Birgit","full_name":"Vogtenhuber, Birgit","last_name":"Vogtenhuber"}],"publist_id":"5581","title":"Representing directed trees as straight skeletons","oa":1,"publisher":"Springer Nature","quality_controlled":"1","year":"2015","publication":"Graph Drawing and Network Visualization","day":"27","page":"335 - 347","date_created":"2018-12-11T11:52:54Z","doi":"10.1007/978-3-319-27261-0_28","date_published":"2015-11-27T00:00:00Z","_id":"1590","conference":{"name":"GD: International Symposium on Graph Drawing","start_date":"2015-09-24","end_date":"2015-09-26","location":"Los Angeles, CA, United States"},"type":"book_chapter","status":"public","date_updated":"2022-01-28T09:10:37Z","department":[{"_id":"HeEd"}],"abstract":[{"text":"The straight skeleton of a polygon is the geometric graph obtained by tracing the vertices during a mitered offsetting process. It is known that the straight skeleton of a simple polygon is a tree, and one can naturally derive directions on the edges of the tree from the propagation of the shrinking process. In this paper, we ask the reverse question: Given a tree with directed edges, can it be the straight skeleton of a polygon? And if so, can we find a suitable simple polygon? We answer these questions for all directed trees where the order of edges around each node is fixed.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1508.01076"}],"alternative_title":["LNCS"],"scopus_import":"1","intvolume":" 9411","month":"11","publication_status":"published","publication_identifier":{"eisbn":["978-3-319-27261-0"],"isbn":["978-3-319-27260-3"]},"language":[{"iso":"eng"}],"volume":9411},{"acknowledgement":"This work is partly supported by the German Research Council (DFG) as part of the Transregional Collaborative Research Center AVACS (SFB/TR 14), by the Czech Science Foundation under grant agreement P202/12/G061, by the EU 7th Framework Programme under grant agreement no. 295261 (MEALS) and 318490 (SENSATION), by the CDZ project 1023 (CAP), by the CAS/SAFEA International Partnership Program for Creative Research Teams, by the EPSRC grant EP/M023656/1, by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007–2013) REA Grant No 291734, by the Austrian Science Fund (FWF) S11407-N23 (RiSE/SHiNE), and by the ERC Start Grant (279307: Graph Games).\r\n","publisher":"Springer","quality_controlled":"1","year":"2015","day":"22","page":"162 - 177","date_created":"2018-12-11T11:52:55Z","date_published":"2015-11-22T00:00:00Z","doi":"10.1007/978-3-662-48899-7_12","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"}],"citation":{"chicago":"Forejt, Vojtěch, Jan Krčál, and Jan Kretinsky. “Controller Synthesis for MDPs and Frequency LTL\\GU,” 9450:162–77. Springer, 2015. https://doi.org/10.1007/978-3-662-48899-7_12.","ista":"Forejt V, Krčál J, Kretinsky J. 2015. Controller synthesis for MDPs and frequency LTL\\GU. LPAR: Logic for Programming, Artificial Intelligence, and Reasoning, LNCS, vol. 9450, 162–177.","mla":"Forejt, Vojtěch, et al. Controller Synthesis for MDPs and Frequency LTL\\GU. Vol. 9450, Springer, 2015, pp. 162–77, doi:10.1007/978-3-662-48899-7_12.","ieee":"V. Forejt, J. Krčál, and J. Kretinsky, “Controller synthesis for MDPs and frequency LTL\\GU,” presented at the LPAR: Logic for Programming, Artificial Intelligence, and Reasoning, Suva, Fiji, 2015, vol. 9450, pp. 162–177.","short":"V. Forejt, J. Krčál, J. Kretinsky, in:, Springer, 2015, pp. 162–177.","ama":"Forejt V, Krčál J, Kretinsky J. Controller synthesis for MDPs and frequency LTL\\GU. In: Vol 9450. Springer; 2015:162-177. doi:10.1007/978-3-662-48899-7_12","apa":"Forejt, V., Krčál, J., & Kretinsky, J. (2015). Controller synthesis for MDPs and frequency LTL\\GU (Vol. 9450, pp. 162–177). Presented at the LPAR: Logic for Programming, Artificial Intelligence, and Reasoning, Suva, Fiji: Springer. https://doi.org/10.1007/978-3-662-48899-7_12"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Vojtěch","last_name":"Forejt","full_name":"Forejt, Vojtěch"},{"full_name":"Krčál, Jan","last_name":"Krčál","first_name":"Jan"},{"first_name":"Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","last_name":"Kretinsky","full_name":"Kretinsky, Jan","orcid":"0000-0002-8122-2881"}],"publist_id":"5577","title":"Controller synthesis for MDPs and frequency LTL\\GU","abstract":[{"lang":"eng","text":"Quantitative extensions of temporal logics have recently attracted significant attention. In this work, we study frequency LTL (fLTL), an extension of LTL which allows to speak about frequencies of events along an execution. Such an extension is particularly useful for probabilistic systems that often cannot fulfil strict qualitative guarantees on the behaviour. It has been recently shown that controller synthesis for Markov decision processes and fLTL is decidable when all the bounds on frequencies are 1. As a step towards a complete quantitative solution, we show that the problem is decidable for the fragment fLTL\\GU, where U does not occur in the scope of G (but still F can). Our solution is based on a novel translation of such quantitative formulae into equivalent deterministic automata."}],"oa_version":"None","alternative_title":["LNCS"],"scopus_import":1,"intvolume":" 9450","month":"11","publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"volume":9450,"_id":"1594","conference":{"start_date":"2015-11-24","location":"Suva, Fiji","end_date":"2015-11-28","name":"LPAR: Logic for Programming, Artificial Intelligence, and Reasoning"},"type":"conference","status":"public","date_updated":"2021-01-12T06:51:50Z","department":[{"_id":"ToHe"},{"_id":"KrCh"}]},{"date_updated":"2022-01-28T09:20:50Z","ddc":["510"],"file_date_updated":"2020-07-14T12:45:04Z","department":[{"_id":"UlWa"}],"_id":"1596","type":"book_chapter","conference":{"name":"GD: Graph Drawing and Network Visualization","start_date":"2015-09-24","end_date":"2015-09-26","location":"Los Angeles, CA, United States"},"status":"public","pubrep_id":"595","publication_identifier":{"isbn":["978-3-319-27260-3"]},"publication_status":"published","file":[{"file_id":"5258","checksum":"eec04f86c5921d04f025d5791db9b965","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:17:06Z","file_name":"IST-2016-595-v1+1_VerticalVisibilityGDRevision.pdf","date_updated":"2020-07-14T12:45:04Z","file_size":312992,"creator":"system"}],"language":[{"iso":"eng"}],"volume":9411,"ec_funded":1,"abstract":[{"lang":"eng","text":"Let C={C1,...,Cn} denote a collection of translates of a regular convex k-gon in the plane with the stacking order. The collection C forms a visibility clique if for everyi < j the intersection Ci and (Ci ∩ Cj)\\⋃i<l<jCl =∅.elements that are stacked between them, i.e., We show that if C forms a visibility clique its size is bounded from above by O(k4) thereby improving the upper bound of 22k from the aforementioned paper. We also obtain an upper bound of 22(k/2)+2 on the size of a visibility clique for homothetes of a convex (not necessarily regular) k-gon."}],"oa_version":"Submitted Version","alternative_title":["LNCS"],"scopus_import":"1","month":"11","intvolume":" 9411","citation":{"apa":"Fulek, R., & Radoičić, R. (2015). Vertical visibility among parallel polygons in three dimensions. In Graph Drawing and Network Visualization (Vol. 9411, pp. 373–379). Los Angeles, CA, United States: Springer Nature. https://doi.org/10.1007/978-3-319-27261-0_31","ama":"Fulek R, Radoičić R. Vertical visibility among parallel polygons in three dimensions. In: Graph Drawing and Network Visualization. Vol 9411. Springer Nature; 2015:373-379. doi:10.1007/978-3-319-27261-0_31","ieee":"R. Fulek and R. Radoičić, “Vertical visibility among parallel polygons in three dimensions,” in Graph Drawing and Network Visualization, vol. 9411, Springer Nature, 2015, pp. 373–379.","short":"R. Fulek, R. Radoičić, in:, Graph Drawing and Network Visualization, Springer Nature, 2015, pp. 373–379.","mla":"Fulek, Radoslav, and Radoš Radoičić. “Vertical Visibility among Parallel Polygons in Three Dimensions.” Graph Drawing and Network Visualization, vol. 9411, Springer Nature, 2015, pp. 373–79, doi:10.1007/978-3-319-27261-0_31.","ista":"Fulek R, Radoičić R. 2015.Vertical visibility among parallel polygons in three dimensions. In: Graph Drawing and Network Visualization. LNCS, vol. 9411, 373–379.","chicago":"Fulek, Radoslav, and Radoš Radoičić. “Vertical Visibility among Parallel Polygons in Three Dimensions.” In Graph Drawing and Network Visualization, 9411:373–79. Springer Nature, 2015. https://doi.org/10.1007/978-3-319-27261-0_31."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publist_id":"5575","author":[{"full_name":"Fulek, Radoslav","orcid":"0000-0001-8485-1774","last_name":"Fulek","first_name":"Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Radoš","full_name":"Radoičić, Radoš","last_name":"Radoičić"}],"article_processing_charge":"No","title":"Vertical visibility among parallel polygons in three dimensions","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"has_accepted_license":"1","year":"2015","day":"27","publication":"Graph Drawing and Network Visualization","page":"373 - 379","doi":"10.1007/978-3-319-27261-0_31","date_published":"2015-11-27T00:00:00Z","date_created":"2018-12-11T11:52:56Z","publisher":"Springer Nature","quality_controlled":"1","oa":1},{"status":"public","type":"conference","conference":{"start_date":"2015-07-18","end_date":"2015-07-24","location":"San Francisco, CA, United States","name":"CAV: Computer Aided Verification"},"_id":"1601","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:45:04Z","ddc":["000"],"date_updated":"2021-01-12T06:51:54Z","month":"07","intvolume":" 9206","scopus_import":1,"alternative_title":["LNCS"],"oa_version":"Submitted Version","abstract":[{"text":"We propose a flexible exchange format for ω-automata, as typically used in formal verification, and implement support for it in a range of established tools. Our aim is to simplify the interaction of tools, helping the research community to build upon other people’s work. A key feature of the format is the use of very generic acceptance conditions, specified by Boolean combinations of acceptance primitives, rather than being limited to common cases such as Büchi, Streett, or Rabin. Such flexibility in the choice of acceptance conditions can be exploited in applications, for example in probabilistic model checking, and furthermore encourages the development of acceptance-agnostic tools for automata manipulations. The format allows acceptance conditions that are either state-based or transition-based, and also supports alternating automata.","lang":"eng"}],"volume":9206,"ec_funded":1,"file":[{"file_name":"2015_CAV_Babiak.pdf","date_created":"2020-05-15T08:38:12Z","file_size":1651779,"date_updated":"2020-07-14T12:45:04Z","creator":"dernst","file_id":"7850","checksum":"5885236fa88a439baba9ac6f3e801e93","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"publication_status":"published","project":[{"name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"The Wittgenstein Prize","grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"}],"title":"The Hanoi omega-automata format","author":[{"last_name":"Babiak","full_name":"Babiak, Tomáš","first_name":"Tomáš"},{"last_name":"Blahoudek","full_name":"Blahoudek, František","first_name":"František"},{"last_name":"Duret Lutz","full_name":"Duret Lutz, Alexandre","first_name":"Alexandre"},{"full_name":"Klein, Joachim","last_name":"Klein","first_name":"Joachim"},{"id":"44CEF464-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","orcid":"0000-0002-8122-2881","full_name":"Kretinsky, Jan","last_name":"Kretinsky"},{"last_name":"Mueller","full_name":"Mueller, Daniel","first_name":"Daniel"},{"full_name":"Parker, David","last_name":"Parker","first_name":"David"},{"first_name":"Jan","last_name":"Strejček","full_name":"Strejček, Jan"}],"publist_id":"5566","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Babiak, T., Blahoudek, F., Duret Lutz, A., Klein, J., Kretinsky, J., Mueller, D., … Strejček, J. (2015). The Hanoi omega-automata format (Vol. 9206, pp. 479–486). Presented at the CAV: Computer Aided Verification, San Francisco, CA, United States: Springer. https://doi.org/10.1007/978-3-319-21690-4_31","ama":"Babiak T, Blahoudek F, Duret Lutz A, et al. The Hanoi omega-automata format. In: Vol 9206. Springer; 2015:479-486. doi:10.1007/978-3-319-21690-4_31","ieee":"T. Babiak et al., “The Hanoi omega-automata format,” presented at the CAV: Computer Aided Verification, San Francisco, CA, United States, 2015, vol. 9206, pp. 479–486.","short":"T. Babiak, F. Blahoudek, A. Duret Lutz, J. Klein, J. Kretinsky, D. Mueller, D. Parker, J. Strejček, in:, Springer, 2015, pp. 479–486.","mla":"Babiak, Tomáš, et al. The Hanoi Omega-Automata Format. Vol. 9206, Springer, 2015, pp. 479–86, doi:10.1007/978-3-319-21690-4_31.","ista":"Babiak T, Blahoudek F, Duret Lutz A, Klein J, Kretinsky J, Mueller D, Parker D, Strejček J. 2015. The Hanoi omega-automata format. CAV: Computer Aided Verification, LNCS, vol. 9206, 479–486.","chicago":"Babiak, Tomáš, František Blahoudek, Alexandre Duret Lutz, Joachim Klein, Jan Kretinsky, Daniel Mueller, David Parker, and Jan Strejček. “The Hanoi Omega-Automata Format,” 9206:479–86. Springer, 2015. https://doi.org/10.1007/978-3-319-21690-4_31."},"publisher":"Springer","quality_controlled":"1","oa":1,"date_published":"2015-07-16T00:00:00Z","doi":"10.1007/978-3-319-21690-4_31","date_created":"2018-12-11T11:52:57Z","page":"479 - 486","day":"16","has_accepted_license":"1","year":"2015"},{"project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"267989","name":"Quantitative Reactive Modeling"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z211","name":"The Wittgenstein Prize"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"citation":{"ista":"Bogomolov S, Schilling C, Bartocci E, Batt G, Kong H, Grosu R. 2015. Abstraction-based parameter synthesis for multiaffine systems. HVC: Haifa Verification Conference, LNCS, vol. 9434, 19–35.","chicago":"Bogomolov, Sergiy, Christian Schilling, Ezio Bartocci, Grégory Batt, Hui Kong, and Radu Grosu. “Abstraction-Based Parameter Synthesis for Multiaffine Systems,” 9434:19–35. Springer, 2015. https://doi.org/10.1007/978-3-319-26287-1_2.","apa":"Bogomolov, S., Schilling, C., Bartocci, E., Batt, G., Kong, H., & Grosu, R. (2015). Abstraction-based parameter synthesis for multiaffine systems (Vol. 9434, pp. 19–35). Presented at the HVC: Haifa Verification Conference, Haifa, Israel: Springer. https://doi.org/10.1007/978-3-319-26287-1_2","ama":"Bogomolov S, Schilling C, Bartocci E, Batt G, Kong H, Grosu R. Abstraction-based parameter synthesis for multiaffine systems. In: Vol 9434. Springer; 2015:19-35. doi:10.1007/978-3-319-26287-1_2","ieee":"S. Bogomolov, C. Schilling, E. Bartocci, G. Batt, H. Kong, and R. Grosu, “Abstraction-based parameter synthesis for multiaffine systems,” presented at the HVC: Haifa Verification Conference, Haifa, Israel, 2015, vol. 9434, pp. 19–35.","short":"S. Bogomolov, C. Schilling, E. Bartocci, G. Batt, H. Kong, R. Grosu, in:, Springer, 2015, pp. 19–35.","mla":"Bogomolov, Sergiy, et al. Abstraction-Based Parameter Synthesis for Multiaffine Systems. Vol. 9434, Springer, 2015, pp. 19–35, doi:10.1007/978-3-319-26287-1_2."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","publist_id":"5561","author":[{"id":"369D9A44-F248-11E8-B48F-1D18A9856A87","first_name":"Sergiy","last_name":"Bogomolov","orcid":"0000-0002-0686-0365","full_name":"Bogomolov, Sergiy"},{"orcid":"0000-0003-3658-1065","full_name":"Schilling, Christian","last_name":"Schilling","first_name":"Christian","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ezio","last_name":"Bartocci","full_name":"Bartocci, Ezio"},{"first_name":"Grégory","full_name":"Batt, Grégory","last_name":"Batt"},{"orcid":"0000-0002-3066-6941","full_name":"Kong, Hui","last_name":"Kong","id":"3BDE25AA-F248-11E8-B48F-1D18A9856A87","first_name":"Hui"},{"first_name":"Radu","last_name":"Grosu","full_name":"Grosu, Radu"}],"title":"Abstraction-based parameter synthesis for multiaffine systems","acknowledgement":"This work was partly supported by the European Research Council (ERC) under grant 267989 (QUAREM), by the Austrian Science Fund (FWF) under grants S11402-N23, S11405-N23 and S11412-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award), and by the German Research Foundation (DFG) as part of the Transregional Collaborative Research Center “Automatic Verification and Analysis of Complex Systems” (SFB/TR 14 AVACS, http://www.avacs.org/).","oa":1,"publisher":"Springer","quality_controlled":"1","year":"2015","has_accepted_license":"1","day":"28","page":"19 - 35","date_created":"2018-12-11T11:52:59Z","date_published":"2015-11-28T00:00:00Z","doi":"10.1007/978-3-319-26287-1_2","_id":"1605","conference":{"name":"HVC: Haifa Verification Conference","end_date":"2015-11-19","location":"Haifa, Israel","start_date":"2015-11-17"},"type":"conference","status":"public","date_updated":"2021-01-12T06:51:56Z","ddc":["000"],"file_date_updated":"2020-07-14T12:45:05Z","department":[{"_id":"ToHe"}],"abstract":[{"lang":"eng","text":"Multiaffine hybrid automata (MHA) represent a powerful formalism to model complex dynamical systems. This formalism is particularly suited for the representation of biological systems which often exhibit highly non-linear behavior. In this paper, we consider the problem of parameter identification for MHA. We present an abstraction of MHA based on linear hybrid automata, which can be analyzed by the SpaceEx model checker. This abstraction enables a precise handling of time-dependent properties. We demonstrate the potential of our approach on a model of a genetic regulatory network and a myocyte model."}],"oa_version":"Submitted Version","alternative_title":["LNCS"],"scopus_import":1,"intvolume":" 9434","month":"11","publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_size":1053207,"date_updated":"2020-07-14T12:45:05Z","creator":"dernst","file_name":"2015_LNCS_Bogomolov.pdf","date_created":"2020-05-15T08:43:19Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"7851","checksum":"3aab260f3f34641d622030ba22645b3e"}],"ec_funded":1,"volume":9434},{"year":"2015","day":"15","publication":"6th International Conference","page":"281 - 286","date_published":"2015-11-15T00:00:00Z","doi":"10.1007/978-3-319-23820-3_19","date_created":"2018-12-11T11:52:59Z","quality_controlled":"1","publisher":"Springer Nature","citation":{"chicago":"Nguyen, Luan, Christian Schilling, Sergiy Bogomolov, and Taylor Johnson. “Runtime Verification for Hybrid Analysis Tools.” In 6th International Conference, 9333:281–86. Springer Nature, 2015. https://doi.org/10.1007/978-3-319-23820-3_19.","ista":"Nguyen L, Schilling C, Bogomolov S, Johnson T. 2015. Runtime verification for hybrid analysis tools. 6th International Conference. RV: Runtime Verification, LNCS, vol. 9333, 281–286.","mla":"Nguyen, Luan, et al. “Runtime Verification for Hybrid Analysis Tools.” 6th International Conference, vol. 9333, Springer Nature, 2015, pp. 281–86, doi:10.1007/978-3-319-23820-3_19.","ieee":"L. Nguyen, C. Schilling, S. Bogomolov, and T. Johnson, “Runtime verification for hybrid analysis tools,” in 6th International Conference, Vienna, Austria, 2015, vol. 9333, pp. 281–286.","short":"L. Nguyen, C. Schilling, S. Bogomolov, T. Johnson, in:, 6th International Conference, Springer Nature, 2015, pp. 281–286.","ama":"Nguyen L, Schilling C, Bogomolov S, Johnson T. Runtime verification for hybrid analysis tools. In: 6th International Conference. Vol 9333. Springer Nature; 2015:281-286. doi:10.1007/978-3-319-23820-3_19","apa":"Nguyen, L., Schilling, C., Bogomolov, S., & Johnson, T. (2015). Runtime verification for hybrid analysis tools. In 6th International Conference (Vol. 9333, pp. 281–286). Vienna, Austria: Springer Nature. https://doi.org/10.1007/978-3-319-23820-3_19"},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publist_id":"5562","author":[{"first_name":"Luan","full_name":"Nguyen, Luan","last_name":"Nguyen"},{"first_name":"Christian","full_name":"Schilling, Christian","last_name":"Schilling"},{"last_name":"Bogomolov","orcid":"0000-0002-0686-0365","full_name":"Bogomolov, Sergiy","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","first_name":"Sergiy"},{"full_name":"Johnson, Taylor","last_name":"Johnson","first_name":"Taylor"}],"article_processing_charge":"No","title":"Runtime verification for hybrid analysis tools","project":[{"name":"Quantitative Reactive Modeling","grant_number":"267989","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z211"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"}],"publication_identifier":{"isbn":["978-3-319-23819-7"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":9333,"ec_funded":1,"abstract":[{"text":"In this paper, we present the first steps toward a runtime verification framework for monitoring hybrid and cyber-physical systems (CPS) development tools based on randomized differential testing. The development tools include hybrid systems reachability analysis tools, model-based development environments like Simulink/Stateflow (SLSF), etc. First, hybrid automaton models are randomly generated. Next, these hybrid automaton models are translated to a number of different tools (currently, SpaceEx, dReach, Flow*, HyCreate, and the MathWorks’ Simulink/Stateflow) using the HyST source transformation and translation tool. Then, the hybrid automaton models are executed in the different tools and their outputs are parsed. The final step is the differential comparison: the outputs of the different tools are compared. If the results do not agree (in the sense that an analysis or verification result from one tool does not match that of another tool, ignoring timeouts, etc.), a candidate bug is flagged and the model is saved for future analysis by the user. The process then repeats and the monitoring continues until the user terminates the process. We present preliminary results that have been useful in identifying a few bugs in the analysis methods of different development tools, and in an earlier version of HyST.","lang":"eng"}],"oa_version":"None","scopus_import":"1","alternative_title":["LNCS"],"month":"11","intvolume":" 9333","date_updated":"2022-02-01T14:52:59Z","department":[{"_id":"ToHe"}],"_id":"1606","type":"conference","conference":{"name":"RV: Runtime Verification","start_date":"2015-09-22","end_date":"2015-09-25","location":"Vienna, Austria"},"status":"public"},{"project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Game Theory","grant_number":"S11407"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"mla":"Chatterjee, Krishnendu, et al. “The Complexity of Synthesis from Probabilistic Components.” 42nd International Colloquium, vol. 9135, Springer Nature, 2015, pp. 108–20, doi:10.1007/978-3-662-47666-6_9.","ama":"Chatterjee K, Doyen L, Vardi M. The complexity of synthesis from probabilistic components. In: 42nd International Colloquium. Vol 9135. Springer Nature; 2015:108-120. doi:10.1007/978-3-662-47666-6_9","apa":"Chatterjee, K., Doyen, L., & Vardi, M. (2015). The complexity of synthesis from probabilistic components. In 42nd International Colloquium (Vol. 9135, pp. 108–120). Kyoto, Japan: Springer Nature. https://doi.org/10.1007/978-3-662-47666-6_9","ieee":"K. Chatterjee, L. Doyen, and M. Vardi, “The complexity of synthesis from probabilistic components,” in 42nd International Colloquium, Kyoto, Japan, 2015, vol. 9135, pp. 108–120.","short":"K. Chatterjee, L. Doyen, M. Vardi, in:, 42nd International Colloquium, Springer Nature, 2015, pp. 108–120.","chicago":"Chatterjee, Krishnendu, Laurent Doyen, and Moshe Vardi. “The Complexity of Synthesis from Probabilistic Components.” In 42nd International Colloquium, 9135:108–20. Springer Nature, 2015. https://doi.org/10.1007/978-3-662-47666-6_9.","ista":"Chatterjee K, Doyen L, Vardi M. 2015. The complexity of synthesis from probabilistic components. 42nd International Colloquium. ICALP: Automata, Languages and Programming, LNCS, vol. 9135, 108–120."},"title":"The complexity of synthesis from probabilistic components","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"full_name":"Doyen, Laurent","last_name":"Doyen","first_name":"Laurent"},{"first_name":"Moshe","full_name":"Vardi, Moshe","last_name":"Vardi"}],"publist_id":"5557","article_processing_charge":"No","acknowledgement":"This research was supported by Austrian Science Fund (FWF) Grant No P23499- N23, FWF NFN Grant No S11407-N23 (SHiNE), ERC Start grant (279307: Graph Games), EU FP7 Project Cassting, NSF grants CNS 1049862 and CCF-1139011, by NSF Expeditions in Computing project “ExCAPE: Expeditions in Computer Augmented Program Engineering”, by BSF grant 9800096, and by gift from Intel.","publisher":"Springer Nature","quality_controlled":"1","oa":1,"day":"20","publication":"42nd International Colloquium","year":"2015","date_published":"2015-06-20T00:00:00Z","doi":"10.1007/978-3-662-47666-6_9","date_created":"2018-12-11T11:53:00Z","page":"108 - 120","_id":"1609","status":"public","type":"conference","conference":{"name":"ICALP: Automata, Languages and Programming","location":"Kyoto, Japan","end_date":"2015-07-10","start_date":"2015-07-06"},"date_updated":"2022-02-01T15:04:44Z","department":[{"_id":"KrCh"}],"oa_version":"Preprint","abstract":[{"text":"The synthesis problem asks for the automatic construction of a system from its specification. In the traditional setting, the system is “constructed from scratch” rather than composed from reusable components. However, this is rare in practice, and almost every non-trivial software system relies heavily on the use of libraries of reusable components. Recently, Lustig and Vardi introduced dataflow and controlflow synthesis from libraries of reusable components. They proved that dataflow synthesis is undecidable, while controlflow synthesis is decidable. The problem of controlflow synthesis from libraries of probabilistic components was considered by Nain, Lustig and Vardi, and was shown to be decidable for qualitative analysis (that asks that the specification be satisfied with probability 1). Our main contribution for controlflow synthesis from probabilistic components is to establish better complexity bounds for the qualitative analysis problem, and to show that the more general quantitative problem is undecidable. For the qualitative analysis, we show that the problem (i) is EXPTIME-complete when the specification is given as a deterministic parity word automaton, improving the previously known 2EXPTIME upper bound; and (ii) belongs to UP ∩ coUP and is parity-games hard, when the specification is given directly as a parity condition on the components, improving the previously known EXPTIME upper bound.","lang":"eng"}],"month":"06","intvolume":" 9135","alternative_title":["LNCS"],"scopus_import":"1","main_file_link":[{"url":"http://arxiv.org/abs/1502.04844","open_access":"1"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-3-662-47665-9"]},"publication_status":"published","volume":9135,"ec_funded":1},{"title":"Perturbed hippocampal synaptic inhibition and γ-oscillations in a neuroligin-4 knockout mouse model of autism","publist_id":"5551","author":[{"first_name":"Matthieu","full_name":"Hammer, Matthieu","last_name":"Hammer"},{"first_name":"Dilja","last_name":"Krueger Burg","full_name":"Krueger Burg, Dilja"},{"first_name":"Liam","full_name":"Tuffy, Liam","last_name":"Tuffy"},{"first_name":"Benjamin","full_name":"Cooper, Benjamin","last_name":"Cooper"},{"first_name":"Holger","last_name":"Taschenberger","full_name":"Taschenberger, Holger"},{"id":"3A578F32-F248-11E8-B48F-1D18A9856A87","first_name":"Sarit","full_name":"Goswami, Sarit","last_name":"Goswami"},{"last_name":"Ehrenreich","full_name":"Ehrenreich, Hannelore","first_name":"Hannelore"},{"first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","last_name":"Jonas"},{"last_name":"Varoqueaux","full_name":"Varoqueaux, Frederique","first_name":"Frederique"},{"full_name":"Rhee, Jeong","last_name":"Rhee","first_name":"Jeong"},{"last_name":"Brose","full_name":"Brose, Nils","first_name":"Nils"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"M. Hammer et al., “Perturbed hippocampal synaptic inhibition and γ-oscillations in a neuroligin-4 knockout mouse model of autism,” Cell Reports, vol. 13, no. 3. Cell Press, pp. 516–523, 2015.","short":"M. Hammer, D. Krueger Burg, L. Tuffy, B. Cooper, H. Taschenberger, S. Goswami, H. Ehrenreich, P.M. Jonas, F. Varoqueaux, J. Rhee, N. Brose, Cell Reports 13 (2015) 516–523.","ama":"Hammer M, Krueger Burg D, Tuffy L, et al. Perturbed hippocampal synaptic inhibition and γ-oscillations in a neuroligin-4 knockout mouse model of autism. Cell Reports. 2015;13(3):516-523. doi:10.1016/j.celrep.2015.09.011","apa":"Hammer, M., Krueger Burg, D., Tuffy, L., Cooper, B., Taschenberger, H., Goswami, S., … Brose, N. (2015). Perturbed hippocampal synaptic inhibition and γ-oscillations in a neuroligin-4 knockout mouse model of autism. Cell Reports. Cell Press. https://doi.org/10.1016/j.celrep.2015.09.011","mla":"Hammer, Matthieu, et al. “Perturbed Hippocampal Synaptic Inhibition and γ-Oscillations in a Neuroligin-4 Knockout Mouse Model of Autism.” Cell Reports, vol. 13, no. 3, Cell Press, 2015, pp. 516–23, doi:10.1016/j.celrep.2015.09.011.","ista":"Hammer M, Krueger Burg D, Tuffy L, Cooper B, Taschenberger H, Goswami S, Ehrenreich H, Jonas PM, Varoqueaux F, Rhee J, Brose N. 2015. Perturbed hippocampal synaptic inhibition and γ-oscillations in a neuroligin-4 knockout mouse model of autism. Cell Reports. 13(3), 516–523.","chicago":"Hammer, Matthieu, Dilja Krueger Burg, Liam Tuffy, Benjamin Cooper, Holger Taschenberger, Sarit Goswami, Hannelore Ehrenreich, et al. “Perturbed Hippocampal Synaptic Inhibition and γ-Oscillations in a Neuroligin-4 Knockout Mouse Model of Autism.” Cell Reports. Cell Press, 2015. https://doi.org/10.1016/j.celrep.2015.09.011."},"oa":1,"publisher":"Cell Press","quality_controlled":"1","acknowledgement":"This work was supported by the Max Planck Society (N.B. and H.E.), the European Commission (EU-AIMS FP7-115300, N.B. and H.E.; Marie Curie IRG, D.K.-B.), the German Research Foundation (CNMPB, N.B., H.E., and F.V.), the Alexander von Humboldt-Foundation (D.K.-B.), and the Austrian Fond zur Förderung der Wissenschaftlichen Forschung (P 24909-B24, P.J.). M.H. was a student of the doctoral program Molecular Physiology of the Brain. Dr. J.-M. Fritschy generously provided the GABAARγ2 antibody. We thank F. Benseler, I. Thanhäuser, D. Schwerdtfeger, A. Ronnenberg, and D. Winkler for valuable advice and excellent technical support. We are grateful to the staff at the animal facility of the Max Planck Institute of Experimental Medicine for mouse husbandry.","date_created":"2018-12-11T11:53:02Z","date_published":"2015-10-20T00:00:00Z","doi":"10.1016/j.celrep.2015.09.011","page":"516 - 523","publication":"Cell Reports","day":"20","year":"2015","has_accepted_license":"1","pubrep_id":"470","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"1615","file_date_updated":"2020-07-14T12:45:07Z","department":[{"_id":"PeJo"}],"ddc":["570"],"date_updated":"2021-01-12T06:52:01Z","intvolume":" 13","month":"10","scopus_import":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Loss-of-function mutations in the synaptic adhesion protein Neuroligin-4 are among the most common genetic abnormalities associated with autism spectrum disorders, but little is known about the function of Neuroligin-4 and the consequences of its loss. We assessed synaptic and network characteristics in Neuroligin-4 knockout mice, focusing on the hippocampus as a model brain region with a critical role in cognition and memory, and found that Neuroligin-4 deletion causes subtle defects of the protein composition and function of GABAergic synapses in the hippocampal CA3 region. Interestingly, these subtle synaptic changes are accompanied by pronounced perturbations of γ-oscillatory network activity, which has been implicated in cognitive function and is altered in multiple psychiatric and neurodevelopmental disorders. Our data provide important insights into the mechanisms by which Neuroligin-4-dependent GABAergic synapses may contribute to autism phenotypes and indicate new strategies for therapeutic approaches."}],"issue":"3","volume":13,"language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"5005","checksum":"44d30fbb543774b076b4938bd36af9d7","creator":"system","file_size":2314406,"date_updated":"2020-07-14T12:45:07Z","file_name":"IST-2016-470-v1+1_1-s2.0-S2211124715010220-main.pdf","date_created":"2018-12-12T10:13:23Z"}],"publication_status":"published"},{"abstract":[{"text":"GABAergic perisoma-inhibiting fast-spiking interneurons (PIIs) effectively control the activity of large neuron populations by their wide axonal arborizations. It is generally assumed that the output of one PII to its target cells is strong and rapid. Here, we show that, unexpectedly, both strength and time course of PII-mediated perisomatic inhibition change with distance between synaptically connected partners in the rodent hippocampus. Synaptic signals become weaker due to lower contact numbers and decay more slowly with distance, very likely resulting from changes in GABAA receptor subunit composition. When distance-dependent synaptic inhibition is introduced to a rhythmically active neuronal network model, randomly driven principal cell assemblies are strongly synchronized by the PIIs, leading to higher precision in principal cell spike times than in a network with uniform synaptic inhibition. ","lang":"eng"}],"pmid":1,"oa_version":"Published Version","scopus_import":1,"intvolume":" 112","month":"01","publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_id":"5838","checksum":"6703309a1f58493cf5a704211fb6ebed","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2019-01-17T07:52:40Z","file_name":"2015_PNAS_Strueber.pdf","date_updated":"2020-07-14T12:45:07Z","file_size":1280860,"creator":"dernst"}],"ec_funded":1,"issue":"4","volume":112,"_id":"1614","type":"journal_article","status":"public","date_updated":"2021-01-12T06:52:01Z","ddc":["570"],"department":[{"_id":"PeJo"}],"file_date_updated":"2020-07-14T12:45:07Z","oa":1,"publisher":"National Academy of Sciences","quality_controlled":"1","year":"2015","has_accepted_license":"1","publication":"PNAS","day":"27","page":"1220 - 1225","date_created":"2018-12-11T11:53:02Z","doi":"10.1073/pnas.1412996112","date_published":"2015-01-27T00:00:00Z","project":[{"_id":"25C26B1E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Mechanisms of transmitter release at GABAergic synapses","grant_number":"P24909-B24"},{"_id":"25C0F108-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"268548","name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons"}],"citation":{"ista":"Strüber M, Jonas PM, Bartos M. 2015. Strength and duration of perisomatic GABAergic inhibition depend on distance between synaptically connected cells. PNAS. 112(4), 1220–1225.","chicago":"Strüber, Michael, Peter M Jonas, and Marlene Bartos. “Strength and Duration of Perisomatic GABAergic Inhibition Depend on Distance between Synaptically Connected Cells.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1412996112.","apa":"Strüber, M., Jonas, P. M., & Bartos, M. (2015). Strength and duration of perisomatic GABAergic inhibition depend on distance between synaptically connected cells. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1412996112","ama":"Strüber M, Jonas PM, Bartos M. Strength and duration of perisomatic GABAergic inhibition depend on distance between synaptically connected cells. PNAS. 2015;112(4):1220-1225. doi:10.1073/pnas.1412996112","short":"M. Strüber, P.M. Jonas, M. Bartos, PNAS 112 (2015) 1220–1225.","ieee":"M. Strüber, P. M. Jonas, and M. Bartos, “Strength and duration of perisomatic GABAergic inhibition depend on distance between synaptically connected cells,” PNAS, vol. 112, no. 4. National Academy of Sciences, pp. 1220–1225, 2015.","mla":"Strüber, Michael, et al. “Strength and Duration of Perisomatic GABAergic Inhibition Depend on Distance between Synaptically Connected Cells.” PNAS, vol. 112, no. 4, National Academy of Sciences, 2015, pp. 1220–25, doi:10.1073/pnas.1412996112."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["25583495"]},"publist_id":"5552","author":[{"first_name":"Michael","last_name":"Strüber","full_name":"Strüber, Michael"},{"full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M"},{"full_name":"Bartos, Marlene","last_name":"Bartos","first_name":"Marlene"}],"title":"Strength and duration of perisomatic GABAergic inhibition depend on distance between synaptically connected cells"},{"project":[{"_id":"255BFFFA-B435-11E9-9278-68D0E5697425","grant_number":"RGY0084/2012","name":"In situ real-time imaging of neurotransmitter signaling using designer optical sensors (HFSP Young Investigator)"}],"external_id":{"pmid":["26061224"]},"publist_id":"5555","author":[{"last_name":"Whitfield","full_name":"Whitfield, Jason","first_name":"Jason"},{"full_name":"Zhang, William","last_name":"Zhang","first_name":"William"},{"last_name":"Herde","full_name":"Herde, Michel","first_name":"Michel"},{"first_name":"Ben","last_name":"Clifton","full_name":"Clifton, Ben"},{"last_name":"Radziejewski","full_name":"Radziejewski, Johanna","first_name":"Johanna"},{"id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","first_name":"Harald L","orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L","last_name":"Janovjak"},{"first_name":"Christian","last_name":"Henneberger","full_name":"Henneberger, Christian"},{"first_name":"Colin","full_name":"Jackson, Colin","last_name":"Jackson"}],"title":"Construction of a robust and sensitive arginine biosensor through ancestral protein reconstruction","citation":{"apa":"Whitfield, J., Zhang, W., Herde, M., Clifton, B., Radziejewski, J., Janovjak, H. L., … Jackson, C. (2015). Construction of a robust and sensitive arginine biosensor through ancestral protein reconstruction. Protein Science. Wiley. https://doi.org/10.1002/pro.2721","ama":"Whitfield J, Zhang W, Herde M, et al. Construction of a robust and sensitive arginine biosensor through ancestral protein reconstruction. Protein Science. 2015;24(9):1412-1422. doi:10.1002/pro.2721","ieee":"J. Whitfield et al., “Construction of a robust and sensitive arginine biosensor through ancestral protein reconstruction,” Protein Science, vol. 24, no. 9. Wiley, pp. 1412–1422, 2015.","short":"J. Whitfield, W. Zhang, M. Herde, B. Clifton, J. Radziejewski, H.L. Janovjak, C. Henneberger, C. Jackson, Protein Science 24 (2015) 1412–1422.","mla":"Whitfield, Jason, et al. “Construction of a Robust and Sensitive Arginine Biosensor through Ancestral Protein Reconstruction.” Protein Science, vol. 24, no. 9, Wiley, 2015, pp. 1412–22, doi:10.1002/pro.2721.","ista":"Whitfield J, Zhang W, Herde M, Clifton B, Radziejewski J, Janovjak HL, Henneberger C, Jackson C. 2015. Construction of a robust and sensitive arginine biosensor through ancestral protein reconstruction. Protein Science. 24(9), 1412–1422.","chicago":"Whitfield, Jason, William Zhang, Michel Herde, Ben Clifton, Johanna Radziejewski, Harald L Janovjak, Christian Henneberger, and Colin Jackson. “Construction of a Robust and Sensitive Arginine Biosensor through Ancestral Protein Reconstruction.” Protein Science. Wiley, 2015. https://doi.org/10.1002/pro.2721."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"quality_controlled":"1","publisher":"Wiley","page":"1412 - 1422","date_created":"2018-12-11T11:53:01Z","date_published":"2015-09-01T00:00:00Z","doi":"10.1002/pro.2721","year":"2015","publication":"Protein Science","day":"01","type":"journal_article","status":"public","_id":"1611","department":[{"_id":"HaJa"}],"date_updated":"2021-01-12T06:52:00Z","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4570536/","open_access":"1"}],"scopus_import":1,"intvolume":" 24","month":"09","abstract":[{"lang":"eng","text":"Biosensors for signaling molecules allow the study of physiological processes by bringing together the fields of protein engineering, fluorescence imaging, and cell biology. Construction of genetically encoded biosensors generally relies on the availability of a binding "core" that is both specific and stable, which can then be combined with fluorescent molecules to create a sensor. However, binding proteins with the desired properties are often not available in nature and substantial improvement to sensors can be required, particularly with regard to their durability. Ancestral protein reconstruction is a powerful protein-engineering tool able to generate highly stable and functional proteins. In this work, we sought to establish the utility of ancestral protein reconstruction to biosensor development, beginning with the construction of an l-arginine biosensor. l-arginine, as the immediate precursor to nitric oxide, is an important molecule in many physiological contexts including brain function. Using a combination of ancestral reconstruction and circular permutation, we constructed a Förster resonance energy transfer (FRET) biosensor for l-arginine (cpFLIPR). cpFLIPR displays high sensitivity and specificity, with a Kd of ∼14 μM and a maximal dynamic range of 35%. Importantly, cpFLIPR was highly robust, enabling accurate l-arginine measurement at physiological temperatures. We established that cpFLIPR is compatible with two-photon excitation fluorescence microscopy and report l-arginine concentrations in brain tissue."}],"pmid":1,"oa_version":"Submitted Version","volume":24,"issue":"9","publication_status":"published","language":[{"iso":"eng"}]}]