[{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"711","ddc":["004","005"],"status":"public","title":"Bidirectional nested weighted automata","intvolume":" 85","pubrep_id":"886","file":[{"access_level":"open_access","file_name":"IST-2017-886-v1+1_LIPIcs-CONCUR-2017-5.pdf","creator":"system","file_size":570294,"content_type":"application/pdf","file_id":"4661","relation":"main_file","checksum":"d2bda4783821a6358333fe27f11f4737","date_updated":"2020-07-14T12:47:49Z","date_created":"2018-12-12T10:08:02Z"}],"oa_version":"Published Version","type":"conference","alternative_title":["LIPIcs"],"abstract":[{"text":"Nested weighted automata (NWA) present a robust and convenient automata-theoretic formalism for quantitative specifications. Previous works have considered NWA that processed input words only in the forward direction. It is natural to allow the automata to process input words backwards as well, for example, to measure the maximal or average time between a response and the preceding request. We therefore introduce and study bidirectional NWA that can process input words in both directions. First, we show that bidirectional NWA can express interesting quantitative properties that are not expressible by forward-only NWA. Second, for the fundamental decision problems of emptiness and universality, we establish decidability and complexity results for the new framework which match the best-known results for the special case of forward-only NWA. Thus, for NWA, the increased expressiveness of bidirectionality is achieved at no additional computational complexity. This is in stark contrast to the unweighted case, where bidirectional finite automata are no more expressive but exponentially more succinct than their forward-only counterparts.","lang":"eng"}],"citation":{"chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Bidirectional Nested Weighted Automata,” Vol. 85. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.CONCUR.2017.5.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","mla":"Chatterjee, Krishnendu, et al. Bidirectional Nested Weighted Automata. Vol. 85, 5, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.CONCUR.2017.5.","ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, “Bidirectional nested weighted automata,” presented at the 28th International Conference on Concurrency Theory, CONCUR, Berlin, Germany, 2017, vol. 85.","apa":"Chatterjee, K., Henzinger, T. A., & Otop, J. (2017). Bidirectional nested weighted automata (Vol. 85). Presented at the 28th International Conference on Concurrency Theory, CONCUR, Berlin, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2017.5","ista":"Chatterjee K, Henzinger TA, Otop J. 2017. Bidirectional nested weighted automata. 28th International Conference on Concurrency Theory, CONCUR, LIPIcs, vol. 85, 5.","ama":"Chatterjee K, Henzinger TA, Otop J. Bidirectional nested weighted automata. In: Vol 85. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.CONCUR.2017.5"},"date_published":"2017-08-01T00:00:00Z","scopus_import":1,"day":"01","has_accepted_license":"1","year":"2017","publication_status":"published","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"author":[{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A"},{"full_name":"Otop, Jan","last_name":"Otop","first_name":"Jan"}],"date_created":"2018-12-11T11:48:04Z","date_updated":"2021-01-12T08:11:53Z","volume":85,"article_number":"5","file_date_updated":"2020-07-14T12:47:49Z","publist_id":"6976","license":"https://creativecommons.org/licenses/by/4.0/","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","conference":{"location":"Berlin, Germany","start_date":"2017-09-05","end_date":"2017-09-08","name":"28th International Conference on Concurrency Theory, CONCUR"},"doi":"10.4230/LIPIcs.CONCUR.2017.5","language":[{"iso":"eng"}],"month":"08","publication_identifier":{"issn":["18688969"]}},{"doi":"10.1016/j.na.2017.03.001","date_published":"2017-08-01T00:00:00Z","language":[{"iso":"eng"}],"publication":"Nonlinear Analysis: Theory, Methods and Applications","oa":1,"citation":{"short":"J.L. Fischer, Nonlinear Analysis: Theory, Methods and Applications 159 (2017) 181–207.","mla":"Fischer, Julian L. “Weak–Strong Uniqueness of Solutions to Entropy Dissipating Reaction–Diffusion Equations.” Nonlinear Analysis: Theory, Methods and Applications, vol. 159, Elsevier, 2017, pp. 181–207, doi:10.1016/j.na.2017.03.001.","chicago":"Fischer, Julian L. “Weak–Strong Uniqueness of Solutions to Entropy Dissipating Reaction–Diffusion Equations.” Nonlinear Analysis: Theory, Methods and Applications. Elsevier, 2017. https://doi.org/10.1016/j.na.2017.03.001.","ama":"Fischer JL. Weak–strong uniqueness of solutions to entropy dissipating reaction–diffusion equations. Nonlinear Analysis: Theory, Methods and Applications. 2017;159:181-207. doi:10.1016/j.na.2017.03.001","ieee":"J. L. Fischer, “Weak–strong uniqueness of solutions to entropy dissipating reaction–diffusion equations,” Nonlinear Analysis: Theory, Methods and Applications, vol. 159. Elsevier, pp. 181–207, 2017.","apa":"Fischer, J. L. (2017). Weak–strong uniqueness of solutions to entropy dissipating reaction–diffusion equations. Nonlinear Analysis: Theory, Methods and Applications. Elsevier. https://doi.org/10.1016/j.na.2017.03.001","ista":"Fischer JL. 2017. Weak–strong uniqueness of solutions to entropy dissipating reaction–diffusion equations. Nonlinear Analysis: Theory, Methods and Applications. 159, 181–207."},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1703.00730"}],"quality_controlled":"1","page":"181 - 207","month":"08","day":"01","publication_identifier":{"issn":["0362546X"]},"scopus_import":1,"author":[{"first_name":"Julian L","last_name":"Fischer","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0479-558X","full_name":"Fischer, Julian L"}],"date_created":"2018-12-11T11:48:05Z","date_updated":"2021-01-12T08:11:55Z","volume":159,"oa_version":"Submitted Version","_id":"712","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","year":"2017","status":"public","title":"Weak–strong uniqueness of solutions to entropy dissipating reaction–diffusion equations","publication_status":"published","intvolume":" 159","department":[{"_id":"JuFi"}],"publisher":"Elsevier","abstract":[{"lang":"eng","text":"We establish a weak–strong uniqueness principle for solutions to entropy-dissipating reaction–diffusion equations: As long as a strong solution to the reaction–diffusion equation exists, any weak solution and even any renormalized solution must coincide with this strong solution. Our assumptions on the reaction rates are just the entropy condition and local Lipschitz continuity; in particular, we do not impose any growth restrictions on the reaction rates. Therefore, our result applies to any single reversible reaction with mass-action kinetics as well as to systems of reversible reactions with mass-action kinetics satisfying the detailed balance condition. Renormalized solutions are known to exist globally in time for reaction–diffusion equations with entropy-dissipating reaction rates; in contrast, the global-in-time existence of weak solutions is in general still an open problem–even for smooth data–, thereby motivating the study of renormalized solutions. The key ingredient of our result is a careful adjustment of the usual relative entropy functional, whose evolution cannot be controlled properly for weak solutions or renormalized solutions."}],"publist_id":"6975","type":"journal_article"},{"day":"01","article_processing_charge":"No","scopus_import":1,"date_published":"2017-09-01T00:00:00Z","article_type":"original","page":"7 - 14","publication":"Drug and Alcohol Dependence","citation":{"short":"G. Brailoiu, E. Deliu, J. Barr, L. Console Bram, A. Ciuciu, M. Abood, E. Unterwald, E. Brǎiloiu, Drug and Alcohol Dependence 178 (2017) 7–14.","mla":"Brailoiu, Gabriela, et al. “HIV Tat Excites D1 Receptor-like Expressing Neurons from Rat Nucleus Accumbens.” Drug and Alcohol Dependence, vol. 178, Elsevier, 2017, pp. 7–14, doi:10.1016/j.drugalcdep.2017.04.015.","chicago":"Brailoiu, Gabriela, Elena Deliu, Jeffrey Barr, Linda Console Bram, Alexandra Ciuciu, Mary Abood, Ellen Unterwald, and Eugen Brǎiloiu. “HIV Tat Excites D1 Receptor-like Expressing Neurons from Rat Nucleus Accumbens.” Drug and Alcohol Dependence. Elsevier, 2017. https://doi.org/10.1016/j.drugalcdep.2017.04.015.","ama":"Brailoiu G, Deliu E, Barr J, et al. HIV Tat excites D1 receptor-like expressing neurons from rat nucleus accumbens. Drug and Alcohol Dependence. 2017;178:7-14. doi:10.1016/j.drugalcdep.2017.04.015","ieee":"G. Brailoiu et al., “HIV Tat excites D1 receptor-like expressing neurons from rat nucleus accumbens,” Drug and Alcohol Dependence, vol. 178. Elsevier, pp. 7–14, 2017.","apa":"Brailoiu, G., Deliu, E., Barr, J., Console Bram, L., Ciuciu, A., Abood, M., … Brǎiloiu, E. (2017). HIV Tat excites D1 receptor-like expressing neurons from rat nucleus accumbens. Drug and Alcohol Dependence. Elsevier. https://doi.org/10.1016/j.drugalcdep.2017.04.015","ista":"Brailoiu G, Deliu E, Barr J, Console Bram L, Ciuciu A, Abood M, Unterwald E, Brǎiloiu E. 2017. HIV Tat excites D1 receptor-like expressing neurons from rat nucleus accumbens. Drug and Alcohol Dependence. 178, 7–14."},"abstract":[{"lang":"eng","text":"Background HIV-1 infection and drug abuse are frequently co-morbid and their association greatly increases the severity of HIV-1-induced neuropathology. While nucleus accumbens (NAcc) function is severely perturbed by drugs of abuse, little is known about how HIV-1 infection affects NAcc. Methods We used calcium and voltage imaging to investigate the effect of HIV-1 trans-activator of transcription (Tat) on rat NAcc. Based on previous neuronal studies, we hypothesized that Tat modulates intracellular Ca2+ homeostasis of NAcc neurons. Results We provide evidence that Tat triggers a Ca2+ signaling cascade in NAcc medium spiny neurons (MSN) expressing D1-like dopamine receptors leading to neuronal depolarization. Firstly, Tat induced inositol 1,4,5-trisphsophate (IP3) receptor-mediated Ca2+ release from endoplasmic reticulum, followed by Ca2+ and Na+ influx via transient receptor potential canonical channels. The influx of cations depolarizes the membrane promoting additional Ca2+ entry through voltage-gated P/Q-type Ca2+ channels and opening of tetrodotoxin-sensitive Na+ channels. By activating this mechanism, Tat elicits a feed-forward depolarization increasing the excitability of D1-phosphatidylinositol-linked NAcc MSN. We previously found that cocaine targets NAcc neurons directly (independent of the inhibition of dopamine transporter) only when IP3-generating mechanisms are concomitantly initiated. When tested here, cocaine produced a dose-dependent potentiation of the effect of Tat on cytosolic Ca2+. Conclusion We describe for the first time a HIV-1 Tat-triggered Ca2+ signaling in MSN of NAcc involving TRPC and depolarization and a potentiation of the effect of Tat by cocaine, which may be relevant for the reward axis in cocaine-abusing HIV-1-positive patients."}],"type":"journal_article","oa_version":"Submitted Version","status":"public","title":"HIV Tat excites D1 receptor-like expressing neurons from rat nucleus accumbens","intvolume":" 178","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"714","month":"09","publication_identifier":{"issn":["03768716"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.drugalcdep.2017.04.015","quality_controlled":"1","oa":1,"external_id":{"pmid":["28623807"]},"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5797705","open_access":"1"}],"publist_id":"6967","date_updated":"2021-01-12T08:12:00Z","date_created":"2018-12-11T11:48:05Z","volume":178,"author":[{"last_name":"Brailoiu","first_name":"Gabriela","full_name":"Brailoiu, Gabriela"},{"last_name":"Deliu","first_name":"Elena","orcid":"0000-0002-7370-5293","id":"37A40D7E-F248-11E8-B48F-1D18A9856A87","full_name":"Deliu, Elena"},{"first_name":"Jeffrey","last_name":"Barr","full_name":"Barr, Jeffrey"},{"full_name":"Console Bram, Linda","first_name":"Linda","last_name":"Console Bram"},{"full_name":"Ciuciu, Alexandra","last_name":"Ciuciu","first_name":"Alexandra"},{"first_name":"Mary","last_name":"Abood","full_name":"Abood, Mary"},{"first_name":"Ellen","last_name":"Unterwald","full_name":"Unterwald, Ellen"},{"last_name":"Brǎiloiu","first_name":"Eugen","full_name":"Brǎiloiu, Eugen"}],"publication_status":"published","publisher":"Elsevier","department":[{"_id":"GaNo"}],"year":"2017","acknowledgement":"This work was supported by the National Institutes of Health grants DA035926 (to MEA), and P30DA013429 (to EMU).","pmid":1},{"date_published":"2017-08-30T00:00:00Z","doi":"10.1126/scitranslmed.aao4218","language":[{"iso":"eng"}],"publication":"Science Translational Medicine","citation":{"ieee":"G. Novarino, “More excitation for Rett syndrome,” Science Translational Medicine, vol. 9, no. 405. American Association for the Advancement of Science, 2017.","apa":"Novarino, G. (2017). More excitation for Rett syndrome. Science Translational Medicine. American Association for the Advancement of Science. https://doi.org/10.1126/scitranslmed.aao4218","ista":"Novarino G. 2017. More excitation for Rett syndrome. Science Translational Medicine. 9(405), aao4218.","ama":"Novarino G. More excitation for Rett syndrome. Science Translational Medicine. 2017;9(405). doi:10.1126/scitranslmed.aao4218","chicago":"Novarino, Gaia. “More Excitation for Rett Syndrome.” Science Translational Medicine. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/scitranslmed.aao4218.","short":"G. Novarino, Science Translational Medicine 9 (2017).","mla":"Novarino, Gaia. “More Excitation for Rett Syndrome.” Science Translational Medicine, vol. 9, no. 405, aao4218, American Association for the Advancement of Science, 2017, doi:10.1126/scitranslmed.aao4218."},"quality_controlled":"1","month":"08","day":"30","publication_identifier":{"issn":["19466234"]},"scopus_import":1,"author":[{"full_name":"Novarino, Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","first_name":"Gaia","last_name":"Novarino"}],"date_updated":"2021-01-12T08:12:04Z","date_created":"2018-12-11T11:48:06Z","volume":9,"oa_version":"None","_id":"715","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2017","status":"public","title":"More excitation for Rett syndrome","publication_status":"published","intvolume":" 9","department":[{"_id":"GaNo"}],"publisher":"American Association for the Advancement of Science","abstract":[{"lang":"eng","text":"D-cycloserine ameliorates breathing abnormalities and survival rate in a mouse model of Rett syndrome."}],"publist_id":"6968","issue":"405","article_number":"aao4218","type":"journal_article"},{"abstract":[{"lang":"eng","text":"Two-player games on graphs are central in many problems in formal verification and program analysis, such as synthesis and verification of open systems. In this work, we consider solving recursive game graphs (or pushdown game graphs) that model the control flow of sequential programs with recursion.While pushdown games have been studied before with qualitative objectives-such as reachability and ?-regular objectives- in this work, we study for the first time such games with the most well-studied quantitative objective, the mean-payoff objective. In pushdown games, two types of strategies are relevant: (1) global strategies, which depend on the entire global history; and (2) modular strategies, which have only local memory and thus do not depend on the context of invocation but rather only on the history of the current invocation of the module. Our main results are as follows: (1) One-player pushdown games with mean-payoff objectives under global strategies are decidable in polynomial time. (2) Two-player pushdown games with mean-payoff objectives under global strategies are undecidable. (3) One-player pushdown games with mean-payoff objectives under modular strategies are NP-hard. (4) Two-player pushdown games with mean-payoff objectives under modular strategies can be solved in NP (i.e., both one-player and two-player pushdown games with mean-payoff objectives under modular strategies are NP-complete). We also establish the optimal strategy complexity by showing that global strategies for mean-payoff objectives require infinite memory even in one-player pushdown games and memoryless modular strategies are sufficient in two-player pushdown games. Finally, we also show that all the problems have the same complexity if the stack boundedness condition is added, where along with the mean-payoff objective the player must also ensure that the stack height is bounded."}],"issue":"5","type":"journal_article","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"716","title":"The complexity of mean-payoff pushdown games","status":"public","intvolume":" 64","day":"01","scopus_import":1,"date_published":"2017-09-01T00:00:00Z","publication":"Journal of the ACM","citation":{"ama":"Chatterjee K, Velner Y. The complexity of mean-payoff pushdown games. Journal of the ACM. 2017;64(5):34. doi:10.1145/3121408","ista":"Chatterjee K, Velner Y. 2017. The complexity of mean-payoff pushdown games. Journal of the ACM. 64(5), 34.","ieee":"K. Chatterjee and Y. Velner, “The complexity of mean-payoff pushdown games,” Journal of the ACM, vol. 64, no. 5. ACM, p. 34, 2017.","apa":"Chatterjee, K., & Velner, Y. (2017). The complexity of mean-payoff pushdown games. Journal of the ACM. ACM. https://doi.org/10.1145/3121408","mla":"Chatterjee, Krishnendu, and Yaron Velner. “The Complexity of Mean-Payoff Pushdown Games.” Journal of the ACM, vol. 64, no. 5, ACM, 2017, p. 34, doi:10.1145/3121408.","short":"K. Chatterjee, Y. Velner, Journal of the ACM 64 (2017) 34.","chicago":"Chatterjee, Krishnendu, and Yaron Velner. “The Complexity of Mean-Payoff Pushdown Games.” Journal of the ACM. ACM, 2017. https://doi.org/10.1145/3121408."},"article_type":"original","page":"34","ec_funded":1,"publist_id":"6964","author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"last_name":"Velner","first_name":"Yaron","full_name":"Velner, Yaron"}],"date_created":"2018-12-11T11:48:06Z","date_updated":"2021-01-12T08:12:08Z","volume":64,"year":"2017","publication_status":"published","publisher":"ACM","department":[{"_id":"KrCh"}],"month":"09","publication_identifier":{"issn":["00045411"]},"doi":"10.1145/3121408","language":[{"iso":"eng"}],"external_id":{"arxiv":["1201.2829"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1201.2829"}],"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"},{"call_identifier":"FWF","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"}]},{"publist_id":"6963","ec_funded":1,"acknowledgement":"The research was supported by Austrian Science Fund (FWF) Grant No. P 23499-N23, FWF NFN Grant No. S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), Microsoft faculty fellows award, the RICH Model Toolkit (ICT COST Action IC0901), and was carried out in partial fulfillment of the requirements for the Ph.D. degree of the second author.","year":"2017","publisher":"Academic Press","department":[{"_id":"KrCh"}],"publication_status":"published","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"2329"}]},"author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"full_name":"Velner, Yaron","first_name":"Yaron","last_name":"Velner"}],"volume":88,"date_created":"2018-12-11T11:48:07Z","date_updated":"2023-02-23T10:38:15Z","month":"09","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1210.3141","open_access":"1"}],"project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","call_identifier":"FWF","name":"Game Theory"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"quality_controlled":"1","doi":"10.1016/j.jcss.2017.04.005","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"text":"We consider finite-state and recursive game graphs with multidimensional mean-payoff objectives. In recursive games two types of strategies are relevant: global strategies and modular strategies. Our contributions are: (1) We show that finite-state multidimensional mean-payoff games can be solved in polynomial time if the number of dimensions and the maximal absolute value of weights are fixed; whereas for arbitrary dimensions the problem is coNP-complete. (2) We show that one-player recursive games with multidimensional mean-payoff objectives can be solved in polynomial time. Both above algorithms are based on hyperplane separation technique. (3) For recursive games we show that under modular strategies the multidimensional problem is undecidable. We show that if the number of modules, exits, and the maximal absolute value of the weights are fixed, then one-dimensional recursive mean-payoff games under modular strategies can be solved in polynomial time, whereas for unbounded number of exits or modules the problem is NP-hard.","lang":"eng"}],"_id":"717","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 88","title":"Hyperplane separation technique for multidimensional mean-payoff games","status":"public","oa_version":"Preprint","scopus_import":1,"day":"01","citation":{"mla":"Chatterjee, Krishnendu, and Yaron Velner. “Hyperplane Separation Technique for Multidimensional Mean-Payoff Games.” Journal of Computer and System Sciences, vol. 88, Academic Press, 2017, pp. 236–59, doi:10.1016/j.jcss.2017.04.005.","short":"K. Chatterjee, Y. Velner, Journal of Computer and System Sciences 88 (2017) 236–259.","chicago":"Chatterjee, Krishnendu, and Yaron Velner. “Hyperplane Separation Technique for Multidimensional Mean-Payoff Games.” Journal of Computer and System Sciences. Academic Press, 2017. https://doi.org/10.1016/j.jcss.2017.04.005.","ama":"Chatterjee K, Velner Y. Hyperplane separation technique for multidimensional mean-payoff games. Journal of Computer and System Sciences. 2017;88:236-259. doi:10.1016/j.jcss.2017.04.005","ista":"Chatterjee K, Velner Y. 2017. Hyperplane separation technique for multidimensional mean-payoff games. Journal of Computer and System Sciences. 88, 236–259.","apa":"Chatterjee, K., & Velner, Y. (2017). Hyperplane separation technique for multidimensional mean-payoff games. Journal of Computer and System Sciences. Academic Press. https://doi.org/10.1016/j.jcss.2017.04.005","ieee":"K. Chatterjee and Y. Velner, “Hyperplane separation technique for multidimensional mean-payoff games,” Journal of Computer and System Sciences, vol. 88. Academic Press, pp. 236–259, 2017."},"publication":"Journal of Computer and System Sciences","page":"236 - 259","date_published":"2017-09-01T00:00:00Z"},{"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"full_name":"Ehlers, Rüdiger","first_name":"Rüdiger","last_name":"Ehlers"}],"date_updated":"2021-01-12T08:12:18Z","date_created":"2018-12-11T11:48:07Z","oa_version":"None","volume":54,"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"719","year":"2017","publication_status":"published","status":"public","title":"Special issue: Synthesis and SYNT 2014","publisher":"Springer","department":[{"_id":"KrCh"}],"intvolume":" 54","abstract":[{"lang":"eng","text":"The ubiquity of computation in modern machines and devices imposes a need to assert the correctness of their behavior. Especially in the case of safety-critical systems, their designers need to take measures that enforce their safe operation. Formal methods has emerged as a research field that addresses this challenge: by rigorously proving that all system executions adhere to their specifications, the correctness of an implementation under concern can be assured. To achieve this goal, a plethora of techniques are nowadays available, all of which are optimized for different system types and application domains."}],"publist_id":"6961","issue":"6","type":"journal_article","date_published":"2017-09-01T00:00:00Z","doi":"10.1007/s00236-017-0299-0","language":[{"iso":"eng"}],"publication":"Acta Informatica","citation":{"chicago":"Chatterjee, Krishnendu, and Rüdiger Ehlers. “Special Issue: Synthesis and SYNT 2014.” Acta Informatica. Springer, 2017. https://doi.org/10.1007/s00236-017-0299-0.","mla":"Chatterjee, Krishnendu, and Rüdiger Ehlers. “Special Issue: Synthesis and SYNT 2014.” Acta Informatica, vol. 54, no. 6, Springer, 2017, pp. 543–44, doi:10.1007/s00236-017-0299-0.","short":"K. Chatterjee, R. Ehlers, Acta Informatica 54 (2017) 543–544.","ista":"Chatterjee K, Ehlers R. 2017. Special issue: Synthesis and SYNT 2014. Acta Informatica. 54(6), 543–544.","apa":"Chatterjee, K., & Ehlers, R. (2017). Special issue: Synthesis and SYNT 2014. Acta Informatica. Springer. https://doi.org/10.1007/s00236-017-0299-0","ieee":"K. Chatterjee and R. Ehlers, “Special issue: Synthesis and SYNT 2014,” Acta Informatica, vol. 54, no. 6. Springer, pp. 543–544, 2017.","ama":"Chatterjee K, Ehlers R. Special issue: Synthesis and SYNT 2014. Acta Informatica. 2017;54(6):543-544. doi:10.1007/s00236-017-0299-0"},"quality_controlled":"1","page":"543 - 544","day":"01","month":"09","publication_identifier":{"issn":["00015903"]},"scopus_import":1},{"year":"2017","department":[{"_id":"GaTk"}],"publisher":"Public Library of Science","publication_status":"published","author":[{"full_name":"Humplik, Jan","last_name":"Humplik","first_name":"Jan","id":"2E9627A8-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","first_name":"Gasper","full_name":"Tkacik, Gasper"}],"volume":13,"date_updated":"2021-01-12T08:12:21Z","date_created":"2018-12-11T11:48:08Z","article_number":"e1005763","publist_id":"6960","file_date_updated":"2020-07-14T12:47:53Z","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"project":[{"name":"Information processing and computation in fish groups","_id":"255008E4-B435-11E9-9278-68D0E5697425","grant_number":"RGP0065/2012"},{"call_identifier":"FWF","name":"Sensitivity to higher-order statistics in natural scenes","_id":"254D1A94-B435-11E9-9278-68D0E5697425","grant_number":"P 25651-N26"}],"quality_controlled":"1","doi":"10.1371/journal.pcbi.1005763","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1553734X"]},"month":"09","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"720","intvolume":" 13","status":"public","ddc":["530","571"],"title":"Probabilistic models for neural populations that naturally capture global coupling and criticality","pubrep_id":"884","file":[{"content_type":"application/pdf","file_size":14167050,"creator":"system","access_level":"open_access","file_name":"IST-2017-884-v1+1_journal.pcbi.1005763.pdf","checksum":"81107096c19771c36ddbe6f0282a3acb","date_updated":"2020-07-14T12:47:53Z","date_created":"2018-12-12T10:18:30Z","relation":"main_file","file_id":"5352"}],"oa_version":"Published Version","type":"journal_article","issue":"9","abstract":[{"lang":"eng","text":"Advances in multi-unit recordings pave the way for statistical modeling of activity patterns in large neural populations. Recent studies have shown that the summed activity of all neurons strongly shapes the population response. A separate recent finding has been that neural populations also exhibit criticality, an anomalously large dynamic range for the probabilities of different population activity patterns. Motivated by these two observations, we introduce a class of probabilistic models which takes into account the prior knowledge that the neural population could be globally coupled and close to critical. These models consist of an energy function which parametrizes interactions between small groups of neurons, and an arbitrary positive, strictly increasing, and twice differentiable function which maps the energy of a population pattern to its probability. We show that: 1) augmenting a pairwise Ising model with a nonlinearity yields an accurate description of the activity of retinal ganglion cells which outperforms previous models based on the summed activity of neurons; 2) prior knowledge that the population is critical translates to prior expectations about the shape of the nonlinearity; 3) the nonlinearity admits an interpretation in terms of a continuous latent variable globally coupling the system whose distribution we can infer from data. Our method is independent of the underlying system’s state space; hence, it can be applied to other systems such as natural scenes or amino acid sequences of proteins which are also known to exhibit criticality."}],"citation":{"chicago":"Humplik, Jan, and Gašper Tkačik. “Probabilistic Models for Neural Populations That Naturally Capture Global Coupling and Criticality.” PLoS Computational Biology. Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005763.","short":"J. Humplik, G. Tkačik, PLoS Computational Biology 13 (2017).","mla":"Humplik, Jan, and Gašper Tkačik. “Probabilistic Models for Neural Populations That Naturally Capture Global Coupling and Criticality.” PLoS Computational Biology, vol. 13, no. 9, e1005763, Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005763.","apa":"Humplik, J., & Tkačik, G. (2017). Probabilistic models for neural populations that naturally capture global coupling and criticality. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005763","ieee":"J. Humplik and G. Tkačik, “Probabilistic models for neural populations that naturally capture global coupling and criticality,” PLoS Computational Biology, vol. 13, no. 9. Public Library of Science, 2017.","ista":"Humplik J, Tkačik G. 2017. Probabilistic models for neural populations that naturally capture global coupling and criticality. PLoS Computational Biology. 13(9), e1005763.","ama":"Humplik J, Tkačik G. Probabilistic models for neural populations that naturally capture global coupling and criticality. PLoS Computational Biology. 2017;13(9). doi:10.1371/journal.pcbi.1005763"},"publication":"PLoS Computational Biology","date_published":"2017-09-19T00:00:00Z","scopus_import":1,"has_accepted_license":"1","article_processing_charge":"Yes","day":"19"},{"page":"1672 - 1705","publication":"Communications on Pure and Applied Mathematics","citation":{"ama":"Ajanki OH, Krüger TH, Erdös L. Singularities of solutions to quadratic vector equations on the complex upper half plane. Communications on Pure and Applied Mathematics. 2017;70(9):1672-1705. doi:10.1002/cpa.21639","apa":"Ajanki, O. H., Krüger, T. H., & Erdös, L. (2017). Singularities of solutions to quadratic vector equations on the complex upper half plane. Communications on Pure and Applied Mathematics. Wiley-Blackwell. https://doi.org/10.1002/cpa.21639","ieee":"O. H. Ajanki, T. H. Krüger, and L. Erdös, “Singularities of solutions to quadratic vector equations on the complex upper half plane,” Communications on Pure and Applied Mathematics, vol. 70, no. 9. Wiley-Blackwell, pp. 1672–1705, 2017.","ista":"Ajanki OH, Krüger TH, Erdös L. 2017. Singularities of solutions to quadratic vector equations on the complex upper half plane. Communications on Pure and Applied Mathematics. 70(9), 1672–1705.","short":"O.H. Ajanki, T.H. Krüger, L. Erdös, Communications on Pure and Applied Mathematics 70 (2017) 1672–1705.","mla":"Ajanki, Oskari H., et al. “Singularities of Solutions to Quadratic Vector Equations on the Complex Upper Half Plane.” Communications on Pure and Applied Mathematics, vol. 70, no. 9, Wiley-Blackwell, 2017, pp. 1672–705, doi:10.1002/cpa.21639.","chicago":"Ajanki, Oskari H, Torben H Krüger, and László Erdös. “Singularities of Solutions to Quadratic Vector Equations on the Complex Upper Half Plane.” Communications on Pure and Applied Mathematics. Wiley-Blackwell, 2017. https://doi.org/10.1002/cpa.21639."},"date_published":"2017-09-01T00:00:00Z","scopus_import":1,"day":"01","status":"public","title":"Singularities of solutions to quadratic vector equations on the complex upper half plane","intvolume":" 70","_id":"721","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","type":"journal_article","abstract":[{"text":"Let S be a positivity-preserving symmetric linear operator acting on bounded functions. The nonlinear equation -1/m=z+Sm with a parameter z in the complex upper half-plane ℍ has a unique solution m with values in ℍ. We show that the z-dependence of this solution can be represented as the Stieltjes transforms of a family of probability measures v on ℝ. Under suitable conditions on S, we show that v has a real analytic density apart from finitely many algebraic singularities of degree at most 3. Our motivation comes from large random matrices. The solution m determines the density of eigenvalues of two prominent matrix ensembles: (i) matrices with centered independent entries whose variances are given by S and (ii) matrices with correlated entries with a translation-invariant correlation structure. Our analysis shows that the limiting eigenvalue density has only square root singularities or cubic root cusps; no other singularities occur.","lang":"eng"}],"issue":"9","quality_controlled":"1","project":[{"grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7"}],"main_file_link":[{"url":"https://arxiv.org/abs/1512.03703","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1002/cpa.21639","month":"09","publication_identifier":{"issn":["00103640"]},"publication_status":"published","publisher":"Wiley-Blackwell","department":[{"_id":"LaEr"}],"year":"2017","date_updated":"2021-01-12T08:12:24Z","date_created":"2018-12-11T11:48:08Z","volume":70,"author":[{"full_name":"Ajanki, Oskari H","id":"36F2FB7E-F248-11E8-B48F-1D18A9856A87","first_name":"Oskari H","last_name":"Ajanki"},{"full_name":"Krüger, Torben H","first_name":"Torben H","last_name":"Krüger","id":"3020C786-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4821-3297"},{"full_name":"Erdös, László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","first_name":"László","last_name":"Erdös"}],"ec_funded":1,"publist_id":"6959"},{"has_accepted_license":"1","day":"11","scopus_import":1,"date_published":"2017-09-11T00:00:00Z","page":"R919 - R930","citation":{"ista":"Morris E, Griffiths M, Golebiowska A, Mairhofer S, Burr Hersey J, Goh T, von Wangenheim D, Atkinson B, Sturrock C, Lynch J, Vissenberg K, Ritz K, Wells D, Mooney S, Bennett M. 2017. Shaping 3D root system architecture. Current Biology. 27(17), R919–R930.","ieee":"E. Morris et al., “Shaping 3D root system architecture,” Current Biology, vol. 27, no. 17. Cell Press, pp. R919–R930, 2017.","apa":"Morris, E., Griffiths, M., Golebiowska, A., Mairhofer, S., Burr Hersey, J., Goh, T., … Bennett, M. (2017). Shaping 3D root system architecture. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2017.06.043","ama":"Morris E, Griffiths M, Golebiowska A, et al. Shaping 3D root system architecture. Current Biology. 2017;27(17):R919-R930. doi:10.1016/j.cub.2017.06.043","chicago":"Morris, Emily, Marcus Griffiths, Agata Golebiowska, Stefan Mairhofer, Jasmine Burr Hersey, Tatsuaki Goh, Daniel von Wangenheim, et al. “Shaping 3D Root System Architecture.” Current Biology. Cell Press, 2017. https://doi.org/10.1016/j.cub.2017.06.043.","mla":"Morris, Emily, et al. “Shaping 3D Root System Architecture.” Current Biology, vol. 27, no. 17, Cell Press, 2017, pp. R919–30, doi:10.1016/j.cub.2017.06.043.","short":"E. Morris, M. Griffiths, A. Golebiowska, S. Mairhofer, J. Burr Hersey, T. Goh, D. von Wangenheim, B. Atkinson, C. Sturrock, J. Lynch, K. Vissenberg, K. Ritz, D. Wells, S. Mooney, M. Bennett, Current Biology 27 (2017) R919–R930."},"publication":"Current Biology","issue":"17","abstract":[{"text":"Plants are sessile organisms rooted in one place. The soil resources that plants require are often distributed in a highly heterogeneous pattern. To aid foraging, plants have evolved roots whose growth and development are highly responsive to soil signals. As a result, 3D root architecture is shaped by myriad environmental signals to ensure resource capture is optimised and unfavourable environments are avoided. The first signals sensed by newly germinating seeds — gravity and light — direct root growth into the soil to aid seedling establishment. Heterogeneous soil resources, such as water, nitrogen and phosphate, also act as signals that shape 3D root growth to optimise uptake. Root architecture is also modified through biotic interactions that include soil fungi and neighbouring plants. This developmental plasticity results in a ‘custom-made’ 3D root system that is best adapted to forage for resources in each soil environment that a plant colonises.","lang":"eng"}],"type":"journal_article","file":[{"checksum":"e45588b21097b408da6276a3e5eedb2e","date_created":"2019-04-17T07:46:40Z","date_updated":"2020-07-14T12:47:54Z","file_id":"6332","relation":"main_file","creator":"dernst","file_size":1576593,"content_type":"application/pdf","access_level":"open_access","file_name":"2017_CurrentBiology_Morris.pdf"}],"oa_version":"Submitted Version","pubrep_id":"982","intvolume":" 27","status":"public","ddc":["581"],"title":"Shaping 3D root system architecture","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"722","publication_identifier":{"issn":["09609822"]},"month":"09","language":[{"iso":"eng"}],"doi":"10.1016/j.cub.2017.06.043","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"external_id":{"pmid":["28898665"]},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","publist_id":"6956","ec_funded":1,"file_date_updated":"2020-07-14T12:47:54Z","volume":27,"date_created":"2018-12-11T11:48:08Z","date_updated":"2021-01-12T08:12:29Z","author":[{"last_name":"Morris","first_name":"Emily","full_name":"Morris, Emily"},{"full_name":"Griffiths, Marcus","last_name":"Griffiths","first_name":"Marcus"},{"first_name":"Agata","last_name":"Golebiowska","full_name":"Golebiowska, Agata"},{"full_name":"Mairhofer, Stefan","last_name":"Mairhofer","first_name":"Stefan"},{"full_name":"Burr Hersey, Jasmine","last_name":"Burr Hersey","first_name":"Jasmine"},{"last_name":"Goh","first_name":"Tatsuaki","full_name":"Goh, Tatsuaki"},{"last_name":"Von Wangenheim","first_name":"Daniel","orcid":"0000-0002-6862-1247","id":"49E91952-F248-11E8-B48F-1D18A9856A87","full_name":"Von Wangenheim, Daniel"},{"last_name":"Atkinson","first_name":"Brian","full_name":"Atkinson, Brian"},{"full_name":"Sturrock, Craig","last_name":"Sturrock","first_name":"Craig"},{"full_name":"Lynch, Jonathan","last_name":"Lynch","first_name":"Jonathan"},{"first_name":"Kris","last_name":"Vissenberg","full_name":"Vissenberg, Kris"},{"full_name":"Ritz, Karl","last_name":"Ritz","first_name":"Karl"},{"last_name":"Wells","first_name":"Darren","full_name":"Wells, Darren"},{"last_name":"Mooney","first_name":"Sacha","full_name":"Mooney, Sacha"},{"last_name":"Bennett","first_name":"Malcolm","full_name":"Bennett, Malcolm"}],"department":[{"_id":"JiFr"}],"publisher":"Cell Press","publication_status":"published","pmid":1,"year":"2017"},{"month":"09","publication_identifier":{"issn":["00278424"]},"quality_controlled":"1","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5617265/","open_access":"1"}],"oa":1,"external_id":{"pmid":["28874581"]},"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1703817114","publist_id":"6953","publication_status":"published","department":[{"_id":"GaTk"}],"publisher":"National Academy of Sciences","year":"2017","pmid":1,"date_updated":"2021-01-12T08:12:36Z","date_created":"2018-12-11T11:48:10Z","volume":114,"author":[{"last_name":"Harpaz","first_name":"Roy","full_name":"Harpaz, Roy"},{"orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","first_name":"Gasper","full_name":"Tkacik, Gasper"},{"last_name":"Schneidman","first_name":"Elad","full_name":"Schneidman, Elad"}],"scopus_import":1,"day":"19","page":"10149 - 10154","publication":"PNAS","citation":{"ieee":"R. Harpaz, G. Tkačik, and E. Schneidman, “Discrete modes of social information processing predict individual behavior of fish in a group,” PNAS, vol. 114, no. 38. National Academy of Sciences, pp. 10149–10154, 2017.","apa":"Harpaz, R., Tkačik, G., & Schneidman, E. (2017). Discrete modes of social information processing predict individual behavior of fish in a group. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1703817114","ista":"Harpaz R, Tkačik G, Schneidman E. 2017. Discrete modes of social information processing predict individual behavior of fish in a group. PNAS. 114(38), 10149–10154.","ama":"Harpaz R, Tkačik G, Schneidman E. Discrete modes of social information processing predict individual behavior of fish in a group. PNAS. 2017;114(38):10149-10154. doi:10.1073/pnas.1703817114","chicago":"Harpaz, Roy, Gašper Tkačik, and Elad Schneidman. “Discrete Modes of Social Information Processing Predict Individual Behavior of Fish in a Group.” PNAS. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1703817114.","short":"R. Harpaz, G. Tkačik, E. Schneidman, PNAS 114 (2017) 10149–10154.","mla":"Harpaz, Roy, et al. “Discrete Modes of Social Information Processing Predict Individual Behavior of Fish in a Group.” PNAS, vol. 114, no. 38, National Academy of Sciences, 2017, pp. 10149–54, doi:10.1073/pnas.1703817114."},"date_published":"2017-09-19T00:00:00Z","type":"journal_article","abstract":[{"text":"Individual computations and social interactions underlying collective behavior in groups of animals are of great ethological, behavioral, and theoretical interest. While complex individual behaviors have successfully been parsed into small dictionaries of stereotyped behavioral modes, studies of collective behavior largely ignored these findings; instead, their focus was on inferring single, mode-independent social interaction rules that reproduced macroscopic and often qualitative features of group behavior. Here, we bring these two approaches together to predict individual swimming patterns of adult zebrafish in a group. We show that fish alternate between an “active” mode, in which they are sensitive to the swimming patterns of conspecifics, and a “passive” mode, where they ignore them. Using a model that accounts for these two modes explicitly, we predict behaviors of individual fish with high accuracy, outperforming previous approaches that assumed a single continuous computation by individuals and simple metric or topological weighing of neighbors’ behavior. At the group level, switching between active and passive modes is uncorrelated among fish, but correlated directional swimming behavior still emerges. Our quantitative approach for studying complex, multi-modal individual behavior jointly with emergent group behavior is readily extensible to additional behavioral modes and their neural correlates as well as to other species.","lang":"eng"}],"issue":"38","title":"Discrete modes of social information processing predict individual behavior of fish in a group","status":"public","intvolume":" 114","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"725","oa_version":"Submitted Version"},{"abstract":[{"lang":"eng","text":"We investigate the stationary and dynamical behavior of an Anderson localized chain coupled to a single central bound state. Although this coupling partially dilutes the Anderson localized peaks towards nearly resonant sites, the most weight of the original peaks remains unchanged. This leads to multifractal wave functions with a frozen spectrum of fractal dimensions, which is characteristic for localized phases in models with power-law hopping. Using a perturbative approach we identify two different dynamical regimes. At weak couplings to the central site, the transport of particles and information is logarithmic in time, a feature usually attributed to many-body localization. We connect such transport to the persistence of the Poisson statistics of level spacings in parts of the spectrum. In contrast, at stronger couplings the level repulsion is established in the entire spectrum, the problem can be mapped to the Fano resonance, and the transport is ballistic."}],"issue":"10","type":"journal_article","oa_version":"Submitted Version","_id":"724","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Noninteracting central site model localization and logarithmic entanglement growth","intvolume":" 96","day":"13","scopus_import":1,"date_published":"2017-09-13T00:00:00Z","publication":"Physical Review B","citation":{"short":"D. Hetterich, M. Serbyn, F. Domínguez, F. Pollmann, B. Trauzettel, Physical Review B 96 (2017).","mla":"Hetterich, Daniel, et al. “Noninteracting Central Site Model Localization and Logarithmic Entanglement Growth.” Physical Review B, vol. 96, no. 10, 104203, American Physical Society, 2017, doi:10.1103/PhysRevB.96.104203.","chicago":"Hetterich, Daniel, Maksym Serbyn, Fernando Domínguez, Frank Pollmann, and Björn Trauzettel. “Noninteracting Central Site Model Localization and Logarithmic Entanglement Growth.” Physical Review B. American Physical Society, 2017. https://doi.org/10.1103/PhysRevB.96.104203.","ama":"Hetterich D, Serbyn M, Domínguez F, Pollmann F, Trauzettel B. Noninteracting central site model localization and logarithmic entanglement growth. Physical Review B. 2017;96(10). doi:10.1103/PhysRevB.96.104203","ieee":"D. Hetterich, M. Serbyn, F. Domínguez, F. Pollmann, and B. Trauzettel, “Noninteracting central site model localization and logarithmic entanglement growth,” Physical Review B, vol. 96, no. 10. American Physical Society, 2017.","apa":"Hetterich, D., Serbyn, M., Domínguez, F., Pollmann, F., & Trauzettel, B. (2017). Noninteracting central site model localization and logarithmic entanglement growth. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.96.104203","ista":"Hetterich D, Serbyn M, Domínguez F, Pollmann F, Trauzettel B. 2017. Noninteracting central site model localization and logarithmic entanglement growth. Physical Review B. 96(10), 104203."},"publist_id":"6955","article_number":"104203","author":[{"full_name":"Hetterich, Daniel","last_name":"Hetterich","first_name":"Daniel"},{"full_name":"Serbyn, Maksym","first_name":"Maksym","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827"},{"last_name":"Domínguez","first_name":"Fernando","full_name":"Domínguez, Fernando"},{"last_name":"Pollmann","first_name":"Frank","full_name":"Pollmann, Frank"},{"full_name":"Trauzettel, Björn","last_name":"Trauzettel","first_name":"Björn"}],"date_updated":"2021-01-12T08:12:35Z","date_created":"2018-12-11T11:48:09Z","volume":96,"year":"2017","acknowledgement":"We would like to thank Dmitry Abanin, Christophe De\r\nBeule, Joel Moore, Romain Vasseur, and Norman Yao for\r\nmany stimulating discussions. Financial support has been\r\nprovided by the Deutsche Forschungsgemeinschaft (DFG)\r\nvia Grant No. TR950/8-1, SFB 1170 “ToCoTronics” and the\r\nENB Graduate School on Topological Insulators. M.S. was\r\nsupported by Gordon and Betty Moore Foundation’s EPiQS\r\nInitiative through Grant No. GBMF4307. F.P. acknowledges\r\nsupport from the DFG Research Unit FOR 1807 through Grant\r\nNo. PO 1370/2-1.","publication_status":"published","publisher":"American Physical Society","department":[{"_id":"MaSe"}],"month":"09","publication_identifier":{"issn":["24699950"]},"doi":"10.1103/PhysRevB.96.104203","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1701.02744"}],"quality_controlled":"1"},{"author":[{"full_name":"Novarino, Gaia","last_name":"Novarino","first_name":"Gaia","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2021-01-12T08:12:57Z","date_created":"2018-12-11T11:48:12Z","volume":9,"oa_version":"None","year":"2017","_id":"731","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication_status":"published","status":"public","title":"The science of love in ASD and ADHD","department":[{"_id":"GaNo"}],"intvolume":" 9","publisher":"American Association for the Advancement of Science","abstract":[{"lang":"eng","text":"Genetic variations in the oxytocin receptor gene affect patients with ASD and ADHD differently."}],"publist_id":"6938","issue":"411","article_number":"eaap8168","type":"journal_article","date_published":"2017-10-11T00:00:00Z","doi":"10.1126/scitranslmed.aap8168","language":[{"iso":"eng"}],"publication":"Science Translational Medicine","citation":{"chicago":"Novarino, Gaia. “The Science of Love in ASD and ADHD.” Science Translational Medicine. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/scitranslmed.aap8168.","mla":"Novarino, Gaia. “The Science of Love in ASD and ADHD.” Science Translational Medicine, vol. 9, no. 411, eaap8168, American Association for the Advancement of Science, 2017, doi:10.1126/scitranslmed.aap8168.","short":"G. Novarino, Science Translational Medicine 9 (2017).","ista":"Novarino G. 2017. The science of love in ASD and ADHD. Science Translational Medicine. 9(411), eaap8168.","apa":"Novarino, G. (2017). The science of love in ASD and ADHD. Science Translational Medicine. American Association for the Advancement of Science. https://doi.org/10.1126/scitranslmed.aap8168","ieee":"G. Novarino, “The science of love in ASD and ADHD,” Science Translational Medicine, vol. 9, no. 411. American Association for the Advancement of Science, 2017.","ama":"Novarino G. The science of love in ASD and ADHD. Science Translational Medicine. 2017;9(411). doi:10.1126/scitranslmed.aap8168"},"quality_controlled":"1","day":"11","month":"10","publication_identifier":{"issn":["19466234"]},"scopus_import":1},{"type":"journal_article","issue":"1","abstract":[{"text":"Inflammation, which is a highly regulated host response against danger signals, may be harmful if it is excessive and deregulated. Ideally, anti-inflammatory therapy should autonomously commence as soon as possible after the onset of inflammation, should be controllable by a physician, and should not systemically block beneficial immune response in the long term. We describe a genetically encoded anti-inflammatory mammalian cell device based on a modular engineered genetic circuit comprising a sensor, an amplifier, a “thresholder” to restrict activation of a positive-feedback loop, a combination of advanced clinically used biopharmaceutical proteins, and orthogonal regulatory elements that linked modules into the functional device. This genetic circuit was autonomously activated by inflammatory signals, including endogenous cecal ligation and puncture (CLP)-induced inflammation in mice and serum from a systemic juvenile idiopathic arthritis (sIJA) patient, and could be reset externally by a chemical signal. The microencapsulated anti-inflammatory device significantly reduced the pathology in dextran sodium sulfate (DSS)-induced acute murine colitis, demonstrating a synthetic immunological approach for autonomous anti-inflammatory therapy.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7360","intvolume":" 25","ddc":["570"],"status":"public","title":"A synthetic mammalian therapeutic gene circuit for sensing and suppressing inflammation","file":[{"file_id":"7561","relation":"main_file","checksum":"ea8b1b28606dd1edab7379ba4fa3641f","date_created":"2020-03-03T10:55:13Z","date_updated":"2020-07-14T12:47:56Z","access_level":"open_access","file_name":"2017_MolecularTherapy_Smole.pdf","creator":"dernst","file_size":3404806,"content_type":"application/pdf"}],"oa_version":"Published Version","has_accepted_license":"1","article_processing_charge":"No","day":"01","citation":{"ista":"Smole A, Lainšček D, Bezeljak U, Horvat S, Jerala R. 2017. A synthetic mammalian therapeutic gene circuit for sensing and suppressing inflammation. Molecular Therapy. 25(1), 102–119.","ieee":"A. Smole, D. Lainšček, U. Bezeljak, S. Horvat, and R. Jerala, “A synthetic mammalian therapeutic gene circuit for sensing and suppressing inflammation,” Molecular Therapy, vol. 25, no. 1. Elsevier, pp. 102–119, 2017.","apa":"Smole, A., Lainšček, D., Bezeljak, U., Horvat, S., & Jerala, R. (2017). A synthetic mammalian therapeutic gene circuit for sensing and suppressing inflammation. Molecular Therapy. Elsevier. https://doi.org/10.1016/j.ymthe.2016.10.005","ama":"Smole A, Lainšček D, Bezeljak U, Horvat S, Jerala R. A synthetic mammalian therapeutic gene circuit for sensing and suppressing inflammation. Molecular Therapy. 2017;25(1):102-119. doi:10.1016/j.ymthe.2016.10.005","chicago":"Smole, Anže, Duško Lainšček, Urban Bezeljak, Simon Horvat, and Roman Jerala. “A Synthetic Mammalian Therapeutic Gene Circuit for Sensing and Suppressing Inflammation.” Molecular Therapy. Elsevier, 2017. https://doi.org/10.1016/j.ymthe.2016.10.005.","mla":"Smole, Anže, et al. “A Synthetic Mammalian Therapeutic Gene Circuit for Sensing and Suppressing Inflammation.” Molecular Therapy, vol. 25, no. 1, Elsevier, 2017, pp. 102–19, doi:10.1016/j.ymthe.2016.10.005.","short":"A. Smole, D. Lainšček, U. Bezeljak, S. Horvat, R. Jerala, Molecular Therapy 25 (2017) 102–119."},"publication":"Molecular Therapy","page":"102-119","article_type":"original","date_published":"2017-01-01T00:00:00Z","file_date_updated":"2020-07-14T12:47:56Z","pmid":1,"year":"2017","department":[{"_id":"MaLo"}],"publisher":"Elsevier","publication_status":"published","author":[{"first_name":"Anže","last_name":"Smole","full_name":"Smole, Anže"},{"last_name":"Lainšček","first_name":"Duško","full_name":"Lainšček, Duško"},{"full_name":"Bezeljak, Urban","id":"2A58201A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1365-5631","first_name":"Urban","last_name":"Bezeljak"},{"full_name":"Horvat, Simon","last_name":"Horvat","first_name":"Simon"},{"full_name":"Jerala, Roman","last_name":"Jerala","first_name":"Roman"}],"volume":25,"date_updated":"2021-01-12T08:13:14Z","date_created":"2020-01-25T15:55:39Z","publication_identifier":{"issn":["1525-0016"]},"month":"01","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"external_id":{"pmid":["28129106"]},"quality_controlled":"1","doi":"10.1016/j.ymthe.2016.10.005","language":[{"iso":"eng"}]},{"publication_status":"published","title":"Optimal geospatial volunteer allocation needs realistic distances","status":"public","department":[{"_id":"ChLa"}],"publisher":"IEEE","_id":"750","year":"2017","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:48:18Z","date_updated":"2021-01-12T08:13:55Z","oa_version":"None","author":[{"full_name":"Pielorz, Jasmin","id":"49BC895A-F248-11E8-B48F-1D18A9856A87","first_name":"Jasmin","last_name":"Pielorz"},{"full_name":"Prandtstetter, Matthias","first_name":"Matthias","last_name":"Prandtstetter"},{"full_name":"Straub, Markus","first_name":"Markus","last_name":"Straub"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","first_name":"Christoph","last_name":"Lampert","full_name":"Lampert, Christoph"}],"type":"conference","abstract":[{"lang":"eng","text":"Modern communication technologies allow first responders to contact thousands of potential volunteers simultaneously for support during a crisis or disaster event. However, such volunteer efforts must be well coordinated and monitored, in order to offer an effective relief to the professionals. In this paper we extend earlier work on optimally assigning volunteers to selected landmark locations. In particular, we emphasize the aspect that obtaining good assignments requires not only advanced computational tools, but also a realistic measure of distance between volunteers and landmarks. Specifically, we propose the use of the Open Street Map (OSM) driving distance instead of he previously used flight distance. We find the OSM driving distance to be better aligned with the interests of volunteers and first responders. Furthermore, we show that relying on the flying distance leads to a substantial underestimation of the number of required volunteers, causing negative side effects in case of an actual crisis situation."}],"publist_id":"6906","quality_controlled":"1","page":"3760 - 3763","publication":"2017 IEEE International Conference on Big Data","citation":{"ama":"Pielorz J, Prandtstetter M, Straub M, Lampert C. Optimal geospatial volunteer allocation needs realistic distances. In: 2017 IEEE International Conference on Big Data. IEEE; 2017:3760-3763. doi:10.1109/BigData.2017.8258375","ieee":"J. Pielorz, M. Prandtstetter, M. Straub, and C. Lampert, “Optimal geospatial volunteer allocation needs realistic distances,” in 2017 IEEE International Conference on Big Data, Boston, MA, United States, 2017, pp. 3760–3763.","apa":"Pielorz, J., Prandtstetter, M., Straub, M., & Lampert, C. (2017). Optimal geospatial volunteer allocation needs realistic distances. In 2017 IEEE International Conference on Big Data (pp. 3760–3763). Boston, MA, United States: IEEE. https://doi.org/10.1109/BigData.2017.8258375","ista":"Pielorz J, Prandtstetter M, Straub M, Lampert C. 2017. Optimal geospatial volunteer allocation needs realistic distances. 2017 IEEE International Conference on Big Data. Big Data, 3760–3763.","short":"J. Pielorz, M. Prandtstetter, M. Straub, C. Lampert, in:, 2017 IEEE International Conference on Big Data, IEEE, 2017, pp. 3760–3763.","mla":"Pielorz, Jasmin, et al. “Optimal Geospatial Volunteer Allocation Needs Realistic Distances.” 2017 IEEE International Conference on Big Data, IEEE, 2017, pp. 3760–63, doi:10.1109/BigData.2017.8258375.","chicago":"Pielorz, Jasmin, Matthias Prandtstetter, Markus Straub, and Christoph Lampert. “Optimal Geospatial Volunteer Allocation Needs Realistic Distances.” In 2017 IEEE International Conference on Big Data, 3760–63. IEEE, 2017. https://doi.org/10.1109/BigData.2017.8258375."},"language":[{"iso":"eng"}],"conference":{"name":"Big Data","start_date":"2017-12-11","location":"Boston, MA, United States","end_date":"2017-12-14"},"doi":"10.1109/BigData.2017.8258375","date_published":"2017-12-01T00:00:00Z","scopus_import":1,"month":"12","day":"01","publication_identifier":{"isbn":["978-153862714-3"]}},{"month":"07","publication_identifier":{"issn":["10778926"]},"doi":"10.37236/6663","language":[{"iso":"eng"}],"oa":1,"quality_controlled":"1","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"file_date_updated":"2020-07-14T12:48:06Z","publist_id":"6859","ec_funded":1,"article_number":"P3.18","author":[{"full_name":"Fulek, Radoslav","last_name":"Fulek","first_name":"Radoslav","orcid":"0000-0001-8485-1774","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jan","last_name":"Kynčl","full_name":"Kynčl, Jan"},{"full_name":"Pálvölgyi, Dömötör","last_name":"Pálvölgyi","first_name":"Dömötör"}],"date_created":"2018-12-11T11:48:32Z","date_updated":"2022-03-18T12:58:53Z","volume":24,"year":"2017","publication_status":"published","publisher":"International Press","department":[{"_id":"UlWa"}],"day":"28","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2017-07-28T00:00:00Z","publication":"Electronic Journal of Combinatorics","citation":{"ista":"Fulek R, Kynčl J, Pálvölgyi D. 2017. Unified Hanani Tutte theorem. Electronic Journal of Combinatorics. 24(3), P3.18.","ieee":"R. Fulek, J. Kynčl, and D. Pálvölgyi, “Unified Hanani Tutte theorem,” Electronic Journal of Combinatorics, vol. 24, no. 3. International Press, 2017.","apa":"Fulek, R., Kynčl, J., & Pálvölgyi, D. (2017). Unified Hanani Tutte theorem. Electronic Journal of Combinatorics. International Press. https://doi.org/10.37236/6663","ama":"Fulek R, Kynčl J, Pálvölgyi D. Unified Hanani Tutte theorem. Electronic Journal of Combinatorics. 2017;24(3). doi:10.37236/6663","chicago":"Fulek, Radoslav, Jan Kynčl, and Dömötör Pálvölgyi. “Unified Hanani Tutte Theorem.” Electronic Journal of Combinatorics. International Press, 2017. https://doi.org/10.37236/6663.","mla":"Fulek, Radoslav, et al. “Unified Hanani Tutte Theorem.” Electronic Journal of Combinatorics, vol. 24, no. 3, P3.18, International Press, 2017, doi:10.37236/6663.","short":"R. Fulek, J. Kynčl, D. Pálvölgyi, Electronic Journal of Combinatorics 24 (2017)."},"article_type":"original","abstract":[{"text":"We introduce a common generalization of the strong Hanani–Tutte theorem and the weak Hanani–Tutte theorem: if a graph G has a drawing D in the plane where every pair of independent edges crosses an even number of times, then G has a planar drawing preserving the rotation of each vertex whose incident edges cross each other evenly in D. The theorem is implicit in the proof of the strong Hanani–Tutte theorem by Pelsmajer, Schaefer and Štefankovič. We give a new, somewhat simpler proof.","lang":"eng"}],"issue":"3","type":"journal_article","file":[{"relation":"main_file","file_id":"5853","date_updated":"2020-07-14T12:48:06Z","date_created":"2019-01-18T14:04:08Z","checksum":"ef320cff0f062051e858f929be6a3581","file_name":"2017_ElectrCombi_Fulek.pdf","access_level":"open_access","file_size":236944,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Published Version","_id":"795","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Unified Hanani Tutte theorem","status":"public","ddc":["000"],"intvolume":" 24"},{"date_created":"2018-12-11T11:48:33Z","date_updated":"2022-03-24T09:16:20Z","oa_version":"None","volume":48,"author":[{"full_name":"Fink, Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","first_name":"Johannes M","last_name":"Fink"}],"status":"public","title":"Photonenblockade aufgelöst","publication_status":"published","department":[{"_id":"JoFi"}],"intvolume":" 48","publisher":"Wiley","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"797","year":"2017","abstract":[{"lang":"ger","text":"Phasenübergänge helfen beim Verständnis von Vielteilchensystemen in der Festkörperphysik und Fluiddynamik bis hin zur Teilchenphysik. Unserer internationalen Kollaboration ist es gelungen, einen neuartigen Phasenübergang in einem Quantensystem zu beobachten [1]. In einem Mikrowellenresonator konnte erstmals die spontane Zustandsänderung von undurchsichtig zu transparent nachgewiesen werden."}],"issue":"3","publist_id":"6856","type":"journal_article","language":[{"iso":"eng"}],"date_published":"2017-05-01T00:00:00Z","doi":"10.1002/piuz.201770305","quality_controlled":"1","article_type":"original","page":"111 - 113","publication":"Physik in unserer Zeit","citation":{"chicago":"Fink, Johannes M. “Photonenblockade Aufgelöst.” Physik in Unserer Zeit. Wiley, 2017. https://doi.org/10.1002/piuz.201770305.","mla":"Fink, Johannes M. “Photonenblockade Aufgelöst.” Physik in Unserer Zeit, vol. 48, no. 3, Wiley, 2017, pp. 111–13, doi:10.1002/piuz.201770305.","short":"J.M. Fink, Physik in Unserer Zeit 48 (2017) 111–113.","ista":"Fink JM. 2017. Photonenblockade aufgelöst. Physik in unserer Zeit. 48(3), 111–113.","ieee":"J. M. Fink, “Photonenblockade aufgelöst,” Physik in unserer Zeit, vol. 48, no. 3. Wiley, pp. 111–113, 2017.","apa":"Fink, J. M. (2017). Photonenblockade aufgelöst. Physik in Unserer Zeit. Wiley. https://doi.org/10.1002/piuz.201770305","ama":"Fink JM. Photonenblockade aufgelöst. Physik in unserer Zeit. 2017;48(3):111-113. doi:10.1002/piuz.201770305"},"day":"01","month":"05","article_processing_charge":"No"},{"volume":6,"date_updated":"2021-12-14T07:54:36Z","date_created":"2021-06-02T14:28:58Z","author":[{"first_name":"David B","last_name":"Lyons","full_name":"Lyons, David B"},{"orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman","first_name":"Daniel","full_name":"Zilberman, Daniel"}],"department":[{"_id":"DaZi"}],"publisher":"eLife Sciences Publications","publication_status":"published","pmid":1,"year":"2017","extern":"1","file_date_updated":"2021-06-02T14:33:36Z","article_number":"e30674","language":[{"iso":"eng"}],"doi":"10.7554/elife.30674","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"},"external_id":{"pmid":["29140247"]},"publication_identifier":{"eissn":["2050-084X"]},"month":"11","oa_version":"Published Version","file":[{"checksum":"4cfcdd67511ae4aed3d993550e46e146","success":1,"date_created":"2021-06-02T14:33:36Z","date_updated":"2021-06-02T14:33:36Z","relation":"main_file","file_id":"9446","content_type":"application/pdf","file_size":1603102,"creator":"cziletti","access_level":"open_access","file_name":"2017_eLife_Lyons.pdf"}],"intvolume":" 6","status":"public","ddc":["570"],"title":"DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes","_id":"9445","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","abstract":[{"lang":"eng","text":"Cytosine methylation regulates essential genome functions across eukaryotes, but the fundamental question of whether nucleosomal or naked DNA is the preferred substrate of plant and animal methyltransferases remains unresolved. Here, we show that genetic inactivation of a single DDM1/Lsh family nucleosome remodeler biases methylation toward inter-nucleosomal linker DNA in Arabidopsis thaliana and mouse. We find that DDM1 enables methylation of DNA bound to the nucleosome, suggesting that nucleosome-free DNA is the preferred substrate of eukaryotic methyltransferases in vivo. Furthermore, we show that simultaneous mutation of DDM1 and linker histone H1 in Arabidopsis reproduces the strong linker-specific methylation patterns of species that diverged from flowering plants and animals over a billion years ago. Our results indicate that in the absence of remodeling, nucleosomes are strong barriers to DNA methyltransferases. Linker-specific methylation can evolve simply by breaking the connection between nucleosome remodeling and DNA methylation."}],"type":"journal_article","date_published":"2017-11-15T00:00:00Z","article_type":"original","citation":{"chicago":"Lyons, David B, and Daniel Zilberman. “DDM1 and Lsh Remodelers Allow Methylation of DNA Wrapped in Nucleosomes.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/elife.30674.","mla":"Lyons, David B., and Daniel Zilberman. “DDM1 and Lsh Remodelers Allow Methylation of DNA Wrapped in Nucleosomes.” ELife, vol. 6, e30674, eLife Sciences Publications, 2017, doi:10.7554/elife.30674.","short":"D.B. Lyons, D. Zilberman, ELife 6 (2017).","ista":"Lyons DB, Zilberman D. 2017. DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes. eLife. 6, e30674.","ieee":"D. B. Lyons and D. Zilberman, “DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes,” eLife, vol. 6. eLife Sciences Publications, 2017.","apa":"Lyons, D. B., & Zilberman, D. (2017). DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.30674","ama":"Lyons DB, Zilberman D. DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes. eLife. 2017;6. doi:10.7554/elife.30674"},"publication":"eLife","has_accepted_license":"1","article_processing_charge":"No","day":"15","scopus_import":"1"},{"publication_identifier":{"issn":["10643745"]},"month":"03","doi":"10.1007/978-1-4939-6940-1_5","language":[{"iso":"eng"}],"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)"}],"quality_controlled":"1","publist_id":"6451","author":[{"last_name":"Clifton","first_name":"Ben","full_name":"Clifton, Ben"},{"first_name":"Jason","last_name":"Whitfield","full_name":"Whitfield, Jason"},{"full_name":"Sanchez Romero, Inmaculada","id":"3D9C5D30-F248-11E8-B48F-1D18A9856A87","last_name":"Sanchez Romero","first_name":"Inmaculada"},{"full_name":"Herde, Michel","last_name":"Herde","first_name":"Michel"},{"full_name":"Henneberger, Christian","last_name":"Henneberger","first_name":"Christian"},{"last_name":"Janovjak","first_name":"Harald L","orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","full_name":"Janovjak, Harald L"},{"full_name":"Jackson, Colin","last_name":"Jackson","first_name":"Colin"}],"volume":1596,"date_created":"2018-12-11T11:49:24Z","date_updated":"2021-01-12T08:22:13Z","year":"2017","publisher":"Springer","department":[{"_id":"HaJa"}],"editor":[{"last_name":"Stein","first_name":"Viktor","full_name":"Stein, Viktor"}],"publication_status":"published","day":"15","scopus_import":1,"series_title":"Synthetic Protein Switches","date_published":"2017-03-15T00:00:00Z","citation":{"chicago":"Clifton, Ben, Jason Whitfield, Inmaculada Sanchez-Romero, Michel Herde, Christian Henneberger, Harald L Janovjak, and Colin Jackson. “Ancestral Protein Reconstruction and Circular Permutation for Improving the Stability and Dynamic Range of FRET Sensors.” In Synthetic Protein Switches, edited by Viktor Stein, 1596:71–87. Synthetic Protein Switches. Springer, 2017. https://doi.org/10.1007/978-1-4939-6940-1_5.","mla":"Clifton, Ben, et al. “Ancestral Protein Reconstruction and Circular Permutation for Improving the Stability and Dynamic Range of FRET Sensors.” Synthetic Protein Switches, edited by Viktor Stein, vol. 1596, Springer, 2017, pp. 71–87, doi:10.1007/978-1-4939-6940-1_5.","short":"B. Clifton, J. Whitfield, I. Sanchez-Romero, M. Herde, C. Henneberger, H.L. Janovjak, C. Jackson, in:, V. Stein (Ed.), Synthetic Protein Switches, Springer, 2017, pp. 71–87.","ista":"Clifton B, Whitfield J, Sanchez-Romero I, Herde M, Henneberger C, Janovjak HL, Jackson C. 2017.Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors. In: Synthetic Protein Switches. Methods in Molecular Biology, vol. 1596, 71–87.","ieee":"B. Clifton et al., “Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors,” in Synthetic Protein Switches, vol. 1596, V. Stein, Ed. Springer, 2017, pp. 71–87.","apa":"Clifton, B., Whitfield, J., Sanchez-Romero, I., Herde, M., Henneberger, C., Janovjak, H. L., & Jackson, C. (2017). Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors. In V. Stein (Ed.), Synthetic Protein Switches (Vol. 1596, pp. 71–87). Springer. https://doi.org/10.1007/978-1-4939-6940-1_5","ama":"Clifton B, Whitfield J, Sanchez-Romero I, et al. Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors. In: Stein V, ed. Synthetic Protein Switches. Vol 1596. Synthetic Protein Switches. Springer; 2017:71-87. doi:10.1007/978-1-4939-6940-1_5"},"publication":"Synthetic Protein Switches","page":"71 - 87","abstract":[{"text":"Small molecule biosensors based on Forster resonance energy transfer (FRET) enable small molecule signaling to be monitored with high spatial and temporal resolution in complex cellular environments. FRET sensors can be constructed by fusing a pair of fluorescent proteins to a suitable recognition domain, such as a member of the solute-binding protein (SBP) superfamily. However, naturally occurring SBPs may be unsuitable for incorporation into FRET sensors due to their low thermostability, which may preclude imaging under physiological conditions, or because the positions of their N- and C-termini may be suboptimal for fusion of fluorescent proteins, which may limit the dynamic range of the resulting sensors. Here, we show how these problems can be overcome using ancestral protein reconstruction and circular permutation. Ancestral protein reconstruction, used as a protein engineering strategy, leverages phylogenetic information to improve the thermostability of proteins, while circular permutation enables the termini of an SBP to be repositioned to maximize the dynamic range of the resulting FRET sensor. We also provide a protocol for cloning the engineered SBPs into FRET sensor constructs using Golden Gate assembly and discuss considerations for in situ characterization of the FRET sensors.","lang":"eng"}],"type":"book_chapter","alternative_title":["Methods in Molecular Biology"],"oa_version":"None","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"957","intvolume":" 1596","status":"public","title":"Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors"},{"_id":"963","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["004"],"title":"Timed network games with clocks","status":"public","intvolume":" 83","pubrep_id":"829","oa_version":"Published Version","file":[{"file_name":"IST-2017-829-v1+1_mfcs-cr.pdf","access_level":"open_access","creator":"system","file_size":369730,"content_type":"application/pdf","file_id":"5059","relation":"main_file","date_created":"2018-12-12T10:14:10Z","date_updated":"2020-07-14T12:48:18Z","checksum":"f55eaf7f3c36ea07801112acfedd17d5"}],"type":"conference","alternative_title":["LIPIcs"],"abstract":[{"lang":"eng","text":"Network games are widely used as a model for selfish resource-allocation problems. In the classical model, each player selects a path connecting her source and target vertex. The cost of traversing an edge depends on the number of players that traverse it. Thus, it abstracts the fact that different users may use a resource at different times and for different durations, which plays an important role in defining the costs of the users in reality. For example, when transmitting packets in a communication network, routing traffic in a road network, or processing a task in a production system, the traversal of the network involves an inherent delay, and so sharing and congestion of resources crucially depends on time. We study timed network games , which add a time component to network games. Each vertex v in the network is associated with a cost function, mapping the load on v to the price that a player pays for staying in v for one time unit with this load. In addition, each edge has a guard, describing time intervals in which the edge can be traversed, forcing the players to spend time on vertices. Unlike earlier work that add a time component to network games, the time in our model is continuous and cannot be discretized. In particular, players have uncountably many strategies, and a game may have uncountably many pure Nash equilibria. We study properties of timed network games with cost-sharing or congestion cost functions: their stability, equilibrium inefficiency, and complexity. In particular, we show that the answer to the question whether we can restrict attention to boundary strategies, namely ones in which edges are traversed only at the boundaries of guards, is mixed. "}],"citation":{"mla":"Avni, Guy, et al. Timed Network Games with Clocks. Vol. 83, 37, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.MFCS.2017.37.","short":"G. Avni, S. Guha, O. Kupferman, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","chicago":"Avni, Guy, Shibashis Guha, and Orna Kupferman. “Timed Network Games with Clocks,” Vol. 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.MFCS.2017.37.","ama":"Avni G, Guha S, Kupferman O. Timed network games with clocks. In: Vol 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.MFCS.2017.37","ista":"Avni G, Guha S, Kupferman O. 2017. Timed network games with clocks. MFCS: Mathematical Foundations of Computer Science (SG), LIPIcs, vol. 83, 37.","ieee":"G. Avni, S. Guha, and O. Kupferman, “Timed network games with clocks,” presented at the MFCS: Mathematical Foundations of Computer Science (SG), Aalborg, Denmark, 2017, vol. 83.","apa":"Avni, G., Guha, S., & Kupferman, O. (2017). Timed network games with clocks (Vol. 83). Presented at the MFCS: Mathematical Foundations of Computer Science (SG), Aalborg, Denmark: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.MFCS.2017.37"},"date_published":"2017-06-01T00:00:00Z","scopus_import":1,"day":"01","has_accepted_license":"1","year":"2017","publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","author":[{"full_name":"Avni, Guy","last_name":"Avni","first_name":"Guy","orcid":"0000-0001-5588-8287","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Guha, Shibashis","last_name":"Guha","first_name":"Shibashis"},{"full_name":"Kupferman, Orna","first_name":"Orna","last_name":"Kupferman"}],"related_material":{"record":[{"status":"public","relation":"later_version","id":"6005"}]},"date_updated":"2023-02-23T12:35:50Z","date_created":"2018-12-11T11:49:26Z","volume":83,"article_number":"37","file_date_updated":"2020-07-14T12:48:18Z","publist_id":"6438","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":[{"grant_number":"S11402-N23","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","name":"Moderne Concurrency Paradigms","call_identifier":"FWF"}],"conference":{"end_date":"2017-08-25","location":"Aalborg, Denmark","start_date":"2017-08-21","name":"MFCS: Mathematical Foundations of Computer Science (SG)"},"doi":"10.4230/LIPIcs.MFCS.2017.37","language":[{"iso":"eng"}],"month":"06","publication_identifier":{"issn":["18688969"]}},{"abstract":[{"text":"Across the nervous system, certain population spiking patterns are observed far more frequently than others. A hypothesis about this structure is that these collective activity patterns function as population codewords–collective modes–carrying information distinct from that of any single cell. We investigate this phenomenon in recordings of ∼150 retinal ganglion cells, the retina’s output. We develop a novel statistical model that decomposes the population response into modes; it predicts the distribution of spiking activity in the ganglion cell population with high accuracy. We found that the modes represent localized features of the visual stimulus that are distinct from the features represented by single neurons. Modes form clusters of activity states that are readily discriminated from one another. When we repeated the same visual stimulus, we found that the same mode was robustly elicited. These results suggest that retinal ganglion cells’ collective signaling is endowed with a form of error-correcting code–a principle that may hold in brain areas beyond retina.","lang":"eng"}],"type":"research_data_reference","date_created":"2021-07-23T11:34:34Z","date_updated":"2023-02-21T16:34:41Z","oa_version":"Published Version","author":[{"full_name":"Prentice, Jason","last_name":"Prentice","first_name":"Jason"},{"full_name":"Marre, Olivier","first_name":"Olivier","last_name":"Marre"},{"last_name":"Ioffe","first_name":"Mark","full_name":"Ioffe, Mark"},{"full_name":"Loback, Adrianna","first_name":"Adrianna","last_name":"Loback"},{"full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","first_name":"Gašper"},{"full_name":"Berry, Michael","first_name":"Michael","last_name":"Berry"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"1197"}]},"status":"public","title":"Data from: Error-robust modes of the retinal population code","publisher":"Dryad","department":[{"_id":"GaTk"}],"_id":"9709","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2017","day":"18","month":"10","article_processing_charge":"No","doi":"10.5061/dryad.1f1rc","date_published":"2017-10-18T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.1f1rc"}],"citation":{"chicago":"Prentice, Jason, Olivier Marre, Mark Ioffe, Adrianna Loback, Gašper Tkačik, and Michael Berry. “Data from: Error-Robust Modes of the Retinal Population Code.” Dryad, 2017. https://doi.org/10.5061/dryad.1f1rc.","mla":"Prentice, Jason, et al. Data from: Error-Robust Modes of the Retinal Population Code. Dryad, 2017, doi:10.5061/dryad.1f1rc.","short":"J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, M. Berry, (2017).","ista":"Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. 2017. Data from: Error-robust modes of the retinal population code, Dryad, 10.5061/dryad.1f1rc.","apa":"Prentice, J., Marre, O., Ioffe, M., Loback, A., Tkačik, G., & Berry, M. (2017). Data from: Error-robust modes of the retinal population code. Dryad. https://doi.org/10.5061/dryad.1f1rc","ieee":"J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, and M. Berry, “Data from: Error-robust modes of the retinal population code.” Dryad, 2017.","ama":"Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. Data from: Error-robust modes of the retinal population code. 2017. doi:10.5061/dryad.1f1rc"},"oa":1},{"month":"12","publication_identifier":{"issn":["15537390"]},"language":[{"iso":"eng"}],"doi":"10.1371/journal.pgen.1007122","quality_controlled":"1","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"file_date_updated":"2020-07-14T12:46:46Z","publist_id":"7275","ec_funded":1,"article_number":"e1007122","date_updated":"2023-02-23T14:10:34Z","date_created":"2018-12-11T11:47:04Z","volume":13,"author":[{"last_name":"Nikolic","first_name":"Nela","orcid":"0000-0001-9068-6090","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","full_name":"Nikolic, Nela"},{"full_name":"Schreiber, Frank","last_name":"Schreiber","first_name":"Frank"},{"last_name":"Dal Co","first_name":"Alma","full_name":"Dal Co, Alma"},{"first_name":"Daniel","last_name":"Kiviet","full_name":"Kiviet, Daniel"},{"full_name":"Bergmiller, Tobias","first_name":"Tobias","last_name":"Bergmiller","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5396-4346"},{"last_name":"Littmann","first_name":"Sten","full_name":"Littmann, Sten"},{"full_name":"Kuypers, Marcel","last_name":"Kuypers","first_name":"Marcel"},{"first_name":"Martin","last_name":"Ackermann","full_name":"Ackermann, Martin"}],"related_material":{"record":[{"id":"9844","relation":"research_data","status":"public"},{"status":"public","relation":"research_data","id":"9845"},{"status":"public","relation":"research_data","id":"9846"}]},"publication_status":"published","department":[{"_id":"CaGu"}],"publisher":"Public Library of Science","year":"2017","day":"18","has_accepted_license":"1","scopus_import":1,"date_published":"2017-12-18T00:00:00Z","publication":"PLoS Genetics","citation":{"ama":"Nikolic N, Schreiber F, Dal Co A, et al. Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations. PLoS Genetics. 2017;13(12). doi:10.1371/journal.pgen.1007122","apa":"Nikolic, N., Schreiber, F., Dal Co, A., Kiviet, D., Bergmiller, T., Littmann, S., … Ackermann, M. (2017). Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1007122","ieee":"N. Nikolic et al., “Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations,” PLoS Genetics, vol. 13, no. 12. Public Library of Science, 2017.","ista":"Nikolic N, Schreiber F, Dal Co A, Kiviet D, Bergmiller T, Littmann S, Kuypers M, Ackermann M. 2017. Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations. PLoS Genetics. 13(12), e1007122.","short":"N. Nikolic, F. Schreiber, A. Dal Co, D. Kiviet, T. Bergmiller, S. Littmann, M. Kuypers, M. Ackermann, PLoS Genetics 13 (2017).","mla":"Nikolic, Nela, et al. “Cell-to-Cell Variation and Specialization in Sugar Metabolism in Clonal Bacterial Populations.” PLoS Genetics, vol. 13, no. 12, e1007122, Public Library of Science, 2017, doi:10.1371/journal.pgen.1007122.","chicago":"Nikolic, Nela, Frank Schreiber, Alma Dal Co, Daniel Kiviet, Tobias Bergmiller, Sten Littmann, Marcel Kuypers, and Martin Ackermann. “Cell-to-Cell Variation and Specialization in Sugar Metabolism in Clonal Bacterial Populations.” PLoS Genetics. Public Library of Science, 2017. https://doi.org/10.1371/journal.pgen.1007122."},"abstract":[{"lang":"eng","text":"While we have good understanding of bacterial metabolism at the population level, we know little about the metabolic behavior of individual cells: do single cells in clonal populations sometimes specialize on different metabolic pathways? Such metabolic specialization could be driven by stochastic gene expression and could provide individual cells with growth benefits of specialization. We measured the degree of phenotypic specialization in two parallel metabolic pathways, the assimilation of glucose and arabinose. We grew Escherichia coli in chemostats, and used isotope-labeled sugars in combination with nanometer-scale secondary ion mass spectrometry and mathematical modeling to quantify sugar assimilation at the single-cell level. We found large variation in metabolic activities between single cells, both in absolute assimilation and in the degree to which individual cells specialize in the assimilation of different sugars. Analysis of transcriptional reporters indicated that this variation was at least partially based on cell-to-cell variation in gene expression. Metabolic differences between cells in clonal populations could potentially reduce metabolic incompatibilities between different pathways, and increase the rate at which parallel reactions can be performed."}],"issue":"12","type":"journal_article","file":[{"relation":"main_file","file_id":"5088","date_updated":"2020-07-14T12:46:46Z","date_created":"2018-12-12T10:14:35Z","checksum":"22426d9382f21554bad5fa5967afcfd0","file_name":"IST-2018-959-v1+1_2017_Nikolic_Cell-to-cell.pdf","access_level":"open_access","file_size":1308475,"content_type":"application/pdf","creator":"system"}],"oa_version":"Published Version","pubrep_id":"959","ddc":["576","579"],"status":"public","title":"Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations","intvolume":" 13","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"541"},{"title":"Supplementary materials and methods; Full data set from effects of mutations in phage restriction sites during escape from restriction–modification","status":"public","publisher":"The Royal Society","department":[{"_id":"CaGu"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9847","year":"2017","date_created":"2021-08-09T13:54:38Z","date_updated":"2023-02-23T12:29:44Z","oa_version":"Published Version","author":[{"id":"4569785E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7460-7479","first_name":"Maros","last_name":"Pleska","full_name":"Pleska, Maros"},{"full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","first_name":"Calin C"}],"related_material":{"record":[{"id":"561","relation":"used_in_publication","status":"public"}]},"type":"research_data_reference","abstract":[{"text":"information on culture conditions, phage mutagenesis, verification and lysate preparation; Raw data","lang":"eng"}],"citation":{"ama":"Pleska M, Guet CC. Supplementary materials and methods; Full data set from effects of mutations in phage restriction sites during escape from restriction–modification. 2017. doi:10.6084/m9.figshare.5633917.v1","ieee":"M. Pleska and C. C. Guet, “Supplementary materials and methods; Full data set from effects of mutations in phage restriction sites during escape from restriction–modification.” The Royal Society, 2017.","apa":"Pleska, M., & Guet, C. C. (2017). Supplementary materials and methods; Full data set from effects of mutations in phage restriction sites during escape from restriction–modification. The Royal Society. https://doi.org/10.6084/m9.figshare.5633917.v1","ista":"Pleska M, Guet CC. 2017. Supplementary materials and methods; Full data set from effects of mutations in phage restriction sites during escape from restriction–modification, The Royal Society, 10.6084/m9.figshare.5633917.v1.","short":"M. Pleska, C.C. Guet, (2017).","mla":"Pleska, Maros, and Calin C. Guet. Supplementary Materials and Methods; Full Data Set from Effects of Mutations in Phage Restriction Sites during Escape from Restriction–Modification. The Royal Society, 2017, doi:10.6084/m9.figshare.5633917.v1.","chicago":"Pleska, Maros, and Calin C Guet. “Supplementary Materials and Methods; Full Data Set from Effects of Mutations in Phage Restriction Sites during Escape from Restriction–Modification.” The Royal Society, 2017. https://doi.org/10.6084/m9.figshare.5633917.v1."},"main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.5633917.v1","open_access":"1"}],"oa":1,"date_published":"2017-11-27T00:00:00Z","doi":"10.6084/m9.figshare.5633917.v1","month":"11","day":"27","article_processing_charge":"No"},{"citation":{"apa":"Nikolic, N., Schreiber, F., Dal Co, A., Kiviet, D., Bergmiller, T., Littmann, S., … Ackermann, M. (2017). Mathematical model. Public Library of Science. https://doi.org/10.1371/journal.pgen.1007122.s017","ieee":"N. Nikolic et al., “Mathematical model.” Public Library of Science, 2017.","ista":"Nikolic N, Schreiber F, Dal Co A, Kiviet D, Bergmiller T, Littmann S, Kuypers M, Ackermann M. 2017. Mathematical model, Public Library of Science, 10.1371/journal.pgen.1007122.s017.","ama":"Nikolic N, Schreiber F, Dal Co A, et al. Mathematical model. 2017. doi:10.1371/journal.pgen.1007122.s017","chicago":"Nikolic, Nela, Frank Schreiber, Alma Dal Co, Daniel Kiviet, Tobias Bergmiller, Sten Littmann, Marcel Kuypers, and Martin Ackermann. “Mathematical Model.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pgen.1007122.s017.","short":"N. Nikolic, F. Schreiber, A. Dal Co, D. Kiviet, T. Bergmiller, S. Littmann, M. Kuypers, M. Ackermann, (2017).","mla":"Nikolic, Nela, et al. Mathematical Model. Public Library of Science, 2017, doi:10.1371/journal.pgen.1007122.s017."},"date_published":"2017-12-18T00:00:00Z","doi":"10.1371/journal.pgen.1007122.s017","article_processing_charge":"No","day":"18","month":"12","year":"2017","_id":"9845","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Public Library of Science","department":[{"_id":"CaGu"}],"status":"public","title":"Mathematical model","related_material":{"record":[{"id":"541","relation":"used_in_publication","status":"public"}]},"author":[{"first_name":"Nela","last_name":"Nikolic","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9068-6090","full_name":"Nikolic, Nela"},{"full_name":"Schreiber, Frank","last_name":"Schreiber","first_name":"Frank"},{"first_name":"Alma","last_name":"Dal Co","full_name":"Dal Co, Alma"},{"first_name":"Daniel","last_name":"Kiviet","full_name":"Kiviet, Daniel"},{"full_name":"Bergmiller, Tobias","orcid":"0000-0001-5396-4346","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","last_name":"Bergmiller","first_name":"Tobias"},{"last_name":"Littmann","first_name":"Sten","full_name":"Littmann, Sten"},{"full_name":"Kuypers, Marcel","last_name":"Kuypers","first_name":"Marcel"},{"last_name":"Ackermann","first_name":"Martin","full_name":"Ackermann, Martin"}],"oa_version":"None","date_updated":"2023-02-23T12:25:04Z","date_created":"2021-08-09T13:31:51Z","type":"research_data_reference","abstract":[{"lang":"eng","text":"Estimates of 13 C-arabinose and 2 H-glucose uptake from the fractions of heavy isotopes measured\tin single cells"}]},{"doi":"10.1371/journal.pcbi.1005609.s001","date_published":"2017-07-18T00:00:00Z","citation":{"ama":"Lukacisinova M, Novak S, Paixao T. 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Paixao, (2017).","chicago":"Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Modelling and Simulation Details.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005609.s001."},"article_processing_charge":"No","month":"07","day":"18","oa_version":"Published Version","date_created":"2021-08-09T14:02:34Z","date_updated":"2023-02-23T12:55:39Z","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"696"}]},"author":[{"full_name":"Lukacisinova, Marta","last_name":"Lukacisinova","first_name":"Marta","orcid":"0000-0002-2519-8004","id":"4342E402-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Novak, Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87","last_name":"Novak","first_name":"Sebastian"},{"orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","last_name":"Paixao","first_name":"Tiago","full_name":"Paixao, Tiago"}],"publisher":"Public Library of Science","department":[{"_id":"ToBo"},{"_id":"NiBa"},{"_id":"CaGu"}],"status":"public","title":"Modelling and simulation details","_id":"9849","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2017","abstract":[{"lang":"eng","text":"This text provides additional information about the model, a derivation of the analytic results in Eq (4), and details about simulations of an additional parameter set."}],"type":"research_data_reference"},{"date_created":"2021-08-09T14:05:24Z","date_updated":"2023-02-23T12:55:39Z","oa_version":"Published Version","author":[{"full_name":"Lukacisinova, Marta","first_name":"Marta","last_name":"Lukacisinova","id":"4342E402-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2519-8004"},{"full_name":"Novak, Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian","last_name":"Novak"},{"full_name":"Paixao, Tiago","first_name":"Tiago","last_name":"Paixao","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"696"}]},"title":"Extensions of the model","status":"public","department":[{"_id":"ToBo"},{"_id":"CaGu"},{"_id":"NiBa"}],"publisher":"Public Library of Science","_id":"9850","year":"2017","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","abstract":[{"text":"In this text, we discuss how a cost of resistance and the possibility of lethal mutations impact our model.","lang":"eng"}],"type":"research_data_reference","date_published":"2017-07-18T00:00:00Z","doi":"10.1371/journal.pcbi.1005609.s002","citation":{"ista":"Lukacisinova M, Novak S, Paixao T. 2017. Extensions of the model, Public Library of Science, 10.1371/journal.pcbi.1005609.s002.","apa":"Lukacisinova, M., Novak, S., & Paixao, T. (2017). Extensions of the model. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005609.s002","ieee":"M. Lukacisinova, S. Novak, and T. Paixao, “Extensions of the model.” Public Library of Science, 2017.","ama":"Lukacisinova M, Novak S, Paixao T. Extensions of the model. 2017. doi:10.1371/journal.pcbi.1005609.s002","chicago":"Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Extensions of the Model.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005609.s002.","mla":"Lukacisinova, Marta, et al. Extensions of the Model. Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005609.s002.","short":"M. Lukacisinova, S. Novak, T. 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Crucially, they also need to compete for the interpretation of those signals with other neurons representing similar features. The form that this competition should take depends critically on the noise corrupting these signals. In this study we show that for the type of noise commonly observed in sensory systems, whose variance scales with the mean signal, sensory neurons should selectively divide their input signals by their predictions, suppressing ambiguous cues while amplifying others. Any change in the stimulus context alters which inputs are suppressed, leading to a deep dynamic reshaping of neural receptive fields going far beyond simple surround suppression. Paradoxically, these highly variable receptive fields go alongside and are in fact required for an invariant representation of external sensory features. In addition to offering a normative account of context-dependent changes in sensory responses, perceptual inference in the presence of signal-dependent noise accounts for ubiquitous features of sensory neurons such as divisive normalization, gain control and contrast dependent temporal dynamics."}],"issue":"6","type":"journal_article","file":[{"file_id":"4645","relation":"main_file","date_updated":"2020-07-14T12:47:40Z","date_created":"2018-12-12T10:07:47Z","checksum":"796a1026076af6f4405a47d985bc7b68","file_name":"IST-2017-898-v1+1_journal.pcbi.1005582.pdf","access_level":"open_access","creator":"system","file_size":14555676,"content_type":"application/pdf"}],"oa_version":"Published Version","pubrep_id":"898","ddc":["571"],"status":"public","title":"Sensory noise predicts divisive reshaping of receptive fields","intvolume":" 13","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"680","day":"01","has_accepted_license":"1","scopus_import":1,"date_published":"2017-06-01T00:00:00Z","publication":"PLoS Computational Biology","citation":{"ieee":"M. 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H., Lo, D., Le Goues, C., & Visser, W. (2017). JFIX: Semantics-based repair of Java programs via symbolic PathFinder. In Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis (pp. 376–379). Santa Barbara, CA, United States: ACM. https://doi.org/10.1145/3092703.3098225","ama":"Le X, Chu DH, Lo D, Le Goues C, Visser W. JFIX: Semantics-based repair of Java programs via symbolic PathFinder. In: Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis. ACM; 2017:376-379. doi:10.1145/3092703.3098225","chicago":"Le, Xuan, Duc Hiep Chu, David Lo, Claire Le Goues, and Willem Visser. “JFIX: Semantics-Based Repair of Java Programs via Symbolic PathFinder.” In Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis, 376–79. ACM, 2017. https://doi.org/10.1145/3092703.3098225.","mla":"Le, Xuan, et al. “JFIX: Semantics-Based Repair of Java Programs via Symbolic PathFinder.” Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis, ACM, 2017, pp. 376–79, doi:10.1145/3092703.3098225.","short":"X. Le, D.H. Chu, D. Lo, C. Le Goues, W. 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Such techniques can be generally classified into two families: syntactic- and semantics-based. Semantics-based APR, on which we focus, typically uses symbolic execution to infer semantic constraints and then program synthesis to construct repairs conforming to them. While syntactic-based APR techniques have been shown successful on bugs in real-world programs written in both C and Java, semantics-based APR techniques mostly target C programs. This leaves empirical comparisons of the APR families not fully explored, and developers without a Java-based semantics APR technique. We present JFix, a semantics-based APR framework that targets Java, and an associated Eclipse plugin. JFix is implemented atop Symbolic PathFinder, a well-known symbolic execution engine for Java programs. It extends one particular APR technique (Angelix), and is designed to be sufficiently generic to support a variety of such techniques. We demonstrate that semantics-based APR can indeed efficiently and effectively repair a variety of classes of bugs in large real-world Java programs. This supports our claim that the framework can both support developers seeking semantics-based repair of bugs in Java programs, as well as enable larger scale empirical studies comparing syntactic- and semantics-based APR targeting Java. The demonstration of our tool is available via the project website at: https://xuanbachle.github.io/semanticsrepair/ ","lang":"eng"}],"type":"conference"},{"month":"05","publication_identifier":{"issn":["1474-760X"],"eissn":["1465-6906"]},"doi":"10.1186/s13059-017-1230-2","language":[{"iso":"eng"}],"external_id":{"pmid":["28486944"]},"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","file_date_updated":"2021-06-07T12:31:36Z","extern":"1","article_number":"87","author":[{"first_name":"Daniel","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel"}],"date_updated":"2021-12-14T07:55:02Z","date_created":"2021-06-07T12:27:39Z","volume":18,"year":"2017","pmid":1,"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"DaZi"}],"day":"09","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2017-05-09T00:00:00Z","publication":"Genome Biology","citation":{"ista":"Zilberman D. 2017. An evolutionary case for functional gene body methylation in plants and animals. Genome Biology. 18(1), 87.","ieee":"D. Zilberman, “An evolutionary case for functional gene body methylation in plants and animals,” Genome Biology, vol. 18, no. 1. Springer Nature, 2017.","apa":"Zilberman, D. (2017). An evolutionary case for functional gene body methylation in plants and animals. Genome Biology. Springer Nature. https://doi.org/10.1186/s13059-017-1230-2","ama":"Zilberman D. An evolutionary case for functional gene body methylation in plants and animals. Genome Biology. 2017;18(1). doi:10.1186/s13059-017-1230-2","chicago":"Zilberman, Daniel. “An Evolutionary Case for Functional Gene Body Methylation in Plants and Animals.” Genome Biology. 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Evolutionary patterns indicate homeostatic functions for this type of methylation.","lang":"eng"}],"issue":"1","type":"journal_article","oa_version":"Published Version","file":[{"file_size":278183,"content_type":"application/pdf","creator":"asandaue","file_name":"2017_GenomeBiology_Zilberman.pdf","access_level":"open_access","date_updated":"2021-06-07T12:31:36Z","date_created":"2021-06-07T12:31:36Z","checksum":"5a455ad914e7d225b1baa4ab07fd925e","success":1,"relation":"main_file","file_id":"9507"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"9506","status":"public","title":"An evolutionary case for functional gene body methylation in plants and animals","ddc":["570"],"intvolume":" 18"},{"publist_id":"6450","author":[{"full_name":"Mitchell, Joshua","first_name":"Joshua","last_name":"Mitchell"},{"full_name":"Zhang, William","first_name":"William","last_name":"Zhang"},{"last_name":"Herde","first_name":"Michel","full_name":"Herde, Michel"},{"full_name":"Henneberger, Christian","first_name":"Christian","last_name":"Henneberger"},{"full_name":"Janovjak, Harald L","first_name":"Harald L","last_name":"Janovjak","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315"},{"full_name":"O'Mara, Megan","first_name":"Megan","last_name":"O'Mara"},{"last_name":"Jackson","first_name":"Colin","full_name":"Jackson, Colin"}],"volume":1596,"date_created":"2018-12-11T11:49:24Z","date_updated":"2021-01-12T08:22:13Z","year":"2017","publisher":"Springer","department":[{"_id":"HaJa"}],"editor":[{"full_name":"Stein, Viktor","first_name":"Viktor","last_name":"Stein"}],"publication_status":"published","publication_identifier":{"issn":["10643745"]},"month":"05","doi":"10.1007/978-1-4939-6940-1_6","language":[{"iso":"eng"}],"quality_controlled":"1","abstract":[{"text":"Biosensors that exploit Forster resonance energy transfer (FRET) can be used to visualize biological and physiological processes and are capable of providing detailed information in both spatial and temporal dimensions. In a FRET-based biosensor, substrate binding is associated with a change in the relative positions of two fluorophores, leading to a change in FRET efficiency that may be observed in the fluorescence spectrum. As a result, their design requires a ligand-binding protein that exhibits a conformational change upon binding. However, not all ligand-binding proteins produce responsive sensors upon conjugation to fluorescent proteins or dyes, and identifying the optimum locations for the fluorophores often involves labor-intensive iterative design or high-throughput screening. Combining the genetic fusion of a fluorescent protein to the ligand-binding protein with site-specific covalent attachment of a fluorescent dye can allow fine control over the positions of the two fluorophores, allowing the construction of very sensitive sensors. This relies upon the accurate prediction of the locations of the two fluorophores in bound and unbound states. In this chapter, we describe a method for computational identification of dye-attachment sites that allows the use of cysteine modification to attach synthetic dyes that can be paired with a fluorescent protein for the purposes of creating FRET sensors.","lang":"eng"}],"type":"book_chapter","alternative_title":["Methods in Molecular Biology"],"oa_version":"None","_id":"958","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","intvolume":" 1596","status":"public","title":"Method for developing optical sensors using a synthetic dye fluorescent protein FRET pair and computational modeling and assessment","day":"15","scopus_import":1,"series_title":"Synthetic Protein Switches","date_published":"2017-05-15T00:00:00Z","citation":{"ista":"Mitchell J, Zhang W, Herde M, Henneberger C, Janovjak HL, O’Mara M, Jackson C. 2017.Method for developing optical sensors using a synthetic dye fluorescent protein FRET pair and computational modeling and assessment. In: Synthetic Protein Switches. Methods in Molecular Biology, vol. 1596, 89–99.","apa":"Mitchell, J., Zhang, W., Herde, M., Henneberger, C., Janovjak, H. L., O’Mara, M., & Jackson, C. (2017). Method for developing optical sensors using a synthetic dye fluorescent protein FRET pair and computational modeling and assessment. In V. Stein (Ed.), Synthetic Protein Switches (Vol. 1596, pp. 89–99). Springer. https://doi.org/10.1007/978-1-4939-6940-1_6","ieee":"J. Mitchell et al., “Method for developing optical sensors using a synthetic dye fluorescent protein FRET pair and computational modeling and assessment,” in Synthetic Protein Switches, vol. 1596, V. Stein, Ed. Springer, 2017, pp. 89–99.","ama":"Mitchell J, Zhang W, Herde M, et al. Method for developing optical sensors using a synthetic dye fluorescent protein FRET pair and computational modeling and assessment. In: Stein V, ed. Synthetic Protein Switches. Vol 1596. Synthetic Protein Switches. Springer; 2017:89-99. doi:10.1007/978-1-4939-6940-1_6","chicago":"Mitchell, Joshua, William Zhang, Michel Herde, Christian Henneberger, Harald L Janovjak, Megan O’Mara, and Colin Jackson. “Method for Developing Optical Sensors Using a Synthetic Dye Fluorescent Protein FRET Pair and Computational Modeling and Assessment.” In Synthetic Protein Switches, edited by Viktor Stein, 1596:89–99. Synthetic Protein Switches. Springer, 2017. https://doi.org/10.1007/978-1-4939-6940-1_6.","mla":"Mitchell, Joshua, et al. “Method for Developing Optical Sensors Using a Synthetic Dye Fluorescent Protein FRET Pair and Computational Modeling and Assessment.” Synthetic Protein Switches, edited by Viktor Stein, vol. 1596, Springer, 2017, pp. 89–99, doi:10.1007/978-1-4939-6940-1_6.","short":"J. Mitchell, W. Zhang, M. Herde, C. Henneberger, H.L. Janovjak, M. O’Mara, C. Jackson, in:, V. Stein (Ed.), Synthetic Protein Switches, Springer, 2017, pp. 89–99."},"publication":"Synthetic Protein Switches","page":"89 - 99"},{"date_published":"2017-01-14T00:00:00Z","doi":"10.5061/dryad.pk16b","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.pk16b"}],"citation":{"short":"P. Riccio, C. Cebrián, H. Zong, S. Hippenmeyer, F. Costantini, (2017).","mla":"Riccio, Paul, et al. Data from: Ret and Etv4 Promote Directed Movements of Progenitor Cells during Renal Branching Morphogenesis. Dryad, 2017, doi:10.5061/dryad.pk16b.","chicago":"Riccio, Paul, Christina Cebrián, Hui Zong, Simon Hippenmeyer, and Frank Costantini. “Data from: Ret and Etv4 Promote Directed Movements of Progenitor Cells during Renal Branching Morphogenesis.” Dryad, 2017. https://doi.org/10.5061/dryad.pk16b.","ama":"Riccio P, Cebrián C, Zong H, Hippenmeyer S, Costantini F. Data from: Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis. 2017. doi:10.5061/dryad.pk16b","apa":"Riccio, P., Cebrián, C., Zong, H., Hippenmeyer, S., & Costantini, F. (2017). Data from: Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis. Dryad. https://doi.org/10.5061/dryad.pk16b","ieee":"P. Riccio, C. Cebrián, H. Zong, S. Hippenmeyer, and F. Costantini, “Data from: Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis.” Dryad, 2017.","ista":"Riccio P, Cebrián C, Zong H, Hippenmeyer S, Costantini F. 2017. Data from: Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis, Dryad, 10.5061/dryad.pk16b."},"oa":1,"day":"14","month":"01","article_processing_charge":"No","author":[{"full_name":"Riccio, Paul","last_name":"Riccio","first_name":"Paul"},{"last_name":"Cebrián","first_name":"Christina","full_name":"Cebrián, Christina"},{"full_name":"Zong, Hui","first_name":"Hui","last_name":"Zong"},{"full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","first_name":"Simon","last_name":"Hippenmeyer"},{"first_name":"Frank","last_name":"Costantini","full_name":"Costantini, Frank"}],"related_material":{"record":[{"status":"deleted","relation":"used_in_publication","id":"9702"}]},"date_updated":"2022-08-25T13:34:55Z","date_created":"2021-07-23T09:39:34Z","oa_version":"Published Version","year":"2017","_id":"9707","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","title":"Data from: Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis","status":"public","publisher":"Dryad","department":[{"_id":"SiHi"}],"abstract":[{"lang":"eng","text":"Branching morphogenesis of the epithelial ureteric bud forms the renal collecting duct system and is critical for normal nephron number, while low nephron number is implicated in hypertension and renal disease. Ureteric bud growth and branching requires GDNF signaling from the surrounding mesenchyme to cells at the ureteric bud tips, via the Ret receptor tyrosine kinase and coreceptor Gfrα1; Ret signaling up-regulates transcription factors Etv4 and Etv5, which are also critical for branching. Despite extensive knowledge of the genetic control of these events, it is not understood, at the cellular level, how renal branching morphogenesis is achieved or how Ret signaling influences epithelial cell behaviors to promote this process. Analysis of chimeric embryos previously suggested a role for Ret signaling in promoting cell rearrangements in the nephric duct, but this method was unsuited to study individual cell behaviors during ureteric bud branching. Here, we use Mosaic Analysis with Double Markers (MADM), combined with organ culture and time-lapse imaging, to trace the movements and divisions of individual ureteric bud tip cells. We first examine wild-type clones and then Ret or Etv4 mutant/wild-type clones in which the mutant and wild-type sister cells are differentially and heritably marked by green and red fluorescent proteins. We find that, in normal kidneys, most individual tip cells behave as self-renewing progenitors, some of whose progeny remain at the tips while others populate the growing UB trunks. In Ret or Etv4 MADM clones, the wild-type cells generated at a UB tip are much more likely to remain at, or move to, the new tips during branching and elongation, while their Ret−/− or Etv4−/− sister cells tend to lag behind and contribute only to the trunks. By tracking successive mitoses in a cell lineage, we find that Ret signaling has little effect on proliferation, in contrast to its effects on cell movement. Our results show that Ret/Etv4 signaling promotes directed cell movements in the ureteric bud tips, and suggest a model in which these cell movements mediate branching morphogenesis."}],"type":"research_data_reference"},{"date_published":"2017-12-18T00:00:00Z","doi":"10.1371/journal.pgen.1007122.s018","citation":{"ama":"Nikolic N, Schreiber F, Dal Co A, et al. Source data for figures and tables. 2017. doi:10.1371/journal.pgen.1007122.s018","apa":"Nikolic, N., Schreiber, F., Dal Co, A., Kiviet, D., Bergmiller, T., Littmann, S., … Ackermann, M. (2017). Source data for figures and tables. Public Library of Science. https://doi.org/10.1371/journal.pgen.1007122.s018","ieee":"N. Nikolic et al., “Source data for figures and tables.” Public Library of Science, 2017.","ista":"Nikolic N, Schreiber F, Dal Co A, Kiviet D, Bergmiller T, Littmann S, Kuypers M, Ackermann M. 2017. Source data for figures and tables, Public Library of Science, 10.1371/journal.pgen.1007122.s018.","short":"N. Nikolic, F. Schreiber, A. Dal Co, D. Kiviet, T. Bergmiller, S. Littmann, M. Kuypers, M. Ackermann, (2017).","mla":"Nikolic, Nela, et al. Source Data for Figures and Tables. Public Library of Science, 2017, doi:10.1371/journal.pgen.1007122.s018.","chicago":"Nikolic, Nela, Frank Schreiber, Alma Dal Co, Daniel Kiviet, Tobias Bergmiller, Sten Littmann, Marcel Kuypers, and Martin Ackermann. “Source Data for Figures and Tables.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pgen.1007122.s018."},"day":"18","month":"12","article_processing_charge":"No","author":[{"orcid":"0000-0001-9068-6090","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","last_name":"Nikolic","first_name":"Nela","full_name":"Nikolic, Nela"},{"full_name":"Schreiber, Frank","first_name":"Frank","last_name":"Schreiber"},{"full_name":"Dal Co, Alma","last_name":"Dal Co","first_name":"Alma"},{"full_name":"Kiviet, Daniel","first_name":"Daniel","last_name":"Kiviet"},{"orcid":"0000-0001-5396-4346","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","last_name":"Bergmiller","first_name":"Tobias","full_name":"Bergmiller, Tobias"},{"first_name":"Sten","last_name":"Littmann","full_name":"Littmann, Sten"},{"full_name":"Kuypers, Marcel","last_name":"Kuypers","first_name":"Marcel"},{"first_name":"Martin","last_name":"Ackermann","full_name":"Ackermann, Martin"}],"related_material":{"record":[{"id":"541","status":"public","relation":"used_in_publication"}]},"date_created":"2021-08-09T13:27:16Z","date_updated":"2023-02-23T12:25:04Z","oa_version":"Published Version","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9844","year":"2017","status":"public","title":"Source data for figures and tables","publisher":"Public Library of Science","department":[{"_id":"CaGu"}],"type":"research_data_reference"},{"publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"Springer","year":"2017","acknowledgement":"This work is partially funded by the DFG project “Verified Model Checkers” and by the Czech Science Foundation, grant No. P202/12/G061.","date_updated":"2023-06-21T13:29:46Z","date_created":"2023-06-21T13:21:14Z","volume":10205,"author":[{"id":"44CEF464-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8122-2881","first_name":"Jan","last_name":"Kretinsky","full_name":"Kretinsky, Jan"},{"full_name":"Meggendorfer, Tobias","first_name":"Tobias","last_name":"Meggendorfer","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","orcid":"0000-0002-1712-2165"},{"last_name":"Waldmann","first_name":"Clara","full_name":"Waldmann, Clara"},{"full_name":"Weininger, Maximilian","last_name":"Weininger","first_name":"Maximilian"}],"quality_controlled":"1","oa":1,"external_id":{"arxiv":["1701.05738"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1701.05738"}],"language":[{"iso":"eng"}],"conference":{"start_date":"2017-04-22","location":"Uppsala, Sweden","end_date":"2017-04-29","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems"},"doi":"10.1007/978-3-662-54577-5_26","month":"03","publication_identifier":{"eisbn":["9783662545775"],"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783662545768"]},"status":"public","title":"Index appearance record for transforming Rabin automata into parity automata","intvolume":" 10205","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13160","oa_version":"Preprint","alternative_title":["LNCS"],"type":"conference","abstract":[{"text":"Transforming deterministic ω\r\n-automata into deterministic parity automata is traditionally done using variants of appearance records. We present a more efficient variant of this approach, tailored to Rabin automata, and several optimizations applicable to all appearance records. We compare the methods experimentally and find out that our method produces smaller automata than previous approaches. Moreover, the experiments demonstrate the potential of our method for LTL synthesis, using LTL-to-Rabin translators. It leads to significantly smaller parity automata when compared to state-of-the-art approaches on complex formulae.","lang":"eng"}],"page":"443-460","publication":"Tools and Algorithms for the Construction and Analysis of Systems","citation":{"ama":"Kretinsky J, Meggendorfer T, Waldmann C, Weininger M. Index appearance record for transforming Rabin automata into parity automata. In: Tools and Algorithms for the Construction and Analysis of Systems. Vol 10205. Springer; 2017:443-460. doi:10.1007/978-3-662-54577-5_26","ista":"Kretinsky J, Meggendorfer T, Waldmann C, Weininger M. 2017. Index appearance record for transforming Rabin automata into parity automata. Tools and Algorithms for the Construction and Analysis of Systems. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 10205, 443–460.","ieee":"J. Kretinsky, T. Meggendorfer, C. Waldmann, and M. Weininger, “Index appearance record for transforming Rabin automata into parity automata,” in Tools and Algorithms for the Construction and Analysis of Systems, Uppsala, Sweden, 2017, vol. 10205, pp. 443–460.","apa":"Kretinsky, J., Meggendorfer, T., Waldmann, C., & Weininger, M. (2017). Index appearance record for transforming Rabin automata into parity automata. In Tools and Algorithms for the Construction and Analysis of Systems (Vol. 10205, pp. 443–460). Uppsala, Sweden: Springer. https://doi.org/10.1007/978-3-662-54577-5_26","mla":"Kretinsky, Jan, et al. “Index Appearance Record for Transforming Rabin Automata into Parity Automata.” Tools and Algorithms for the Construction and Analysis of Systems, vol. 10205, Springer, 2017, pp. 443–60, doi:10.1007/978-3-662-54577-5_26.","short":"J. Kretinsky, T. Meggendorfer, C. Waldmann, M. Weininger, in:, Tools and Algorithms for the Construction and Analysis of Systems, Springer, 2017, pp. 443–460.","chicago":"Kretinsky, Jan, Tobias Meggendorfer, Clara Waldmann, and Maximilian Weininger. “Index Appearance Record for Transforming Rabin Automata into Parity Automata.” In Tools and Algorithms for the Construction and Analysis of Systems, 10205:443–60. Springer, 2017. https://doi.org/10.1007/978-3-662-54577-5_26."},"date_published":"2017-03-31T00:00:00Z","day":"31","article_processing_charge":"No"},{"abstract":[{"lang":"eng","text":"Two-player games on graphs are widely studied in formal methods as they model the interaction between a system and its environment. The game is played by moving a token throughout a graph to produce an infinite path. There are several common modes to determine how the players move the token through the graph; e.g., in turn-based games the players alternate turns in moving the token. We study the bidding mode of moving the token, which, to the best of our knowledge, has never been studied in infinite-duration games. Both players have separate budgets, which sum up to $1$. In each turn, a bidding takes place. Both players submit bids simultaneously, and a bid is legal if it does not exceed the available budget. The winner of the bidding pays his bid to the other player and moves the token. For reachability objectives, repeated bidding games have been studied and are called Richman games. There, a central question is the existence and computation of threshold budgets; namely, a value t\\in [0,1] such that if\\PO's budget exceeds $t$, he can win the game, and if\\PT's budget exceeds 1-t, he can win the game. We focus on parity games and mean-payoff games. We show the existence of threshold budgets in these games, and reduce the problem of finding them to Richman games. We also determine the strategy-complexity of an optimal strategy. Our most interesting result shows that memoryless strategies suffice for mean-payoff bidding games. \r\n"}],"type":"conference","alternative_title":["LIPIcs"],"pubrep_id":"844","file":[{"access_level":"open_access","file_name":"IST-2017-844-v1+1_concur-cr.pdf","creator":"system","content_type":"application/pdf","file_size":335170,"file_id":"5318","relation":"main_file","checksum":"6d5cccf755207b91ccbef95d8275b013","date_updated":"2020-07-14T12:48:16Z","date_created":"2018-12-12T10:18:00Z"}],"oa_version":"Published Version","_id":"950","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 85","status":"public","ddc":["000"],"title":"Infinite-duration bidding games","has_accepted_license":"1","day":"01","scopus_import":1,"date_published":"2017-09-01T00:00:00Z","citation":{"ista":"Avni G, Henzinger TA, Chonev VK. 2017. Infinite-duration bidding games. CONCUR: Concurrency Theory, LIPIcs, vol. 85, 17.","apa":"Avni, G., Henzinger, T. A., & Chonev, V. K. (2017). Infinite-duration bidding games (Vol. 85). Presented at the CONCUR: Concurrency Theory, Berlin, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2017.21","ieee":"G. Avni, T. A. Henzinger, and V. K. Chonev, “Infinite-duration bidding games,” presented at the CONCUR: Concurrency Theory, Berlin, Germany, 2017, vol. 85.","ama":"Avni G, Henzinger TA, Chonev VK. Infinite-duration bidding games. In: Vol 85. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.CONCUR.2017.21","chicago":"Avni, Guy, Thomas A Henzinger, and Ventsislav K Chonev. “Infinite-Duration Bidding Games,” Vol. 85. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.CONCUR.2017.21.","mla":"Avni, Guy, et al. Infinite-Duration Bidding Games. Vol. 85, 17, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.CONCUR.2017.21.","short":"G. Avni, T.A. Henzinger, V.K. Chonev, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017."},"publist_id":"6466","file_date_updated":"2020-07-14T12:48:16Z","article_number":"17","related_material":{"record":[{"status":"public","relation":"later_version","id":"6752"}]},"author":[{"id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5588-8287","first_name":"Guy","last_name":"Avni","full_name":"Avni, Guy"},{"first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"last_name":"Chonev","first_name":"Ventsislav K","id":"36CBE2E6-F248-11E8-B48F-1D18A9856A87","full_name":"Chonev, Ventsislav K"}],"volume":85,"date_created":"2018-12-11T11:49:22Z","date_updated":"2023-08-29T07:02:13Z","year":"2017","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"publication_status":"published","publication_identifier":{"issn":["1868-8969"]},"month":"09","doi":"10.4230/LIPIcs.CONCUR.2017.21","conference":{"name":"CONCUR: Concurrency Theory","location":"Berlin, Germany","start_date":"2017-09-05","end_date":"2017-09-07"},"language":[{"iso":"eng"}],"external_id":{"arxiv":["1705.01433"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1"},{"file_date_updated":"2020-07-14T12:47:41Z","publist_id":"7033","article_number":"49","author":[{"full_name":"Lubiw, Anna","last_name":"Lubiw","first_name":"Anna"},{"full_name":"Masárová, Zuzana","orcid":"0000-0002-6660-1322","id":"45CFE238-F248-11E8-B48F-1D18A9856A87","last_name":"Masárová","first_name":"Zuzana"},{"first_name":"Uli","last_name":"Wagner","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli"}],"related_material":{"record":[{"relation":"later_version","status":"public","id":"5986"}]},"date_created":"2018-12-11T11:47:54Z","date_updated":"2023-09-05T15:01:43Z","volume":77,"year":"2017","publication_status":"published","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"UlWa"}],"month":"06","conference":{"start_date":"2017-07-04","location":"Brisbane, Australia","end_date":"2017-07-07","name":"SoCG: Symposium on Computational Geometry"},"doi":"10.4230/LIPIcs.SoCG.2017.49","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","abstract":[{"text":"Given a triangulation of a point set in the plane, a flip deletes an edge e whose removal leaves a convex quadrilateral, and replaces e by the opposite diagonal of the quadrilateral. It is well known that any triangulation of a point set can be reconfigured to any other triangulation by some sequence of flips. We explore this question in the setting where each edge of a triangulation has a label, and a flip transfers the label of the removed edge to the new edge. It is not true that every labelled triangulation of a point set can be reconfigured to every other labelled triangulation via a sequence of flips, but we characterize when this is possible. There is an obvious necessary condition: for each label l, if edge e has label l in the first triangulation and edge f has label l in the second triangulation, then there must be some sequence of flips that moves label l from e to f, ignoring all other labels. Bose, Lubiw, Pathak and Verdonschot formulated the Orbit Conjecture, which states that this necessary condition is also sufficient, i.e. that all labels can be simultaneously mapped to their destination if and only if each label individually can be mapped to its destination. We prove this conjecture. Furthermore, we give a polynomial-time algorithm to find a sequence of flips to reconfigure one labelled triangulation to another, if such a sequence exists, and we prove an upper bound of O(n7) on the length of the flip sequence. Our proof uses the topological result that the sets of pairwise non-crossing edges on a planar point set form a simplicial complex that is homeomorphic to a high-dimensional ball (this follows from a result of Orden and Santos; we give a different proof based on a shelling argument). The dual cell complex of this simplicial ball, called the flip complex, has the usual flip graph as its 1-skeleton. We use properties of the 2-skeleton of the flip complex to prove the Orbit Conjecture.","lang":"eng"}],"type":"conference","alternative_title":["LIPIcs"],"pubrep_id":"896","file":[{"file_name":"IST-2017-896-v1+1_LIPIcs-SoCG-2017-49.pdf","access_level":"open_access","content_type":"application/pdf","file_size":710007,"creator":"system","relation":"main_file","file_id":"5265","date_created":"2018-12-12T10:17:12Z","date_updated":"2020-07-14T12:47:41Z","checksum":"24fdde981cc513352a78dcf9b0660ae9"}],"oa_version":"Published Version","_id":"683","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","ddc":["514","516"],"title":"A proof of the orbit conjecture for flipping edge labelled triangulations","intvolume":" 77","day":"01","has_accepted_license":"1","scopus_import":1,"date_published":"2017-06-01T00:00:00Z","citation":{"mla":"Lubiw, Anna, et al. A Proof of the Orbit Conjecture for Flipping Edge Labelled Triangulations. Vol. 77, 49, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.SoCG.2017.49.","short":"A. Lubiw, Z. Masárová, U. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","chicago":"Lubiw, Anna, Zuzana Masárová, and Uli Wagner. “A Proof of the Orbit Conjecture for Flipping Edge Labelled Triangulations,” Vol. 77. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.SoCG.2017.49.","ama":"Lubiw A, Masárová Z, Wagner U. A proof of the orbit conjecture for flipping edge labelled triangulations. In: Vol 77. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.SoCG.2017.49","ista":"Lubiw A, Masárová Z, Wagner U. 2017. A proof of the orbit conjecture for flipping edge labelled triangulations. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 77, 49.","apa":"Lubiw, A., Masárová, Z., & Wagner, U. (2017). A proof of the orbit conjecture for flipping edge labelled triangulations (Vol. 77). Presented at the SoCG: Symposium on Computational Geometry, Brisbane, Australia: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2017.49","ieee":"A. Lubiw, Z. Masárová, and U. Wagner, “A proof of the orbit conjecture for flipping edge labelled triangulations,” presented at the SoCG: Symposium on Computational Geometry, Brisbane, Australia, 2017, vol. 77."}},{"has_accepted_license":"1","article_processing_charge":"No","day":"02","citation":{"ista":"Daca P. 2017. Statistical and logical methods for property checking. Institute of Science and Technology Austria.","ieee":"P. Daca, “Statistical and logical methods for property checking,” Institute of Science and Technology Austria, 2017.","apa":"Daca, P. (2017). Statistical and logical methods for property checking. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH_730","ama":"Daca P. Statistical and logical methods for property checking. 2017. doi:10.15479/AT:ISTA:TH_730","chicago":"Daca, Przemyslaw. “Statistical and Logical Methods for Property Checking.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:TH_730.","mla":"Daca, Przemyslaw. Statistical and Logical Methods for Property Checking. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:TH_730.","short":"P. Daca, Statistical and Logical Methods for Property Checking, Institute of Science and Technology Austria, 2017."},"page":"163","date_published":"2017-01-02T00:00:00Z","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"This dissertation concerns the automatic verification of probabilistic systems and programs with arrays by statistical and logical methods. Although statistical and logical methods are different in nature, we show that they can be successfully combined for system analysis. In the first part of the dissertation we present a new statistical algorithm for the verification of probabilistic systems with respect to unbounded properties, including linear temporal logic. Our algorithm often performs faster than the previous approaches, and at the same time requires less information about the system. In addition, our method can be generalized to unbounded quantitative properties such as mean-payoff bounds. In the second part, we introduce two techniques for comparing probabilistic systems. Probabilistic systems are typically compared using the notion of equivalence, which requires the systems to have the equal probability of all behaviors. However, this notion is often too strict, since probabilities are typically only empirically estimated, and any imprecision may break the relation between processes. On the one hand, we propose to replace the Boolean notion of equivalence by a quantitative distance of similarity. For this purpose, we introduce a statistical framework for estimating distances between Markov chains based on their simulation runs, and we investigate which distances can be approximated in our framework. On the other hand, we propose to compare systems with respect to a new qualitative logic, which expresses that behaviors occur with probability one or a positive probability. This qualitative analysis is robust with respect to modeling errors and applicable to many domains. In the last part, we present a new quantifier-free logic for integer arrays, which allows us to express counting. Counting properties are prevalent in array-manipulating programs, however they cannot be expressed in the quantified fragments of the theory of arrays. We present a decision procedure for our logic, and provide several complexity results."}],"_id":"1155","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","ddc":["004","005"],"title":"Statistical and logical methods for property checking","pubrep_id":"730","file":[{"file_id":"4880","relation":"main_file","checksum":"1406a681cb737508234fde34766be2c2","date_created":"2018-12-12T10:11:26Z","date_updated":"2020-07-14T12:44:34Z","access_level":"open_access","file_name":"IST-2017-730-v1+1_Statistical_and_Logical_Methods_for_Property_Checking.pdf","creator":"system","content_type":"application/pdf","file_size":1028586}],"oa_version":"Published Version","publication_identifier":{"issn":["2663-337X"]},"month":"01","oa":1,"project":[{"name":"Quantitative Reactive Modeling","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"}],"doi":"10.15479/AT:ISTA:TH_730","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"}],"ec_funded":1,"publist_id":"6203","file_date_updated":"2020-07-14T12:44:34Z","acknowledgement":" First of all, I want to thank my advisor, prof. Thomas A. Henzinger, for his guidance during my PhD program. I am grateful for the freedom I was given to pursue my research interests, and his continuous support. Working with prof. Henzinger was a truly inspiring experience and taught me what it means to be a scientist. I want to express my gratitude to my collaborators: Nikola Beneš, Krishnendu Chatterjee, Martin Chmelík, Ashutosh Gupta, Willibald Krenn, Jan Kˇretínský, Dejan Nickovic, Andrey Kupriyanov, and Tatjana Petrov. I have learned a great deal from my collaborators, and without their help this thesis would not be possible. In addition, I want to thank the members of my thesis committee: Dirk Beyer, Dejan Nickovic, and Georg Weissenbacher for their advice and reviewing this dissertation. I would especially like to acknowledge the late Helmut Veith, who was a member of my committee. I will remember Helmut for his kindness, enthusiasm, and wit, as well as for being an inspiring scientist. Finally, I would like to thank my colleagues for making my stay at IST such a pleasant experience: Guy Avni, Sergiy Bogomolov, Ventsislav Chonev, Rasmus Ibsen-Jensen, Mirco Giacobbe, Bernhard Kragl, Hui Kong, Petr Novotný, Jan Otop, Andreas Pavlogiannis, Tantjana Petrov, Arjun Radhakrishna, Jakob Ruess, Thorsten Tarrach, as well as other members of groups Henzinger and Chatterjee. ","year":"2017","department":[{"_id":"ToHe"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","related_material":{"record":[{"id":"1093","status":"public","relation":"part_of_dissertation"},{"id":"1230","status":"public","relation":"part_of_dissertation"},{"id":"1234","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"1391"},{"id":"1501","status":"public","relation":"part_of_dissertation"},{"id":"1502","relation":"part_of_dissertation","status":"public"},{"id":"2063","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"2167"}]},"author":[{"first_name":"Przemyslaw","last_name":"Daca","id":"49351290-F248-11E8-B48F-1D18A9856A87","full_name":"Daca, Przemyslaw"}],"date_created":"2018-12-11T11:50:27Z","date_updated":"2023-09-07T11:58:34Z"},{"date_published":"2017-02-01T00:00:00Z","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Bollback, Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4624-4612","first_name":"Jonathan P","last_name":"Bollback"},{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"citation":{"ama":"Payne P. Bacterial herd and social immunity to phages. 2017.","ista":"Payne P. 2017. Bacterial herd and social immunity to phages. Institute of Science and Technology Austria.","ieee":"P. Payne, “Bacterial herd and social immunity to phages,” Institute of Science and Technology Austria, 2017.","apa":"Payne, P. (2017). Bacterial herd and social immunity to phages. Institute of Science and Technology Austria.","mla":"Payne, Pavel. Bacterial Herd and Social Immunity to Phages. Institute of Science and Technology Austria, 2017.","short":"P. Payne, Bacterial Herd and Social Immunity to Phages, Institute of Science and Technology Austria, 2017.","chicago":"Payne, Pavel. “Bacterial Herd and Social Immunity to Phages.” Institute of Science and Technology Austria, 2017."},"oa":1,"page":"83","article_processing_charge":"No","has_accepted_license":"1","publication_identifier":{"issn":["2663-337X"]},"month":"02","day":"01","author":[{"full_name":"Payne, Pavel","id":"35F78294-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2711-9453","first_name":"Pavel","last_name":"Payne"}],"oa_version":"Published Version","file":[{"file_id":"6292","relation":"main_file","checksum":"a0fc5c26a89c0ea759947ffba87d0d8f","date_created":"2019-04-09T15:15:32Z","date_updated":"2020-07-14T12:47:27Z","access_level":"closed","file_name":"thesis_pavel_payne_final_w_signature_page.pdf","creator":"dernst","content_type":"application/pdf","file_size":3025175},{"checksum":"af531e921a7f64a9e0af4cd8783b2226","success":1,"date_updated":"2021-02-22T13:45:59Z","date_created":"2021-02-22T13:45:59Z","relation":"main_file","file_id":"9187","file_size":3111536,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2017_Payne_Thesis.pdf"}],"date_updated":"2023-09-07T12:00:00Z","date_created":"2019-04-09T15:16:45Z","_id":"6291","year":"2017","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"publisher":"Institute of Science and Technology Austria","status":"public","publication_status":"published","title":"Bacterial herd and social immunity to phages","ddc":["570"],"file_date_updated":"2021-02-22T13:45:59Z","abstract":[{"text":"Bacteria and their pathogens – phages – are the most abundant living entities on Earth. Throughout their coevolution, bacteria have evolved multiple immune systems to overcome the ubiquitous threat from the phages. Although the molecu- lar details of these immune systems’ functions are relatively well understood, their epidemiological consequences for the phage-bacterial communities have been largely neglected. In this thesis we employed both experimental and theoretical methods to explore whether herd and social immunity may arise in bacterial popu- lations. Using our experimental system consisting of Escherichia coli strains with a CRISPR based immunity to the T7 phage we show that herd immunity arises in phage-bacterial communities and that it is accentuated when the populations are spatially structured. By fitting a mathematical model, we inferred expressions for the herd immunity threshold and the velocity of spread of a phage epidemic in partially resistant bacterial populations, which both depend on the bacterial growth rate, phage burst size and phage latent period. We also investigated the poten- tial for social immunity in Streptococcus thermophilus and its phage 2972 using a bioinformatic analysis of potentially coding short open reading frames with a signalling signature, encoded within the CRISPR associated genes. Subsequently, we tested one identified potentially signalling peptide and found that its addition to a phage-challenged culture increases probability of survival of bacteria two fold, although the results were only marginally significant. Together, these results demonstrate that the ubiquitous arms races between bacteria and phages have further consequences at the level of the population.","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"]},{"publist_id":"7253","article_number":"20170646","related_material":{"record":[{"relation":"research_data","status":"public","id":"9847"},{"status":"public","relation":"dissertation_contains","id":"202"}]},"author":[{"full_name":"Pleska, Maros","id":"4569785E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7460-7479","first_name":"Maros","last_name":"Pleska"},{"full_name":"Guet, Calin C","last_name":"Guet","first_name":"Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"}],"volume":13,"date_created":"2018-12-11T11:47:11Z","date_updated":"2023-09-07T11:59:32Z","pmid":1,"year":"2017","acknowledgement":"This work was funded by an HFSP Young Investigators' grant RGY0079/2011 (C.C.G.). M.P. is a recipient of a DOC Fellowship of the Austrian Academy of Science at the Institute of Science and Technology Austria.","publisher":"The Royal Society","department":[{"_id":"CaGu"}],"publication_status":"published","publication_identifier":{"issn":["1744-9561"]},"month":"12","doi":"10.1098/rsbl.2017.0646","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1098/rsbl.2017.0646","open_access":"1"}],"oa":1,"external_id":{"pmid":["29237814"]},"project":[{"name":"Multi-Level Conflicts in Evolutionary Dynamics of Restriction-Modification Systems (HFSP Young investigators' grant)","_id":"251BCBEC-B435-11E9-9278-68D0E5697425","grant_number":"RGY0079/2011"},{"name":"Effects of Stochasticity on the Function of Restriction-Modi cation Systems at the Single-Cell Level (DOC Fellowship)","_id":"251D65D8-B435-11E9-9278-68D0E5697425","grant_number":"24210"}],"quality_controlled":"1","issue":"12","abstract":[{"lang":"eng","text":"Restriction–modification systems are widespread genetic elements that protect bacteria from bacteriophage infections by recognizing and cleaving heterologous DNA at short, well-defined sequences called restriction sites. Bioinformatic evidence shows that restriction sites are significantly underrepresented in bacteriophage genomes, presumably because bacteriophages with fewer restriction sites are more likely to escape cleavage by restriction–modification systems. However, how mutations in restriction sites affect the likelihood of bacteriophage escape is unknown. Using the bacteriophage l and the restriction–modification system EcoRI, we show that while mutation effects at different restriction sites are unequal, they are independent. As a result, the probability of bacteriophage escape increases with each mutated restriction site. Our results experimentally support the role of restriction site avoidance as a response to selection imposed by restriction–modification systems and offer an insight into the events underlying the process of bacteriophage escape."}],"type":"journal_article","oa_version":"Published Version","_id":"561","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 13","title":"Effects of mutations in phage restriction sites during escape from restriction–modification","status":"public","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2017-12-01T00:00:00Z","citation":{"ieee":"M. Pleska and C. C. Guet, “Effects of mutations in phage restriction sites during escape from restriction–modification,” Biology Letters, vol. 13, no. 12. The Royal Society, 2017.","apa":"Pleska, M., & Guet, C. C. (2017). Effects of mutations in phage restriction sites during escape from restriction–modification. Biology Letters. The Royal Society. https://doi.org/10.1098/rsbl.2017.0646","ista":"Pleska M, Guet CC. 2017. Effects of mutations in phage restriction sites during escape from restriction–modification. Biology Letters. 13(12), 20170646.","ama":"Pleska M, Guet CC. Effects of mutations in phage restriction sites during escape from restriction–modification. Biology Letters. 2017;13(12). doi:10.1098/rsbl.2017.0646","chicago":"Pleska, Maros, and Calin C Guet. “Effects of Mutations in Phage Restriction Sites during Escape from Restriction–Modification.” Biology Letters. The Royal Society, 2017. https://doi.org/10.1098/rsbl.2017.0646.","short":"M. Pleska, C.C. Guet, Biology Letters 13 (2017).","mla":"Pleska, Maros, and Calin C. Guet. “Effects of Mutations in Phage Restriction Sites during Escape from Restriction–Modification.” Biology Letters, vol. 13, no. 12, 20170646, The Royal Society, 2017, doi:10.1098/rsbl.2017.0646."},"publication":"Biology Letters","article_type":"original"},{"day":"27","article_processing_charge":"No","has_accepted_license":"1","date_published":"2017-09-27T00:00:00Z","citation":{"chicago":"Mitosch, Karin. “Timing, Variability and Cross-Protection in Bacteria – Insights from Dynamic Gene Expression Responses to Antibiotics.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_862.","short":"K. Mitosch, Timing, Variability and Cross-Protection in Bacteria – Insights from Dynamic Gene Expression Responses to Antibiotics, Institute of Science and Technology Austria, 2017.","mla":"Mitosch, Karin. Timing, Variability and Cross-Protection in Bacteria – Insights from Dynamic Gene Expression Responses to Antibiotics. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_862.","ieee":"K. Mitosch, “Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics,” Institute of Science and Technology Austria, 2017.","apa":"Mitosch, K. (2017). Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_862","ista":"Mitosch K. 2017. Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics. Institute of Science and Technology Austria.","ama":"Mitosch K. Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics. 2017. doi:10.15479/AT:ISTA:th_862"},"page":"113","abstract":[{"text":"Antibiotics have diverse effects on bacteria, including massive changes in bacterial gene expression. Whereas the gene expression changes under many antibiotics have been measured, the temporal organization of these responses and their dependence on the bacterial growth rate are unclear. As described in Chapter 1, we quantified the temporal gene expression changes in the bacterium Escherichia coli in response to the sudden exposure to antibiotics using a fluorescent reporter library and a robotic system. Our data show temporally structured gene expression responses, with response times for individual genes ranging from tens of minutes to several hours. We observed that many stress response genes were activated in response to antibiotics. As certain stress responses cross-protect bacteria from other stressors, we then asked whether cellular responses to antibiotics have a similar protective role in Chapter 2. Indeed, we found that the trimethoprim-induced acid stress response protects bacteria from subsequent acid stress. We combined microfluidics with time-lapse imaging to monitor survival, intracellular pH, and acid stress response in single cells. This approach revealed that the variable expression of the acid resistance operon gadBC strongly correlates with single-cell survival time. Cells with higher gadBC expression following trimethoprim maintain higher intracellular pH and survive the acid stress longer. Overall, we provide a way to identify single-cell cross-protection between antibiotics and environmental stressors from temporal gene expression data, and show how antibiotics can increase bacterial fitness in changing environments. While gene expression changes to antibiotics show a clear temporal structure at the population-level, it is unclear whether this clear temporal order is followed by every single cell. Using dual-reporter strains described in Chapter 3, we measured gene expression dynamics of promoter pairs in the same cells using microfluidics and microscopy. Chapter 4 shows that the oxidative stress response and the DNA stress response showed little timing variability and a clear temporal order under the antibiotic nitrofurantoin. In contrast, the acid stress response under trimethoprim ran independently from all other activated response programs including the DNA stress response, which showed particularly high timing variability in this stress condition. In summary, this approach provides insight into the temporal organization of gene expression programs at the single-cell level and suggests dependencies between response programs and the underlying variability-introducing mechanisms. Altogether, this work advances our understanding of the diverse effects that antibiotics have on bacteria. These results were obtained by taking into account gene expression dynamics, which allowed us to identify general principles, molecular mechanisms, and dependencies between genes. Our findings may have implications for infectious disease treatments, and microbial communities in the human body and in nature. ","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"pubrep_id":"862","file":[{"file_id":"6210","relation":"source_file","date_created":"2019-04-05T08:48:51Z","date_updated":"2020-07-14T12:48:09Z","checksum":"da3993c5f90f59a8e8623cc31ad501dd","file_name":"Thesis_KarinMitosch.docx","access_level":"closed","creator":"dernst","file_size":6331071,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"},{"content_type":"application/pdf","file_size":9289852,"creator":"dernst","file_name":"Thesis_KarinMitosch.pdf","access_level":"open_access","date_created":"2019-04-05T08:48:51Z","date_updated":"2020-07-14T12:48:09Z","checksum":"24c3d9e51992f1b721f3df55aa13fcb8","relation":"main_file","file_id":"6211"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"818","ddc":["571","579"],"status":"public","title":"Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics","month":"09","publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/AT:ISTA:th_862","degree_awarded":"PhD","supervisor":[{"full_name":"Bollenbach, Mark Tobias","orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach","first_name":"Mark Tobias"}],"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"},"file_date_updated":"2020-07-14T12:48:09Z","publist_id":"6831","author":[{"full_name":"Mitosch, Karin","first_name":"Karin","last_name":"Mitosch","id":"39B66846-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"2001"},{"id":"666","status":"public","relation":"part_of_dissertation"}]},"date_created":"2018-12-11T11:48:40Z","date_updated":"2023-09-07T12:00:26Z","acknowledgement":"First of all, I would like to express great gratitude to my PhD supervisor Tobias Bollenbach. Through his open and trusting attitude I had the freedom to explore different scientific directions during this project, and follow the research lines of my interest. I am thankful for constructive and often extensive discussions and his support and commitment during the different stages of my PhD. I want to thank my committee members, Călin Guet, Terry Hwa and Nassos Typas for their interest and their valuable input to this project. Special thanks to Nassos for career guidance, and for accepting me in his lab. A big thank you goes to the past, present and affiliated members of the Bollenbach group: Guillaume Chevereau, Marjon de Vos, Marta Lukačišinová, Veronika Bierbaum, Qi Qin, Marcin Zagórski, Martin Lukačišin, Andreas Angermayr, Bor Kavčič, Julia Tischler, Dilay Ayhan, Jaroslav Ferenc, and Georg Rieckh. I enjoyed working and discussing with you very much and I will miss our lengthy group meetings, our inspiring journal clubs, and our common lunches. Special thanks to Bor for great mental and professional support during the hard months of thesis writing, and to Marta for very creative times during the beginning of our PhDs. May the ‘Bacterial Survival Guide’ decorate the walls of IST forever! A great thanks to my friend and collaborator Georg Rieckh for his enthusiasm and for getting so involved in these projects, for his endurance and for his company throughout the years. Thanks to the FriSBi crowd at IST Austria for interesting meetings and discussions. In particular I want to thank Magdalena Steinrück, and Anna Andersson for inspiring exchange, and enjoyable time together. Thanks to everybody who contributed to the cover for Cell Systems: The constructive input from Tobias Bollenbach, Bor Kavčič, Georg Rieckh, Marta Lukačišinová, and Sebastian Nozzi, and the professional implementation by the graphic designer Martina Markus from the University of Cologne. Thanks to all my office mates in the first floor Bertalanffy building throughout the years: for ensuring a pleasant working atmosphere, and for your company! In general, I want to thank all the people that make IST such a great environment, with the many possibilities to shape our own social and research environment. I want to thank my family for all kind of practical support during the years, and my second family in Argentina for their enthusiasm. Thanks to my brother Bernhard and my sister Martina for being great siblings, and to Helena and Valentin for the joy you brought to my life. My deep gratitude goes to Sebastian Nozzi, for constant support, patience, love and for believing in me. ","year":"2017","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"ToBo"}]},{"publication_identifier":{"issn":["24054712"]},"month":"04","doi":"10.1016/j.cels.2017.03.001","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"project":[{"call_identifier":"FP7","name":"Optimality principles in responses to antibiotics","grant_number":"303507","_id":"25E83C2C-B435-11E9-9278-68D0E5697425"},{"_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","grant_number":"P27201-B22","name":"Revealing the mechanisms underlying drug interactions","call_identifier":"FWF"},{"name":"Revealing the fundamental limits of cell growth","_id":"25EB3A80-B435-11E9-9278-68D0E5697425","grant_number":"RGP0042/2013"}],"quality_controlled":"1","publist_id":"7061","ec_funded":1,"file_date_updated":"2020-07-14T12:47:35Z","related_material":{"record":[{"id":"818","status":"public","relation":"dissertation_contains"}]},"author":[{"full_name":"Mitosch, Karin","first_name":"Karin","last_name":"Mitosch","id":"39B66846-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Georg","last_name":"Rieckh","id":"34DA8BD6-F248-11E8-B48F-1D18A9856A87","full_name":"Rieckh, Georg"},{"last_name":"Bollenbach","first_name":"Tobias","orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","full_name":"Bollenbach, Tobias"}],"volume":4,"date_updated":"2023-09-07T12:00:25Z","date_created":"2018-12-11T11:47:48Z","year":"2017","department":[{"_id":"ToBo"},{"_id":"GaTk"}],"publisher":"Cell Press","publication_status":"published","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","day":"26","scopus_import":1,"date_published":"2017-04-26T00:00:00Z","citation":{"chicago":"Mitosch, Karin, Georg Rieckh, and Mark Tobias Bollenbach. “Noisy Response to Antibiotic Stress Predicts Subsequent Single Cell Survival in an Acidic Environment.” Cell Systems. Cell Press, 2017. https://doi.org/10.1016/j.cels.2017.03.001.","mla":"Mitosch, Karin, et al. “Noisy Response to Antibiotic Stress Predicts Subsequent Single Cell Survival in an Acidic Environment.” Cell Systems, vol. 4, no. 4, Cell Press, 2017, pp. 393–403, doi:10.1016/j.cels.2017.03.001.","short":"K. Mitosch, G. Rieckh, M.T. Bollenbach, Cell Systems 4 (2017) 393–403.","ista":"Mitosch K, Rieckh G, Bollenbach MT. 2017. Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment. Cell Systems. 4(4), 393–403.","ieee":"K. Mitosch, G. Rieckh, and M. T. Bollenbach, “Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment,” Cell Systems, vol. 4, no. 4. Cell Press, pp. 393–403, 2017.","apa":"Mitosch, K., Rieckh, G., & Bollenbach, M. T. (2017). Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment. Cell Systems. Cell Press. https://doi.org/10.1016/j.cels.2017.03.001","ama":"Mitosch K, Rieckh G, Bollenbach MT. Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment. Cell Systems. 2017;4(4):393-403. doi:10.1016/j.cels.2017.03.001"},"publication":"Cell Systems","page":"393 - 403","issue":"4","abstract":[{"lang":"eng","text":"Antibiotics elicit drastic changes in microbial gene expression, including the induction of stress response genes. While certain stress responses are known to “cross-protect” bacteria from other stressors, it is unclear whether cellular responses to antibiotics have a similar protective role. By measuring the genome-wide transcriptional response dynamics of Escherichia coli to four antibiotics, we found that trimethoprim induces a rapid acid stress response that protects bacteria from subsequent exposure to acid. Combining microfluidics with time-lapse imaging to monitor survival and acid stress response in single cells revealed that the noisy expression of the acid resistance operon gadBC correlates with single-cell survival. Cells with higher gadBC expression following trimethoprim maintain higher intracellular pH and survive the acid stress longer. The seemingly random single-cell survival under acid stress can therefore be predicted from gadBC expression and rationalized in terms of GadB/C molecular function. Overall, we provide a roadmap for identifying the molecular mechanisms of single-cell cross-protection between antibiotics and other stressors."}],"type":"journal_article","pubrep_id":"901","file":[{"date_updated":"2020-07-14T12:47:35Z","date_created":"2018-12-12T10:13:54Z","checksum":"04ff20011c3d9a601c514aa999a5fe1a","relation":"main_file","file_id":"5041","content_type":"application/pdf","file_size":2438660,"creator":"system","file_name":"IST-2017-901-v1+1_1-s2.0-S2405471217300868-main.pdf","access_level":"open_access"}],"oa_version":"Published Version","_id":"666","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 4","ddc":["576","610"],"title":"Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment","status":"public"},{"license":"https://creativecommons.org/licenses/by-nd/4.0/","ec_funded":1,"publist_id":"6828","file_date_updated":"2020-07-14T12:48:10Z","date_created":"2018-12-11T11:48:41Z","date_updated":"2023-09-07T12:01:59Z","related_material":{"record":[{"id":"1071","relation":"part_of_dissertation","status":"public"},{"id":"1437","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"1602"},{"status":"public","relation":"part_of_dissertation","id":"1604"},{"id":"1607","status":"public","relation":"part_of_dissertation"},{"id":"1714","relation":"part_of_dissertation","status":"public"}]},"author":[{"id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722","first_name":"Andreas","last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas"}],"department":[{"_id":"KrCh"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","acknowledgement":"First, I am thankful to my advisor, Krishnendu Chatterjee, for offering me the opportunity to\r\nmaterialize my scientific curiosity in a remarkably wide range of interesting topics, as well as for his constant availability and continuous support throughout my doctoral studies. I have had the privilege of collaborating with, discussing and getting inspired by all members of my committee: Thomas A. Henzinger, Ulrich Schmid and Martin A. Nowak. The role of the above four people has been very instrumental both to the research carried out for this dissertation, and to the researcher I evolved to in the process.\r\nI have greatly enjoyed my numerous brainstorming sessions with Rasmus Ibsen-Jensen, many\r\nof which led to results on low-treewidth graphs presented here. I thank Alex Kößler for our\r\ndiscussions on modeling and analyzing real-time scheduling algorithms, Yaron Velner for our\r\ncollaboration on the Quantitative Interprocedural Analysis framework, and Nishant Sinha for our initial discussions on partial order reduction techniques in stateless model checking. I also thank Jan Otop, Ben Adlam, Bernhard Kragl and Josef Tkadlec for our fruitful collaborations on\r\ntopics outside the scope of this dissertation, as well as the interns Prateesh Goyal, Amir Kafshdar Goharshady, Samarth Mishra, Bhavya Choudhary and Marek Chalupa, with whom I have shared my excitement on various research topics. Together with my collaborators, I thank officemates and members of the Chatterjee and Henzinger groups throughout the years, Thorsten Tarrach, Ventsi Chonev, Roopsha Samanta, Przemek Daca, Mirco Giacobbe, Tanja Petrov, Ashutosh\r\nGupta, Arjun Radhakrishna, Petr Novontý, Christian Hilbe, Jakob Ruess, Martin Chmelik,\r\nCezara Dragoi, Johannes Reiter, Andrey Kupriyanov, Guy Avni, Sasha Rubin, Jessica Davies, Hongfei Fu, Thomas Ferrère, Pavol Cerný, Ali Sezgin, Jan Kretínský, Sergiy Bogomolov, Hui\r\nKong, Benjamin Aminof, Duc-Hiep Chu, and Damien Zufferey. Besides collaborations and office spaces, with many of the above people I have been fortunate to share numerous whiteboard\r\ndiscussions, as well as memorable long walks and amicable meals accompanied by stimulating\r\nconversations. I am highly indebted to Elisabeth Hacker for her continuous assistance in matters\r\nthat often exceeded her official duties, and who made my integration in Austria a smooth process.","year":"2017","publication_identifier":{"issn":["2663-337X"]},"month":"08","language":[{"iso":"eng"}],"supervisor":[{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"}],"degree_awarded":"PhD","doi":"10.15479/AT:ISTA:th_854","project":[{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"}],"oa":1,"tmp":{"short":"CC BY-ND (4.0)","image":"/image/cc_by_nd.png","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode"},"abstract":[{"lang":"eng","text":"This dissertation focuses on algorithmic aspects of program verification, and presents modeling and complexity advances on several problems related to the\r\nstatic analysis of programs, the stateless model checking of concurrent programs, and the competitive analysis of real-time scheduling algorithms.\r\nOur contributions can be broadly grouped into five categories.\r\n\r\nOur first contribution is a set of new algorithms and data structures for the quantitative and data-flow analysis of programs, based on the graph-theoretic notion of treewidth.\r\nIt has been observed that the control-flow graphs of typical programs have special structure, and are characterized as graphs of small treewidth.\r\nWe utilize this structural property to provide faster algorithms for the quantitative and data-flow analysis of recursive and concurrent programs.\r\nIn most cases we make an algebraic treatment of the considered problem,\r\nwhere several interesting analyses, such as the reachability, shortest path, and certain kind of data-flow analysis problems follow as special cases. \r\nWe exploit the constant-treewidth property to obtain algorithmic improvements for on-demand versions of the problems, \r\nand provide data structures with various tradeoffs between the resources spent in the preprocessing and querying phase.\r\nWe also improve on the algorithmic complexity of quantitative problems outside the algebraic path framework,\r\nnamely of the minimum mean-payoff, minimum ratio, and minimum initial credit for energy problems.\r\n\r\n\r\nOur second contribution is a set of algorithms for Dyck reachability with applications to data-dependence analysis and alias analysis.\r\nIn particular, we develop an optimal algorithm for Dyck reachability on bidirected graphs, which are ubiquitous in context-insensitive, field-sensitive points-to analysis.\r\nAdditionally, we develop an efficient algorithm for context-sensitive data-dependence analysis via Dyck reachability,\r\nwhere the task is to obtain analysis summaries of library code in the presence of callbacks.\r\nOur algorithm preprocesses libraries in almost linear time, after which the contribution of the library in the complexity of the client analysis is (i)~linear in the number of call sites and (ii)~only logarithmic in the size of the whole library, as opposed to linear in the size of the whole library.\r\nFinally, we prove that Dyck reachability is Boolean Matrix Multiplication-hard in general, and the hardness also holds for graphs of constant treewidth.\r\nThis hardness result strongly indicates that there exist no combinatorial algorithms for Dyck reachability with truly subcubic complexity.\r\n\r\n\r\nOur third contribution is the formalization and algorithmic treatment of the Quantitative Interprocedural Analysis framework.\r\nIn this framework, the transitions of a recursive program are annotated as good, bad or neutral, and receive a weight which measures\r\nthe magnitude of their respective effect.\r\nThe Quantitative Interprocedural Analysis problem asks to determine whether there exists an infinite run of the program where the long-run ratio of the bad weights over the good weights is above a given threshold.\r\nWe illustrate how several quantitative problems related to static analysis of recursive programs can be instantiated in this framework,\r\nand present some case studies to this direction.\r\n\r\n\r\nOur fourth contribution is a new dynamic partial-order reduction for the stateless model checking of concurrent programs. Traditional approaches rely on the standard Mazurkiewicz equivalence between traces, by means of partitioning the trace space into equivalence classes, and attempting to explore a few representatives from each class.\r\nWe present a new dynamic partial-order reduction method called the Data-centric Partial Order Reduction (DC-DPOR).\r\nOur algorithm is based on a new equivalence between traces, called the observation equivalence.\r\nDC-DPOR explores a coarser partitioning of the trace space than any exploration method based on the standard Mazurkiewicz equivalence.\r\nDepending on the program, the new partitioning can be even exponentially coarser.\r\nAdditionally, DC-DPOR spends only polynomial time in each explored class.\r\n\r\n\r\nOur fifth contribution is the use of automata and game-theoretic verification techniques in the competitive analysis and synthesis of real-time scheduling algorithms for firm-deadline tasks.\r\nOn the analysis side, we leverage automata on infinite words to compute the competitive ratio of real-time schedulers subject to various environmental constraints.\r\nOn the synthesis side, we introduce a new instance of two-player mean-payoff partial-information games, and show\r\nhow the synthesis of an optimal real-time scheduler can be reduced to computing winning strategies in this new type of games."}],"alternative_title":["ISTA Thesis"],"type":"dissertation","file":[{"relation":"main_file","file_id":"4900","checksum":"3a3ec003f6ee73f41f82a544d63dfc77","date_created":"2018-12-12T10:11:44Z","date_updated":"2020-07-14T12:48:10Z","access_level":"open_access","file_name":"IST-2017-854-v1+1_Pavlogiannis_Thesis_PubRep.pdf","file_size":4103115,"content_type":"application/pdf","creator":"system"},{"access_level":"closed","file_name":"2017_thesis_Pavlogiannis.zip","content_type":"application/zip","file_size":14744374,"creator":"dernst","relation":"source_file","file_id":"6201","checksum":"bd2facc45ff8a2e20c5ed313c2ccaa83","date_created":"2019-04-05T07:59:31Z","date_updated":"2020-07-14T12:48:10Z"}],"oa_version":"Published Version","pubrep_id":"854","ddc":["000"],"title":"Algorithmic advances in program analysis and their applications","status":"public","_id":"821","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","has_accepted_license":"1","article_processing_charge":"No","day":"09","date_published":"2017-08-09T00:00:00Z","page":"418","citation":{"ista":"Pavlogiannis A. 2017. Algorithmic advances in program analysis and their applications. Institute of Science and Technology Austria.","ieee":"A. Pavlogiannis, “Algorithmic advances in program analysis and their applications,” Institute of Science and Technology Austria, 2017.","apa":"Pavlogiannis, A. (2017). Algorithmic advances in program analysis and their applications. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_854","ama":"Pavlogiannis A. Algorithmic advances in program analysis and their applications. 2017. doi:10.15479/AT:ISTA:th_854","chicago":"Pavlogiannis, Andreas. “Algorithmic Advances in Program Analysis and Their Applications.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_854.","mla":"Pavlogiannis, Andreas. Algorithmic Advances in Program Analysis and Their Applications. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_854.","short":"A. Pavlogiannis, Algorithmic Advances in Program Analysis and Their Applications, Institute of Science and Technology Austria, 2017."}},{"acknowledgement":"ERC H2020 programme (grant agreement no. 648440)\r\nThanks to Jon Bollback for giving me the chance to do this work, for sharing the ideas that lay at the basis of this work, for his honesty and openness, showing himself to me as a person and not just as a boss. Thanks to Nick Barton for his guidance at the last stage, reading and commenting extensively on several versions of this manuscript, and for his encouragement; thanks to both Jon and Nick for their kindness and patience. Thanks to Erik van Nimwegen and Calin Guet for their time and willingness to be in my thesis committee, and to Erik van Nimwegen especially for agreeing to enter my thesis committee at the last moment, and for his very sharp, helpful and relevant comments during and after the defense. Thanks to my collaborators and discussion partners: Anne Kupczok, for her guidance, ideas and discussions during the construction of the manuscript of Chapter Two, and her comments on the manuscript; Georg Rieckh for making me aware of the issue of parameter identifiability, suggesting how to solve it, and for his unfortunate idea to start the plasmid enterprise in the first place; Murat Tugrul for sharing his model, for his enthusiasm, and his comments on Chapter Three; Srdjan Sarikas for his collaboration on the Monod model fitting, fast forwarding the analysis to turbo speed and making beautiful figures, and making the discussion fun on top of it all; Vanessa Barone for her last minute comments, especially on Chapter Three, providing a sharp and very helpful experimentalist perspective at the last moment; Maros Pleska and Marjon de Vos for their comments on the manuscript of Chapter Two; Gasper Tkacik for his crucial input on the relation between growth rate and lactose concentration; Bor Kavcic for his input on growth rate modeling and error propagation. Thanks to the Bollback, Bollenbach, Barton, Guet and Tkacik group members for both pro- viding an inspiring and supportive scientific environment to work in, as well as a lot of warmth and colour to everyday life. And thanks to the friends I found here, to the people who were there for me and to the people who changed my life, making it stranger and more beautiful than I could have imagined, Maros, Vanessa, Tade, Suzi, Andrej, Peter, Tiago, Kristof, Karin, Irene, Misha, Mato, Guillaume and Zanin. ","year":"2017","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"JoBo"}],"author":[{"id":"4C8C26A4-F248-11E8-B48F-1D18A9856A87","first_name":"Fabienne","last_name":"Jesse","full_name":"Jesse, Fabienne"}],"date_updated":"2023-09-07T12:01:21Z","date_created":"2018-12-11T11:48:41Z","file_date_updated":"2020-07-14T12:48:10Z","publist_id":"6829","ec_funded":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"},"project":[{"call_identifier":"H2020","name":"Selective Barriers to Horizontal Gene Transfer","grant_number":"648440","_id":"2578D616-B435-11E9-9278-68D0E5697425"}],"doi":"10.15479/AT:ISTA:th_857","supervisor":[{"first_name":"Jonathan P","last_name":"Bollback","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4624-4612","full_name":"Bollback, Jonathan P"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"month":"08","publication_identifier":{"issn":["2663-337X"]},"_id":"820","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"The lac operon in the wild","ddc":["576","577","579"],"status":"public","pubrep_id":"857","file":[{"relation":"main_file","file_id":"5252","checksum":"c62257a7bff0c5f39e1abffc6bfcca5c","date_created":"2018-12-12T10:17:00Z","date_updated":"2020-07-14T12:48:10Z","access_level":"open_access","file_name":"IST-2017-857-v1+1_thesis_fabienne.pdf","file_size":3417773,"content_type":"application/pdf","creator":"system"},{"relation":"source_file","file_id":"6212","date_created":"2019-04-05T08:51:59Z","date_updated":"2020-07-14T12:48:10Z","checksum":"fc87d7d72fce52824a3ae7dcad0413a8","file_name":"2017_thesis_Jesse_source.tex","access_level":"closed","content_type":"application/x-tex","file_size":215899,"creator":"dernst"}],"oa_version":"Published Version","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"The lac operon is a classic model system for bacterial gene regulation, and has been studied extensively in E. coli, a classic model organism. However, not much is known about E. coli’s ecology and life outside the laboratory, in particular in soil and water environments. The natural diversity of the lac operon outside the laboratory, its role in the ecology of E. coli and the selection pressures it is exposed to, are similarly unknown.\r\nIn Chapter Two of this thesis, I explore the genetic diversity, phylogenetic history and signatures of selection of the lac operon across 20 natural isolates of E. coli and divergent clades of Escherichia. I found that complete lac operons were present in all isolates examined, which in all but one case were functional. The lac operon phylogeny conformed to the whole-genome phylogeny of the divergent Escherichia clades, which excludes horizontal gene transfer as an explanation for the presence of functional lac operons in these clades. All lac operon genes showed a signature of purifying selection; this signature was strongest for the lacY gene. Lac operon genes of human and environmental isolates showed similar signatures of selection, except the lacZ gene, which showed a stronger signature of selection in environmental isolates.\r\nIn Chapter Three, I try to identify the natural genetic variation relevant for phenotype and fitness in the lac operon, comparing growth rate on lactose and LacZ activity of the lac operons of these wild isolates in a common genetic background. Sequence variation in the lac promoter region, upstream of the -10 and -35 RNA polymerase binding motif, predicted variation in LacZ activity at full induction, using a thermodynamic model of polymerase binding (Tugrul, 2016). However, neither variation in LacZ activity, nor RNA polymerase binding predicted by the model correlated with variation in growth rate. Lac operons of human and environmental isolates did not differ systematically in either growth rate on lactose or LacZ protein activity, suggesting that these lac operons have been exposed to similar selection pressures. We thus have no evidence that the phenotypic variation we measured is relevant for fitness.\r\nTo start assessing the effect of genomic background on the growth phenotype conferred by the lac operon, I compared growth on minimal medium with lactose between lac operon constructs and the corresponding original isolates, I found that maximal growth rate was determined by genomic background, with almost all backgrounds conferring higher growth rates than lab strain K12 MG1655. However, I found no evidence that the lactose concentration at which growth was half maximal depended on genomic background.","lang":"eng"}],"citation":{"ama":"Jesse F. The lac operon in the wild. 2017. doi:10.15479/AT:ISTA:th_857","ista":"Jesse F. 2017. The lac operon in the wild. Institute of Science and Technology Austria.","ieee":"F. Jesse, “The lac operon in the wild,” Institute of Science and Technology Austria, 2017.","apa":"Jesse, F. (2017). The lac operon in the wild. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_857","mla":"Jesse, Fabienne. The Lac Operon in the Wild. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_857.","short":"F. Jesse, The Lac Operon in the Wild, Institute of Science and Technology Austria, 2017.","chicago":"Jesse, Fabienne. “The Lac Operon in the Wild.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_857."},"page":"87","date_published":"2017-08-25T00:00:00Z","day":"25","article_processing_charge":"No","has_accepted_license":"1"},{"date_published":"2017-06-26T00:00:00Z","citation":{"mla":"Rybar, Michal. (The Exact Security of) Message Authentication Codes. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_828.","short":"M. Rybar, (The Exact Security of) Message Authentication Codes, Institute of Science and Technology Austria, 2017.","chicago":"Rybar, Michal. “(The Exact Security of) Message Authentication Codes.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_828.","ama":"Rybar M. (The exact security of) Message authentication codes. 2017. doi:10.15479/AT:ISTA:th_828","ista":"Rybar M. 2017. (The exact security of) Message authentication codes. Institute of Science and Technology Austria.","apa":"Rybar, M. (2017). (The exact security of) Message authentication codes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_828","ieee":"M. Rybar, “(The exact security of) Message authentication codes,” Institute of Science and Technology Austria, 2017."},"page":"86","day":"26","has_accepted_license":"1","article_processing_charge":"No","pubrep_id":"828","file":[{"file_name":"IST-2017-828-v1+3_2017_Rybar_thesis.pdf","access_level":"open_access","content_type":"application/pdf","file_size":847400,"creator":"system","relation":"main_file","file_id":"4799","date_updated":"2020-07-14T12:48:12Z","date_created":"2018-12-12T10:10:13Z","checksum":"ff8639ec4bded6186f44c7bd3ee26804"},{"file_name":"2017_Thesis_Rybar_source.zip","access_level":"closed","creator":"dernst","file_size":26054879,"content_type":"application/zip","file_id":"6202","relation":"source_file","date_updated":"2020-07-14T12:48:12Z","date_created":"2019-04-05T08:24:11Z","checksum":"3462101745ce8ad199c2d0f75dae4a7e"}],"oa_version":"Published Version","_id":"838","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["000"],"title":"(The exact security of) Message authentication codes","status":"public","abstract":[{"lang":"eng","text":"In this thesis we discuss the exact security of message authentications codes HMAC , NMAC , and PMAC . NMAC is a mode of operation which turns a fixed input-length keyed hash function f into a variable input-length function. A practical single-key variant of NMAC called HMAC is a very popular and widely deployed message authentication code (MAC). PMAC is a block-cipher based mode of operation, which also happens to be the most famous fully parallel MAC. NMAC was introduced by Bellare, Canetti and Krawczyk Crypto’96, who proved it to be a secure pseudorandom function (PRF), and thus also a MAC, under two assumptions. Unfortunately, for many instantiations of HMAC one of them has been found to be wrong. To restore the provable guarantees for NMAC , Bellare [Crypto’06] showed its security without this assumption. PMAC was introduced by Black and Rogaway at Eurocrypt 2002. If instantiated with a pseudorandom permutation over n -bit strings, PMAC constitutes a provably secure variable input-length PRF. For adversaries making q queries, each of length at most ` (in n -bit blocks), and of total length σ ≤ q` , the original paper proves an upper bound on the distinguishing advantage of O ( σ 2 / 2 n ), while the currently best bound is O ( qσ/ 2 n ). In this work we show that this bound is tight by giving an attack with advantage Ω( q 2 `/ 2 n ). In the PMAC construction one initially XORs a mask to every message block, where the mask for the i th block is computed as τ i := γ i · L , where L is a (secret) random value, and γ i is the i -th codeword of the Gray code. Our attack applies more generally to any sequence of γ i ’s which contains a large coset of a subgroup of GF (2 n ). As for NMAC , our first contribution is a simpler and uniform proof: If f is an ε -secure PRF (against q queries) and a δ - non-adaptively secure PRF (against q queries), then NMAC f is an ( ε + `qδ )-secure PRF against q queries of length at most ` blocks each. We also show that this ε + `qδ bound is basically tight by constructing an f for which an attack with advantage `qδ exists. Moreover, we analyze the PRF-security of a modification of NMAC called NI by An and Bellare that avoids the constant rekeying on multi-block messages in NMAC and allows for an information-theoretic analysis. We carry out such an analysis, obtaining a tight `q 2 / 2 c bound for this step, improving over the trivial bound of ` 2 q 2 / 2 c . Finally, we investigate, if the security of PMAC can be further improved by using τ i ’s that are k -wise independent, for k > 1 (the original has k = 1). We observe that the security of PMAC will not increase in general if k = 2, and then prove that the security increases to O ( q 2 / 2 n ), if the k = 4. Due to simple extension attacks, this is the best bound one can hope for, using any distribution on the masks. Whether k = 3 is already sufficient to get this level of security is left as an open problem. Keywords: Message authentication codes, Pseudorandom functions, HMAC, PMAC. "}],"type":"dissertation","alternative_title":["ISTA Thesis"],"doi":"10.15479/AT:ISTA:th_828","degree_awarded":"PhD","language":[{"iso":"eng"}],"oa":1,"month":"06","publication_identifier":{"issn":["2663-337X"]},"author":[{"full_name":"Rybar, Michal","id":"2B3E3DE8-F248-11E8-B48F-1D18A9856A87","last_name":"Rybar","first_name":"Michal"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"2082"},{"status":"public","relation":"part_of_dissertation","id":"6196"}]},"date_updated":"2023-09-07T12:02:28Z","date_created":"2018-12-11T11:48:46Z","year":"2017","publication_status":"published","department":[{"_id":"KrPi"}],"publisher":"Institute of Science and Technology Austria","file_date_updated":"2020-07-14T12:48:12Z","publist_id":"6810"},{"date_created":"2019-04-04T13:48:23Z","date_updated":"2023-09-07T12:02:27Z","volume":2016,"author":[{"last_name":"Gazi","first_name":"Peter","id":"3E0BFE38-F248-11E8-B48F-1D18A9856A87","full_name":"Gazi, Peter"},{"full_name":"Pietrzak, Krzysztof Z","first_name":"Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654"},{"last_name":"Rybar","first_name":"Michal","id":"2B3E3DE8-F248-11E8-B48F-1D18A9856A87","full_name":"Rybar, Michal"}],"related_material":{"record":[{"id":"838","status":"public","relation":"dissertation_contains"}]},"publication_status":"published","department":[{"_id":"KrPi"}],"publisher":"Ruhr University Bochum","year":"2017","file_date_updated":"2020-07-14T12:47:24Z","ec_funded":1,"language":[{"iso":"eng"}],"doi":"10.13154/TOSC.V2016.I2.145-161","quality_controlled":"1","project":[{"name":"Teaching Old Crypto New Tricks","call_identifier":"H2020","grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"month":"02","publication_identifier":{"eissn":["2519-173X"]},"oa_version":"Published Version","file":[{"file_id":"6197","relation":"main_file","checksum":"f23161d685dd957ae8d7274132999684","date_created":"2019-04-04T13:53:58Z","date_updated":"2020-07-14T12:47:24Z","access_level":"open_access","file_name":"2017_IACR_Gazi.pdf","creator":"dernst","file_size":597335,"content_type":"application/pdf"}],"status":"public","title":"The exact security of PMAC","ddc":["000"],"intvolume":" 2016","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"6196","abstract":[{"lang":"eng","text":"PMAC is a simple and parallel block-cipher mode of operation, which was introduced by Black and Rogaway at Eurocrypt 2002. If instantiated with a (pseudo)random permutation over n-bit strings, PMAC constitutes a provably secure variable input-length (pseudo)random function. For adversaries making q queries, each of length at most l (in n-bit blocks), and of total length σ ≤ ql, the original paper proves an upper bound on the distinguishing advantage of Ο(σ2/2n), while the currently best bound is Ο (qσ/2n).In this work we show that this bound is tight by giving an attack with advantage Ω (q2l/2n). In the PMAC construction one initially XORs a mask to every message block, where the mask for the ith block is computed as τi := γi·L, where L is a (secret) random value, and γi is the i-th codeword of the Gray code. Our attack applies more generally to any sequence of γi’s which contains a large coset of a subgroup of GF(2n). We then investigate if the security of PMAC can be further improved by using τi’s that are k-wise independent, for k > 1 (the original distribution is only 1-wise independent). We observe that the security of PMAC will not increase in general, even if the masks are chosen from a 2-wise independent distribution, and then prove that the security increases to O(q<2/2n), if the τi are 4-wise independent. Due to simple extension attacks, this is the best bound one can hope for, using any distribution on the masks. Whether 3-wise independence is already sufficient to get this level of security is left as an open problem."}],"issue":"2","type":"journal_article","date_published":"2017-02-03T00:00:00Z","page":"145-161","publication":"IACR Transactions on Symmetric Cryptology","citation":{"short":"P. Gazi, K.Z. Pietrzak, M. Rybar, IACR Transactions on Symmetric Cryptology 2016 (2017) 145–161.","mla":"Gazi, Peter, et al. “The Exact Security of PMAC.” IACR Transactions on Symmetric Cryptology, vol. 2016, no. 2, Ruhr University Bochum, 2017, pp. 145–61, doi:10.13154/TOSC.V2016.I2.145-161.","chicago":"Gazi, Peter, Krzysztof Z Pietrzak, and Michal Rybar. “The Exact Security of PMAC.” IACR Transactions on Symmetric Cryptology. Ruhr University Bochum, 2017. https://doi.org/10.13154/TOSC.V2016.I2.145-161.","ama":"Gazi P, Pietrzak KZ, Rybar M. The exact security of PMAC. IACR Transactions on Symmetric Cryptology. 2017;2016(2):145-161. doi:10.13154/TOSC.V2016.I2.145-161","ieee":"P. Gazi, K. Z. Pietrzak, and M. Rybar, “The exact security of PMAC,” IACR Transactions on Symmetric Cryptology, vol. 2016, no. 2. Ruhr University Bochum, pp. 145–161, 2017.","apa":"Gazi, P., Pietrzak, K. Z., & Rybar, M. (2017). The exact security of PMAC. IACR Transactions on Symmetric Cryptology. Ruhr University Bochum. https://doi.org/10.13154/TOSC.V2016.I2.145-161","ista":"Gazi P, Pietrzak KZ, Rybar M. 2017. The exact security of PMAC. IACR Transactions on Symmetric Cryptology. 2016(2), 145–161."},"day":"03","has_accepted_license":"1"},{"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"5828"}]},"author":[{"id":"310349D0-F248-11E8-B48F-1D18A9856A87","first_name":"Haibing","last_name":"Xu","full_name":"Xu, Haibing"}],"date_created":"2018-12-11T11:48:46Z","date_updated":"2023-09-07T12:06:38Z","acknowledgement":"I am very grateful for the opportunity I have had as a graduate student to explore and incredibly interesting branch of neuroscience, and for the people who made it possible. Firstly, I would like to offer my thanks to my supervisor Professor Jozsef Csicsvari for his great support, guidance and patience offered over the years. The door to his office was always open whenever I had questions. I have learned a lot from him about carefully designing experiments, asking interesting questions and how to integrate results into a broader picture. I also express my gratitude to the remarkable post- doc , Dr. Joseph O’Neill. He is a gre at scientific role model who is always willing to teach , and advice and talk through problems with his full attention. Many thanks to my wonderful “office mates” over the years and their support and encouragement, Alice Avernhe, Philipp Schönenberger, Desiree Dickerson, Karel Blahna, Charlotte Boccara, Igor Gridchyn, Peter Baracskay, Krisztián Kovács, Dámaris Rangel, Karola Käfer and Federico Stella. They were the ones in the lab for the many useful discussions about science and for making the laboratory such a nice and friendly place to work in. A special thank goes to Michael LoBianco and Jago Wallenschus for wonderful technical support. I would also like to thank Professor Peter Jonas and Professor David M Bannerman for being my qualifying exam and thesi s committee members despite their busy schedule. I am also very thankful to IST Austria for their support all throughout my PhD. ","year":"2017","publisher":"Institute of Science and Technology Austria","department":[{"_id":"JoCs"}],"publication_status":"published","publist_id":"6811","file_date_updated":"2020-07-14T12:48:12Z","doi":"10.15479/AT:ISTA:th_858","language":[{"iso":"eng"}],"supervisor":[{"orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari","first_name":"Jozsef L","full_name":"Csicsvari, Jozsef L"}],"degree_awarded":"PhD","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"},"publication_identifier":{"issn":["2663-337X"]},"month":"08","pubrep_id":"858","oa_version":"Published Version","file":[{"file_id":"6213","relation":"source_file","checksum":"f11925fbbce31e495124b6bc4f10573c","date_updated":"2020-07-14T12:48:12Z","date_created":"2019-04-05T08:59:51Z","access_level":"closed","file_name":"2017_Xu_Haibing_Thesis_Source.docx","creator":"dernst","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":3589490},{"date_created":"2019-04-05T08:59:51Z","date_updated":"2020-07-14T12:48:12Z","checksum":"ffb10749a537d615fab1ef0937ccb157","file_id":"6214","relation":"main_file","creator":"dernst","file_size":11668613,"content_type":"application/pdf","file_name":"2017_Xu_Thesis_IST.pdf","access_level":"open_access"}],"_id":"837","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["571"],"status":"public","title":"Reactivation of the hippocampal cognitive map in goal-directed spatial tasks","abstract":[{"text":"The hippocampus is a key brain region for memory and notably for spatial memory, and is needed for both spatial working and reference memories. Hippocampal place cells selectively discharge in specific locations of the environment to form mnemonic represen tations of space. Several behavioral protocols have been designed to test spatial memory which requires the experimental subject to utilize working memory and reference memory. However, less is known about how these memory traces are presented in the hippo campus, especially considering tasks that require both spatial working and long -term reference memory demand. The aim of my thesis was to elucidate how spatial working memory, reference memory, and the combination of both are represented in the hippocampus. In this thesis, using a radial eight -arm maze, I examined how the combined demand on these memories influenced place cell assemblies while reference memories were partially updated by changing some of the reward- arms. This was contrasted with task varian ts requiring working or reference memories only. Reference memory update led to gradual place field shifts towards the rewards on the switched arms. Cells developed enhanced firing in passes between newly -rewarded arms as compared to those containing an unchanged reward. The working memory task did not show such gradual changes. Place assemblies on occasions replayed trajectories of the maze; at decision points the next arm choice was preferentially replayed in tasks needing reference memory while in the pure working memory task the previously visited arm was replayed. Hence trajectory replay only reflected the decision of the animal in tasks needing reference memory update. At the reward locations, in all three tasks outbound trajectories of the current arm were preferentially replayed, showing the animals’ next path to the center. At reward locations trajectories were replayed preferentially in reverse temporal order. Moreover, in the center reverse replay was seen in the working memory task but in the other tasks forward replay was seen. Hence, the direction of reactivation was determined by the goal locations so that part of the trajectory which was closer to the goal was reactivated later in an HSE while places further away from the goal were reactivated earlier. Altogether my work demonstrated that reference memory update triggers several levels of reorganization of the hippocampal cognitive map which are not seen in simpler working memory demand s. Moreover, hippocampus is likely to be involved in spatial decisions through reactivating planned trajectories when reference memory recall is required for such a decision. ","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"date_published":"2017-08-23T00:00:00Z","citation":{"chicago":"Xu, Haibing. “Reactivation of the Hippocampal Cognitive Map in Goal-Directed Spatial Tasks.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_858.","mla":"Xu, Haibing. Reactivation of the Hippocampal Cognitive Map in Goal-Directed Spatial Tasks. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_858.","short":"H. Xu, Reactivation of the Hippocampal Cognitive Map in Goal-Directed Spatial Tasks, Institute of Science and Technology Austria, 2017.","ista":"Xu H. 2017. Reactivation of the hippocampal cognitive map in goal-directed spatial tasks. Institute of Science and Technology Austria.","apa":"Xu, H. (2017). Reactivation of the hippocampal cognitive map in goal-directed spatial tasks. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_858","ieee":"H. Xu, “Reactivation of the hippocampal cognitive map in goal-directed spatial tasks,” Institute of Science and Technology Austria, 2017.","ama":"Xu H. Reactivation of the hippocampal cognitive map in goal-directed spatial tasks. 2017. doi:10.15479/AT:ISTA:th_858"},"page":"93","has_accepted_license":"1","article_processing_charge":"No","day":"23"},{"file_date_updated":"2020-07-14T12:48:15Z","publist_id":"6483","year":"2017","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"JiFr"}],"author":[{"full_name":"Adamowski, Maciek","orcid":"0000-0001-6463-5257","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","last_name":"Adamowski","first_name":"Maciek"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"1591"}]},"date_updated":"2023-09-07T12:06:09Z","date_created":"2018-12-11T11:49:18Z","month":"06","publication_identifier":{"issn":["2663-337X"]},"oa":1,"doi":"10.15479/AT:ISTA:th_842","degree_awarded":"PhD","supervisor":[{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří"}],"language":[{"iso":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"The thesis encompasses several topics of plant cell biology which were studied in the model plant Arabidopsis thaliana. Chapter 1 concerns the plant hormone auxin and its polar transport through cells and tissues. The highly controlled, directional transport of auxin is facilitated by plasma membrane-localized transporters. Transporters from the PIN family direct auxin transport due to their polarized localizations at cell membranes. Substantial effort has been put into research on cellular trafficking of PIN proteins, which is thought to underlie their polar distribution. I participated in a forward genetic screen aimed at identifying novel regulators of PIN polarity. The screen yielded several genes which may be involved in PIN polarity regulation or participate in polar auxin transport by other means. Chapter 2 focuses on the endomembrane system, with particular attention to clathrin-mediated endocytosis. The project started with identification of several proteins that interact with clathrin light chains. Among them, I focused on two putative homologues of auxilin, which in non-plant systems is an endocytotic factor known for uncoating clathrin-coated vesicles in the final step of endocytosis. The body of my work consisted of an in-depth characterization of transgenic A. thaliana lines overexpressing these putative auxilins in an inducible manner. Overexpression of these proteins leads to an inhibition of endocytosis, as documented by imaging of cargoes and clathrin-related endocytic machinery. An extension of this work is an investigation into a concept of homeostatic regulation acting between distinct transport processes in the endomembrane system. With auxilin overexpressing lines, where endocytosis is blocked specifically, I made observations on the mutual relationship between two opposite trafficking processes of secretion and endocytosis. In Chapter 3, I analyze cortical microtubule arrays and their relationship to auxin signaling and polarized growth in elongating cells. In plants, microtubules are organized into arrays just below the plasma membrane, and it is thought that their function is to guide membrane-docked cellulose synthase complexes. These, in turn, influence cell wall structure and cell shape by directed deposition of cellulose fibres. In elongating cells, cortical microtubule arrays are able to reorient in relation to long cell axis, and these reorientations have been linked to cell growth and to signaling of growth-regulating factors such as auxin or light. In this chapter, I am addressing the causal relationship between microtubule array reorientation, growth, and auxin signaling. I arrive at a model where array reorientation is not guided by auxin directly, but instead is only controlled by growth, which, in turn, is regulated by auxin.","lang":"eng"}],"_id":"938","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana ","ddc":["581","583","580"],"pubrep_id":"842","oa_version":"Published Version","file":[{"file_name":"2017_Adamowski-Thesis_Source.docx","access_level":"closed","creator":"dernst","file_size":46903863,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"6215","relation":"source_file","date_updated":"2020-07-14T12:48:15Z","date_created":"2019-04-05T09:03:20Z","checksum":"193425764d9aaaed3ac57062a867b315"},{"file_name":"2017_Adamowski-Thesis.pdf","access_level":"open_access","file_size":8698888,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"6216","date_updated":"2020-07-14T12:48:15Z","date_created":"2019-04-05T09:03:19Z","checksum":"df5ab01be81f821e1b958596a1ec8d21"}],"day":"02","article_processing_charge":"No","has_accepted_license":"1","citation":{"chicago":"Adamowski, Maciek. “Investigations into Cell Polarity and Trafficking in the Plant Model Arabidopsis Thaliana .” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_842.","mla":"Adamowski, Maciek. Investigations into Cell Polarity and Trafficking in the Plant Model Arabidopsis Thaliana . Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_842.","short":"M. Adamowski, Investigations into Cell Polarity and Trafficking in the Plant Model Arabidopsis Thaliana , Institute of Science and Technology Austria, 2017.","ista":"Adamowski M. 2017. Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana . Institute of Science and Technology Austria.","apa":"Adamowski, M. (2017). Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_842","ieee":"M. Adamowski, “Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana ,” Institute of Science and Technology Austria, 2017.","ama":"Adamowski M. Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana . 2017. doi:10.15479/AT:ISTA:th_842"},"page":"117","date_published":"2017-06-02T00:00:00Z"}]