[{"_id":"471","type":"journal_article","status":"public","date_updated":"2023-02-21T16:48:11Z","department":[{"_id":"ToHe"}],"abstract":[{"text":"We present a new algorithm for the statistical model checking of Markov chains with respect to unbounded temporal properties, including full linear temporal logic. The main idea is that we monitor each simulation run on the fly, in order to detect quickly if a bottom strongly connected component is entered with high probability, in which case the simulation run can be terminated early. As a result, our simulation runs are often much shorter than required by termination bounds that are computed a priori for a desired level of confidence on a large state space. In comparison to previous algorithms for statistical model checking our method is not only faster in many cases but also requires less information about the system, namely, only the minimum transition probability that occurs in the Markov chain. In addition, our method can be generalised to unbounded quantitative properties such as mean-payoff bounds. ","lang":"eng"}],"oa_version":"Submitted Version","main_file_link":[{"url":"https://arxiv.org/abs/1504.05739","open_access":"1"}],"scopus_import":1,"intvolume":" 18","month":"05","publication_status":"published","publication_identifier":{"issn":["15293785"]},"language":[{"iso":"eng"}],"ec_funded":1,"issue":"2","volume":18,"related_material":{"record":[{"status":"public","id":"1234","relation":"earlier_version"}]},"article_number":"12","project":[{"grant_number":"267989","name":"Quantitative Reactive Modeling","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","name":"Moderne Concurrency Paradigms","grant_number":"S11402-N23"},{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","grant_number":"Z211"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"citation":{"mla":"Daca, Przemyslaw, et al. “Faster Statistical Model Checking for Unbounded Temporal Properties.” ACM Transactions on Computational Logic (TOCL), vol. 18, no. 2, 12, ACM, 2017, doi:10.1145/3060139.","short":"P. Daca, T.A. Henzinger, J. Kretinsky, T. Petrov, ACM Transactions on Computational Logic (TOCL) 18 (2017).","ieee":"P. Daca, T. A. Henzinger, J. Kretinsky, and T. Petrov, “Faster statistical model checking for unbounded temporal properties,” ACM Transactions on Computational Logic (TOCL), vol. 18, no. 2. ACM, 2017.","apa":"Daca, P., Henzinger, T. A., Kretinsky, J., & Petrov, T. (2017). Faster statistical model checking for unbounded temporal properties. ACM Transactions on Computational Logic (TOCL). ACM. https://doi.org/10.1145/3060139","ama":"Daca P, Henzinger TA, Kretinsky J, Petrov T. Faster statistical model checking for unbounded temporal properties. ACM Transactions on Computational Logic (TOCL). 2017;18(2). doi:10.1145/3060139","chicago":"Daca, Przemyslaw, Thomas A Henzinger, Jan Kretinsky, and Tatjana Petrov. “Faster Statistical Model Checking for Unbounded Temporal Properties.” ACM Transactions on Computational Logic (TOCL). ACM, 2017. https://doi.org/10.1145/3060139.","ista":"Daca P, Henzinger TA, Kretinsky J, Petrov T. 2017. Faster statistical model checking for unbounded temporal properties. ACM Transactions on Computational Logic (TOCL). 18(2), 12."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"7349","author":[{"last_name":"Daca","full_name":"Daca, Przemyslaw","first_name":"Przemyslaw","id":"49351290-F248-11E8-B48F-1D18A9856A87"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"full_name":"Kretinsky, Jan","orcid":"0000-0002-8122-2881","last_name":"Kretinsky","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"},{"full_name":"Petrov, Tatjana","orcid":"0000-0002-9041-0905","last_name":"Petrov","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","first_name":"Tatjana"}],"title":"Faster statistical model checking for unbounded temporal properties","oa":1,"quality_controlled":"1","publisher":"ACM","year":"2017","publication":"ACM Transactions on Computational Logic (TOCL)","day":"01","date_created":"2018-12-11T11:46:39Z","date_published":"2017-05-01T00:00:00Z","doi":"10.1145/3060139"},{"day":"13","publication":"International Journal of Computational Geometry and Applications","has_accepted_license":"1","year":"2017","date_published":"2017-04-13T00:00:00Z","doi":"10.1142/S0218195916600050","date_created":"2018-12-11T11:46:43Z","page":"211 - 229","acknowledgement":"Supported by NSERC and the Ross and Muriel Cheriton Fellowship. Research supported by Austrian Science Fund (FWF): P25816-N15.","quality_controlled":"1","publisher":"World Scientific Publishing","oa":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Biedl T, Huber S, Palfrader P. 2017. Planar matchings for weighted straight skeletons. International Journal of Computational Geometry and Applications. 26(3–4), 211–229.","chicago":"Biedl, Therese, Stefan Huber, and Peter Palfrader. “Planar Matchings for Weighted Straight Skeletons.” International Journal of Computational Geometry and Applications. World Scientific Publishing, 2017. https://doi.org/10.1142/S0218195916600050.","ieee":"T. Biedl, S. Huber, and P. Palfrader, “Planar matchings for weighted straight skeletons,” International Journal of Computational Geometry and Applications, vol. 26, no. 3–4. World Scientific Publishing, pp. 211–229, 2017.","short":"T. Biedl, S. Huber, P. Palfrader, International Journal of Computational Geometry and Applications 26 (2017) 211–229.","ama":"Biedl T, Huber S, Palfrader P. Planar matchings for weighted straight skeletons. International Journal of Computational Geometry and Applications. 2017;26(3-4):211-229. doi:10.1142/S0218195916600050","apa":"Biedl, T., Huber, S., & Palfrader, P. (2017). Planar matchings for weighted straight skeletons. International Journal of Computational Geometry and Applications. World Scientific Publishing. https://doi.org/10.1142/S0218195916600050","mla":"Biedl, Therese, et al. “Planar Matchings for Weighted Straight Skeletons.” International Journal of Computational Geometry and Applications, vol. 26, no. 3–4, World Scientific Publishing, 2017, pp. 211–29, doi:10.1142/S0218195916600050."},"title":"Planar matchings for weighted straight skeletons","author":[{"last_name":"Biedl","full_name":"Biedl, Therese","first_name":"Therese"},{"id":"4700A070-F248-11E8-B48F-1D18A9856A87","first_name":"Stefan","full_name":"Huber, Stefan","orcid":"0000-0002-8871-5814","last_name":"Huber"},{"full_name":"Palfrader, Peter","last_name":"Palfrader","first_name":"Peter"}],"publist_id":"7338","file":[{"file_name":"IST-2018-949-v1+1_2016_huber_PLanar_matchings.pdf","date_created":"2018-12-12T10:09:34Z","file_size":769296,"date_updated":"2020-07-14T12:46:35Z","creator":"system","file_id":"4758","checksum":"f79e8558bfe4b368dfefeb8eec2e3a5e","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":26,"related_material":{"record":[{"id":"10892","status":"public","relation":"earlier_version"}]},"issue":"3-4","license":"https://creativecommons.org/licenses/by/4.0/","oa_version":"Published Version","abstract":[{"text":"We introduce planar matchings on directed pseudo-line arrangements, which yield a planar set of pseudo-line segments such that only matching-partners are adjacent. By translating the planar matching problem into a corresponding stable roommates problem we show that such matchings always exist. Using our new framework, we establish, for the first time, a complete, rigorous definition of weighted straight skeletons, which are based on a so-called wavefront propagation process. We present a generalized and unified approach to treat structural changes in the wavefront that focuses on the restoration of weak planarity by finding planar matchings.","lang":"eng"}],"month":"04","intvolume":" 26","scopus_import":1,"ddc":["004","514","516"],"date_updated":"2023-02-21T16:06:22Z","file_date_updated":"2020-07-14T12:46:35Z","department":[{"_id":"HeEd"}],"_id":"481","status":"public","pubrep_id":"949","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"}},{"_id":"484","type":"journal_article","status":"public","date_updated":"2021-01-12T08:00:58Z","department":[{"_id":"RoSe"}],"abstract":[{"text":"We consider the dynamics of a large quantum system of N identical bosons in 3D interacting via a two-body potential of the form N3β-1w(Nβ(x - y)). For fixed 0 = β < 1/3 and large N, we obtain a norm approximation to the many-body evolution in the Nparticle Hilbert space. The leading order behaviour of the dynamics is determined by Hartree theory while the second order is given by Bogoliubov theory.","lang":"eng"}],"oa_version":"Submitted Version","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1509.04631"}],"scopus_import":1,"intvolume":" 21","month":"01","publication_status":"published","publication_identifier":{"issn":["10950761"]},"language":[{"iso":"eng"}],"ec_funded":1,"volume":21,"issue":"3","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"},{"grant_number":"P27533_N27","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","call_identifier":"FWF","_id":"25C878CE-B435-11E9-9278-68D0E5697425"}],"citation":{"mla":"Nam, Phan, and Marcin M. Napiórkowski. “Bogoliubov Correction to the Mean-Field Dynamics of Interacting Bosons.” Advances in Theoretical and Mathematical Physics, vol. 21, no. 3, International Press, 2017, pp. 683–738, doi:10.4310/ATMP.2017.v21.n3.a4.","short":"P. Nam, M.M. Napiórkowski, Advances in Theoretical and Mathematical Physics 21 (2017) 683–738.","ieee":"P. Nam and M. M. Napiórkowski, “Bogoliubov correction to the mean-field dynamics of interacting bosons,” Advances in Theoretical and Mathematical Physics, vol. 21, no. 3. International Press, pp. 683–738, 2017.","ama":"Nam P, Napiórkowski MM. Bogoliubov correction to the mean-field dynamics of interacting bosons. Advances in Theoretical and Mathematical Physics. 2017;21(3):683-738. doi:10.4310/ATMP.2017.v21.n3.a4","apa":"Nam, P., & Napiórkowski, M. M. (2017). Bogoliubov correction to the mean-field dynamics of interacting bosons. Advances in Theoretical and Mathematical Physics. International Press. https://doi.org/10.4310/ATMP.2017.v21.n3.a4","chicago":"Nam, Phan, and Marcin M Napiórkowski. “Bogoliubov Correction to the Mean-Field Dynamics of Interacting Bosons.” Advances in Theoretical and Mathematical Physics. International Press, 2017. https://doi.org/10.4310/ATMP.2017.v21.n3.a4.","ista":"Nam P, Napiórkowski MM. 2017. Bogoliubov correction to the mean-field dynamics of interacting bosons. Advances in Theoretical and Mathematical Physics. 21(3), 683–738."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Phan","id":"404092F4-F248-11E8-B48F-1D18A9856A87","last_name":"Nam","full_name":"Nam, Phan"},{"last_name":"Napiórkowski","full_name":"Napiórkowski, Marcin M","first_name":"Marcin M","id":"4197AD04-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7336","title":"Bogoliubov correction to the mean-field dynamics of interacting bosons","oa":1,"publisher":"International Press","quality_controlled":"1","year":"2017","publication":"Advances in Theoretical and Mathematical Physics","day":"01","page":"683 - 738","date_created":"2018-12-11T11:46:43Z","date_published":"2017-01-01T00:00:00Z","doi":"10.4310/ATMP.2017.v21.n3.a4"},{"date_updated":"2021-01-12T08:00:57Z","department":[{"_id":"LaEr"}],"_id":"483","status":"public","type":"journal_article","language":[{"iso":"eng"}],"publication_identifier":{"issn":["10950761"]},"publication_status":"published","volume":21,"issue":"3","ec_funded":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"We prove the universality for the eigenvalue gap statistics in the bulk of the spectrum for band matrices, in the regime where the band width is comparable with the dimension of the matrix, W ~ N. All previous results concerning universality of non-Gaussian random matrices are for mean-field models. By relying on a new mean-field reduction technique, we deduce universality from quantum unique ergodicity for band matrices."}],"month":"08","intvolume":" 21","scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1602.02312"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Bourgade P, Erdös L, Yau H, Yin J. 2017. Universality for a class of random band matrices. Advances in Theoretical and Mathematical Physics. 21(3), 739–800.","chicago":"Bourgade, Paul, László Erdös, Horng Yau, and Jun Yin. “Universality for a Class of Random Band Matrices.” Advances in Theoretical and Mathematical Physics. International Press, 2017. https://doi.org/10.4310/ATMP.2017.v21.n3.a5.","ieee":"P. Bourgade, L. Erdös, H. Yau, and J. Yin, “Universality for a class of random band matrices,” Advances in Theoretical and Mathematical Physics, vol. 21, no. 3. International Press, pp. 739–800, 2017.","short":"P. Bourgade, L. Erdös, H. Yau, J. Yin, Advances in Theoretical and Mathematical Physics 21 (2017) 739–800.","ama":"Bourgade P, Erdös L, Yau H, Yin J. Universality for a class of random band matrices. Advances in Theoretical and Mathematical Physics. 2017;21(3):739-800. doi:10.4310/ATMP.2017.v21.n3.a5","apa":"Bourgade, P., Erdös, L., Yau, H., & Yin, J. (2017). Universality for a class of random band matrices. Advances in Theoretical and Mathematical Physics. International Press. https://doi.org/10.4310/ATMP.2017.v21.n3.a5","mla":"Bourgade, Paul, et al. “Universality for a Class of Random Band Matrices.” Advances in Theoretical and Mathematical Physics, vol. 21, no. 3, International Press, 2017, pp. 739–800, doi:10.4310/ATMP.2017.v21.n3.a5."},"title":"Universality for a class of random band matrices","author":[{"last_name":"Bourgade","full_name":"Bourgade, Paul","first_name":"Paul"},{"first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","full_name":"Erdös, László","last_name":"Erdös"},{"first_name":"Horng","last_name":"Yau","full_name":"Yau, Horng"},{"first_name":"Jun","last_name":"Yin","full_name":"Yin, Jun"}],"publist_id":"7337","project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"338804","name":"Random matrices, universality and disordered quantum systems"}],"day":"25","publication":"Advances in Theoretical and Mathematical Physics","year":"2017","doi":"10.4310/ATMP.2017.v21.n3.a5","date_published":"2017-08-25T00:00:00Z","date_created":"2018-12-11T11:46:43Z","page":"739 - 800","publisher":"International Press","quality_controlled":"1","oa":1},{"quality_controlled":"1","publisher":"Nature Publishing Group","oa":1,"date_published":"2017-07-01T00:00:00Z","doi":"10.1038/ncomms16032","date_created":"2018-12-11T11:46:54Z","day":"01","publication":"Nature Communications","has_accepted_license":"1","year":"2017","article_number":"16032","title":"Activity dependent feedback inhibition may maintain head direction signals in mouse presubiculum","publist_id":"7305","author":[{"last_name":"Simonnet","full_name":"Simonnet, Jean","first_name":"Jean"},{"last_name":"Nassar","full_name":"Nassar, Mérie","first_name":"Mérie"},{"last_name":"Stella","full_name":"Stella, Federico","orcid":"0000-0001-9439-3148","id":"39AF1E74-F248-11E8-B48F-1D18A9856A87","first_name":"Federico"},{"last_name":"Cohen","full_name":"Cohen, Ivan","first_name":"Ivan"},{"first_name":"Bertrand","last_name":"Mathon","full_name":"Mathon, Bertrand"},{"last_name":"Boccara","full_name":"Boccara, Charlotte","orcid":"0000-0001-7237-5109","first_name":"Charlotte","id":"3FC06552-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Miles","full_name":"Miles, Richard","first_name":"Richard"},{"first_name":"Desdemona","last_name":"Fricker","full_name":"Fricker, Desdemona"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"J. Simonnet et al., “Activity dependent feedback inhibition may maintain head direction signals in mouse presubiculum,” Nature Communications, vol. 8. Nature Publishing Group, 2017.","short":"J. Simonnet, M. Nassar, F. Stella, I. Cohen, B. Mathon, C.N. Boccara, R. Miles, D. Fricker, Nature Communications 8 (2017).","ama":"Simonnet J, Nassar M, Stella F, et al. Activity dependent feedback inhibition may maintain head direction signals in mouse presubiculum. Nature Communications. 2017;8. doi:10.1038/ncomms16032","apa":"Simonnet, J., Nassar, M., Stella, F., Cohen, I., Mathon, B., Boccara, C. N., … Fricker, D. (2017). Activity dependent feedback inhibition may maintain head direction signals in mouse presubiculum. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms16032","mla":"Simonnet, Jean, et al. “Activity Dependent Feedback Inhibition May Maintain Head Direction Signals in Mouse Presubiculum.” Nature Communications, vol. 8, 16032, Nature Publishing Group, 2017, doi:10.1038/ncomms16032.","ista":"Simonnet J, Nassar M, Stella F, Cohen I, Mathon B, Boccara CN, Miles R, Fricker D. 2017. Activity dependent feedback inhibition may maintain head direction signals in mouse presubiculum. Nature Communications. 8, 16032.","chicago":"Simonnet, Jean, Mérie Nassar, Federico Stella, Ivan Cohen, Bertrand Mathon, Charlotte N. Boccara, Richard Miles, and Desdemona Fricker. “Activity Dependent Feedback Inhibition May Maintain Head Direction Signals in Mouse Presubiculum.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/ncomms16032."},"month":"07","intvolume":" 8","scopus_import":1,"oa_version":"Published Version","abstract":[{"text":"Orientation in space is represented in specialized brain circuits. Persistent head direction signals are transmitted from anterior thalamus to the presubiculum, but the identity of the presubicular target neurons, their connectivity and function in local microcircuits are unknown. Here, we examine how thalamic afferents recruit presubicular principal neurons and Martinotti interneurons, and the ensuing synaptic interactions between these cells. Pyramidal neuron activation of Martinotti cells in superficial layers is strongly facilitating such that high-frequency head directional stimulation efficiently unmutes synaptic excitation. Martinotti-cell feedback plays a dual role: precisely timed spikes may not inhibit the firing of in-tune head direction cells, while exerting lateral inhibition. Autonomous attractor dynamics emerge from a modelled network implementing wiring motifs and timing sensitive synaptic interactions in the pyramidal - Martinotti-cell feedback loop. This inhibitory microcircuit is therefore tuned to refine and maintain head direction information in the presubiculum.","lang":"eng"}],"volume":8,"file":[{"file_id":"5083","checksum":"76d8a2b72a58e56adb410ec37dfa7eee","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"IST-2018-937-v1+1_2017_Stella_Activity_dependent.pdf","date_created":"2018-12-12T10:14:31Z","file_size":2948357,"date_updated":"2020-07-14T12:46:36Z","creator":"system"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["20411723"]},"publication_status":"published","status":"public","pubrep_id":"937","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"514","file_date_updated":"2020-07-14T12:46:36Z","department":[{"_id":"JoCs"}],"ddc":["571"],"date_updated":"2021-01-12T08:01:16Z"},{"oa":1,"publisher":"Nature Publishing Group","quality_controlled":"1","page":"800 - 808","date_created":"2018-12-11T11:46:54Z","doi":"10.1038/nsmb.3460","date_published":"2017-10-05T00:00:00Z","year":"2017","has_accepted_license":"1","publication":"Nature Structural and Molecular Biology","day":"05","project":[{"call_identifier":"H2020","_id":"2590DB08-B435-11E9-9278-68D0E5697425","grant_number":"701309","name":"Atomic-Resolution Structures of Mitochondrial Respiratory Chain Supercomplexes (H2020)"}],"publist_id":"7304","author":[{"last_name":"Letts","full_name":"Letts, James A","orcid":"0000-0002-9864-3586","id":"322DA418-F248-11E8-B48F-1D18A9856A87","first_name":"James A"},{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A","last_name":"Sazanov","orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A"}],"title":"Clarifying the supercomplex: The higher-order organization of the mitochondrial electron transport chain","citation":{"ista":"Letts JA, Sazanov LA. 2017. Clarifying the supercomplex: The higher-order organization of the mitochondrial electron transport chain. Nature Structural and Molecular Biology. 24(10), 800–808.","chicago":"Letts, James A, and Leonid A Sazanov. “Clarifying the Supercomplex: The Higher-Order Organization of the Mitochondrial Electron Transport Chain.” Nature Structural and Molecular Biology. Nature Publishing Group, 2017. https://doi.org/10.1038/nsmb.3460.","apa":"Letts, J. A., & Sazanov, L. A. (2017). Clarifying the supercomplex: The higher-order organization of the mitochondrial electron transport chain. Nature Structural and Molecular Biology. Nature Publishing Group. https://doi.org/10.1038/nsmb.3460","ama":"Letts JA, Sazanov LA. Clarifying the supercomplex: The higher-order organization of the mitochondrial electron transport chain. Nature Structural and Molecular Biology. 2017;24(10):800-808. doi:10.1038/nsmb.3460","ieee":"J. A. Letts and L. A. Sazanov, “Clarifying the supercomplex: The higher-order organization of the mitochondrial electron transport chain,” Nature Structural and Molecular Biology, vol. 24, no. 10. Nature Publishing Group, pp. 800–808, 2017.","short":"J.A. Letts, L.A. Sazanov, Nature Structural and Molecular Biology 24 (2017) 800–808.","mla":"Letts, James A., and Leonid A. Sazanov. “Clarifying the Supercomplex: The Higher-Order Organization of the Mitochondrial Electron Transport Chain.” Nature Structural and Molecular Biology, vol. 24, no. 10, Nature Publishing Group, 2017, pp. 800–08, doi:10.1038/nsmb.3460."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"intvolume":" 24","month":"10","abstract":[{"lang":"eng","text":"The oxidative phosphorylation electron transport chain (OXPHOS-ETC) of the inner mitochondrial membrane is composed of five large protein complexes, named CI-CV. These complexes convert energy from the food we eat into ATP, a small molecule used to power a multitude of essential reactions throughout the cell. OXPHOS-ETC complexes are organized into supercomplexes (SCs) of defined stoichiometry: CI forms a supercomplex with CIII2 and CIV (SC I+III2+IV, known as the respirasome), as well as with CIII2 alone (SC I+III2). CIII2 forms a supercomplex with CIV (SC III2+IV) and CV forms dimers (CV2). Recent cryo-EM studies have revealed the structures of SC I+III2+IV and SC I+III2. Furthermore, recent work has shed light on the assembly and function of the SCs. Here we review and compare these recent studies and discuss how they have advanced our understanding of mitochondrial electron transport."}],"oa_version":"Submitted Version","ec_funded":1,"volume":24,"issue":"10","publication_status":"published","publication_identifier":{"issn":["15459993"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2019-11-07T12:51:07Z","file_name":"29893_2_merged_1501257589_red.pdf","creator":"lsazanov","date_updated":"2020-07-14T12:46:36Z","file_size":4118385,"file_id":"6993","checksum":"9bc7e8c41b43636dd7566289e511f096","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"type":"journal_article","article_type":"original","status":"public","_id":"515","department":[{"_id":"LeSa"}],"file_date_updated":"2020-07-14T12:46:36Z","date_updated":"2021-01-12T08:01:17Z","ddc":["572"]},{"author":[{"last_name":"Klotz","orcid":"0000-0003-1740-7635","full_name":"Klotz, Lukasz","id":"2C9AF1C2-F248-11E8-B48F-1D18A9856A87","first_name":"Lukasz"},{"full_name":"Lemoult, Grégoire M","last_name":"Lemoult","first_name":"Grégoire M","id":"4787FE80-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Idalia","full_name":"Frontczak, Idalia","last_name":"Frontczak"},{"first_name":"Laurette","last_name":"Tuckerman","full_name":"Tuckerman, Laurette"},{"first_name":"José","last_name":"Wesfreid","full_name":"Wesfreid, José"}],"publist_id":"7306","title":"Couette-Poiseuille flow experiment with zero mean advection velocity: Subcritical transition to turbulence","department":[{"_id":"BjHo"}],"citation":{"chicago":"Klotz, Lukasz, Grégoire M Lemoult, Idalia Frontczak, Laurette Tuckerman, and José Wesfreid. “Couette-Poiseuille Flow Experiment with Zero Mean Advection Velocity: Subcritical Transition to Turbulence.” Physical Review Fluids. American Physical Society, 2017. https://doi.org/10.1103/PhysRevFluids.2.043904.","ista":"Klotz L, Lemoult GM, Frontczak I, Tuckerman L, Wesfreid J. 2017. Couette-Poiseuille flow experiment with zero mean advection velocity: Subcritical transition to turbulence. Physical Review Fluids. 2(4), 043904.","mla":"Klotz, Lukasz, et al. “Couette-Poiseuille Flow Experiment with Zero Mean Advection Velocity: Subcritical Transition to Turbulence.” Physical Review Fluids, vol. 2, no. 4, 043904, American Physical Society, 2017, doi:10.1103/PhysRevFluids.2.043904.","short":"L. Klotz, G.M. Lemoult, I. Frontczak, L. Tuckerman, J. Wesfreid, Physical Review Fluids 2 (2017).","ieee":"L. Klotz, G. M. Lemoult, I. Frontczak, L. Tuckerman, and J. Wesfreid, “Couette-Poiseuille flow experiment with zero mean advection velocity: Subcritical transition to turbulence,” Physical Review Fluids, vol. 2, no. 4. American Physical Society, 2017.","ama":"Klotz L, Lemoult GM, Frontczak I, Tuckerman L, Wesfreid J. Couette-Poiseuille flow experiment with zero mean advection velocity: Subcritical transition to turbulence. Physical Review Fluids. 2017;2(4). doi:10.1103/PhysRevFluids.2.043904","apa":"Klotz, L., Lemoult, G. M., Frontczak, I., Tuckerman, L., & Wesfreid, J. (2017). Couette-Poiseuille flow experiment with zero mean advection velocity: Subcritical transition to turbulence. Physical Review Fluids. American Physical Society. https://doi.org/10.1103/PhysRevFluids.2.043904"},"date_updated":"2021-01-12T08:01:16Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","status":"public","_id":"513","article_number":"043904","volume":2,"issue":"4","date_published":"2017-04-01T00:00:00Z","doi":"10.1103/PhysRevFluids.2.043904","date_created":"2018-12-11T11:46:54Z","publication_status":"published","year":"2017","day":"01","language":[{"iso":"eng"}],"publication":"Physical Review Fluids","scopus_import":1,"publisher":"American Physical Society","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1704.02619","open_access":"1"}],"oa":1,"month":"04","intvolume":" 2","abstract":[{"text":"We present an experimental setup that creates a shear flow with zero mean advection velocity achieved by counterbalancing the nonzero streamwise pressure gradient by moving boundaries, which generates plane Couette-Poiseuille flow. We obtain experimental results in the transitional regime for this flow. Using flow visualization, we characterize the subcritical transition to turbulence in Couette-Poiseuille flow and show the existence of turbulent spots generated by a permanent perturbation. Due to the zero mean advection velocity of the base profile, these turbulent structures are nearly stationary. We distinguish two regions of the turbulent spot: the active turbulent core, which is characterized by waviness of the streaks similar to traveling waves, and the surrounding region, which includes in addition the weak undisturbed streaks and oblique waves at the laminar-turbulent interface. We also study the dependence of the size of these two regions on Reynolds number. Finally, we show that the traveling waves move in the downstream (Poiseuille) direction.","lang":"eng"}],"oa_version":"Preprint"},{"publist_id":"7299","author":[{"last_name":"Austin","full_name":"Austin, Kyle","first_name":"Kyle"},{"id":"2E36B656-F248-11E8-B48F-1D18A9856A87","first_name":"Ziga","full_name":"Virk, Ziga","last_name":"Virk"}],"title":"Higson compactification and dimension raising","department":[{"_id":"HeEd"}],"date_updated":"2021-01-12T08:01:21Z","citation":{"ama":"Austin K, Virk Z. Higson compactification and dimension raising. Topology and its Applications. 2017;215:45-57. doi:10.1016/j.topol.2016.10.005","apa":"Austin, K., & Virk, Z. (2017). Higson compactification and dimension raising. Topology and Its Applications. Elsevier. https://doi.org/10.1016/j.topol.2016.10.005","short":"K. Austin, Z. Virk, Topology and Its Applications 215 (2017) 45–57.","ieee":"K. Austin and Z. Virk, “Higson compactification and dimension raising,” Topology and its Applications, vol. 215. Elsevier, pp. 45–57, 2017.","mla":"Austin, Kyle, and Ziga Virk. “Higson Compactification and Dimension Raising.” Topology and Its Applications, vol. 215, Elsevier, 2017, pp. 45–57, doi:10.1016/j.topol.2016.10.005.","ista":"Austin K, Virk Z. 2017. Higson compactification and dimension raising. Topology and its Applications. 215, 45–57.","chicago":"Austin, Kyle, and Ziga Virk. “Higson Compactification and Dimension Raising.” Topology and Its Applications. Elsevier, 2017. https://doi.org/10.1016/j.topol.2016.10.005."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","status":"public","_id":"521","page":"45 - 57","date_published":"2017-01-01T00:00:00Z","doi":"10.1016/j.topol.2016.10.005","volume":215,"date_created":"2018-12-11T11:46:56Z","publication_identifier":{"issn":["01668641"]},"publication_status":"published","year":"2017","day":"01","language":[{"iso":"eng"}],"publication":"Topology and its Applications","publisher":"Elsevier","quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1608.03954v1","open_access":"1"}],"month":"01","intvolume":" 215","abstract":[{"text":"Let X and Y be proper metric spaces. We show that a coarsely n-to-1 map f:X→Y induces an n-to-1 map of Higson coronas. This viewpoint turns out to be successful in showing that the classical dimension raising theorems hold in large scale; that is, if f:X→Y is a coarsely n-to-1 map between proper metric spaces X and Y then asdim(Y)≤asdim(X)+n−1. Furthermore we introduce coarsely open coarsely n-to-1 maps, which include the natural quotient maps via a finite group action, and prove that they preserve the asymptotic dimension.","lang":"eng"}],"oa_version":"Submitted Version"},{"publication":"Current Biology","file":[{"creator":"system","file_size":2840413,"date_updated":"2020-07-14T12:46:38Z","file_name":"IST-2018-983-v1+1_Plant_biology_Building_barriers__in_roots.pdf","date_created":"2018-12-12T10:18:11Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"81fd4475c5a2a2c6f4313beeab215ed9","file_id":"5330"}],"day":"06","year":"2017","publication_status":"published","date_created":"2018-12-11T11:46:58Z","issue":"5","doi":"10.1016/j.cub.2017.01.060","date_published":"2017-03-06T00:00:00Z","volume":27,"page":"R172 - R174","acknowledgement":"Biotechnology and Biological Sciences Research Council:\tBBSRC BB/M001806/1 and BB/H020314/1\t","abstract":[{"text":"The Casparian strip is an important barrier regulating water and nutrient uptake into root tissues. New research reveals two peptide signals and their co-receptors play critical roles patterning and maintaining barrier integrity. ","lang":"eng"}],"intvolume":" 27","month":"03","main_file_link":[{"url":"https://repository.ist.ac.at/id/eprint/983","open_access":"1"}],"oa":1,"quality_controlled":0,"publisher":"Cell Press","extern":1,"citation":{"ista":"von Wangenheim D, Goh T, Dietrich D, Bennett M. 2017. Plant biology: Building barriers… in roots. Current Biology. 27(5), R172–R174.","chicago":"Wangenheim, Daniel von, Tatsuaki Goh, Daniela Dietrich, and Malcolm Bennett. “Plant Biology: Building Barriers… in Roots.” Current Biology. Cell Press, 2017. https://doi.org/10.1016/j.cub.2017.01.060.","ieee":"D. von Wangenheim, T. Goh, D. Dietrich, and M. Bennett, “Plant biology: Building barriers… in roots,” Current Biology, vol. 27, no. 5. Cell Press, pp. R172–R174, 2017.","short":"D. von Wangenheim, T. Goh, D. Dietrich, M. Bennett, Current Biology 27 (2017) R172–R174.","ama":"von Wangenheim D, Goh T, Dietrich D, Bennett M. Plant biology: Building barriers… in roots. Current Biology. 2017;27(5):R172-R174. doi:10.1016/j.cub.2017.01.060","apa":"von Wangenheim, D., Goh, T., Dietrich, D., & Bennett, M. (2017). Plant biology: Building barriers… in roots. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2017.01.060","mla":"von Wangenheim, Daniel, et al. “Plant Biology: Building Barriers… in Roots.” Current Biology, vol. 27, no. 5, Cell Press, 2017, pp. R172–74, doi:10.1016/j.cub.2017.01.060."},"date_updated":"2021-01-12T08:01:23Z","file_date_updated":"2020-07-14T12:46:38Z","title":"Plant biology: Building barriers… in roots","author":[{"first_name":"Daniel","id":"49E91952-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6862-1247","full_name":"Daniel von Wangenheim","last_name":"Von Wangenheim"},{"first_name":"Tatsuaki","full_name":"Goh, Tatsuaki","last_name":"Goh"},{"last_name":"Dietrich","full_name":"Dietrich, Daniela","first_name":"Daniela"},{"last_name":"Bennett","full_name":"Bennett, Malcolm J","first_name":"Malcolm"}],"publist_id":"7294","_id":"525","pubrep_id":"983","status":"public","type":"journal_article"},{"article_processing_charge":"No","external_id":{"arxiv":["1602.07907"]},"author":[{"full_name":"Burton, Benjamin","last_name":"Burton","first_name":"Benjamin"},{"last_name":"De Mesmay","full_name":"De Mesmay, Arnaud N","id":"3DB2F25C-F248-11E8-B48F-1D18A9856A87","first_name":"Arnaud N"},{"last_name":"Wagner","full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568","first_name":"Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7283","title":"Finding non-orientable surfaces in 3-Manifolds","citation":{"ista":"Burton B, de Mesmay AN, Wagner U. 2017. Finding non-orientable surfaces in 3-Manifolds. Discrete & Computational Geometry. 58(4), 871–888.","chicago":"Burton, Benjamin, Arnaud N de Mesmay, and Uli Wagner. “Finding Non-Orientable Surfaces in 3-Manifolds.” Discrete & Computational Geometry. Springer, 2017. https://doi.org/10.1007/s00454-017-9900-0.","apa":"Burton, B., de Mesmay, A. N., & Wagner, U. (2017). Finding non-orientable surfaces in 3-Manifolds. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-017-9900-0","ama":"Burton B, de Mesmay AN, Wagner U. Finding non-orientable surfaces in 3-Manifolds. Discrete & Computational Geometry. 2017;58(4):871-888. doi:10.1007/s00454-017-9900-0","ieee":"B. Burton, A. N. de Mesmay, and U. Wagner, “Finding non-orientable surfaces in 3-Manifolds,” Discrete & Computational Geometry, vol. 58, no. 4. Springer, pp. 871–888, 2017.","short":"B. Burton, A.N. de Mesmay, U. Wagner, Discrete & Computational Geometry 58 (2017) 871–888.","mla":"Burton, Benjamin, et al. “Finding Non-Orientable Surfaces in 3-Manifolds.” Discrete & Computational Geometry, vol. 58, no. 4, Springer, 2017, pp. 871–88, doi:10.1007/s00454-017-9900-0."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"publisher":"Springer","quality_controlled":"1","page":"871 - 888","date_created":"2018-12-11T11:47:01Z","date_published":"2017-06-09T00:00:00Z","doi":"10.1007/s00454-017-9900-0","year":"2017","publication":"Discrete & Computational Geometry","day":"09","type":"journal_article","article_type":"original","status":"public","_id":"534","department":[{"_id":"UlWa"}],"date_updated":"2023-02-21T17:01:34Z","main_file_link":[{"url":"https://arxiv.org/abs/1602.07907","open_access":"1"}],"scopus_import":1,"intvolume":" 58","month":"06","abstract":[{"text":"We investigate the complexity of finding an embedded non-orientable surface of Euler genus g in a triangulated 3-manifold. This problem occurs both as a natural question in low-dimensional topology, and as a first non-trivial instance of embeddability of complexes into 3-manifolds. We prove that the problem is NP-hard, thus adding to the relatively few hardness results that are currently known in 3-manifold topology. In addition, we show that the problem lies in NP when the Euler genus g is odd, and we give an explicit algorithm in this case.","lang":"eng"}],"oa_version":"Preprint","issue":"4","related_material":{"record":[{"id":"1379","status":"public","relation":"earlier_version"}]},"volume":58,"publication_status":"published","publication_identifier":{"issn":["01795376"]},"language":[{"iso":"eng"}]},{"file_date_updated":"2020-07-14T12:46:39Z","department":[{"_id":"CaGu"},{"_id":"HaJa"}],"date_updated":"2021-01-12T08:01:33Z","ddc":["571"],"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"932","_id":"538","volume":129,"issue":"16","ec_funded":1,"publication_status":"published","file":[{"file_id":"5007","checksum":"d66fee867e7cdbfa3fe276c2fb0778bb","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:13:24Z","file_name":"IST-2018-932-v1+1_Kainrath_et_al-2017-Angewandte_Chemie.pdf","creator":"system","date_updated":"2020-07-14T12:46:39Z","file_size":1668557}],"language":[{"iso":"eng"}],"month":"05","intvolume":" 129","abstract":[{"text":"Optogenetik und Photopharmakologie ermöglichen präzise räumliche und zeitliche Kontrolle von Proteinwechselwirkung und -funktion in Zellen und Tieren. Optogenetische Methoden, die auf grünes Licht ansprechen und zum Trennen von Proteinkomplexen geeignet sind, sind nichtweitläufig verfügbar, würden jedoch mehrfarbige Experimente zur Beantwortung von biologischen Fragestellungen ermöglichen. Hier demonstrieren wir die Verwendung von Cobalamin(Vitamin B12)-bindenden Domänen von bakteriellen CarH-Transkriptionsfaktoren zur Grünlicht-induzierten Dissoziation von Rezeptoren. Fusioniert mit dem Fibroblasten-W achstumsfaktor-Rezeptor 1 führten diese im Dunkeln in kultivierten Zellen zu Signalaktivität durch Oligomerisierung, welche durch Beleuchten umgehend aufgehoben wurde. In Zebrafischembryonen, die einen derartigen Rezeptor exprimieren, ermöglichte grünes Licht die Kontrolle über abnormale Signalaktivität während der Embryonalentwicklung. ","lang":"ger"}],"oa_version":"Published Version","publist_id":"7279","author":[{"full_name":"Kainrath, Stephanie","last_name":"Kainrath","id":"32CFBA64-F248-11E8-B48F-1D18A9856A87","first_name":"Stephanie"},{"full_name":"Stadler, Manuela","last_name":"Stadler","first_name":"Manuela"},{"orcid":"0000-0002-7218-7738","full_name":"Gschaider-Reichhart, Eva","last_name":"Gschaider-Reichhart","id":"3FEE232A-F248-11E8-B48F-1D18A9856A87","first_name":"Eva"},{"first_name":"Martin","full_name":"Distel, Martin","last_name":"Distel"},{"first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L","last_name":"Janovjak"}],"title":"Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen","citation":{"ista":"Kainrath S, Stadler M, Gschaider-Reichhart E, Distel M, Janovjak HL. 2017. Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen. Angewandte Chemie. 129(16), 4679–4682.","chicago":"Kainrath, Stephanie, Manuela Stadler, Eva Gschaider-Reichhart, Martin Distel, and Harald L Janovjak. “Grünlicht-Induzierte Rezeptorinaktivierung Durch Cobalamin-Bindende Domänen.” Angewandte Chemie. Wiley, 2017. https://doi.org/10.1002/ange.201611998.","short":"S. Kainrath, M. Stadler, E. Gschaider-Reichhart, M. Distel, H.L. Janovjak, Angewandte Chemie 129 (2017) 4679–4682.","ieee":"S. Kainrath, M. Stadler, E. Gschaider-Reichhart, M. Distel, and H. L. Janovjak, “Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen,” Angewandte Chemie, vol. 129, no. 16. Wiley, pp. 4679–4682, 2017.","apa":"Kainrath, S., Stadler, M., Gschaider-Reichhart, E., Distel, M., & Janovjak, H. L. (2017). Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen. Angewandte Chemie. Wiley. https://doi.org/10.1002/ange.201611998","ama":"Kainrath S, Stadler M, Gschaider-Reichhart E, Distel M, Janovjak HL. Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen. Angewandte Chemie. 2017;129(16):4679-4682. doi:10.1002/ange.201611998","mla":"Kainrath, Stephanie, et al. “Grünlicht-Induzierte Rezeptorinaktivierung Durch Cobalamin-Bindende Domänen.” Angewandte Chemie, vol. 129, no. 16, Wiley, 2017, pp. 4679–82, doi:10.1002/ange.201611998."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"25548C20-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Microbial Ion Channels for Synthetic Neurobiology","grant_number":"303564"},{"grant_number":"W1232-B24","name":"Molecular Drug Targets","_id":"255A6082-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"page":"4679 - 4682","doi":"10.1002/ange.201611998","date_published":"2017-05-20T00:00:00Z","date_created":"2018-12-11T11:47:02Z","has_accepted_license":"1","year":"2017","day":"20","publication":"Angewandte Chemie","quality_controlled":"1","publisher":"Wiley","oa":1},{"volume":13,"issue":"12","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"1aa20f19a1e90664fadce6e7d5284fdc","file_id":"4944","date_updated":"2020-07-14T12:46:44Z","file_size":4106772,"creator":"system","date_created":"2018-12-12T10:12:26Z","file_name":"IST-2018-931-v1+1_journal.ppat.1006758.pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["15537366"]},"publication_status":"published","month":"12","intvolume":" 13","scopus_import":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"RNA-dependent RNA polymerases (RdRps) play a key role in the life cycle of RNA viruses and impact their immunobiology. The arenavirus lymphocytic choriomeningitis virus (LCMV) strain Clone 13 provides a benchmark model for studying chronic infection. A major genetic determinant for its ability to persist maps to a single amino acid exchange in the viral L protein, which exhibits RdRp activity, yet its functional consequences remain elusive. To unravel the L protein interactions with the host proteome, we engineered infectious L protein-tagged LCMV virions by reverse genetics. A subsequent mass-spectrometric analysis of L protein pulldowns from infected human cells revealed a comprehensive network of interacting host proteins. The obtained LCMV L protein interactome was bioinformatically integrated with known host protein interactors of RdRps from other RNA viruses, emphasizing interconnected modules of human proteins. Functional characterization of selected interactors highlighted proviral (DDX3X) as well as antiviral (NKRF, TRIM21) host factors. To corroborate these findings, we infected Trim21-/-mice with LCMV and found impaired virus control in chronic infection. These results provide insights into the complex interactions of the arenavirus LCMV and other viral RdRps with the host proteome and contribute to a better molecular understanding of how chronic viruses interact with their host."}],"department":[{"_id":"GaNo"}],"file_date_updated":"2020-07-14T12:46:44Z","ddc":["576","616"],"date_updated":"2021-01-12T08:01:48Z","status":"public","pubrep_id":"931","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"540","doi":"10.1371/journal.ppat.1006758","date_published":"2017-12-01T00:00:00Z","date_created":"2018-12-11T11:47:03Z","day":"01","publication":"PLoS Pathogens","has_accepted_license":"1","year":"2017","quality_controlled":"1","publisher":"Public Library of Science","oa":1,"title":"Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein","author":[{"full_name":"Khamina, Kseniya","last_name":"Khamina","first_name":"Kseniya"},{"full_name":"Lercher, Alexander","last_name":"Lercher","first_name":"Alexander"},{"first_name":"Michael","full_name":"Caldera, Michael","last_name":"Caldera"},{"first_name":"Christopher","full_name":"Schliehe, Christopher","last_name":"Schliehe"},{"first_name":"Bojan","full_name":"Vilagos, Bojan","last_name":"Vilagos"},{"last_name":"Sahin","full_name":"Sahin, Mehmet","first_name":"Mehmet"},{"last_name":"Kosack","full_name":"Kosack, Lindsay","first_name":"Lindsay"},{"last_name":"Bhattacharya","full_name":"Bhattacharya, Anannya","first_name":"Anannya"},{"first_name":"Peter","last_name":"Májek","full_name":"Májek, Peter"},{"last_name":"Stukalov","full_name":"Stukalov, Alexey","first_name":"Alexey"},{"last_name":"Sacco","full_name":"Sacco, Roberto","first_name":"Roberto","id":"42C9F57E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Leo","full_name":"James, Leo","last_name":"James"},{"first_name":"Daniel","last_name":"Pinschewer","full_name":"Pinschewer, Daniel"},{"first_name":"Keiryn","last_name":"Bennett","full_name":"Bennett, Keiryn"},{"first_name":"Jörg","last_name":"Menche","full_name":"Menche, Jörg"},{"first_name":"Andreas","full_name":"Bergthaler, Andreas","last_name":"Bergthaler"}],"publist_id":"7276","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"K. Khamina, A. Lercher, M. Caldera, C. Schliehe, B. Vilagos, M. Sahin, L. Kosack, A. Bhattacharya, P. Májek, A. Stukalov, R. Sacco, L. James, D. Pinschewer, K. Bennett, J. Menche, A. Bergthaler, PLoS Pathogens 13 (2017).","ieee":"K. Khamina et al., “Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein,” PLoS Pathogens, vol. 13, no. 12. Public Library of Science, 2017.","apa":"Khamina, K., Lercher, A., Caldera, M., Schliehe, C., Vilagos, B., Sahin, M., … Bergthaler, A. (2017). Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein. PLoS Pathogens. Public Library of Science. https://doi.org/10.1371/journal.ppat.1006758","ama":"Khamina K, Lercher A, Caldera M, et al. Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein. PLoS Pathogens. 2017;13(12). doi:10.1371/journal.ppat.1006758","mla":"Khamina, Kseniya, et al. “Characterization of Host Proteins Interacting with the Lymphocytic Choriomeningitis Virus L Protein.” PLoS Pathogens, vol. 13, no. 12, e1006758, Public Library of Science, 2017, doi:10.1371/journal.ppat.1006758.","ista":"Khamina K, Lercher A, Caldera M, Schliehe C, Vilagos B, Sahin M, Kosack L, Bhattacharya A, Májek P, Stukalov A, Sacco R, James L, Pinschewer D, Bennett K, Menche J, Bergthaler A. 2017. Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein. PLoS Pathogens. 13(12), e1006758.","chicago":"Khamina, Kseniya, Alexander Lercher, Michael Caldera, Christopher Schliehe, Bojan Vilagos, Mehmet Sahin, Lindsay Kosack, et al. “Characterization of Host Proteins Interacting with the Lymphocytic Choriomeningitis Virus L Protein.” PLoS Pathogens. Public Library of Science, 2017. https://doi.org/10.1371/journal.ppat.1006758."},"article_number":"e1006758"},{"scopus_import":1,"intvolume":" 13","month":"07","abstract":[{"text":"We consider Markov decision processes (MDPs) with multiple limit-average (or mean-payoff) objectives. There exist two different views: (i) the expectation semantics, where the goal is to optimize the expected mean-payoff objective, and (ii) the satisfaction semantics, where the goal is to maximize the probability of runs such that the mean-payoff value stays above a given vector. We consider optimization with respect to both objectives at once, thus unifying the existing semantics. Precisely, the goal is to optimize the expectation while ensuring the satisfaction constraint. Our problem captures the notion of optimization with respect to strategies that are risk-averse (i.e., ensure certain probabilistic guarantee). Our main results are as follows: First, we present algorithms for the decision problems which are always polynomial in the size of the MDP. We also show that an approximation of the Pareto-curve can be computed in time polynomial in the size of the MDP, and the approximation factor, but exponential in the number of dimensions. Second, we present a complete characterization of the strategy complexity (in terms of memory bounds and randomization) required to solve our problem. ","lang":"eng"}],"oa_version":"Published Version","ec_funded":1,"license":"https://creativecommons.org/licenses/by-nd/4.0/","volume":13,"related_material":{"record":[{"relation":"earlier_version","id":"1657","status":"public"},{"status":"public","id":"5429","relation":"earlier_version"},{"relation":"earlier_version","status":"public","id":"5435"}]},"issue":"2","publication_status":"published","publication_identifier":{"issn":["18605974"]},"language":[{"iso":"eng"}],"file":[{"file_name":"IST-2018-957-v1+1_2017_Chatterjee_Unifying_two.pdf","date_created":"2018-12-12T10:18:32Z","creator":"system","file_size":511832,"date_updated":"2020-07-14T12:46:33Z","checksum":"bfa405385ec6229ad5ead89ab5751639","file_id":"5354","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","image":"/image/cc_by_nd.png","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","short":"CC BY-ND (4.0)"},"type":"journal_article","pubrep_id":"957","status":"public","_id":"466","file_date_updated":"2020-07-14T12:46:33Z","department":[{"_id":"KrCh"}],"date_updated":"2023-02-23T12:26:16Z","ddc":["004"],"oa":1,"quality_controlled":"1","publisher":"International Federation of Computational Logic","date_created":"2018-12-11T11:46:38Z","doi":"10.23638/LMCS-13(2:15)2017","date_published":"2017-07-03T00:00:00Z","year":"2017","has_accepted_license":"1","publication":"Logical Methods in Computer Science","day":"03","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"},{"call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Atomic-Resolution Structures of Mitochondrial Respiratory Chain Supercomplexes (H2020)","grant_number":"701309","call_identifier":"H2020","_id":"2590DB08-B435-11E9-9278-68D0E5697425"}],"article_number":"15","publist_id":"7355","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"full_name":"Křetínská, Zuzana","last_name":"Křetínská","first_name":"Zuzana"},{"id":"44CEF464-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","full_name":"Kretinsky, Jan","orcid":"0000-0002-8122-2881","last_name":"Kretinsky"}],"title":"Unifying two views on multiple mean-payoff objectives in Markov decision processes","citation":{"chicago":"Chatterjee, Krishnendu, Zuzana Křetínská, and Jan Kretinsky. “Unifying Two Views on Multiple Mean-Payoff Objectives in Markov Decision Processes.” Logical Methods in Computer Science. International Federation of Computational Logic, 2017. https://doi.org/10.23638/LMCS-13(2:15)2017.","ista":"Chatterjee K, Křetínská Z, Kretinsky J. 2017. Unifying two views on multiple mean-payoff objectives in Markov decision processes. Logical Methods in Computer Science. 13(2), 15.","mla":"Chatterjee, Krishnendu, et al. “Unifying Two Views on Multiple Mean-Payoff Objectives in Markov Decision Processes.” Logical Methods in Computer Science, vol. 13, no. 2, 15, International Federation of Computational Logic, 2017, doi:10.23638/LMCS-13(2:15)2017.","short":"K. Chatterjee, Z. Křetínská, J. Kretinsky, Logical Methods in Computer Science 13 (2017).","ieee":"K. Chatterjee, Z. Křetínská, and J. Kretinsky, “Unifying two views on multiple mean-payoff objectives in Markov decision processes,” Logical Methods in Computer Science, vol. 13, no. 2. International Federation of Computational Logic, 2017.","ama":"Chatterjee K, Křetínská Z, Kretinsky J. Unifying two views on multiple mean-payoff objectives in Markov decision processes. Logical Methods in Computer Science. 2017;13(2). doi:10.23638/LMCS-13(2:15)2017","apa":"Chatterjee, K., Křetínská, Z., & Kretinsky, J. (2017). Unifying two views on multiple mean-payoff objectives in Markov decision processes. Logical Methods in Computer Science. International Federation of Computational Logic. https://doi.org/10.23638/LMCS-13(2:15)2017"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"author":[{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","full_name":"Otop, Jan","last_name":"Otop"}],"publist_id":"7354","external_id":{"arxiv":["1606.03598"]},"title":"Nested weighted automata","citation":{"ama":"Chatterjee K, Henzinger TA, Otop J. Nested weighted automata. ACM Transactions on Computational Logic (TOCL). 2017;18(4). doi:10.1145/3152769","apa":"Chatterjee, K., Henzinger, T. A., & Otop, J. (2017). Nested weighted automata. ACM Transactions on Computational Logic (TOCL). ACM. https://doi.org/10.1145/3152769","short":"K. Chatterjee, T.A. Henzinger, J. Otop, ACM Transactions on Computational Logic (TOCL) 18 (2017).","ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, “Nested weighted automata,” ACM Transactions on Computational Logic (TOCL), vol. 18, no. 4. ACM, 2017.","mla":"Chatterjee, Krishnendu, et al. “Nested Weighted Automata.” ACM Transactions on Computational Logic (TOCL), vol. 18, no. 4, 31, ACM, 2017, doi:10.1145/3152769.","ista":"Chatterjee K, Henzinger TA, Otop J. 2017. Nested weighted automata. ACM Transactions on Computational Logic (TOCL). 18(4), 31.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Nested Weighted Automata.” ACM Transactions on Computational Logic (TOCL). ACM, 2017. https://doi.org/10.1145/3152769."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z211"},{"call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"article_number":"31","doi":"10.1145/3152769","date_published":"2017-12-01T00:00:00Z","date_created":"2018-12-11T11:46:38Z","year":"2017","day":"01","publication":"ACM Transactions on Computational Logic (TOCL)","publisher":"ACM","quality_controlled":"1","oa":1,"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"date_updated":"2023-02-23T12:26:19Z","type":"journal_article","status":"public","_id":"467","related_material":{"record":[{"status":"public","id":"1656","relation":"earlier_version"},{"id":"5415","status":"public","relation":"earlier_version"},{"relation":"earlier_version","status":"public","id":"5436"}]},"volume":18,"issue":"4","ec_funded":1,"publication_identifier":{"issn":["15293785"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1606.03598"}],"month":"12","intvolume":" 18","abstract":[{"text":"Recently there has been a significant effort to handle quantitative properties in formal verification and synthesis. While weighted automata over finite and infinite words provide a natural and flexible framework to express quantitative properties, perhaps surprisingly, some basic system properties such as average response time cannot be expressed using weighted automata or in any other known decidable formalism. In this work, we introduce nested weighted automata as a natural extension of weighted automata, which makes it possible to express important quantitative properties such as average response time. In nested weighted automata, a master automaton spins off and collects results from weighted slave automata, each of which computes a quantity along a finite portion of an infinite word. Nested weighted automata can be viewed as the quantitative analogue of monitor automata, which are used in runtime verification. We establish an almost-complete decidability picture for the basic decision problems about nested weighted automata and illustrate their applicability in several domains. In particular, nested weighted automata can be used to decide average response time properties.","lang":"eng"}],"oa_version":"Preprint"},{"project":[{"call_identifier":"FWF","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23","name":"Moderne Concurrency Paradigms"},{"call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z211"},{"name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Chatterjee, K., Henzinger, T. A., Ibsen-Jensen, R., & Otop, J. (2017). Edit distance for pushdown automata. Logical Methods in Computer Science. International Federation of Computational Logic. https://doi.org/10.23638/LMCS-13(3:23)2017","ama":"Chatterjee K, Henzinger TA, Ibsen-Jensen R, Otop J. Edit distance for pushdown automata. Logical Methods in Computer Science. 2017;13(3). doi:10.23638/LMCS-13(3:23)2017","short":"K. Chatterjee, T.A. Henzinger, R. Ibsen-Jensen, J. Otop, Logical Methods in Computer Science 13 (2017).","ieee":"K. Chatterjee, T. A. Henzinger, R. Ibsen-Jensen, and J. Otop, “Edit distance for pushdown automata,” Logical Methods in Computer Science, vol. 13, no. 3. International Federation of Computational Logic, 2017.","mla":"Chatterjee, Krishnendu, et al. “Edit Distance for Pushdown Automata.” Logical Methods in Computer Science, vol. 13, no. 3, International Federation of Computational Logic, 2017, doi:10.23638/LMCS-13(3:23)2017.","ista":"Chatterjee K, Henzinger TA, Ibsen-Jensen R, Otop J. 2017. Edit distance for pushdown automata. Logical Methods in Computer Science. 13(3).","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, Rasmus Ibsen-Jensen, and Jan Otop. “Edit Distance for Pushdown Automata.” Logical Methods in Computer Science. International Federation of Computational Logic, 2017. https://doi.org/10.23638/LMCS-13(3:23)2017."},"title":"Edit distance for pushdown automata","publist_id":"7356","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"},{"last_name":"Ibsen-Jensen","orcid":"0000-0003-4783-0389","full_name":"Ibsen-Jensen, Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87","first_name":"Rasmus"},{"full_name":"Otop, Jan","last_name":"Otop","first_name":"Jan"}],"oa":1,"publisher":"International Federation of Computational Logic","quality_controlled":"1","publication":"Logical Methods in Computer Science","day":"13","year":"2017","has_accepted_license":"1","date_created":"2018-12-11T11:46:37Z","date_published":"2017-09-13T00:00:00Z","doi":"10.23638/LMCS-13(3:23)2017","_id":"465","pubrep_id":"955","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","image":"/image/cc_by_nd.png","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","short":"CC BY-ND (4.0)"},"type":"journal_article","ddc":["004"],"date_updated":"2023-02-23T12:26:25Z","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:46:33Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"The edit distance between two words w 1 , w 2 is the minimal number of word operations (letter insertions, deletions, and substitutions) necessary to transform w 1 to w 2 . The edit distance generalizes to languages L 1 , L 2 , where the edit distance from L 1 to L 2 is the minimal number k such that for every word from L 1 there exists a word in L 2 with edit distance at most k . We study the edit distance computation problem between pushdown automata and their subclasses. The problem of computing edit distance to a pushdown automaton is undecidable, and in practice, the interesting question is to compute the edit distance from a pushdown automaton (the implementation, a standard model for programs with recursion) to a regular language (the specification). In this work, we present a complete picture of decidability and complexity for the following problems: (1) deciding whether, for a given threshold k , the edit distance from a pushdown automaton to a finite automaton is at most k , and (2) deciding whether the edit distance from a pushdown automaton to a finite automaton is finite. "}],"intvolume":" 13","month":"09","scopus_import":1,"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"08041379ba408d40664f449eb5907a8f","file_id":"5090","date_updated":"2020-07-14T12:46:33Z","file_size":279071,"creator":"system","date_created":"2018-12-12T10:14:37Z","file_name":"IST-2015-321-v1+1_main.pdf"},{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"08041379ba408d40664f449eb5907a8f","file_id":"5091","file_size":279071,"date_updated":"2020-07-14T12:46:33Z","creator":"system","file_name":"IST-2018-955-v1+1_2017_Chatterjee_Edit_distance.pdf","date_created":"2018-12-12T10:14:38Z"}],"publication_status":"published","publication_identifier":{"issn":["18605974"]},"ec_funded":1,"volume":13,"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"1610"},{"relation":"earlier_version","id":"5438","status":"public"}]},"issue":"3"},{"date_updated":"2023-02-23T12:26:57Z","ddc":["004"],"file_date_updated":"2020-07-14T12:46:36Z","department":[{"_id":"KrCh"}],"_id":"512","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"938","status":"public","publication_status":"published","publication_identifier":{"issn":["20452322"]},"language":[{"iso":"eng"}],"file":[{"file_name":"IST-2018-938-v1+1_2017_Pavlogiannis_Amplification_on.pdf","date_created":"2018-12-12T10:18:35Z","file_size":1536783,"date_updated":"2020-07-14T12:46:36Z","creator":"system","checksum":"7d05cbdd914e194a019c0f91fb64e9a8","file_id":"5357","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"ec_funded":1,"volume":7,"issue":"1","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"5449"}]},"abstract":[{"lang":"eng","text":"The fixation probability is the probability that a new mutant introduced in a homogeneous population eventually takes over the entire population. The fixation probability is a fundamental quantity of natural selection, and known to depend on the population structure. Amplifiers of natural selection are population structures which increase the fixation probability of advantageous mutants, as compared to the baseline case of well-mixed populations. In this work we focus on symmetric population structures represented as undirected graphs. In the regime of undirected graphs, the strongest amplifier known has been the Star graph, and the existence of undirected graphs with stronger amplification properties has remained open for over a decade. In this work we present the Comet and Comet-swarm families of undirected graphs. We show that for a range of fitness values of the mutants, the Comet and Cometswarm graphs have fixation probability strictly larger than the fixation probability of the Star graph, for fixed population size and at the limit of large populations, respectively. "}],"oa_version":"Published Version","scopus_import":1,"intvolume":" 7","month":"03","citation":{"ama":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. Amplification on undirected population structures: Comets beat stars. Scientific Reports. 2017;7(1). doi:10.1038/s41598-017-00107-w","apa":"Pavlogiannis, A., Tkadlec, J., Chatterjee, K., & Nowak, M. (2017). Amplification on undirected population structures: Comets beat stars. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/s41598-017-00107-w","short":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M. Nowak, Scientific Reports 7 (2017).","ieee":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. Nowak, “Amplification on undirected population structures: Comets beat stars,” Scientific Reports, vol. 7, no. 1. Nature Publishing Group, 2017.","mla":"Pavlogiannis, Andreas, et al. “Amplification on Undirected Population Structures: Comets Beat Stars.” Scientific Reports, vol. 7, no. 1, 82, Nature Publishing Group, 2017, doi:10.1038/s41598-017-00107-w.","ista":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. 2017. Amplification on undirected population structures: Comets beat stars. Scientific Reports. 7(1), 82.","chicago":"Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. “Amplification on Undirected Population Structures: Comets Beat Stars.” Scientific Reports. 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The input is a graph where the edges are labeled with different types of opening and closing parentheses, and the reachability information is computed via paths whose parentheses are properly matched. We present new results for Dyck reachability problems with applications to alias analysis and data-dependence analysis. Our main contributions, that include improved upper bounds as well as lower bounds that establish optimality guarantees, are as follows: First, we consider Dyck reachability on bidirected graphs, which is the standard way of performing field-sensitive points-to analysis. Given a bidirected graph with n nodes and m edges, we present: (i) an algorithm with worst-case running time O(m + n · α(n)), where α(n) is the inverse Ackermann function, improving the previously known O(n2) time bound; (ii) a matching lower bound that shows that our algorithm is optimal wrt to worst-case complexity; and (iii) an optimal average-case upper bound of O(m) time, improving the previously known O(m · logn) bound. Second, we consider the problem of context-sensitive data-dependence analysis, where the task is to obtain analysis summaries of library code in the presence of callbacks. Our algorithm preprocesses libraries in almost linear time, after which the contribution of the library in the complexity of the client analysis is only linear, and only wrt the number of call sites. Third, we prove that combinatorial algorithms for Dyck reachability on general graphs with truly sub-cubic bounds cannot be obtained without obtaining sub-cubic combinatorial algorithms for Boolean Matrix Multiplication, which is a long-standing open problem. Thus we establish that the existing combinatorial algorithms for Dyck reachability are (conditionally) optimal for general graphs. We also show that the same hardness holds for graphs of constant treewidth. Finally, we provide a prototype implementation of our algorithms for both alias analysis and data-dependence analysis. Our experimental evaluation demonstrates that the new algorithms significantly outperform all existing methods on the two problems, over real-world benchmarks.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 2","month":"12","citation":{"ista":"Chatterjee K, Choudhary B, Pavlogiannis A. 2017. Optimal Dyck reachability for data-dependence and Alias analysis. 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POPL, 30, Association for Computing Machinery, 2017, doi:10.1145/3158118."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","external_id":{"arxiv":["1910.00241"]},"article_processing_charge":"No","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Choudhary","full_name":"Choudhary, Bhavya","first_name":"Bhavya"},{"first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722"}],"title":"Optimal Dyck reachability for data-dependence and Alias analysis","article_number":"30","project":[{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"year":"2017","has_accepted_license":"1","publication":"Proceedings of the ACM on Programming Languages","day":"27","date_created":"2021-12-05T23:01:48Z","doi":"10.1145/3158118","date_published":"2017-12-27T00:00:00Z","acknowledgement":"The research was partly supported by Austrian Science Fund (FWF) Grant No P23499-N23, FWF NFN Grant No S11407-N23 (RiSE/SHiNE), and ERC Start grant (279307: Graph Games).\r\n","oa":1,"quality_controlled":"1","publisher":"Association for Computing Machinery"},{"publisher":"IST Austria","oa":1,"page":"37","date_published":"2017-10-23T00:00:00Z","doi":"10.15479/AT:IST-2017-870-v1-1","date_created":"2018-12-12T11:39:26Z","has_accepted_license":"1","year":"2017","day":"23","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"full_name":"Choudhary, Bhavya","last_name":"Choudhary","first_name":"Bhavya"},{"id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722","last_name":"Pavlogiannis"}],"article_processing_charge":"No","title":"Optimal Dyck reachability for data-dependence and alias analysis","citation":{"ista":"Chatterjee K, Choudhary B, Pavlogiannis A. 2017. Optimal Dyck reachability for data-dependence and alias analysis, IST Austria, 37p.","chicago":"Chatterjee, Krishnendu, Bhavya Choudhary, and Andreas Pavlogiannis. Optimal Dyck Reachability for Data-Dependence and Alias Analysis. IST Austria, 2017. https://doi.org/10.15479/AT:IST-2017-870-v1-1.","ieee":"K. Chatterjee, B. Choudhary, and A. Pavlogiannis, Optimal Dyck reachability for data-dependence and alias analysis. IST Austria, 2017.","short":"K. Chatterjee, B. Choudhary, A. Pavlogiannis, Optimal Dyck Reachability for Data-Dependence and Alias Analysis, IST Austria, 2017.","apa":"Chatterjee, K., Choudhary, B., & Pavlogiannis, A. (2017). Optimal Dyck reachability for data-dependence and alias analysis. IST Austria. https://doi.org/10.15479/AT:IST-2017-870-v1-1","ama":"Chatterjee K, Choudhary B, Pavlogiannis A. Optimal Dyck Reachability for Data-Dependence and Alias Analysis. IST Austria; 2017. doi:10.15479/AT:IST-2017-870-v1-1","mla":"Chatterjee, Krishnendu, et al. Optimal Dyck Reachability for Data-Dependence and Alias Analysis. IST Austria, 2017, doi:10.15479/AT:IST-2017-870-v1-1."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","alternative_title":["IST Austria Technical Report"],"month":"10","abstract":[{"text":"A fundamental algorithmic problem at the heart of static analysis is Dyck reachability. The input is a graphwhere the edges are labeled with different types of opening and closing parentheses, and the reachabilityinformation is computed via paths whose parentheses are properly matched. We present new results for Dyckreachability problems with applications to alias analysis and data-dependence analysis. Our main contributions,that include improved upper bounds as well as lower bounds that establish optimality guarantees, are asfollows:First, we consider Dyck reachability on bidirected graphs, which is the standard way of performing field-sensitive points-to analysis. Given a bidirected graph withnnodes andmedges, we present: (i) an algorithmwith worst-case running timeO(m+n·α(n)), whereα(n)is the inverse Ackermann function, improving thepreviously knownO(n2)time bound; (ii) a matching lower bound that shows that our algorithm is optimalwrt to worst-case complexity; and (iii) an optimal average-case upper bound ofO(m)time, improving thepreviously knownO(m·logn)bound.Second, we consider the problem of context-sensitive data-dependence analysis, where the task is to obtainanalysis summaries of library code in the presence of callbacks. Our algorithm preprocesses libraries in almostlinear time, after which the contribution of the library in the complexity of the client analysis is only linear,and only wrt the number of call sites.Third, we prove that combinatorial algorithms for Dyck reachability on general graphs with truly sub-cubic bounds cannot be obtained without obtaining sub-cubic combinatorial algorithms for Boolean MatrixMultiplication, which is a long-standing open problem. Thus we establish that the existing combinatorialalgorithms for Dyck reachability are (conditionally) optimal for general graphs. We also show that the samehardness holds for graphs of constant treewidth.Finally, we provide a prototype implementation of our algorithms for both alias analysis and data-dependenceanalysis. Our experimental evaluation demonstrates that the new algorithms significantly outperform allexisting methods on the two problems, over real-world benchmarks.","lang":"eng"}],"oa_version":"Published Version","related_material":{"record":[{"relation":"later_version","id":"10416","status":"public"}]},"publication_identifier":{"issn":["2664-1690"]},"publication_status":"published","file":[{"checksum":"177a84a46e3ac17e87b31534ad16a4c9","file_id":"5524","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T11:54:02Z","file_name":"IST-2017-870-v1+1_main.pdf","date_updated":"2020-07-14T12:46:59Z","file_size":960491,"creator":"system"}],"language":[{"iso":"eng"}],"type":"technical_report","status":"public","pubrep_id":"870","_id":"5455","file_date_updated":"2020-07-14T12:46:59Z","department":[{"_id":"KrCh"}],"date_updated":"2023-02-21T15:54:10Z","ddc":["000"]},{"extern":0,"citation":{"ista":"Petritsch B. 2017. Implementing the institutional data repository IST DataRep, IST Austria,p.","chicago":"Petritsch, Barbara. Implementing the Institutional Data Repository IST DataRep. IST Austria, 2017.","ieee":"B. Petritsch, Implementing the institutional data repository IST DataRep. IST Austria, 2017.","short":"B. Petritsch, Implementing the Institutional Data Repository IST DataRep, IST Austria, 2017.","ama":"Petritsch B. Implementing the Institutional Data Repository IST DataRep. IST Austria; 2017.","apa":"Petritsch, B. (2017). Implementing the institutional data repository IST DataRep. IST Austria.","mla":"Petritsch, Barbara. Implementing the Institutional Data Repository IST DataRep. IST Austria, 2017."},"date_updated":"2020-07-14T23:05:03Z","title":"Implementing the institutional data repository IST DataRep","file_date_updated":"2020-07-14T12:46:59Z","department":[{"_id":"E-Lib"}],"author":[{"first_name":"Barbara","id":"406048EC-F248-11E8-B48F-1D18A9856A87","last_name":"Petritsch","full_name":"Barbara Petritsch","orcid":"0000-0003-2724-4614"}],"_id":"5450","status":"public","pubrep_id":"724","type":"report","day":"26","file":[{"checksum":"6321792dcfa82bf490f17615a9b22355","file_id":"5483","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T11:53:22Z","file_name":"IST-2017-724-v1+1_DataRep_Project_Report_2017.pdf","date_updated":"2020-07-14T12:46:59Z","file_size":3460985,"creator":"system"}],"year":"2017","date_published":"2017-06-26T00:00:00Z","date_created":"2018-12-12T11:39:24Z","publication_date":"2017-06-26","abstract":[{"text":"In this report the implementation of the institutional data repository IST DataRep at IST Austria will be covered: Starting with the research phase when requirements for a repository were established, the procedure of choosing a repository-software and its customization based on the results of user-testings will be discussed. Followed by reflections on the marketing strategies in regard of impact, and at the end sharing some experiences of one year operating IST DataRep.","lang":"eng"}],"month":"06","publisher":"IST Austria","oa":1,"main_file_link":[{"url":"https://repository.ist.ac.at/id/eprint/724.","open_access":"1"}]},{"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["2475-1421"]},"ec_funded":1,"issue":"POPL","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"5448"},{"relation":"earlier_version","id":"5456","status":"public"}]},"volume":2,"oa_version":"Published Version","abstract":[{"text":"We present a new dynamic partial-order reduction method for stateless model checking of concurrent programs. A common approach for exploring program behaviors relies on enumerating the traces of the program, without storing the visited states (aka stateless exploration). As the number of distinct traces grows exponentially, dynamic partial-order reduction (DPOR) techniques have been successfully used to partition the space of traces into equivalence classes (Mazurkiewicz partitioning), with the goal of exploring only few representative traces from each class.\r\n\r\nWe introduce a new equivalence on traces under sequential consistency semantics, which we call the observation equivalence. Two traces are observationally equivalent if every read event observes the same write event in both traces. While the traditional Mazurkiewicz equivalence is control-centric, our new definition is data-centric. We show that our observation equivalence is coarser than the Mazurkiewicz equivalence, and in many cases even exponentially coarser. We devise a DPOR exploration of the trace space, called data-centric DPOR, based on the observation equivalence.","lang":"eng"}],"intvolume":" 2","month":"12","main_file_link":[{"url":"https://dl.acm.org/doi/10.1145/3158119","open_access":"1"}],"scopus_import":"1","date_updated":"2023-02-23T12:27:16Z","department":[{"_id":"KrCh"}],"_id":"10417","status":"public","conference":{"end_date":"2018-01-13","location":"Los Angeles, CA, United States","start_date":"2018-01-07","name":"POPL: Programming Languages"},"type":"journal_article","article_type":"original","publication":"Proceedings of the ACM on Programming Languages","day":"27","year":"2017","date_created":"2021-12-05T23:01:49Z","date_published":"2017-12-27T00:00:00Z","doi":"10.1145/3158119","acknowledgement":"The research was partly supported by Austrian Science Fund (FWF) Grant No P23499- N23, FWF\r\nNFN Grant No S11407-N23 (RiSE/SHiNE), ERC Start grant (279307: Graph Games), and Czech\r\nScience Foundation grant GBP202/12/G061.","oa":1,"publisher":"Association for Computing Machinery","quality_controlled":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"apa":"Chalupa, M., Chatterjee, K., Pavlogiannis, A., Sinha, N., & Vaidya, K. (2017). Data-centric dynamic partial order reduction. Proceedings of the ACM on Programming Languages. Los Angeles, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3158119","ama":"Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. Data-centric dynamic partial order reduction. Proceedings of the ACM on Programming Languages. 2017;2(POPL). doi:10.1145/3158119","short":"M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, K. Vaidya, Proceedings of the ACM on Programming Languages 2 (2017).","ieee":"M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, and K. Vaidya, “Data-centric dynamic partial order reduction,” Proceedings of the ACM on Programming Languages, vol. 2, no. POPL. Association for Computing Machinery, 2017.","mla":"Chalupa, Marek, et al. “Data-Centric Dynamic Partial Order Reduction.” Proceedings of the ACM on Programming Languages, vol. 2, no. POPL, 31, Association for Computing Machinery, 2017, doi:10.1145/3158119.","ista":"Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. 2017. Data-centric dynamic partial order reduction. Proceedings of the ACM on Programming Languages. 2(POPL), 31.","chicago":"Chalupa, Marek, Krishnendu Chatterjee, Andreas Pavlogiannis, Nishant Sinha, and Kapil Vaidya. “Data-Centric Dynamic Partial Order Reduction.” Proceedings of the ACM on Programming Languages. Association for Computing Machinery, 2017. https://doi.org/10.1145/3158119."},"title":"Data-centric dynamic partial order reduction","article_processing_charge":"No","external_id":{"arxiv":["1610.01188"]},"author":[{"first_name":"Marek","last_name":"Chalupa","full_name":"Chalupa, Marek"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722","last_name":"Pavlogiannis","first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Nishant","last_name":"Sinha","full_name":"Sinha, Nishant"},{"first_name":"Kapil","last_name":"Vaidya","full_name":"Vaidya, Kapil"}],"article_number":"31","project":[{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}]},{"month":"10","publisher":"IST Austria","alternative_title":["IST Austria Technical Report"],"oa":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"We present a new dynamic partial-order reduction method for stateless model checking of concurrent programs. A common approach for exploring program behaviors relies on enumerating the traces of the program, without storing the visited states (aka stateless exploration). As the number of distinct traces grows exponentially, dynamic partial-order reduction (DPOR) techniques have been successfully used to partition the space of traces into equivalence classes (Mazurkiewicz partitioning), with the goal of exploring only few representative traces from each class.\r\nWe introduce a new equivalence on traces under sequential consistency semantics, which we call the observation equivalence. Two traces are observationally equivalent if every read event observes the same write event in both traces. While the traditional Mazurkiewicz equivalence is control-centric, our new definition is data-centric. We show that our observation equivalence is coarser than the Mazurkiewicz equivalence, and in many cases even exponentially coarser. We devise a DPOR exploration of the trace space, called data-centric DPOR, based on the observation equivalence.\r\n1. For acyclic architectures, our algorithm is guaranteed to explore exactly one representative trace from each observation class, while spending polynomial time per class. Hence, our algorithm is optimal wrt the observation equivalence, and in several cases explores exponentially fewer traces than any enumerative method based on the Mazurkiewicz equivalence.\r\n2. For cyclic architectures, we consider an equivalence between traces which is finer than the observation equivalence; but coarser than the Mazurkiewicz equivalence, and in some cases is exponentially coarser. Our data-centric DPOR algorithm remains optimal under this trace equivalence. \r\nFinally, we perform a basic experimental comparison between the existing Mazurkiewicz-based DPOR and our data-centric DPOR on a set of academic benchmarks. Our results show a significant reduction in both running time and the number of explored equivalence classes."}],"date_published":"2017-10-23T00:00:00Z","doi":"10.15479/AT:IST-2017-872-v1-1","related_material":{"record":[{"relation":"later_version","id":"10417","status":"public"},{"id":"5448","status":"public","relation":"earlier_version"}]},"date_created":"2018-12-12T11:39:26Z","page":"36","day":"23","file":[{"file_id":"5487","checksum":"d2635c4cf013000f0a1b09e80f9e4ab7","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T11:53:26Z","file_name":"IST-2017-872-v1+1_main.pdf","date_updated":"2020-07-14T12:46:59Z","file_size":910347,"creator":"system"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2664-1690"]},"has_accepted_license":"1","publication_status":"published","year":"2017","status":"public","pubrep_id":"872","type":"technical_report","_id":"5456","department":[{"_id":"KrCh"}],"title":"Data-centric dynamic partial order reduction","file_date_updated":"2020-07-14T12:46:59Z","author":[{"first_name":"Marek","full_name":"Chalupa, Marek","last_name":"Chalupa"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"last_name":"Pavlogiannis","orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas","first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sinha, Nishant","last_name":"Sinha","first_name":"Nishant"},{"first_name":"Kapil","full_name":"Vaidya, Kapil","last_name":"Vaidya"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"citation":{"mla":"Chalupa, Marek, et al. Data-Centric Dynamic Partial Order Reduction. IST Austria, 2017, doi:10.15479/AT:IST-2017-872-v1-1.","apa":"Chalupa, M., Chatterjee, K., Pavlogiannis, A., Sinha, N., & Vaidya, K. (2017). Data-centric dynamic partial order reduction. IST Austria. https://doi.org/10.15479/AT:IST-2017-872-v1-1","ama":"Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. Data-Centric Dynamic Partial Order Reduction. IST Austria; 2017. doi:10.15479/AT:IST-2017-872-v1-1","ieee":"M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, and K. Vaidya, Data-centric dynamic partial order reduction. IST Austria, 2017.","short":"M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, K. Vaidya, Data-Centric Dynamic Partial Order Reduction, IST Austria, 2017.","chicago":"Chalupa, Marek, Krishnendu Chatterjee, Andreas Pavlogiannis, Nishant Sinha, and Kapil Vaidya. Data-Centric Dynamic Partial Order Reduction. IST Austria, 2017. https://doi.org/10.15479/AT:IST-2017-872-v1-1.","ista":"Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. 2017. Data-centric dynamic partial order reduction, IST Austria, 36p."},"date_updated":"2023-02-23T12:26:54Z"},{"citation":{"ista":"Chatterjee K, Ibsen-Jensen R, Nowak M. 2017. Faster Monte Carlo algorithms for fixation probability of the Moran process on undirected graphs. Leibniz International Proceedings in Informatics. MFCS: Mathematical Foundations of Computer Science (SG), LIPIcs, vol. 83, 61.","chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Martin Nowak. “Faster Monte Carlo Algorithms for Fixation Probability of the Moran Process on Undirected Graphs.” In Leibniz International Proceedings in Informatics, Vol. 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.MFCS.2017.61.","apa":"Chatterjee, K., Ibsen-Jensen, R., & Nowak, M. (2017). Faster Monte Carlo algorithms for fixation probability of the Moran process on undirected graphs. In Leibniz International Proceedings in Informatics (Vol. 83). Aalborg, Denmark: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.MFCS.2017.61","ama":"Chatterjee K, Ibsen-Jensen R, Nowak M. Faster Monte Carlo algorithms for fixation probability of the Moran process on undirected graphs. In: Leibniz International Proceedings in Informatics. Vol 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.MFCS.2017.61","ieee":"K. Chatterjee, R. Ibsen-Jensen, and M. Nowak, “Faster Monte Carlo algorithms for fixation probability of the Moran process on undirected graphs,” in Leibniz International Proceedings in Informatics, Aalborg, Denmark, 2017, vol. 83.","short":"K. Chatterjee, R. Ibsen-Jensen, M. Nowak, in:, Leibniz International Proceedings in Informatics, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","mla":"Chatterjee, Krishnendu, et al. “Faster Monte Carlo Algorithms for Fixation Probability of the Moran Process on Undirected Graphs.” Leibniz International Proceedings in Informatics, vol. 83, 61, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.MFCS.2017.61."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"first_name":"Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87","last_name":"Ibsen-Jensen","orcid":"0000-0003-4783-0389","full_name":"Ibsen-Jensen, Rasmus"},{"first_name":"Martin","full_name":"Nowak, Martin","last_name":"Nowak"}],"publist_id":"7263","title":"Faster Monte Carlo algorithms for fixation probability of the Moran process on undirected graphs","article_number":"61","year":"2017","has_accepted_license":"1","publication":"Leibniz International Proceedings in Informatics","day":"01","date_created":"2018-12-11T11:47:08Z","doi":"10.4230/LIPIcs.MFCS.2017.61","date_published":"2017-11-01T00:00:00Z","oa":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","date_updated":"2021-01-12T08:02:34Z","ddc":["004"],"file_date_updated":"2020-07-14T12:47:00Z","department":[{"_id":"KrCh"}],"_id":"551","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"name":"MFCS: Mathematical Foundations of Computer Science (SG)","end_date":"2017-08-25","location":"Aalborg, Denmark","start_date":"2017-08-21"},"type":"conference","pubrep_id":"924","status":"public","publication_status":"published","publication_identifier":{"isbn":["978-395977046-0"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"2eed5224c0e4e259484a1d71acb8ba6a","file_id":"5322","date_updated":"2020-07-14T12:47:00Z","file_size":535077,"creator":"system","date_created":"2018-12-12T10:18:04Z","file_name":"IST-2018-924-v1+1_LIPIcs-MFCS-2017-61.pdf"}],"volume":83,"abstract":[{"lang":"eng","text":"Evolutionary graph theory studies the evolutionary dynamics in a population structure given as a connected graph. Each node of the graph represents an individual of the population, and edges determine how offspring are placed. We consider the classical birth-death Moran process where there are two types of individuals, namely, the residents with fitness 1 and mutants with fitness r. The fitness indicates the reproductive strength. The evolutionary dynamics happens as follows: in the initial step, in a population of all resident individuals a mutant is introduced, and then at each step, an individual is chosen proportional to the fitness of its type to reproduce, and the offspring replaces a neighbor uniformly at random. The process stops when all individuals are either residents or mutants. The probability that all individuals in the end are mutants is called the fixation probability, which is a key factor in the rate of evolution. We consider the problem of approximating the fixation probability. The class of algorithms that is extremely relevant for approximation of the fixation probabilities is the Monte-Carlo simulation of the process. Previous results present a polynomial-time Monte-Carlo algorithm for undirected graphs when r is given in unary. First, we present a simple modification: instead of simulating each step, we discard ineffective steps, where no node changes type (i.e., either residents replace residents, or mutants replace mutants). Using the above simple modification and our result that the number of effective steps is concentrated around the expected number of effective steps, we present faster polynomial-time Monte-Carlo algorithms for undirected graphs. Our algorithms are always at least a factor O(n2/ log n) faster as compared to the previous algorithms, where n is the number of nodes, and is polynomial even if r is given in binary. We also present lower bounds showing that the upper bound on the expected number of effective steps we present is asymptotically tight for undirected graphs. "}],"oa_version":"Published Version","alternative_title":["LIPIcs"],"scopus_import":1,"intvolume":" 83","month":"11"},{"quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","oa":1,"has_accepted_license":"1","year":"2017","day":"01","publication":"Leibniz International Proceedings in Informatics","doi":"10.4230/LIPIcs.MFCS.2017.39","date_published":"2017-11-01T00:00:00Z","date_created":"2018-12-11T11:47:08Z","article_number":"39","project":[{"name":"Game Theory","grant_number":"S11407","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"}],"citation":{"apa":"Chatterjee, K., Henzinger, M. H., & Svozil, A. (2017). Faster algorithms for mean-payoff parity games. In Leibniz International Proceedings in Informatics (Vol. 83). Aalborg, Denmark: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.MFCS.2017.39","ama":"Chatterjee K, Henzinger MH, Svozil A. Faster algorithms for mean-payoff parity games. In: Leibniz International Proceedings in Informatics. Vol 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.MFCS.2017.39","short":"K. Chatterjee, M.H. Henzinger, A. Svozil, in:, Leibniz International Proceedings in Informatics, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","ieee":"K. Chatterjee, M. H. Henzinger, and A. Svozil, “Faster algorithms for mean-payoff parity games,” in Leibniz International Proceedings in Informatics, Aalborg, Denmark, 2017, vol. 83.","mla":"Chatterjee, Krishnendu, et al. “Faster Algorithms for Mean-Payoff Parity Games.” Leibniz International Proceedings in Informatics, vol. 83, 39, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.MFCS.2017.39.","ista":"Chatterjee K, Henzinger MH, Svozil A. 2017. Faster algorithms for mean-payoff parity games. Leibniz International Proceedings in Informatics. MFCS: Mathematical Foundations of Computer Science (SG), LIPIcs, vol. 83, 39.","chicago":"Chatterjee, Krishnendu, Monika H Henzinger, and Alexander Svozil. “Faster Algorithms for Mean-Payoff Parity Games.” In Leibniz International Proceedings in Informatics, Vol. 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.MFCS.2017.39."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"7262","author":[{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","last_name":"Henzinger","first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"full_name":"Svozil, Alexander","last_name":"Svozil","first_name":"Alexander"}],"article_processing_charge":"No","title":"Faster algorithms for mean-payoff parity games","abstract":[{"text":"Graph games provide the foundation for modeling and synthesis of reactive processes. Such games are played over graphs where the vertices are controlled by two adversarial players. We consider graph games where the objective of the first player is the conjunction of a qualitative objective (specified as a parity condition) and a quantitative objective (specified as a meanpayoff condition). There are two variants of the problem, namely, the threshold problem where the quantitative goal is to ensure that the mean-payoff value is above a threshold, and the value problem where the quantitative goal is to ensure the optimal mean-payoff value; in both cases ensuring the qualitative parity objective. The previous best-known algorithms for game graphs with n vertices, m edges, parity objectives with d priorities, and maximal absolute reward value W for mean-payoff objectives, are as follows: O(nd+1 . m . w) for the threshold problem, and O(nd+2 · m · W) for the value problem. Our main contributions are faster algorithms, and the running times of our algorithms are as follows: O(nd-1 · m ·W) for the threshold problem, and O(nd · m · W · log(n · W)) for the value problem. For mean-payoff parity objectives with two priorities, our algorithms match the best-known bounds of the algorithms for mean-payoff games (without conjunction with parity objectives). Our results are relevant in synthesis of reactive systems with both functional requirement (given as a qualitative objective) and performance requirement (given as a quantitative objective).","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","alternative_title":["LIPIcs"],"month":"11","intvolume":" 83","publication_identifier":{"isbn":["978-395977046-0"]},"publication_status":"published","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"5248","checksum":"c67f4866ddbfd555afef1f63ae9a8fc7","creator":"system","date_updated":"2020-07-14T12:47:00Z","file_size":610339,"date_created":"2018-12-12T10:16:57Z","file_name":"IST-2018-923-v1+1_LIPIcs-MFCS-2017-39.pdf"}],"language":[{"iso":"eng"}],"volume":83,"ec_funded":1,"license":"https://creativecommons.org/licenses/by/3.0/","_id":"552","type":"conference","conference":{"location":"Aalborg, Denmark","end_date":"2017-08-25","start_date":"2017-08-21","name":"MFCS: Mathematical Foundations of Computer Science (SG)"},"tmp":{"short":"CC BY (3.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)"},"status":"public","pubrep_id":"923","date_updated":"2023-02-14T10:06:46Z","ddc":["004"],"department":[{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:47:00Z"},{"date_updated":"2021-01-12T08:02:35Z","ddc":["004"],"file_date_updated":"2020-07-14T12:47:00Z","department":[{"_id":"KrCh"}],"_id":"553","conference":{"start_date":"2017-08-21","location":"Aalborg, Denmark","end_date":"2017-08-25","name":"MFCS: Mathematical Foundations of Computer Science (SG)"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"conference","pubrep_id":"922","status":"public","publication_status":"published","publication_identifier":{"isbn":["978-395977046-0"]},"language":[{"iso":"eng"}],"file":[{"creator":"system","file_size":549967,"date_updated":"2020-07-14T12:47:00Z","file_name":"IST-2018-922-v1+1_LIPIcs-MFCS-2017-55.pdf","date_created":"2018-12-12T10:09:29Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"4753","checksum":"7101facb56ade363205c695d72dbd173"}],"volume":83,"abstract":[{"text":"We consider two player, zero-sum, finite-state concurrent reachability games, played for an infinite number of rounds, where in every round, each player simultaneously and independently of the other players chooses an action, whereafter the successor state is determined by a probability distribution given by the current state and the chosen actions. Player 1 wins iff a designated goal state is eventually visited. We are interested in the complexity of stationary strategies measured by their patience, which is defined as the inverse of the smallest non-zero probability employed. Our main results are as follows: We show that: (i) the optimal bound on the patience of optimal and -optimal strategies, for both players is doubly exponential; and (ii) even in games with a single non-absorbing state exponential (in the number of actions) patience is necessary. ","lang":"eng"}],"oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1506.02434"}],"scopus_import":1,"alternative_title":["LIPIcs"],"intvolume":" 83","month":"11","citation":{"ama":"Chatterjee K, Hansen K, Ibsen-Jensen R. Strategy complexity of concurrent safety games. In: Leibniz International Proceedings in Informatics. Vol 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.MFCS.2017.55","apa":"Chatterjee, K., Hansen, K., & Ibsen-Jensen, R. (2017). Strategy complexity of concurrent safety games. In Leibniz International Proceedings in Informatics (Vol. 83). Aalborg, Denmark: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.MFCS.2017.55","ieee":"K. Chatterjee, K. Hansen, and R. Ibsen-Jensen, “Strategy complexity of concurrent safety games,” in Leibniz International Proceedings in Informatics, Aalborg, Denmark, 2017, vol. 83.","short":"K. Chatterjee, K. Hansen, R. Ibsen-Jensen, in:, Leibniz International Proceedings in Informatics, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","mla":"Chatterjee, Krishnendu, et al. “Strategy Complexity of Concurrent Safety Games.” Leibniz International Proceedings in Informatics, vol. 83, 55, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.MFCS.2017.55.","ista":"Chatterjee K, Hansen K, Ibsen-Jensen R. 2017. Strategy complexity of concurrent safety games. Leibniz International Proceedings in Informatics. MFCS: Mathematical Foundations of Computer Science (SG), LIPIcs, vol. 83, 55.","chicago":"Chatterjee, Krishnendu, Kristofer Hansen, and Rasmus Ibsen-Jensen. “Strategy Complexity of Concurrent Safety Games.” In Leibniz International Proceedings in Informatics, Vol. 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.MFCS.2017.55."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"7261","author":[{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hansen","full_name":"Hansen, Kristofer","first_name":"Kristofer"},{"last_name":"Ibsen-Jensen","orcid":"0000-0003-4783-0389","full_name":"Ibsen-Jensen, Rasmus","first_name":"Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87"}],"title":"Strategy complexity of concurrent safety games","article_number":"55","year":"2017","has_accepted_license":"1","publication":"Leibniz International Proceedings in Informatics","day":"01","date_created":"2018-12-11T11:47:08Z","doi":"10.4230/LIPIcs.MFCS.2017.55","date_published":"2017-11-01T00:00:00Z","oa":1,"quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik"},{"date_updated":"2021-01-12T08:03:04Z","department":[{"_id":"JaMa"}],"_id":"560","status":"public","type":"journal_article","language":[{"iso":"eng"}],"publication_identifier":{"issn":["13645021"]},"publication_status":"published","volume":473,"issue":"2207","ec_funded":1,"oa_version":"Submitted Version","abstract":[{"text":"In a recent article (Jentzen et al. 2016 Commun. Math. Sci. 14, 1477–1500 (doi:10.4310/CMS.2016.v14. n6.a1)), it has been established that, for every arbitrarily slow convergence speed and every natural number d ? {4, 5, . . .}, there exist d-dimensional stochastic differential equations with infinitely often differentiable and globally bounded coefficients such that no approximation method based on finitely many observations of the driving Brownian motion can converge in absolute mean to the solution faster than the given speed of convergence. In this paper, we strengthen the above result by proving that this slow convergence phenomenon also arises in two (d = 2) and three (d = 3) space dimensions.","lang":"eng"}],"month":"11","intvolume":" 473","scopus_import":1,"main_file_link":[{"url":"https://arxiv.org/abs/1702.03229","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Gerencser, Mate, Arnulf Jentzen, and Diyora Salimova. “On Stochastic Differential Equations with Arbitrarily Slow Convergence Rates for Strong Approximation in Two Space Dimensions.” Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. Royal Society of London, 2017. https://doi.org/10.1098/rspa.2017.0104.","ista":"Gerencser M, Jentzen A, Salimova D. 2017. On stochastic differential equations with arbitrarily slow convergence rates for strong approximation in two space dimensions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. 473(2207), 0104.","mla":"Gerencser, Mate, et al. “On Stochastic Differential Equations with Arbitrarily Slow Convergence Rates for Strong Approximation in Two Space Dimensions.” Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol. 473, no. 2207, 0104, Royal Society of London, 2017, doi:10.1098/rspa.2017.0104.","apa":"Gerencser, M., Jentzen, A., & Salimova, D. (2017). On stochastic differential equations with arbitrarily slow convergence rates for strong approximation in two space dimensions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. Royal Society of London. https://doi.org/10.1098/rspa.2017.0104","ama":"Gerencser M, Jentzen A, Salimova D. On stochastic differential equations with arbitrarily slow convergence rates for strong approximation in two space dimensions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. 2017;473(2207). doi:10.1098/rspa.2017.0104","ieee":"M. Gerencser, A. Jentzen, and D. Salimova, “On stochastic differential equations with arbitrarily slow convergence rates for strong approximation in two space dimensions,” Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol. 473, no. 2207. Royal Society of London, 2017.","short":"M. Gerencser, A. Jentzen, D. Salimova, Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 473 (2017)."},"title":"On stochastic differential equations with arbitrarily slow convergence rates for strong approximation in two space dimensions","author":[{"full_name":"Gerencser, Mate","last_name":"Gerencser","first_name":"Mate","id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Jentzen, Arnulf","last_name":"Jentzen","first_name":"Arnulf"},{"first_name":"Diyora","last_name":"Salimova","full_name":"Salimova, Diyora"}],"publist_id":"7256","article_number":"0104","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"day":"01","publication":"Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences","year":"2017","date_published":"2017-11-01T00:00:00Z","doi":"10.1098/rspa.2017.0104","date_created":"2018-12-11T11:47:11Z","publisher":"Royal Society of London","quality_controlled":"1","oa":1},{"doi":"10.4310/HHA.2017.v19.n2.a16","date_published":"2017-01-01T00:00:00Z","date_created":"2018-12-11T11:47:14Z","page":"313 - 342","day":"01","publication":"Homology, Homotopy and Applications","year":"2017","quality_controlled":"1","publisher":"International Press","oa":1,"title":"Persistence of zero sets","publist_id":"7246","author":[{"id":"473294AE-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","last_name":"Franek","full_name":"Franek, Peter"},{"last_name":"Krcál","full_name":"Krcál, Marek","id":"33E21118-F248-11E8-B48F-1D18A9856A87","first_name":"Marek"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Franek, Peter, and Marek Krcál. “Persistence of Zero Sets.” Homology, Homotopy and Applications. International Press, 2017. https://doi.org/10.4310/HHA.2017.v19.n2.a16.","ista":"Franek P, Krcál M. 2017. Persistence of zero sets. Homology, Homotopy and Applications. 19(2), 313–342.","mla":"Franek, Peter, and Marek Krcál. “Persistence of Zero Sets.” Homology, Homotopy and Applications, vol. 19, no. 2, International Press, 2017, pp. 313–42, doi:10.4310/HHA.2017.v19.n2.a16.","short":"P. Franek, M. Krcál, Homology, Homotopy and Applications 19 (2017) 313–342.","ieee":"P. Franek and M. Krcál, “Persistence of zero sets,” Homology, Homotopy and Applications, vol. 19, no. 2. International Press, pp. 313–342, 2017.","ama":"Franek P, Krcál M. Persistence of zero sets. Homology, Homotopy and Applications. 2017;19(2):313-342. doi:10.4310/HHA.2017.v19.n2.a16","apa":"Franek, P., & Krcál, M. (2017). Persistence of zero sets. Homology, Homotopy and Applications. International Press. https://doi.org/10.4310/HHA.2017.v19.n2.a16"},"project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"701309","name":"Atomic-Resolution Structures of Mitochondrial Respiratory Chain Supercomplexes (H2020)","call_identifier":"H2020","_id":"2590DB08-B435-11E9-9278-68D0E5697425"}],"volume":19,"issue":"2","ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["15320073"]},"publication_status":"published","month":"01","intvolume":" 19","scopus_import":1,"main_file_link":[{"url":"https://arxiv.org/abs/1507.04310","open_access":"1"}],"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"We study robust properties of zero sets of continuous maps f: X → ℝn. Formally, we analyze the family Z< r(f) := (g-1(0): ||g - f|| < r) of all zero sets of all continuous maps g closer to f than r in the max-norm. All of these sets are outside A := (x: |f(x)| ≥ r) and we claim that Z< r(f) is fully determined by A and an element of a certain cohomotopy group which (by a recent result) is computable whenever the dimension of X is at most 2n - 3. By considering all r > 0 simultaneously, the pointed cohomotopy groups form a persistence module-a structure leading to persistence diagrams as in the case of persistent homology or well groups. Eventually, we get a descriptor of persistent robust properties of zero sets that has better descriptive power (Theorem A) and better computability status (Theorem B) than the established well diagrams. Moreover, if we endow every point of each zero set with gradients of the perturbation, the robust description of the zero sets by elements of cohomotopy groups is in some sense the best possible (Theorem C)."}],"department":[{"_id":"UlWa"},{"_id":"HeEd"}],"date_updated":"2021-01-12T08:03:12Z","status":"public","type":"journal_article","_id":"568"},{"date_created":"2018-12-11T11:47:14Z","date_published":"2017-11-13T00:00:00Z","doi":"10.7554/eLife.28921","publication":"eLife","day":"13","year":"2017","has_accepted_license":"1","oa":1,"quality_controlled":"1","publisher":"eLife Sciences Publications","title":"Regulatory network structure determines patterns of intermolecular epistasis","author":[{"last_name":"Lagator","full_name":"Lagator, Mato","first_name":"Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sarikas, Srdjan","last_name":"Sarikas","id":"35F0286E-F248-11E8-B48F-1D18A9856A87","first_name":"Srdjan"},{"id":"2DDF136A-F248-11E8-B48F-1D18A9856A87","first_name":"Hande","orcid":"0000-0003-1986-9753","full_name":"Acar, Hande","last_name":"Acar"},{"full_name":"Bollback, Jonathan P","orcid":"0000-0002-4624-4612","last_name":"Bollback","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","first_name":"Jonathan P"},{"first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052"}],"publist_id":"7244","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Lagator M, Sarikas S, Acar H, Bollback JP, Guet CC. 2017. Regulatory network structure determines patterns of intermolecular epistasis. eLife. 6, e28921.","chicago":"Lagator, Mato, Srdjan Sarikas, Hande Acar, Jonathan P Bollback, and Calin C Guet. “Regulatory Network Structure Determines Patterns of Intermolecular Epistasis.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.28921.","ama":"Lagator M, Sarikas S, Acar H, Bollback JP, Guet CC. Regulatory network structure determines patterns of intermolecular epistasis. eLife. 2017;6. doi:10.7554/eLife.28921","apa":"Lagator, M., Sarikas, S., Acar, H., Bollback, J. P., & Guet, C. C. (2017). Regulatory network structure determines patterns of intermolecular epistasis. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.28921","short":"M. Lagator, S. Sarikas, H. Acar, J.P. Bollback, C.C. Guet, ELife 6 (2017).","ieee":"M. Lagator, S. Sarikas, H. Acar, J. P. Bollback, and C. C. Guet, “Regulatory network structure determines patterns of intermolecular epistasis,” eLife, vol. 6. eLife Sciences Publications, 2017.","mla":"Lagator, Mato, et al. “Regulatory Network Structure Determines Patterns of Intermolecular Epistasis.” ELife, vol. 6, e28921, eLife Sciences Publications, 2017, doi:10.7554/eLife.28921."},"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"},{"name":"Selective Barriers to Horizontal Gene Transfer","grant_number":"648440","_id":"2578D616-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_number":"e28921","ec_funded":1,"volume":6,"language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-12T10:14:42Z","file_name":"IST-2017-918-v1+1_elife-28921-figures-v3.pdf","creator":"system","date_updated":"2020-07-14T12:47:10Z","file_size":8453470,"checksum":"273ab17f33305e4eaafd911ff88e7c5b","file_id":"5096","access_level":"open_access","relation":"main_file","content_type":"application/pdf"},{"file_size":1953221,"date_updated":"2020-07-14T12:47:10Z","creator":"system","file_name":"IST-2017-918-v1+2_elife-28921-v3.pdf","date_created":"2018-12-12T10:14:43Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5097","checksum":"b433f90576c7be597cd43367946f8e7f"}],"publication_status":"published","publication_identifier":{"issn":["2050084X"]},"intvolume":" 6","month":"11","scopus_import":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Most phenotypes are determined by molecular systems composed of specifically interacting molecules. However, unlike for individual components, little is known about the distributions of mutational effects of molecular systems as a whole. We ask how the distribution of mutational effects of a transcriptional regulatory system differs from the distributions of its components, by first independently, and then simultaneously, mutating a transcription factor and the associated promoter it represses. We find that the system distribution exhibits increased phenotypic variation compared to individual component distributions - an effect arising from intermolecular epistasis between the transcription factor and its DNA-binding site. In large part, this epistasis can be qualitatively attributed to the structure of the transcriptional regulatory system and could therefore be a common feature in prokaryotes. Counter-intuitively, intermolecular epistasis can alleviate the constraints of individual components, thereby increasing phenotypic variation that selection could act on and facilitating adaptive evolution. "}],"file_date_updated":"2020-07-14T12:47:10Z","department":[{"_id":"CaGu"},{"_id":"JoBo"},{"_id":"NiBa"}],"ddc":["576"],"date_updated":"2021-01-12T08:03:15Z","pubrep_id":"918","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"570"},{"title":"Cytokinesis in vertebrate cells initiates by contraction of an equatorial actomyosin network composed of randomly oriented filaments","publist_id":"7245","author":[{"full_name":"Spira, Felix","last_name":"Spira","first_name":"Felix"},{"first_name":"Sara","last_name":"Cuylen Haering","full_name":"Cuylen Haering, Sara"},{"first_name":"Shalin","last_name":"Mehta","full_name":"Mehta, Shalin"},{"first_name":"Matthias","full_name":"Samwer, Matthias","last_name":"Samwer"},{"id":"35B76592-F248-11E8-B48F-1D18A9856A87","first_name":"Anne","last_name":"Reversat","orcid":"0000-0003-0666-8928","full_name":"Reversat, Anne"},{"first_name":"Amitabh","full_name":"Verma, Amitabh","last_name":"Verma"},{"last_name":"Oldenbourg","full_name":"Oldenbourg, Rudolf","first_name":"Rudolf"},{"last_name":"Sixt","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Gerlich, Daniel","last_name":"Gerlich","first_name":"Daniel"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Spira, Felix, et al. “Cytokinesis in Vertebrate Cells Initiates by Contraction of an Equatorial Actomyosin Network Composed of Randomly Oriented Filaments.” ELife, vol. 6, e30867, eLife Sciences Publications, 2017, doi:10.7554/eLife.30867.","apa":"Spira, F., Cuylen Haering, S., Mehta, S., Samwer, M., Reversat, A., Verma, A., … Gerlich, D. (2017). Cytokinesis in vertebrate cells initiates by contraction of an equatorial actomyosin network composed of randomly oriented filaments. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.30867","ama":"Spira F, Cuylen Haering S, Mehta S, et al. Cytokinesis in vertebrate cells initiates by contraction of an equatorial actomyosin network composed of randomly oriented filaments. eLife. 2017;6. doi:10.7554/eLife.30867","ieee":"F. Spira et al., “Cytokinesis in vertebrate cells initiates by contraction of an equatorial actomyosin network composed of randomly oriented filaments,” eLife, vol. 6. eLife Sciences Publications, 2017.","short":"F. Spira, S. Cuylen Haering, S. Mehta, M. Samwer, A. Reversat, A. Verma, R. Oldenbourg, M.K. Sixt, D. Gerlich, ELife 6 (2017).","chicago":"Spira, Felix, Sara Cuylen Haering, Shalin Mehta, Matthias Samwer, Anne Reversat, Amitabh Verma, Rudolf Oldenbourg, Michael K Sixt, and Daniel Gerlich. “Cytokinesis in Vertebrate Cells Initiates by Contraction of an Equatorial Actomyosin Network Composed of Randomly Oriented Filaments.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.30867.","ista":"Spira F, Cuylen Haering S, Mehta S, Samwer M, Reversat A, Verma A, Oldenbourg R, Sixt MK, Gerlich D. 2017. Cytokinesis in vertebrate cells initiates by contraction of an equatorial actomyosin network composed of randomly oriented filaments. eLife. 6, e30867."},"article_number":"e30867","date_created":"2018-12-11T11:47:14Z","date_published":"2017-11-06T00:00:00Z","doi":"10.7554/eLife.30867","publication":"eLife","day":"06","year":"2017","has_accepted_license":"1","oa":1,"publisher":"eLife Sciences Publications","quality_controlled":"1","file_date_updated":"2020-07-14T12:47:10Z","department":[{"_id":"MiSi"}],"ddc":["570"],"date_updated":"2023-02-23T12:30:29Z","pubrep_id":"919","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"569","volume":6,"language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"4829","checksum":"ba09c1451153d39e4f4b7cee013e314c","creator":"system","file_size":9666973,"date_updated":"2020-07-14T12:47:10Z","file_name":"IST-2017-919-v1+1_elife-30867-figures-v1.pdf","date_created":"2018-12-12T10:10:40Z"},{"file_id":"4830","checksum":"01eb51f1d6ad679947415a51c988e137","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"IST-2017-919-v1+2_elife-30867-v1.pdf","date_created":"2018-12-12T10:10:41Z","file_size":5951246,"date_updated":"2020-07-14T12:47:10Z","creator":"system"}],"publication_status":"published","publication_identifier":{"issn":["2050084X"]},"intvolume":" 6","month":"11","scopus_import":1,"oa_version":"Published Version","abstract":[{"text":"The actomyosin ring generates force to ingress the cytokinetic cleavage furrow in animal cells, yet its filament organization and the mechanism of contractility is not well understood. We quantified actin filament order in human cells using fluorescence polarization microscopy and found that cleavage furrow ingression initiates by contraction of an equatorial actin network with randomly oriented filaments. The network subsequently gradually reoriented actin filaments along the cell equator. This strictly depended on myosin II activity, suggesting local network reorganization by mechanical forces. Cortical laser microsurgery revealed that during cytokinesis progression, mechanical tension increased substantially along the direction of the cell equator, while the network contracted laterally along the pole-to-pole axis without a detectable increase in tension. Our data suggest that an asymmetric increase in cortical tension promotes filament reorientation along the cytokinetic cleavage furrow, which might have implications for diverse other biological processes involving actomyosin rings.","lang":"eng"}]},{"date_published":"2017-12-01T00:00:00Z","doi":"10.3390/ijms18122587","date_created":"2018-12-11T11:47:15Z","has_accepted_license":"1","year":"2017","day":"01","publication":"International Journal of Molecular Sciences","quality_controlled":"1","publisher":"MDPI","oa":1,"publist_id":"7242","author":[{"last_name":"Olatunji","full_name":"Olatunji, Damilola","first_name":"Damilola"},{"last_name":"Geelen","full_name":"Geelen, Danny","first_name":"Danny"},{"first_name":"Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7241-2328","full_name":"Verstraeten, Inge","last_name":"Verstraeten"}],"article_processing_charge":"No","title":"Control of endogenous auxin levels in plant root development","citation":{"mla":"Olatunji, Damilola, et al. “Control of Endogenous Auxin Levels in Plant Root Development.” International Journal of Molecular Sciences, vol. 18, no. 12, 2587, MDPI, 2017, doi:10.3390/ijms18122587.","ieee":"D. Olatunji, D. Geelen, and I. Verstraeten, “Control of endogenous auxin levels in plant root development,” International Journal of Molecular Sciences, vol. 18, no. 12. MDPI, 2017.","short":"D. Olatunji, D. Geelen, I. Verstraeten, International Journal of Molecular Sciences 18 (2017).","ama":"Olatunji D, Geelen D, Verstraeten I. Control of endogenous auxin levels in plant root development. International Journal of Molecular Sciences. 2017;18(12). doi:10.3390/ijms18122587","apa":"Olatunji, D., Geelen, D., & Verstraeten, I. (2017). Control of endogenous auxin levels in plant root development. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms18122587","chicago":"Olatunji, Damilola, Danny Geelen, and Inge Verstraeten. “Control of Endogenous Auxin Levels in Plant Root Development.” International Journal of Molecular Sciences. MDPI, 2017. https://doi.org/10.3390/ijms18122587.","ista":"Olatunji D, Geelen D, Verstraeten I. 2017. Control of endogenous auxin levels in plant root development. International Journal of Molecular Sciences. 18(12), 2587."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","article_number":"2587","volume":18,"issue":"12","publication_status":"published","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"82d51f11e493f7eec02976d9a9a9805e","file_id":"4718","creator":"system","date_updated":"2020-07-14T12:47:10Z","file_size":920962,"date_created":"2018-12-12T10:08:55Z","file_name":"IST-2017-917-v1+1_ijms-18-02587.pdf"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"12","intvolume":" 18","abstract":[{"text":"In this review, we summarize the different biosynthesis-related pathways that contribute to the regulation of endogenous auxin in plants. We demonstrate that all known genes involved in auxin biosynthesis also have a role in root formation, from the initiation of a root meristem during embryogenesis to the generation of a functional root system with a primary root, secondary lateral root branches and adventitious roots. Furthermore, the versatile adaptation of root development in response to environmental challenges is mediated by both local and distant control of auxin biosynthesis. In conclusion, auxin homeostasis mediated by spatial and temporal regulation of auxin biosynthesis plays a central role in determining root architecture.","lang":"eng"}],"oa_version":"Published Version","file_date_updated":"2020-07-14T12:47:10Z","department":[{"_id":"JiFr"}],"date_updated":"2021-01-12T08:03:16Z","ddc":["580"],"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"917","_id":"572"},{"article_number":"012004","citation":{"chicago":"Camus, Nicolas, Enderalp Yakaboylu, Lutz Fechner, Michael Klaiber, Martin Laux, Yonghao Mi, Karen Hatsagortsyan, Thomas Pfeifer, Cristoph Keitel, and Robert Moshammer. “Experimental Evidence for Wigner’s Tunneling Time,” Vol. 999. American Physical Society, 2017. https://doi.org/10.1088/1742-6596/999/1/012004.","ista":"Camus N, Yakaboylu E, Fechner L, Klaiber M, Laux M, Mi Y, Hatsagortsyan K, Pfeifer T, Keitel C, Moshammer R. 2017. Experimental evidence for Wigner’s tunneling time. Annual International Laser Physics Workshop LPHYS, Journal of Physics: Conference Series, vol. 999, 012004.","mla":"Camus, Nicolas, et al. Experimental Evidence for Wigner’s Tunneling Time. Vol. 999, no. 1, 012004, American Physical Society, 2017, doi:10.1088/1742-6596/999/1/012004.","ieee":"N. Camus et al., “Experimental evidence for Wigner’s tunneling time,” presented at the Annual International Laser Physics Workshop LPHYS, Kazan, Russian Federation, 2017, vol. 999, no. 1.","short":"N. Camus, E. Yakaboylu, L. Fechner, M. Klaiber, M. Laux, Y. Mi, K. Hatsagortsyan, T. Pfeifer, C. Keitel, R. Moshammer, in:, American Physical Society, 2017.","ama":"Camus N, Yakaboylu E, Fechner L, et al. Experimental evidence for Wigner’s tunneling time. In: Vol 999. American Physical Society; 2017. doi:10.1088/1742-6596/999/1/012004","apa":"Camus, N., Yakaboylu, E., Fechner, L., Klaiber, M., Laux, M., Mi, Y., … Moshammer, R. (2017). Experimental evidence for Wigner’s tunneling time (Vol. 999). Presented at the Annual International Laser Physics Workshop LPHYS, Kazan, Russian Federation: American Physical Society. https://doi.org/10.1088/1742-6596/999/1/012004"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["1611.03701"]},"author":[{"first_name":"Nicolas","last_name":"Camus","full_name":"Camus, Nicolas"},{"last_name":"Yakaboylu","full_name":"Yakaboylu, Enderalp","orcid":"0000-0001-5973-0874","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87","first_name":"Enderalp"},{"full_name":"Fechner, Lutz","last_name":"Fechner","first_name":"Lutz"},{"first_name":"Michael","last_name":"Klaiber","full_name":"Klaiber, Michael"},{"full_name":"Laux, Martin","last_name":"Laux","first_name":"Martin"},{"first_name":"Yonghao","full_name":"Mi, Yonghao","last_name":"Mi"},{"last_name":"Hatsagortsyan","full_name":"Hatsagortsyan, Karen","first_name":"Karen"},{"first_name":"Thomas","full_name":"Pfeifer, Thomas","last_name":"Pfeifer"},{"first_name":"Cristoph","last_name":"Keitel","full_name":"Keitel, Cristoph"},{"first_name":"Robert","last_name":"Moshammer","full_name":"Moshammer, Robert"}],"publist_id":"7552","title":"Experimental evidence for Wigner's tunneling time","oa":1,"publisher":"American Physical Society","quality_controlled":"1","year":"2017","has_accepted_license":"1","day":"14","date_created":"2018-12-11T11:45:46Z","date_published":"2017-07-14T00:00:00Z","doi":"10.1088/1742-6596/999/1/012004","_id":"313","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"name":"Annual International Laser Physics Workshop LPHYS","location":"Kazan, Russian Federation","end_date":"2017-08-21","start_date":"2017-08-17"},"type":"conference","status":"public","date_updated":"2023-02-23T12:36:07Z","ddc":["530"],"department":[{"_id":"MiLe"}],"file_date_updated":"2020-07-14T12:46:00Z","abstract":[{"text":"Tunneling of a particle through a potential barrier remains one of the most remarkable quantum phenomena. Owing to advances in laser technology, electric fields comparable to those electrons experience in atoms are readily generated and open opportunities to dynamically investigate the process of electron tunneling through the potential barrier formed by the superposition of both laser and atomic fields. Attosecond-time and angstrom-space resolution of the strong laser-field technique allow to address fundamental questions related to tunneling, which are still open and debated: Which time is spent under the barrier and what momentum is picked up by the particle in the meantime? In this combined experimental and theoretical study we demonstrate that for strong-field ionization the leading quantum mechanical Wigner treatment for the time resolved description of tunneling is valid. We achieve a high sensitivity on the tunneling barrier and unambiguously isolate its effects by performing a differential study of two systems with almost identical tunneling geometry. Moreover, working with a low frequency laser, we essentially limit the non-adiabaticity of the process as a major source of uncertainty. The agreement between experiment and theory implies two substantial corrections with respect to the widely employed quasiclassical treatment: In addition to a non-vanishing longitudinal momentum along the laser field-direction we provide clear evidence for a non-zero tunneling time delay. This addresses also the fundamental question how the transition occurs from the tunnel barrier to free space classical evolution of the ejected electron.","lang":"eng"}],"oa_version":"Published Version","alternative_title":["Journal of Physics: Conference Series"],"scopus_import":1,"intvolume":" 999","month":"07","publication_status":"published","publication_identifier":{"issn":["17426588"]},"language":[{"iso":"eng"}],"file":[{"checksum":"6e70b525a84f6d5fb175c48e9f5cb59a","file_id":"5871","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2017_Physics_Camus.pdf","date_created":"2019-01-22T08:34:10Z","file_size":949321,"date_updated":"2020-07-14T12:46:00Z","creator":"dernst"}],"volume":999,"related_material":{"record":[{"id":"6013","status":"public","relation":"later_version"}]},"issue":"1"},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","status":"public","_id":"601","file_date_updated":"2020-07-14T12:47:16Z","date_updated":"2021-01-12T08:05:40Z","ddc":["570"],"extern":"1","intvolume":" 8","month":"06","abstract":[{"text":"The conserved polymerase-Associated factor 1 complex (Paf1C) plays multiple roles in chromatin transcription and genomic regulation. Paf1C comprises the five subunits Paf1, Leo1, Ctr9, Cdc73 and Rtf1, and binds to the RNA polymerase II (Pol II) transcription elongation complex (EC). Here we report the reconstitution of Paf1C from Saccharomyces cerevisiae, and a structural analysis of Paf1C bound to a Pol II EC containing the elongation factor TFIIS. Cryo-electron microscopy and crosslinking data reveal that Paf1C is highly mobile and extends over the outer Pol II surface from the Rpb2 to the Rpb3 subunit. The Paf1-Leo1 heterodimer and Cdc73 form opposite ends of Paf1C, whereas Ctr9 bridges between them. Consistent with the structural observations, the initiation factor TFIIF impairs Paf1C binding to Pol II, whereas the elongation factor TFIIS enhances it. We further show that Paf1C is globally required for normal mRNA transcription in yeast. These results provide a three-dimensional framework for further analysis of Paf1C function in transcription through chromatin. ","lang":"eng"}],"oa_version":"Published Version","volume":8,"publication_status":"published","publication_identifier":{"issn":["20411723"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2019-01-21T14:48:10Z","file_name":"2017_NatureComm_Xu.pdf","creator":"dernst","date_updated":"2020-07-14T12:47:16Z","file_size":3018075,"checksum":"940742282a9a285dc4aeae0c2b5ebe96","file_id":"5865","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"article_number":"15741","article_processing_charge":"No","publist_id":"7203","author":[{"first_name":"Youwei","full_name":"Xu, Youwei","last_name":"Xu"},{"full_name":"Bernecky, Carrie A","orcid":"0000-0003-0893-7036","last_name":"Bernecky","first_name":"Carrie A","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Chung","last_name":"Lee","full_name":"Lee, Chung"},{"last_name":"Maier","full_name":"Maier, Kerstin","first_name":"Kerstin"},{"first_name":"Björn","last_name":"Schwalb","full_name":"Schwalb, Björn"},{"last_name":"Tegunov","full_name":"Tegunov, Dimitri","first_name":"Dimitri"},{"first_name":"Jürgen","full_name":"Plitzko, Jürgen","last_name":"Plitzko"},{"full_name":"Urlaub, Henning","last_name":"Urlaub","first_name":"Henning"},{"first_name":"Patrick","full_name":"Cramer, Patrick","last_name":"Cramer"}],"title":"Architecture of the RNA polymerase II-Paf1C-TFIIS transcription elongation complex","citation":{"ama":"Xu Y, Bernecky C, Lee C, et al. Architecture of the RNA polymerase II-Paf1C-TFIIS transcription elongation complex. Nature Communications. 2017;8. doi:10.1038/ncomms15741","apa":"Xu, Y., Bernecky, C., Lee, C., Maier, K., Schwalb, B., Tegunov, D., … Cramer, P. (2017). Architecture of the RNA polymerase II-Paf1C-TFIIS transcription elongation complex. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms15741","ieee":"Y. Xu et al., “Architecture of the RNA polymerase II-Paf1C-TFIIS transcription elongation complex,” Nature Communications, vol. 8. Nature Publishing Group, 2017.","short":"Y. Xu, C. Bernecky, C. Lee, K. Maier, B. Schwalb, D. Tegunov, J. Plitzko, H. Urlaub, P. Cramer, Nature Communications 8 (2017).","mla":"Xu, Youwei, et al. “Architecture of the RNA Polymerase II-Paf1C-TFIIS Transcription Elongation Complex.” Nature Communications, vol. 8, 15741, Nature Publishing Group, 2017, doi:10.1038/ncomms15741.","ista":"Xu Y, Bernecky C, Lee C, Maier K, Schwalb B, Tegunov D, Plitzko J, Urlaub H, Cramer P. 2017. Architecture of the RNA polymerase II-Paf1C-TFIIS transcription elongation complex. Nature Communications. 8, 15741.","chicago":"Xu, Youwei, Carrie Bernecky, Chung Lee, Kerstin Maier, Björn Schwalb, Dimitri Tegunov, Jürgen Plitzko, Henning Urlaub, and Patrick Cramer. “Architecture of the RNA Polymerase II-Paf1C-TFIIS Transcription Elongation Complex.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/ncomms15741."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"publisher":"Nature Publishing Group","quality_controlled":"1","date_created":"2018-12-11T11:47:25Z","date_published":"2017-06-06T00:00:00Z","doi":"10.1038/ncomms15741","year":"2017","has_accepted_license":"1","publication":"Nature Communications","day":"06"},{"department":[{"_id":"MiLe"}],"date_updated":"2023-02-23T11:13:36Z","type":"journal_article","status":"public","_id":"6013","issue":"2","volume":119,"related_material":{"record":[{"relation":"earlier_version","id":"313","status":"public"}]},"publication_status":"published","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1611.03701"}],"scopus_import":1,"intvolume":" 119","month":"07","abstract":[{"lang":"eng","text":"The first hundred attoseconds of the electron dynamics during strong field tunneling ionization are investigated. We quantify theoretically how the electron’s classical trajectories in the continuum emerge from the tunneling process and test the results with those achieved in parallel from attoclock measurements. An especially high sensitivity on the tunneling barrier is accomplished here by comparing the momentum distributions of two atomic species of slightly deviating atomic potentials (argon and krypton) being ionized under absolutely identical conditions with near-infrared laser pulses (1300 nm). The agreement between experiment and theory provides clear evidence for a nonzero tunneling time delay and a nonvanishing longitudinal momentum of the electron at the “tunnel exit.”"}],"oa_version":"Preprint","external_id":{"arxiv":["1611.03701"]},"author":[{"last_name":"Camus","full_name":"Camus, Nicolas","first_name":"Nicolas"},{"first_name":"Enderalp","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87","last_name":"Yakaboylu","full_name":"Yakaboylu, Enderalp","orcid":"0000-0001-5973-0874"},{"first_name":"Lutz","last_name":"Fechner","full_name":"Fechner, Lutz"},{"full_name":"Klaiber, Michael","last_name":"Klaiber","first_name":"Michael"},{"first_name":"Martin","full_name":"Laux, Martin","last_name":"Laux"},{"last_name":"Mi","full_name":"Mi, Yonghao","first_name":"Yonghao"},{"full_name":"Hatsagortsyan, Karen Z.","last_name":"Hatsagortsyan","first_name":"Karen Z."},{"last_name":"Pfeifer","full_name":"Pfeifer, Thomas","first_name":"Thomas"},{"first_name":"Christoph H.","last_name":"Keitel","full_name":"Keitel, Christoph H."},{"first_name":"Robert","full_name":"Moshammer, Robert","last_name":"Moshammer"}],"title":"Experimental evidence for quantum tunneling time","citation":{"ista":"Camus N, Yakaboylu E, Fechner L, Klaiber M, Laux M, Mi Y, Hatsagortsyan KZ, Pfeifer T, Keitel CH, Moshammer R. 2017. Experimental evidence for quantum tunneling time. Physical Review Letters. 119(2), 023201.","chicago":"Camus, Nicolas, Enderalp Yakaboylu, Lutz Fechner, Michael Klaiber, Martin Laux, Yonghao Mi, Karen Z. Hatsagortsyan, Thomas Pfeifer, Christoph H. Keitel, and Robert Moshammer. “Experimental Evidence for Quantum Tunneling Time.” Physical Review Letters. American Physical Society, 2017. https://doi.org/10.1103/PhysRevLett.119.023201.","short":"N. Camus, E. Yakaboylu, L. Fechner, M. Klaiber, M. Laux, Y. Mi, K.Z. Hatsagortsyan, T. Pfeifer, C.H. Keitel, R. Moshammer, Physical Review Letters 119 (2017).","ieee":"N. Camus et al., “Experimental evidence for quantum tunneling time,” Physical Review Letters, vol. 119, no. 2. American Physical Society, 2017.","ama":"Camus N, Yakaboylu E, Fechner L, et al. Experimental evidence for quantum tunneling time. Physical Review Letters. 2017;119(2). doi:10.1103/PhysRevLett.119.023201","apa":"Camus, N., Yakaboylu, E., Fechner, L., Klaiber, M., Laux, M., Mi, Y., … Moshammer, R. (2017). Experimental evidence for quantum tunneling time. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.119.023201","mla":"Camus, Nicolas, et al. “Experimental Evidence for Quantum Tunneling Time.” Physical Review Letters, vol. 119, no. 2, 023201, American Physical Society, 2017, doi:10.1103/PhysRevLett.119.023201."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"023201","date_created":"2019-02-14T15:24:13Z","date_published":"2017-07-14T00:00:00Z","doi":"10.1103/PhysRevLett.119.023201","year":"2017","publication":"Physical Review Letters","day":"14","oa":1,"quality_controlled":"1","publisher":"American Physical Society"},{"date_updated":"2021-01-12T08:05:53Z","department":[{"_id":"KrPi"}],"_id":"605","status":"public","type":"conference","conference":{"end_date":"2017-11-15","location":"Baltimore, MD, United States","start_date":"2017-11-12","name":"TCC: Theory of Cryptography Conference"},"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-331970499-9"]},"publication_status":"published","volume":10677,"ec_funded":1,"oa_version":"Submitted Version","abstract":[{"text":"Position based cryptography (PBC), proposed in the seminal work of Chandran, Goyal, Moriarty, and Ostrovsky (SIAM J. Computing, 2014), aims at constructing cryptographic schemes in which the identity of the user is his geographic position. Chandran et al. construct PBC schemes for secure positioning and position-based key agreement in the bounded-storage model (Maurer, J. Cryptology, 1992). Apart from bounded memory, their security proofs need a strong additional restriction on the power of the adversary: he cannot compute joint functions of his inputs. Removing this assumption is left as an open problem. We show that an answer to this question would resolve a long standing open problem in multiparty communication complexity: finding a function that is hard to compute with low communication complexity in the simultaneous message model, but easy to compute in the fully adaptive model. On a more positive side: we also show some implications in the other direction, i.e.: we prove that lower bounds on the communication complexity of certain multiparty problems imply existence of PBC primitives. Using this result we then show two attractive ways to “bypass” our hardness result: the first uses the random oracle model, the second weakens the locality requirement in the bounded-storage model to online computability. The random oracle construction is arguably one of the simplest proposed so far in this area. Our results indicate that constructing improved provably secure protocols for PBC requires a better understanding of multiparty communication complexity. This is yet another example where negative results in one area (in our case: lower bounds in multiparty communication complexity) can be used to construct secure cryptographic schemes.","lang":"eng"}],"month":"11","intvolume":" 10677","alternative_title":["LNCS"],"scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2016/536"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Brody, Joshua, et al. Position Based Cryptography and Multiparty Communication Complexity. Edited by Yael Kalai and Leonid Reyzin, vol. 10677, Springer, 2017, pp. 56–81, doi:10.1007/978-3-319-70500-2_3.","short":"J. Brody, S. Dziembowski, S. Faust, K.Z. Pietrzak, in:, Y. Kalai, L. Reyzin (Eds.), Springer, 2017, pp. 56–81.","ieee":"J. Brody, S. Dziembowski, S. Faust, and K. Z. Pietrzak, “Position based cryptography and multiparty communication complexity,” presented at the TCC: Theory of Cryptography Conference, Baltimore, MD, United States, 2017, vol. 10677, pp. 56–81.","apa":"Brody, J., Dziembowski, S., Faust, S., & Pietrzak, K. Z. (2017). Position based cryptography and multiparty communication complexity. In Y. Kalai & L. Reyzin (Eds.) (Vol. 10677, pp. 56–81). Presented at the TCC: Theory of Cryptography Conference, Baltimore, MD, United States: Springer. https://doi.org/10.1007/978-3-319-70500-2_3","ama":"Brody J, Dziembowski S, Faust S, Pietrzak KZ. Position based cryptography and multiparty communication complexity. In: Kalai Y, Reyzin L, eds. Vol 10677. Springer; 2017:56-81. doi:10.1007/978-3-319-70500-2_3","chicago":"Brody, Joshua, Stefan Dziembowski, Sebastian Faust, and Krzysztof Z Pietrzak. “Position Based Cryptography and Multiparty Communication Complexity.” edited by Yael Kalai and Leonid Reyzin, 10677:56–81. Springer, 2017. https://doi.org/10.1007/978-3-319-70500-2_3.","ista":"Brody J, Dziembowski S, Faust S, Pietrzak KZ. 2017. Position based cryptography and multiparty communication complexity. TCC: Theory of Cryptography Conference, LNCS, vol. 10677, 56–81."},"title":"Position based cryptography and multiparty communication complexity","editor":[{"first_name":"Yael","last_name":"Kalai","full_name":"Kalai, Yael"},{"last_name":"Reyzin","full_name":"Reyzin, Leonid","first_name":"Leonid"}],"publist_id":"7200","author":[{"first_name":"Joshua","full_name":"Brody, Joshua","last_name":"Brody"},{"last_name":"Dziembowski","full_name":"Dziembowski, Stefan","first_name":"Stefan"},{"first_name":"Sebastian","full_name":"Faust, Sebastian","last_name":"Faust"},{"first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654"}],"project":[{"call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","name":"Teaching Old Crypto New Tricks","grant_number":"682815"}],"day":"05","year":"2017","doi":"10.1007/978-3-319-70500-2_3","date_published":"2017-11-05T00:00:00Z","date_created":"2018-12-11T11:47:27Z","page":"56 - 81","quality_controlled":"1","publisher":"Springer","oa":1},{"oa":1,"quality_controlled":"1","publisher":"The Royal Society of Chemistry","year":"2017","publication":"Cold Chemistry: Molecular Scattering and Reactivity Near Absolute Zero ","day":"14","page":"444 - 495","date_created":"2018-12-11T11:47:27Z","date_published":"2017-12-14T00:00:00Z","doi":"10.1039/9781782626800-00444","citation":{"ista":"Lemeshko M, Schmidt R. 2017.Molecular impurities interacting with a many-particle environment: From ultracold gases to helium nanodroplets. In: Cold Chemistry: Molecular Scattering and Reactivity Near Absolute Zero . Theoretical and Computational Chemistry Series, vol. 11, 444–495.","chicago":"Lemeshko, Mikhail, and Richard Schmidt. “Molecular Impurities Interacting with a Many-Particle Environment: From Ultracold Gases to Helium Nanodroplets.” In Cold Chemistry: Molecular Scattering and Reactivity Near Absolute Zero , edited by Oliver Dulieu and Andreas Osterwalder, 11:444–95. Theoretical and Computational Chemistry Series. The Royal Society of Chemistry, 2017. https://doi.org/10.1039/9781782626800-00444.","short":"M. Lemeshko, R. Schmidt, in:, O. Dulieu, A. Osterwalder (Eds.), Cold Chemistry: Molecular Scattering and Reactivity Near Absolute Zero , The Royal Society of Chemistry, 2017, pp. 444–495.","ieee":"M. Lemeshko and R. Schmidt, “Molecular impurities interacting with a many-particle environment: From ultracold gases to helium nanodroplets,” in Cold Chemistry: Molecular Scattering and Reactivity Near Absolute Zero , vol. 11, O. Dulieu and A. Osterwalder, Eds. The Royal Society of Chemistry, 2017, pp. 444–495.","ama":"Lemeshko M, Schmidt R. Molecular impurities interacting with a many-particle environment: From ultracold gases to helium nanodroplets. In: Dulieu O, Osterwalder A, eds. Cold Chemistry: Molecular Scattering and Reactivity Near Absolute Zero . Vol 11. Theoretical and Computational Chemistry Series. The Royal Society of Chemistry; 2017:444-495. doi:10.1039/9781782626800-00444","apa":"Lemeshko, M., & Schmidt, R. (2017). Molecular impurities interacting with a many-particle environment: From ultracold gases to helium nanodroplets. In O. Dulieu & A. Osterwalder (Eds.), Cold Chemistry: Molecular Scattering and Reactivity Near Absolute Zero (Vol. 11, pp. 444–495). The Royal Society of Chemistry. https://doi.org/10.1039/9781782626800-00444","mla":"Lemeshko, Mikhail, and Richard Schmidt. “Molecular Impurities Interacting with a Many-Particle Environment: From Ultracold Gases to Helium Nanodroplets.” Cold Chemistry: Molecular Scattering and Reactivity Near Absolute Zero , edited by Oliver Dulieu and Andreas Osterwalder, vol. 11, The Royal Society of Chemistry, 2017, pp. 444–95, doi:10.1039/9781782626800-00444."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"7201","author":[{"last_name":"Lemeshko","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail"},{"first_name":"Richard","last_name":"Schmidt","full_name":"Schmidt, Richard"}],"title":"Molecular impurities interacting with a many-particle environment: From ultracold gases to helium nanodroplets","editor":[{"first_name":"Oliver","last_name":"Dulieu","full_name":"Dulieu, Oliver"},{"first_name":"Andreas","full_name":"Osterwalder, Andreas","last_name":"Osterwalder"}],"abstract":[{"text":"In several settings of physics and chemistry one has to deal with molecules interacting with some kind of an external environment, be it a gas, a solution, or a crystal surface. Understanding molecular processes in the presence of such a many-particle bath is inherently challenging, and usually requires large-scale numerical computations. Here, we present an alternative approach to the problem, based on the notion of the angulon quasiparticle. We show that molecules rotating inside superfluid helium nanodroplets and Bose–Einstein condensates form angulons, and therefore can be described by straightforward solutions of a simple microscopic Hamiltonian. Casting the problem in the language of angulons allows us not only to greatly simplify it, but also to gain insights into the origins of the observed phenomena and to make predictions for future experimental studies.","lang":"eng"}],"oa_version":"Submitted Version","main_file_link":[{"url":"https://arxiv.org/abs/1703.06753","open_access":"1"}],"alternative_title":["Theoretical and Computational Chemistry Series"],"scopus_import":1,"intvolume":" 11","month":"12","publication_status":"published","publication_identifier":{"issn":["20413181"]},"language":[{"iso":"eng"}],"volume":11,"_id":"604","series_title":"Theoretical and Computational Chemistry Series","type":"book_chapter","status":"public","date_updated":"2021-01-12T08:05:50Z","department":[{"_id":"MiLe"}]},{"status":"public","conference":{"name":"TCC: Theory of Cryptography","location":"Baltimore, MD, United States","end_date":"2017-11-15","start_date":"2017-11-12"},"type":"conference","_id":"609","department":[{"_id":"KrPi"}],"date_updated":"2021-01-12T08:06:04Z","intvolume":" 10677","month":"11","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2017/945"}],"scopus_import":1,"alternative_title":["LNCS"],"oa_version":"Submitted Version","abstract":[{"text":"Several cryptographic schemes and applications are based on functions that are both reasonably efficient to compute and moderately hard to invert, including client puzzles for Denial-of-Service protection, password protection via salted hashes, or recent proof-of-work blockchain systems. Despite their wide use, a definition of this concept has not yet been distilled and formalized explicitly. Instead, either the applications are proven directly based on the assumptions underlying the function, or some property of the function is proven, but the security of the application is argued only informally. The goal of this work is to provide a (universal) definition that decouples the efforts of designing new moderately hard functions and of building protocols based on them, serving as an interface between the two. On a technical level, beyond the mentioned definitions, we instantiate the model for four different notions of hardness. We extend the work of Alwen and Serbinenko (STOC 2015) by providing a general tool for proving security for the first notion of memory-hard functions that allows for provably secure applications. The tool allows us to recover all of the graph-theoretic techniques developed for proving security under the older, non-composable, notion of security used by Alwen and Serbinenko. As an application of our definition of moderately hard functions, we prove the security of two different schemes for proofs of effort (PoE). We also formalize and instantiate the concept of a non-interactive proof of effort (niPoE), in which the proof is not bound to a particular communication context but rather any bit-string chosen by the prover.","lang":"eng"}],"volume":10677,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"isbn":["978-331970499-9"]},"editor":[{"first_name":"Yael","full_name":"Kalai, Yael","last_name":"Kalai"},{"full_name":"Reyzin, Leonid","last_name":"Reyzin","first_name":"Leonid"}],"title":"Moderately hard functions: Definition, instantiations, and applications","publist_id":"7196","author":[{"last_name":"Alwen","full_name":"Alwen, Joel F","first_name":"Joel F","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Tackmann","full_name":"Tackmann, Björn","first_name":"Björn"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Alwen JF, Tackmann B. 2017. Moderately hard functions: Definition, instantiations, and applications. TCC: Theory of Cryptography, LNCS, vol. 10677, 493–526.","chicago":"Alwen, Joel F, and Björn Tackmann. “Moderately Hard Functions: Definition, Instantiations, and Applications.” edited by Yael Kalai and Leonid Reyzin, 10677:493–526. Springer, 2017. https://doi.org/10.1007/978-3-319-70500-2_17.","ama":"Alwen JF, Tackmann B. Moderately hard functions: Definition, instantiations, and applications. In: Kalai Y, Reyzin L, eds. Vol 10677. Springer; 2017:493-526. doi:10.1007/978-3-319-70500-2_17","apa":"Alwen, J. F., & Tackmann, B. (2017). Moderately hard functions: Definition, instantiations, and applications. In Y. Kalai & L. Reyzin (Eds.) (Vol. 10677, pp. 493–526). Presented at the TCC: Theory of Cryptography, Baltimore, MD, United States: Springer. https://doi.org/10.1007/978-3-319-70500-2_17","ieee":"J. F. Alwen and B. Tackmann, “Moderately hard functions: Definition, instantiations, and applications,” presented at the TCC: Theory of Cryptography, Baltimore, MD, United States, 2017, vol. 10677, pp. 493–526.","short":"J.F. Alwen, B. Tackmann, in:, Y. Kalai, L. Reyzin (Eds.), Springer, 2017, pp. 493–526.","mla":"Alwen, Joel F., and Björn Tackmann. Moderately Hard Functions: Definition, Instantiations, and Applications. Edited by Yael Kalai and Leonid Reyzin, vol. 10677, Springer, 2017, pp. 493–526, doi:10.1007/978-3-319-70500-2_17."},"oa":1,"publisher":"Springer","quality_controlled":"1","date_created":"2018-12-11T11:47:28Z","date_published":"2017-11-05T00:00:00Z","doi":"10.1007/978-3-319-70500-2_17","page":"493 - 526","day":"05","year":"2017"},{"type":"journal_article","status":"public","_id":"610","department":[{"_id":"UlWa"}],"date_updated":"2023-02-23T10:02:13Z","scopus_import":1,"main_file_link":[{"url":"https://arxiv.org/abs/1610.09063","open_access":"1"}],"month":"10","intvolume":" 222","abstract":[{"text":"The fact that the complete graph K5 does not embed in the plane has been generalized in two independent directions. On the one hand, the solution of the classical Heawood problem for graphs on surfaces established that the complete graph Kn embeds in a closed surface M (other than the Klein bottle) if and only if (n−3)(n−4) ≤ 6b1(M), where b1(M) is the first Z2-Betti number of M. On the other hand, van Kampen and Flores proved that the k-skeleton of the n-dimensional simplex (the higher-dimensional analogue of Kn+1) embeds in R2k if and only if n ≤ 2k + 1. Two decades ago, Kühnel conjectured that the k-skeleton of the n-simplex embeds in a compact, (k − 1)-connected 2k-manifold with kth Z2-Betti number bk only if the following generalized Heawood inequality holds: (k+1 n−k−1) ≤ (k+1 2k+1)bk. This is a common generalization of the case of graphs on surfaces as well as the van Kampen–Flores theorem. In the spirit of Kühnel’s conjecture, we prove that if the k-skeleton of the n-simplex embeds in a compact 2k-manifold with kth Z2-Betti number bk, then n ≤ 2bk(k 2k+2)+2k+4. This bound is weaker than the generalized Heawood inequality, but does not require the assumption that M is (k−1)-connected. Our results generalize to maps without q-covered points, in the spirit of Tverberg’s theorem, for q a prime power. Our proof uses a result of Volovikov about maps that satisfy a certain homological triviality condition.","lang":"eng"}],"oa_version":"Preprint","volume":222,"related_material":{"record":[{"relation":"earlier_version","id":"1511","status":"public"}]},"issue":"2","ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}],"project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"author":[{"first_name":"Xavier","full_name":"Goaoc, Xavier","last_name":"Goaoc"},{"last_name":"Mabillard","full_name":"Mabillard, Isaac","id":"32BF9DAA-F248-11E8-B48F-1D18A9856A87","first_name":"Isaac"},{"full_name":"Paták, Pavel","last_name":"Paták","first_name":"Pavel"},{"id":"48B57058-F248-11E8-B48F-1D18A9856A87","first_name":"Zuzana","last_name":"Patakova","full_name":"Patakova, Zuzana","orcid":"0000-0002-3975-1683"},{"first_name":"Martin","id":"38AC689C-F248-11E8-B48F-1D18A9856A87","last_name":"Tancer","full_name":"Tancer, Martin","orcid":"0000-0002-1191-6714"},{"orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli","last_name":"Wagner","first_name":"Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7194","title":"On generalized Heawood inequalities for manifolds: A van Kampen–Flores type nonembeddability result","citation":{"chicago":"Goaoc, Xavier, Isaac Mabillard, Pavel Paták, Zuzana Patakova, Martin Tancer, and Uli Wagner. “On Generalized Heawood Inequalities for Manifolds: A van Kampen–Flores Type Nonembeddability Result.” Israel Journal of Mathematics. Springer, 2017. https://doi.org/10.1007/s11856-017-1607-7.","ista":"Goaoc X, Mabillard I, Paták P, Patakova Z, Tancer M, Wagner U. 2017. On generalized Heawood inequalities for manifolds: A van Kampen–Flores type nonembeddability result. Israel Journal of Mathematics. 222(2), 841–866.","mla":"Goaoc, Xavier, et al. “On Generalized Heawood Inequalities for Manifolds: A van Kampen–Flores Type Nonembeddability Result.” Israel Journal of Mathematics, vol. 222, no. 2, Springer, 2017, pp. 841–66, doi:10.1007/s11856-017-1607-7.","short":"X. Goaoc, I. Mabillard, P. Paták, Z. Patakova, M. Tancer, U. Wagner, Israel Journal of Mathematics 222 (2017) 841–866.","ieee":"X. Goaoc, I. Mabillard, P. Paták, Z. Patakova, M. Tancer, and U. Wagner, “On generalized Heawood inequalities for manifolds: A van Kampen–Flores type nonembeddability result,” Israel Journal of Mathematics, vol. 222, no. 2. Springer, pp. 841–866, 2017.","ama":"Goaoc X, Mabillard I, Paták P, Patakova Z, Tancer M, Wagner U. On generalized Heawood inequalities for manifolds: A van Kampen–Flores type nonembeddability result. Israel Journal of Mathematics. 2017;222(2):841-866. doi:10.1007/s11856-017-1607-7","apa":"Goaoc, X., Mabillard, I., Paták, P., Patakova, Z., Tancer, M., & Wagner, U. (2017). On generalized Heawood inequalities for manifolds: A van Kampen–Flores type nonembeddability result. Israel Journal of Mathematics. Springer. https://doi.org/10.1007/s11856-017-1607-7"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer","quality_controlled":"1","oa":1,"acknowledgement":"The work by Z. P. was partially supported by the Israel Science Foundation grant ISF-768/12. The work by Z. P. and M. T. was partially supported by the project CE-ITI (GACR P202/12/G061) of the Czech Science Foundation and by the ERC Advanced Grant No. 267165. Part of the research work of M.T. was conducted at IST Austria, supported by an IST Fellowship. The research of P. P. was supported by the ERC Advanced grant no. 320924. The work by I. M. and U. W. was supported by the Swiss National Science Foundation (grants SNSF-200020-138230 and SNSF-PP00P2-138948). The collaboration between U. W. and X. G. was partially supported by the LabEx Bézout (ANR-10-LABX-58).","page":"841 - 866","doi":"10.1007/s11856-017-1607-7","date_published":"2017-10-01T00:00:00Z","date_created":"2018-12-11T11:47:29Z","year":"2017","day":"01","publication":"Israel Journal of Mathematics"},{"oa":1,"quality_controlled":"1","publisher":"National Academy of Sciences","year":"2017","has_accepted_license":"1","publication":"Proceedings of the National Academy of Sciences","day":"18","page":"4195-4200","date_created":"2019-03-19T13:46:36Z","date_published":"2017-04-18T00:00:00Z","doi":"10.1073/pnas.1618934114","citation":{"chicago":"Fenk, Lorenz A., and Mario de Bono. “Memory of Recent Oxygen Experience Switches Pheromone Valence InCaenorhabditis Elegans.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1618934114.","ista":"Fenk LA, de Bono M. 2017. Memory of recent oxygen experience switches pheromone valence inCaenorhabditis elegans. Proceedings of the National Academy of Sciences. 114(16), 4195–4200.","mla":"Fenk, Lorenz A., and Mario de Bono. “Memory of Recent Oxygen Experience Switches Pheromone Valence InCaenorhabditis Elegans.” Proceedings of the National Academy of Sciences, vol. 114, no. 16, National Academy of Sciences, 2017, pp. 4195–200, doi:10.1073/pnas.1618934114.","short":"L.A. Fenk, M. de Bono, Proceedings of the National Academy of Sciences 114 (2017) 4195–4200.","ieee":"L. A. Fenk and M. de Bono, “Memory of recent oxygen experience switches pheromone valence inCaenorhabditis elegans,” Proceedings of the National Academy of Sciences, vol. 114, no. 16. National Academy of Sciences, pp. 4195–4200, 2017.","ama":"Fenk LA, de Bono M. Memory of recent oxygen experience switches pheromone valence inCaenorhabditis elegans. Proceedings of the National Academy of Sciences. 2017;114(16):4195-4200. doi:10.1073/pnas.1618934114","apa":"Fenk, L. A., & de Bono, M. (2017). Memory of recent oxygen experience switches pheromone valence inCaenorhabditis elegans. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1618934114"},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["28373553"]},"author":[{"first_name":"Lorenz A.","full_name":"Fenk, Lorenz A.","last_name":"Fenk"},{"full_name":"de Bono, Mario","orcid":"0000-0001-8347-0443","last_name":"de Bono","first_name":"Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87"}],"title":"Memory of recent oxygen experience switches pheromone valence inCaenorhabditis elegans","abstract":[{"lang":"eng","text":"Animals adjust their behavioral priorities according to momentary needs and prior experience. We show that Caenorhabditis elegans changes how it processes sensory information according to the oxygen environment it experienced recently. C. elegans acclimated to 7% O2 are aroused by CO2 and repelled by pheromones that attract animals acclimated to 21% O2. This behavioral plasticity arises from prolonged activity differences in a circuit that continuously signals O2 levels. A sustained change in the activity of O2-sensing neurons reprograms the properties of their postsynaptic partners, the RMG hub interneurons. RMG is gap-junctionally coupled to the ASK and ADL pheromone sensors that respectively drive pheromone attraction and repulsion. Prior O2 experience has opposite effects on the pheromone responsiveness of these neurons. These circuit changes provide a physiological correlate of altered pheromone valence. Our results suggest C. elegans stores a memory of recent O2 experience in the RMG circuit and illustrate how a circuit is flexibly sculpted to guide behavioral decisions in a context-dependent manner."}],"pmid":1,"oa_version":"Published Version","intvolume":" 114","month":"04","publication_status":"published","publication_identifier":{"issn":["0027-8424","1091-6490"]},"language":[{"iso":"eng"}],"file":[{"file_id":"6116","checksum":"1801bc8319b752fa17598004ec375279","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2019-03-19T14:00:42Z","file_name":"2017_PNAS_Fenk.pdf","date_updated":"2020-07-14T12:47:20Z","file_size":1217696,"creator":"kschuh"}],"volume":114,"issue":"16","_id":"6115","type":"journal_article","status":"public","date_updated":"2021-01-12T08:06:11Z","ddc":["570"],"extern":"1","file_date_updated":"2020-07-14T12:47:20Z"},{"day":"02","publication":"Nature","year":"2017","date_published":"2017-02-02T00:00:00Z","doi":"10.1038/nature20818","date_created":"2019-03-19T14:06:41Z","page":"43-48","publisher":"Springer Nature","quality_controlled":"1","oa":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Chen C, Itakura E, Nelson GM, Sheng M, Laurent P, Fenk LA, Butcher RA, Hegde RS, de Bono M. 2017. IL-17 is a neuromodulator of Caenorhabditis elegans sensory responses. Nature. 542(7639), 43–48.","chicago":"Chen, Changchun, Eisuke Itakura, Geoffrey M. Nelson, Ming Sheng, Patrick Laurent, Lorenz A. Fenk, Rebecca A. Butcher, Ramanujan S. Hegde, and Mario de Bono. “IL-17 Is a Neuromodulator of Caenorhabditis Elegans Sensory Responses.” Nature. Springer Nature, 2017. https://doi.org/10.1038/nature20818.","short":"C. Chen, E. Itakura, G.M. Nelson, M. Sheng, P. Laurent, L.A. Fenk, R.A. Butcher, R.S. Hegde, M. de Bono, Nature 542 (2017) 43–48.","ieee":"C. Chen et al., “IL-17 is a neuromodulator of Caenorhabditis elegans sensory responses,” Nature, vol. 542, no. 7639. Springer Nature, pp. 43–48, 2017.","ama":"Chen C, Itakura E, Nelson GM, et al. IL-17 is a neuromodulator of Caenorhabditis elegans sensory responses. Nature. 2017;542(7639):43-48. doi:10.1038/nature20818","apa":"Chen, C., Itakura, E., Nelson, G. M., Sheng, M., Laurent, P., Fenk, L. A., … de Bono, M. (2017). IL-17 is a neuromodulator of Caenorhabditis elegans sensory responses. Nature. Springer Nature. https://doi.org/10.1038/nature20818","mla":"Chen, Changchun, et al. “IL-17 Is a Neuromodulator of Caenorhabditis Elegans Sensory Responses.” Nature, vol. 542, no. 7639, Springer Nature, 2017, pp. 43–48, doi:10.1038/nature20818."},"title":"IL-17 is a neuromodulator of Caenorhabditis elegans sensory responses","author":[{"first_name":"Changchun","last_name":"Chen","full_name":"Chen, Changchun"},{"full_name":"Itakura, Eisuke","last_name":"Itakura","first_name":"Eisuke"},{"first_name":"Geoffrey M.","full_name":"Nelson, Geoffrey M.","last_name":"Nelson"},{"last_name":"Sheng","full_name":"Sheng, Ming","first_name":"Ming"},{"full_name":"Laurent, Patrick","last_name":"Laurent","first_name":"Patrick"},{"first_name":"Lorenz A.","last_name":"Fenk","full_name":"Fenk, Lorenz A."},{"full_name":"Butcher, Rebecca A.","last_name":"Butcher","first_name":"Rebecca A."},{"full_name":"Hegde, Ramanujan S.","last_name":"Hegde","first_name":"Ramanujan S."},{"last_name":"de Bono","orcid":"0000-0001-8347-0443","full_name":"de Bono, Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","first_name":"Mario"}],"external_id":{"pmid":[" 28099418"]},"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0028-0836","1476-4687"]},"publication_status":"published","issue":"7639","volume":542,"pmid":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Interleukin-17 (IL-17) is a major pro-inflammatory cytokine: it mediates responses to pathogens or tissue damage, and drives autoimmune diseases. Little is known about its role in the nervous system. Here we show that IL-17 has neuromodulator-like properties in Caenorhabditis elegans. IL-17 can act directly on neurons to alter their response properties and contribution to behaviour. Using unbiased genetic screens, we delineate an IL-17 signalling pathway and show that it acts in the RMG hub interneurons. Disrupting IL-17 signalling reduces RMG responsiveness to input from oxygen sensors, and renders sustained escape from 21% oxygen transient and contingent on additional stimuli. Over-activating IL-17 receptors abnormally heightens responses to 21% oxygen in RMG neurons and whole animals. IL-17 deficiency can be bypassed by optogenetic stimulation of RMG. Inducing IL-17 expression in adults can rescue mutant defects within 6 h. These findings reveal a non-immunological role of IL-17 modulating circuit function and behaviour."}],"month":"02","intvolume":" 542","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/28099418","open_access":"1"}],"extern":"1","date_updated":"2021-01-12T08:06:12Z","_id":"6117","status":"public","type":"journal_article"},{"day":"06","publication":"Proceedings of the National Academy of Sciences","has_accepted_license":"1","year":"2017","date_published":"2017-06-06T00:00:00Z","doi":"10.1073/pnas.1614596114","date_created":"2019-03-19T13:29:51Z","page":"E4658-E4665","quality_controlled":"1","publisher":"National Academy of Sciences","oa":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Oda, Shigekazu, Yu Toyoshima, and Mario de Bono. “Modulation of Sensory Information Processing by a Neuroglobin in Caenorhabditis Elegans.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1614596114.","ista":"Oda S, Toyoshima Y, de Bono M. 2017. Modulation of sensory information processing by a neuroglobin in Caenorhabditis elegans. Proceedings of the National Academy of Sciences. 114(23), E4658–E4665.","mla":"Oda, Shigekazu, et al. “Modulation of Sensory Information Processing by a Neuroglobin in Caenorhabditis Elegans.” Proceedings of the National Academy of Sciences, vol. 114, no. 23, National Academy of Sciences, 2017, pp. E4658–65, doi:10.1073/pnas.1614596114.","ama":"Oda S, Toyoshima Y, de Bono M. Modulation of sensory information processing by a neuroglobin in Caenorhabditis elegans. Proceedings of the National Academy of Sciences. 2017;114(23):E4658-E4665. doi:10.1073/pnas.1614596114","apa":"Oda, S., Toyoshima, Y., & de Bono, M. (2017). Modulation of sensory information processing by a neuroglobin in Caenorhabditis elegans. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1614596114","ieee":"S. Oda, Y. Toyoshima, and M. de Bono, “Modulation of sensory information processing by a neuroglobin in Caenorhabditis elegans,” Proceedings of the National Academy of Sciences, vol. 114, no. 23. National Academy of Sciences, pp. E4658–E4665, 2017.","short":"S. Oda, Y. Toyoshima, M. de Bono, Proceedings of the National Academy of Sciences 114 (2017) E4658–E4665."},"title":"Modulation of sensory information processing by a neuroglobin in Caenorhabditis elegans","author":[{"full_name":"Oda, Shigekazu","last_name":"Oda","first_name":"Shigekazu"},{"full_name":"Toyoshima, Yu","last_name":"Toyoshima","first_name":"Yu"},{"last_name":"de Bono","orcid":"0000-0001-8347-0443","full_name":"de Bono, Mario","first_name":"Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"pmid":["28536200"]},"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"9e42ce47090ecdad7d76f2dbdebb924e","file_id":"6114","creator":"kschuh","date_updated":"2020-07-14T12:47:19Z","file_size":1469622,"date_created":"2019-03-19T13:42:58Z","file_name":"2017_PNAS_Oda.pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0027-8424","1091-6490"]},"publication_status":"published","volume":114,"issue":"23","oa_version":"Published Version","pmid":1,"month":"06","intvolume":" 114","extern":"1","ddc":["570"],"date_updated":"2021-01-12T08:06:11Z","file_date_updated":"2020-07-14T12:47:19Z","_id":"6113","status":"public","type":"journal_article"},{"title":"Shaping bacterial population behavior through computer interfaced control of individual cells","author":[{"id":"3464AE84-F248-11E8-B48F-1D18A9856A87","first_name":"Remy P","last_name":"Chait","orcid":"0000-0003-0876-3187","full_name":"Chait, Remy P"},{"id":"4A245D00-F248-11E8-B48F-1D18A9856A87","first_name":"Jakob","last_name":"Ruess","full_name":"Ruess, Jakob","orcid":"0000-0003-1615-3282"},{"first_name":"Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","last_name":"Bergmiller","orcid":"0000-0001-5396-4346","full_name":"Bergmiller, Tobias"},{"last_name":"Tkacik","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper"},{"last_name":"Guet","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7191","article_processing_charge":"Yes (in subscription journal)","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Chait, Remy P, Jakob Ruess, Tobias Bergmiller, Gašper Tkačik, and Calin C Guet. “Shaping Bacterial Population Behavior through Computer Interfaced Control of Individual Cells.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/s41467-017-01683-1.","ista":"Chait RP, Ruess J, Bergmiller T, Tkačik G, Guet CC. 2017. Shaping bacterial population behavior through computer interfaced control of individual cells. Nature Communications. 8(1), 1535.","mla":"Chait, Remy P., et al. “Shaping Bacterial Population Behavior through Computer Interfaced Control of Individual Cells.” Nature Communications, vol. 8, no. 1, 1535, Nature Publishing Group, 2017, doi:10.1038/s41467-017-01683-1.","ieee":"R. P. Chait, J. Ruess, T. Bergmiller, G. Tkačik, and C. C. Guet, “Shaping bacterial population behavior through computer interfaced control of individual cells,” Nature Communications, vol. 8, no. 1. Nature Publishing Group, 2017.","short":"R.P. Chait, J. Ruess, T. Bergmiller, G. Tkačik, C.C. Guet, Nature Communications 8 (2017).","ama":"Chait RP, Ruess J, Bergmiller T, Tkačik G, Guet CC. Shaping bacterial population behavior through computer interfaced control of individual cells. Nature Communications. 2017;8(1). doi:10.1038/s41467-017-01683-1","apa":"Chait, R. P., Ruess, J., Bergmiller, T., Tkačik, G., & Guet, C. C. (2017). Shaping bacterial population behavior through computer interfaced control of individual cells. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-01683-1"},"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"},{"_id":"254E9036-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P28844-B27","name":"Biophysics of information processing in gene regulation"}],"article_number":"1535","date_published":"2017-12-01T00:00:00Z","doi":"10.1038/s41467-017-01683-1","date_created":"2018-12-11T11:47:30Z","day":"01","publication":"Nature Communications","has_accepted_license":"1","year":"2017","publisher":"Nature Publishing Group","quality_controlled":"1","oa":1,"acknowledgement":"We are grateful to M. Lang, H. Janovjak, M. Khammash, A. Milias-Argeitis, M. Rullan, G. Batt, A. Bosma-Moody, Aryan, S. Leibler, and members of the Guet and Tkačik groups for helpful discussion, comments, and suggestions. We thank A. Moglich, T. Mathes, J. Tabor, and S. Schmidl for kind gifts of strains, and R. Hauschild, B. Knep, M. Lang, T. Asenov, E. Papusheva, T. Menner, T. Adletzberger, and J. Merrin for technical assistance. The research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007–2013) under REA grant agreement no. [291734]. (to R.C. and J.R.), Austrian Science Fund grant FWF P28844 (to G.T.), and internal IST Austria Interdisciplinary Project Support. J.R. acknowledges support from the Agence Nationale de la Recherche (ANR) under Grant Nos. ANR-16-CE33-0018 (MEMIP), ANR-16-CE12-0025 (COGEX) and ANR-10-BINF-06-01 (ICEBERG).","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"file_date_updated":"2020-07-14T12:47:20Z","ddc":["576","579"],"date_updated":"2021-01-12T08:06:15Z","status":"public","pubrep_id":"911","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"613","volume":8,"issue":"1","ec_funded":1,"file":[{"date_created":"2018-12-12T10:16:05Z","file_name":"IST-2017-911-v1+1_s41467-017-01683-1.pdf","date_updated":"2020-07-14T12:47:20Z","file_size":1951699,"creator":"system","file_id":"5190","checksum":"44bb5d0229926c23a9955d9fe0f9723f","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["20411723"]},"publication_status":"published","month":"12","intvolume":" 8","scopus_import":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Bacteria in groups vary individually, and interact with other bacteria and the environment to produce population-level patterns of gene expression. Investigating such behavior in detail requires measuring and controlling populations at the single-cell level alongside precisely specified interactions and environmental characteristics. Here we present an automated, programmable platform that combines image-based gene expression and growth measurements with on-line optogenetic expression control for hundreds of individual Escherichia coli cells over days, in a dynamically adjustable environment. This integrated platform broadly enables experiments that bridge individual and population behaviors. We demonstrate: (i) population structuring by independent closed-loop control of gene expression in many individual cells, (ii) cell-cell variation control during antibiotic perturbation, (iii) hybrid bio-digital circuits in single cells, and freely specifiable digital communication between individual bacteria. These examples showcase the potential for real-time integration of theoretical models with measurement and control of many individual cells to investigate and engineer microbial population behavior."}]},{"date_updated":"2021-01-12T08:06:22Z","department":[{"_id":"LaEr"}],"_id":"615","type":"journal_article","status":"public","publication_identifier":{"issn":["02460203"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":53,"issue":"4","ec_funded":1,"abstract":[{"text":"We show that the Dyson Brownian Motion exhibits local universality after a very short time assuming that local rigidity and level repulsion of the eigenvalues hold. These conditions are verified, hence bulk spectral universality is proven, for a large class of Wigner-like matrices, including deformed Wigner ensembles and ensembles with non-stochastic variance matrices whose limiting densities differ from Wigner's semicircle law.","lang":"eng"}],"oa_version":"Submitted Version","scopus_import":1,"main_file_link":[{"url":"https://arxiv.org/abs/1504.00650","open_access":"1"}],"month":"11","intvolume":" 53","citation":{"mla":"Erdös, László, and Kevin Schnelli. “Universality for Random Matrix Flows with Time Dependent Density.” Annales de l’institut Henri Poincare (B) Probability and Statistics, vol. 53, no. 4, Institute of Mathematical Statistics, 2017, pp. 1606–56, doi:10.1214/16-AIHP765.","apa":"Erdös, L., & Schnelli, K. (2017). Universality for random matrix flows with time dependent density. Annales de l’institut Henri Poincare (B) Probability and Statistics. Institute of Mathematical Statistics. https://doi.org/10.1214/16-AIHP765","ama":"Erdös L, Schnelli K. Universality for random matrix flows with time dependent density. Annales de l’institut Henri Poincare (B) Probability and Statistics. 2017;53(4):1606-1656. doi:10.1214/16-AIHP765","short":"L. Erdös, K. Schnelli, Annales de l’institut Henri Poincare (B) Probability and Statistics 53 (2017) 1606–1656.","ieee":"L. Erdös and K. Schnelli, “Universality for random matrix flows with time dependent density,” Annales de l’institut Henri Poincare (B) Probability and Statistics, vol. 53, no. 4. Institute of Mathematical Statistics, pp. 1606–1656, 2017.","chicago":"Erdös, László, and Kevin Schnelli. “Universality for Random Matrix Flows with Time Dependent Density.” Annales de l’institut Henri Poincare (B) Probability and Statistics. Institute of Mathematical Statistics, 2017. https://doi.org/10.1214/16-AIHP765.","ista":"Erdös L, Schnelli K. 2017. Universality for random matrix flows with time dependent density. Annales de l’institut Henri Poincare (B) Probability and Statistics. 53(4), 1606–1656."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"7189","author":[{"first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","orcid":"0000-0001-5366-9603","full_name":"Erdös, László"},{"first_name":"Kevin","id":"434AD0AE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0954-3231","full_name":"Schnelli, Kevin","last_name":"Schnelli"}],"title":"Universality for random matrix flows with time dependent density","project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"338804","name":"Random matrices, universality and disordered quantum systems"}],"year":"2017","day":"01","publication":"Annales de l'institut Henri Poincare (B) Probability and Statistics","page":"1606 - 1656","date_published":"2017-11-01T00:00:00Z","doi":"10.1214/16-AIHP765","date_created":"2018-12-11T11:47:30Z","quality_controlled":"1","publisher":"Institute of Mathematical Statistics","oa":1},{"title":"Environmental temperature variation influences fitness trade-offs in a fish-tapeworm association ","author":[{"last_name":"Franke","full_name":"Franke, Frederik","first_name":"Frederik"},{"last_name":"Armitage","full_name":"Armitage, Sophie","first_name":"Sophie"},{"full_name":"Kutzer, Megan","orcid":"0000-0002-8696-6978","last_name":"Kutzer","first_name":"Megan","id":"29D0B332-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Joachim","last_name":"Kurtz","full_name":"Kurtz, Joachim"},{"first_name":"Jörn","full_name":"Scharsack, Jörn","last_name":"Scharsack"}],"publist_id":"7186","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Franke F, Armitage S, Kutzer M, Kurtz J, Scharsack J. 2017. Environmental temperature variation influences fitness trade-offs in a fish-tapeworm association . Parasites & Vectors. 10(252), 52.","chicago":"Franke, Frederik, Sophie Armitage, Megan Kutzer, Joachim Kurtz, and Jörn Scharsack. “Environmental Temperature Variation Influences Fitness Trade-Offs in a Fish-Tapeworm Association .” Parasites & Vectors. BioMed Central, 2017. https://doi.org/10.1186/s13071-017-2192-7.","ieee":"F. Franke, S. Armitage, M. Kutzer, J. Kurtz, and J. Scharsack, “Environmental temperature variation influences fitness trade-offs in a fish-tapeworm association ,” Parasites & Vectors, vol. 10, no. 252. BioMed Central, 2017.","short":"F. Franke, S. Armitage, M. Kutzer, J. Kurtz, J. Scharsack, Parasites & Vectors 10 (2017).","apa":"Franke, F., Armitage, S., Kutzer, M., Kurtz, J., & Scharsack, J. (2017). Environmental temperature variation influences fitness trade-offs in a fish-tapeworm association . Parasites & Vectors. BioMed Central. https://doi.org/10.1186/s13071-017-2192-7","ama":"Franke F, Armitage S, Kutzer M, Kurtz J, Scharsack J. Environmental temperature variation influences fitness trade-offs in a fish-tapeworm association . Parasites & Vectors. 2017;10(252). doi:10.1186/s13071-017-2192-7","mla":"Franke, Frederik, et al. “Environmental Temperature Variation Influences Fitness Trade-Offs in a Fish-Tapeworm Association .” Parasites & Vectors, vol. 10, no. 252, 52, BioMed Central, 2017, doi:10.1186/s13071-017-2192-7."},"article_number":"52","date_created":"2018-12-11T11:47:31Z","doi":"10.1186/s13071-017-2192-7","date_published":"2017-06-02T00:00:00Z","publication":"Parasites & Vectors","day":"02","year":"2017","has_accepted_license":"1","oa":1,"publisher":"BioMed Central","quality_controlled":"1","file_date_updated":"2020-07-14T12:47:22Z","ddc":["570"],"extern":"1","date_updated":"2021-01-12T08:06:35Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"618","issue":"252","volume":10,"language":[{"iso":"eng"}],"file":[{"file_size":671807,"date_updated":"2020-07-14T12:47:22Z","creator":"dernst","file_name":"2017_Parasites_Franke.pdf","date_created":"2019-01-21T13:45:36Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"742943377a38ee208108705b8e2f4dbf","file_id":"5864"}],"publication_status":"published","publication_identifier":{"issn":["17563305"]},"intvolume":" 10","month":"06","oa_version":"Published Version","abstract":[{"text":"Background: Increasing temperatures are predicted to strongly impact host-parasite interactions, but empirical tests are rare. Host species that are naturally exposed to a broad temperature spectrum offer the possibility to investigate the effects of elevated temperatures on hosts and parasites. Using three-spined sticklebacks, Gasterosteus aculeatus L., and tapeworms, Schistocephalus solidus (Müller, 1776), originating from a cold and a warm water site of a volcanic lake, we subjected sympatric and allopatric host-parasite combinations to cold and warm conditions in a fully crossed design. We predicted that warm temperatures would promote the development of the parasites, while the hosts might benefit from cooler temperatures. We further expected adaptations to the local temperature and mutual adaptations of local host-parasite pairs. Results: Overall, S. solidus parasites grew faster at warm temperatures and stickleback hosts at cold temperatures. On a finer scale, we observed that parasites were able to exploit their hosts more efficiently at the parasite’s temperature of origin. In contrast, host tolerance towards parasite infection was higher when sticklebacks were infected with parasites at the parasite’s ‘foreign’ temperature. Cold-origin sticklebacks tended to grow faster and parasite infection induced a stronger immune response. Conclusions: Our results suggest that increasing environmental temperatures promote the parasite rather than the host and that host tolerance is dependent on the interaction between parasite infection and temperature. Sticklebacks might use tolerance mechanisms towards parasite infection in combination with their high plasticity towards temperature changes to cope with increasing parasite infection pressures and rising temperatures.","lang":"eng"}]},{"has_accepted_license":"1","year":"2017","day":"01","publication":"Theoretical Population Biology","page":"50 - 73","doi":"10.1016/j.tpb.2017.06.001","date_published":"2017-12-01T00:00:00Z","date_created":"2018-12-11T11:47:34Z","quality_controlled":"1","publisher":"Academic Press","oa":1,"citation":{"ista":"Barton NH, Etheridge A, Véber A. 2017. The infinitesimal model: Definition derivation and implications. Theoretical Population Biology. 118, 50–73.","chicago":"Barton, Nicholas H, Alison Etheridge, and Amandine Véber. “The Infinitesimal Model: Definition Derivation and Implications.” Theoretical Population Biology. Academic Press, 2017. https://doi.org/10.1016/j.tpb.2017.06.001.","short":"N.H. Barton, A. Etheridge, A. Véber, Theoretical Population Biology 118 (2017) 50–73.","ieee":"N. H. Barton, A. Etheridge, and A. Véber, “The infinitesimal model: Definition derivation and implications,” Theoretical Population Biology, vol. 118. Academic Press, pp. 50–73, 2017.","ama":"Barton NH, Etheridge A, Véber A. The infinitesimal model: Definition derivation and implications. Theoretical Population Biology. 2017;118:50-73. doi:10.1016/j.tpb.2017.06.001","apa":"Barton, N. H., Etheridge, A., & Véber, A. (2017). The infinitesimal model: Definition derivation and implications. Theoretical Population Biology. Academic Press. https://doi.org/10.1016/j.tpb.2017.06.001","mla":"Barton, Nicholas H., et al. “The Infinitesimal Model: Definition Derivation and Implications.” Theoretical Population Biology, vol. 118, Academic Press, 2017, pp. 50–73, doi:10.1016/j.tpb.2017.06.001."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"},{"first_name":"Alison","full_name":"Etheridge, Alison","last_name":"Etheridge"},{"full_name":"Véber, Amandine","last_name":"Véber","first_name":"Amandine"}],"publist_id":"7169","title":"The infinitesimal model: Definition derivation and implications","project":[{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152"}],"publication_identifier":{"issn":["00405809"]},"publication_status":"published","file":[{"creator":"system","file_size":1133924,"date_updated":"2020-07-14T12:47:25Z","file_name":"IST-2017-908-v1+1_1-s2.0-S0040580917300886-main_1_.pdf","date_created":"2018-12-12T10:12:45Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"7dd02bfcfe8f244f4a6c19091aedf2c8","file_id":"4964"}],"language":[{"iso":"eng"}],"volume":118,"ec_funded":1,"abstract":[{"lang":"eng","text":"Our focus here is on the infinitesimal model. In this model, one or several quantitative traits are described as the sum of a genetic and a non-genetic component, the first being distributed within families as a normal random variable centred at the average of the parental genetic components, and with a variance independent of the parental traits. Thus, the variance that segregates within families is not perturbed by selection, and can be predicted from the variance components. This does not necessarily imply that the trait distribution across the whole population should be Gaussian, and indeed selection or population structure may have a substantial effect on the overall trait distribution. One of our main aims is to identify some general conditions on the allelic effects for the infinitesimal model to be accurate. We first review the long history of the infinitesimal model in quantitative genetics. Then we formulate the model at the phenotypic level in terms of individual trait values and relationships between individuals, but including different evolutionary processes: genetic drift, recombination, selection, mutation, population structure, …. We give a range of examples of its application to evolutionary questions related to stabilising selection, assortative mating, effective population size and response to selection, habitat preference and speciation. We provide a mathematical justification of the model as the limit as the number M of underlying loci tends to infinity of a model with Mendelian inheritance, mutation and environmental noise, when the genetic component of the trait is purely additive. We also show how the model generalises to include epistatic effects. We prove in particular that, within each family, the genetic components of the individual trait values in the current generation are indeed normally distributed with a variance independent of ancestral traits, up to an error of order 1∕M. Simulations suggest that in some cases the convergence may be as fast as 1∕M."}],"oa_version":"Published Version","scopus_import":1,"month":"12","intvolume":" 118","date_updated":"2021-01-12T08:06:50Z","ddc":["576"],"file_date_updated":"2020-07-14T12:47:25Z","department":[{"_id":"NiBa"}],"_id":"626","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"908"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"K. Chatterjee, L. Doyen, T.A. Henzinger, in:, L. Aceto, G. Bacci, A. Ingólfsdóttir, A. Legay, R. Mardare (Eds.), Models, Algorithms, Logics and Tools, Springer, 2017, pp. 367–381.","ieee":"K. Chatterjee, L. Doyen, and T. A. Henzinger, “The cost of exactness in quantitative reachability,” in Models, Algorithms, Logics and Tools, vol. 10460, L. Aceto, G. Bacci, A. Ingólfsdóttir, A. Legay, and R. Mardare, Eds. Springer, 2017, pp. 367–381.","ama":"Chatterjee K, Doyen L, Henzinger TA. The cost of exactness in quantitative reachability. In: Aceto L, Bacci G, Ingólfsdóttir A, Legay A, Mardare R, eds. Models, Algorithms, Logics and Tools. Vol 10460. Theoretical Computer Science and General Issues. Springer; 2017:367-381. doi:10.1007/978-3-319-63121-9_18","apa":"Chatterjee, K., Doyen, L., & Henzinger, T. A. (2017). The cost of exactness in quantitative reachability. In L. Aceto, G. Bacci, A. Ingólfsdóttir, A. Legay, & R. Mardare (Eds.), Models, Algorithms, Logics and Tools (Vol. 10460, pp. 367–381). Springer. https://doi.org/10.1007/978-3-319-63121-9_18","mla":"Chatterjee, Krishnendu, et al. “The Cost of Exactness in Quantitative Reachability.” Models, Algorithms, Logics and Tools, edited by Luca Aceto et al., vol. 10460, Springer, 2017, pp. 367–81, doi:10.1007/978-3-319-63121-9_18.","ista":"Chatterjee K, Doyen L, Henzinger TA. 2017.The cost of exactness in quantitative reachability. In: Models, Algorithms, Logics and Tools. LNCS, vol. 10460, 367–381.","chicago":"Chatterjee, Krishnendu, Laurent Doyen, and Thomas A Henzinger. “The Cost of Exactness in Quantitative Reachability.” In Models, Algorithms, Logics and Tools, edited by Luca Aceto, Giorgio Bacci, Anna Ingólfsdóttir, Axel Legay, and Radu Mardare, 10460:367–81. Theoretical Computer Science and General Issues. Springer, 2017. https://doi.org/10.1007/978-3-319-63121-9_18."},"title":"The cost of exactness in quantitative reachability","editor":[{"first_name":"Luca","full_name":"Aceto, Luca","last_name":"Aceto"},{"first_name":"Giorgio","last_name":"Bacci","full_name":"Bacci, Giorgio"},{"first_name":"Anna","last_name":"Ingólfsdóttir","full_name":"Ingólfsdóttir, Anna"},{"last_name":"Legay","full_name":"Legay, Axel","first_name":"Axel"},{"first_name":"Radu","last_name":"Mardare","full_name":"Mardare, Radu"}],"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"last_name":"Doyen","full_name":"Doyen, Laurent","first_name":"Laurent"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"}],"publist_id":"7170","article_processing_charge":"No","project":[{"call_identifier":"FWF","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","name":"Moderne Concurrency Paradigms","grant_number":"S11402-N23"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Game Theory","grant_number":"S11407"},{"name":"The Wittgenstein Prize","grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425"}],"day":"25","publication":"Models, Algorithms, Logics and Tools","has_accepted_license":"1","year":"2017","date_published":"2017-07-25T00:00:00Z","doi":"10.1007/978-3-319-63121-9_18","date_created":"2018-12-11T11:47:34Z","page":"367 - 381","acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grants S11402-N23 and S11407-N23 (RiSE/SHiNE), and Z211-N23 (Wittgenstein Award), ERC Start grant (279307: Graph Games), Vienna Science and Technology Fund (WWTF) through project ICT15-003.","quality_controlled":"1","publisher":"Springer","oa":1,"ddc":["000"],"date_updated":"2022-05-23T08:54:02Z","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:47:25Z","_id":"625","series_title":"Theoretical Computer Science and General Issues","status":"public","type":"book_chapter","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"7048","checksum":"b2402766ec02c79801aac634bd8f9f6c","date_updated":"2020-07-14T12:47:25Z","file_size":192826,"creator":"dernst","date_created":"2019-11-19T08:06:50Z","file_name":"2017_ModelsAlgorithms_Chatterjee.pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0302-9743"],"isbn":["978-3-319-63120-2"]},"publication_status":"published","volume":10460,"ec_funded":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"In the analysis of reactive systems a quantitative objective assigns a real value to every trace of the system. The value decision problem for a quantitative objective requires a trace whose value is at least a given threshold, and the exact value decision problem requires a trace whose value is exactly the threshold. We compare the computational complexity of the value and exact value decision problems for classical quantitative objectives, such as sum, discounted sum, energy, and mean-payoff for two standard models of reactive systems, namely, graphs and graph games."}],"month":"07","intvolume":" 10460","scopus_import":"1","alternative_title":["LNCS"]},{"author":[{"last_name":"Nikolic","full_name":"Nikolic, Nela","orcid":"0000-0001-9068-6090","first_name":"Nela","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Didara, Zrinka","last_name":"Didara","first_name":"Zrinka"},{"full_name":"Moll, Isabella","last_name":"Moll","first_name":"Isabella"}],"publist_id":"7172","title":"MazF activation promotes translational heterogeneity of the grcA mRNA in Escherichia coli populations","citation":{"mla":"Nikolic, Nela, et al. “MazF Activation Promotes Translational Heterogeneity of the GrcA MRNA in Escherichia Coli Populations.” PeerJ, vol. 2017, no. 9, 3830, PeerJ, 2017, doi:10.7717/peerj.3830.","apa":"Nikolic, N., Didara, Z., & Moll, I. (2017). MazF activation promotes translational heterogeneity of the grcA mRNA in Escherichia coli populations. PeerJ. PeerJ. https://doi.org/10.7717/peerj.3830","ama":"Nikolic N, Didara Z, Moll I. MazF activation promotes translational heterogeneity of the grcA mRNA in Escherichia coli populations. PeerJ. 2017;2017(9). doi:10.7717/peerj.3830","ieee":"N. Nikolic, Z. Didara, and I. Moll, “MazF activation promotes translational heterogeneity of the grcA mRNA in Escherichia coli populations,” PeerJ, vol. 2017, no. 9. PeerJ, 2017.","short":"N. Nikolic, Z. Didara, I. Moll, PeerJ 2017 (2017).","chicago":"Nikolic, Nela, Zrinka Didara, and Isabella Moll. “MazF Activation Promotes Translational Heterogeneity of the GrcA MRNA in Escherichia Coli Populations.” PeerJ. PeerJ, 2017. https://doi.org/10.7717/peerj.3830.","ista":"Nikolic N, Didara Z, Moll I. 2017. MazF activation promotes translational heterogeneity of the grcA mRNA in Escherichia coli populations. PeerJ. 2017(9), 3830."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"3830","date_created":"2018-12-11T11:47:33Z","doi":"10.7717/peerj.3830","date_published":"2017-09-21T00:00:00Z","year":"2017","has_accepted_license":"1","publication":"PeerJ","day":"21","oa":1,"quality_controlled":"1","publisher":"PeerJ","acknowledgement":"Austrian Science Fund (FWF): M1697, P22249; Swiss National Science Foundation (SNF): 145706; European Commission;FWF Special Research Program: RNA-REG F43","file_date_updated":"2020-07-14T12:47:24Z","department":[{"_id":"CaGu"}],"date_updated":"2021-01-12T08:06:48Z","ddc":["579"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"909","status":"public","_id":"624","volume":2017,"issue":"9","publication_status":"published","publication_identifier":{"issn":["21678359"]},"language":[{"iso":"eng"}],"file":[{"checksum":"3d79ae6b6eabc90b0eaaed82ff3493b0","file_id":"4908","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:11:51Z","file_name":"IST-2017-909-v1+1_peerj-3830.pdf","date_updated":"2020-07-14T12:47:24Z","file_size":682064,"creator":"system"}],"scopus_import":1,"intvolume":" 2017","month":"09","abstract":[{"lang":"eng","text":"Bacteria adapt to adverse environmental conditions by altering gene expression patterns. Recently, a novel stress adaptation mechanism has been described that allows Escherichia coli to alter gene expression at the post-transcriptional level. The key player in this regulatory pathway is the endoribonuclease MazF, the toxin component of the toxin-antitoxin module mazEF that is triggered by various stressful conditions. In general, MazF degrades the majority of transcripts by cleaving at ACA sites, which results in the retardation of bacterial growth. Furthermore, MazF can process a small subset of mRNAs and render them leaderless by removing their ribosome binding site. MazF concomitantly modifies ribosomes, making them selective for the translation of leaderless mRNAs. In this study, we employed fluorescent reporter-systems to investigate mazEF expression during stressful conditions, and to infer consequences of the mRNA processing mediated by MazF on gene expression at the single-cell level. Our results suggest that mazEF transcription is maintained at low levels in single cells encountering adverse conditions, such as antibiotic stress or amino acid starvation. Moreover, using the grcA mRNA as a model for MazF-mediated mRNA processing, we found that MazF activation promotes heterogeneity in the grcA reporter expression, resulting in a subpopulation of cells with increased levels of GrcA reporter protein."}],"oa_version":"Published Version"},{"date_updated":"2021-01-12T08:06:55Z","department":[{"_id":"KrCh"}],"_id":"628","status":"public","conference":{"location":"Heidelberg, Germany","end_date":"2017-07-28","start_date":"2017-07-24","name":"CAV: Computer Aided Verification"},"type":"conference","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"isbn":["978-331963386-2"]},"ec_funded":1,"volume":10426,"oa_version":"Submitted Version","abstract":[{"text":"We consider the problem of developing automated techniques for solving recurrence relations to aid the expected-runtime analysis of programs. The motivation is that several classical textbook algorithms have quite efficient expected-runtime complexity, whereas the corresponding worst-case bounds are either inefficient (e.g., Quick-Sort), or completely ineffective (e.g., Coupon-Collector). Since the main focus of expected-runtime analysis is to obtain efficient bounds, we consider bounds that are either logarithmic, linear or almost-linear (O(log n), O(n), O(n · log n), respectively, where n represents the input size). Our main contribution is an efficient (simple linear-time algorithm) sound approach for deriving such expected-runtime bounds for the analysis of recurrence relations induced by randomized algorithms. The experimental results show that our approach can efficiently derive asymptotically optimal expected-runtime bounds for recurrences of classical randomized algorithms, including Randomized-Search, Quick-Sort, Quick-Select, Coupon-Collector, where the worst-case bounds are either inefficient (such as linear as compared to logarithmic expected-runtime complexity, or quadratic as compared to linear or almost-linear expected-runtime complexity), or ineffective.","lang":"eng"}],"intvolume":" 10426","month":"01","main_file_link":[{"url":"https://arxiv.org/abs/1705.00314","open_access":"1"}],"scopus_import":1,"alternative_title":["LNCS"],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Chatterjee, Krishnendu, et al. Automated Recurrence Analysis for Almost Linear Expected Runtime Bounds. Edited by Rupak Majumdar and Viktor Kunčak, vol. 10426, Springer, 2017, pp. 118–39, doi:10.1007/978-3-319-63387-9_6.","apa":"Chatterjee, K., Fu, H., & Murhekar, A. (2017). Automated recurrence analysis for almost linear expected runtime bounds. In R. Majumdar & V. Kunčak (Eds.) (Vol. 10426, pp. 118–139). Presented at the CAV: Computer Aided Verification, Heidelberg, Germany: Springer. https://doi.org/10.1007/978-3-319-63387-9_6","ama":"Chatterjee K, Fu H, Murhekar A. Automated recurrence analysis for almost linear expected runtime bounds. In: Majumdar R, Kunčak V, eds. Vol 10426. Springer; 2017:118-139. doi:10.1007/978-3-319-63387-9_6","ieee":"K. Chatterjee, H. Fu, and A. Murhekar, “Automated recurrence analysis for almost linear expected runtime bounds,” presented at the CAV: Computer Aided Verification, Heidelberg, Germany, 2017, vol. 10426, pp. 118–139.","short":"K. Chatterjee, H. Fu, A. Murhekar, in:, R. Majumdar, V. Kunčak (Eds.), Springer, 2017, pp. 118–139.","chicago":"Chatterjee, Krishnendu, Hongfei Fu, and Aniket Murhekar. “Automated Recurrence Analysis for Almost Linear Expected Runtime Bounds.” edited by Rupak Majumdar and Viktor Kunčak, 10426:118–39. Springer, 2017. https://doi.org/10.1007/978-3-319-63387-9_6.","ista":"Chatterjee K, Fu H, Murhekar A. 2017. Automated recurrence analysis for almost linear expected runtime bounds. CAV: Computer Aided Verification, LNCS, vol. 10426, 118–139."},"editor":[{"full_name":"Majumdar, Rupak","last_name":"Majumdar","first_name":"Rupak"},{"first_name":"Viktor","last_name":"Kunčak","full_name":"Kunčak, Viktor"}],"title":"Automated recurrence analysis for almost linear expected runtime bounds","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"first_name":"Hongfei","full_name":"Fu, Hongfei","last_name":"Fu"},{"first_name":"Aniket","full_name":"Murhekar, Aniket","last_name":"Murhekar"}],"publist_id":"7166","project":[{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Game Theory","grant_number":"S11407"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"day":"01","year":"2017","date_created":"2018-12-11T11:47:35Z","doi":"10.1007/978-3-319-63387-9_6","date_published":"2017-01-01T00:00:00Z","page":"118 - 139","oa":1,"publisher":"Springer","quality_controlled":"1"},{"file":[{"file_size":443635,"date_updated":"2020-07-14T12:47:27Z","creator":"system","file_name":"IST-2017-906-v1+1_SHTI236-0356.pdf","date_created":"2018-12-12T10:11:56Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"1254dcc5b04a996d97fad9a726b42727","file_id":"4913"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-161499758-0"]},"publication_status":"published","volume":236,"license":"https://creativecommons.org/licenses/by-nc/4.0/","oa_version":"Published Version","abstract":[{"text":"Background: Standards have become available to share semantically encoded vital parameters from medical devices, as required for example by personal healthcare records. Standardised sharing of biosignal data largely remains open. Objectives: The goal of this work is to explore available biosignal file format and data exchange standards and profiles, and to conceptualise end-To-end solutions. Methods: The authors reviewed and discussed available biosignal file format standards with other members of international standards development organisations (SDOs). Results: A raw concept for standards based acquisition, storage, archiving and sharing of biosignals was developed. The GDF format may serve for storing biosignals. Signals can then be shared using FHIR resources and may be stored on FHIR servers or in DICOM archives, with DICOM waveforms as one possible format. Conclusion: Currently a group of international SDOs (e.g. HL7, IHE, DICOM, IEEE) is engaged in intensive discussions. This discussion extends existing work that already was adopted by large implementer communities. The concept presented here only reports the current status of the discussion in Austria. The discussion will continue internationally, with results to be expected over the coming years.","lang":"eng"}],"month":"01","intvolume":" 236","alternative_title":["Studies in Health Technology and Informatics"],"scopus_import":1,"ddc":["005"],"date_updated":"2021-01-12T08:06:59Z","department":[{"_id":"ScienComp"},{"_id":"PeJo"}],"file_date_updated":"2020-07-14T12:47:27Z","_id":"630","status":"public","pubrep_id":"906","type":"conference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"conference":{"start_date":"2017-05-23","end_date":"2017-05-24","location":"Vienna, Austria","name":"eHealth: Health Informatics Meets eHealth"},"day":"01","has_accepted_license":"1","year":"2017","date_published":"2017-01-01T00:00:00Z","doi":"10.3233/978-1-61499-759-7-356","date_created":"2018-12-11T11:47:36Z","page":"356 - 362","publisher":"IOS Press","quality_controlled":"1","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Sauermann, Stefan, et al. Biosignals Standards and FHIR: The Way to Go. Vol. 236, IOS Press, 2017, pp. 356–62, doi:10.3233/978-1-61499-759-7-356.","short":"S. Sauermann, V. David, A. Schlögl, R. Egelkraut, M. Frohner, B. Pohn, P. Urbauer, A. Mense, in:, IOS Press, 2017, pp. 356–362.","ieee":"S. Sauermann et al., “Biosignals standards and FHIR: The way to go,” presented at the eHealth: Health Informatics Meets eHealth, Vienna, Austria, 2017, vol. 236, pp. 356–362.","apa":"Sauermann, S., David, V., Schlögl, A., Egelkraut, R., Frohner, M., Pohn, B., … Mense, A. (2017). Biosignals standards and FHIR: The way to go (Vol. 236, pp. 356–362). Presented at the eHealth: Health Informatics Meets eHealth, Vienna, Austria: IOS Press. https://doi.org/10.3233/978-1-61499-759-7-356","ama":"Sauermann S, David V, Schlögl A, et al. Biosignals standards and FHIR: The way to go. In: Vol 236. IOS Press; 2017:356-362. doi:10.3233/978-1-61499-759-7-356","chicago":"Sauermann, Stefan, Veronika David, Alois Schlögl, Reinhard Egelkraut, Matthias Frohner, Birgit Pohn, Philipp Urbauer, and Alexander Mense. “Biosignals Standards and FHIR: The Way to Go,” 236:356–62. IOS Press, 2017. https://doi.org/10.3233/978-1-61499-759-7-356.","ista":"Sauermann S, David V, Schlögl A, Egelkraut R, Frohner M, Pohn B, Urbauer P, Mense A. 2017. Biosignals standards and FHIR: The way to go. eHealth: Health Informatics Meets eHealth, Studies in Health Technology and Informatics, vol. 236, 356–362."},"title":"Biosignals standards and FHIR: The way to go","publist_id":"7164","author":[{"last_name":"Sauermann","full_name":"Sauermann, Stefan","first_name":"Stefan"},{"full_name":"David, Veronika","last_name":"David","first_name":"Veronika"},{"orcid":"0000-0002-5621-8100","full_name":"Schlögl, Alois","last_name":"Schlögl","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","first_name":"Alois"},{"last_name":"Egelkraut","full_name":"Egelkraut, Reinhard","first_name":"Reinhard"},{"last_name":"Frohner","full_name":"Frohner, Matthias","first_name":"Matthias"},{"first_name":"Birgit","last_name":"Pohn","full_name":"Pohn, Birgit"},{"full_name":"Urbauer, Philipp","last_name":"Urbauer","first_name":"Philipp"},{"first_name":"Alexander","full_name":"Mense, Alexander","last_name":"Mense"}]},{"day":"01","publication":"Proceedings of the American Mathematical Society","year":"2017","date_published":"2017-01-01T00:00:00Z","doi":"10.1090/proc/13468","date_created":"2018-12-11T11:47:36Z","page":"2441 - 2454","quality_controlled":"1","publisher":"American Mathematical Society","oa":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Lewin, Mathieu, Phan Nam, and Nicolas Rougerie. “A Note on 2D Focusing Many Boson Systems.” Proceedings of the American Mathematical Society. American Mathematical Society, 2017. https://doi.org/10.1090/proc/13468.","ista":"Lewin M, Nam P, Rougerie N. 2017. A note on 2D focusing many boson systems. Proceedings of the American Mathematical Society. 145(6), 2441–2454.","mla":"Lewin, Mathieu, et al. “A Note on 2D Focusing Many Boson Systems.” Proceedings of the American Mathematical Society, vol. 145, no. 6, American Mathematical Society, 2017, pp. 2441–54, doi:10.1090/proc/13468.","ieee":"M. Lewin, P. Nam, and N. Rougerie, “A note on 2D focusing many boson systems,” Proceedings of the American Mathematical Society, vol. 145, no. 6. American Mathematical Society, pp. 2441–2454, 2017.","short":"M. Lewin, P. Nam, N. Rougerie, Proceedings of the American Mathematical Society 145 (2017) 2441–2454.","ama":"Lewin M, Nam P, Rougerie N. A note on 2D focusing many boson systems. Proceedings of the American Mathematical Society. 2017;145(6):2441-2454. doi:10.1090/proc/13468","apa":"Lewin, M., Nam, P., & Rougerie, N. (2017). A note on 2D focusing many boson systems. Proceedings of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/proc/13468"},"title":"A note on 2D focusing many boson systems","publist_id":"7160","author":[{"first_name":"Mathieu","last_name":"Lewin","full_name":"Lewin, Mathieu"},{"id":"404092F4-F248-11E8-B48F-1D18A9856A87","first_name":"Phan","last_name":"Nam","full_name":"Nam, Phan"},{"last_name":"Rougerie","full_name":"Rougerie, Nicolas","first_name":"Nicolas"}],"project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"language":[{"iso":"eng"}],"publication_status":"published","issue":"6","volume":145,"ec_funded":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"We consider a 2D quantum system of N bosons in a trapping potential |x|s, interacting via a pair potential of the form N2β−1 w(Nβ x). We show that for all 0 < β < (s + 1)/(s + 2), the leading order behavior of ground states of the many-body system is described in the large N limit by the corresponding cubic nonlinear Schrödinger energy functional. Our result covers the focusing case (w < 0) where even the stability of the many-body system is not obvious. This answers an open question mentioned by X. Chen and J. Holmer for harmonic traps (s = 2). Together with the BBGKY hierarchy approach used by these authors, our result implies the convergence of the many-body quantum dynamics to the focusing NLS equation with harmonic trap for all 0 < β < 3/4. "}],"month":"01","intvolume":" 145","scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1509.09045"}],"date_updated":"2021-01-12T08:07:03Z","department":[{"_id":"RoSe"}],"_id":"632","status":"public","type":"journal_article"},{"project":[{"call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","name":"Teaching Old Crypto New Tricks","grant_number":"682815"}],"publist_id":"7154","author":[{"first_name":"Joel F","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","last_name":"Alwen","full_name":"Alwen, Joel F"},{"full_name":"Chen, Binchi","last_name":"Chen","first_name":"Binchi"},{"full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654","last_name":"Pietrzak","first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Reyzin","full_name":"Reyzin, Leonid","first_name":"Leonid"},{"first_name":"Stefano","full_name":"Tessaro, Stefano","last_name":"Tessaro"}],"editor":[{"first_name":"Jean-Sébastien","full_name":"Coron, Jean-Sébastien","last_name":"Coron"},{"first_name":"Jesper","last_name":"Buus Nielsen","full_name":"Buus Nielsen, Jesper"}],"title":"Scrypt is maximally memory hard","citation":{"short":"J.F. Alwen, B. Chen, K.Z. Pietrzak, L. Reyzin, S. Tessaro, in:, J.-S. Coron, J. Buus Nielsen (Eds.), Springer, 2017, pp. 33–62.","ieee":"J. F. Alwen, B. Chen, K. Z. Pietrzak, L. Reyzin, and S. Tessaro, “Scrypt is maximally memory hard,” presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Paris, France, 2017, vol. 10212, pp. 33–62.","apa":"Alwen, J. F., Chen, B., Pietrzak, K. Z., Reyzin, L., & Tessaro, S. (2017). Scrypt is maximally memory hard. In J.-S. Coron & J. Buus Nielsen (Eds.) (Vol. 10212, pp. 33–62). Presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Paris, France: Springer. https://doi.org/10.1007/978-3-319-56617-7_2","ama":"Alwen JF, Chen B, Pietrzak KZ, Reyzin L, Tessaro S. Scrypt is maximally memory hard. In: Coron J-S, Buus Nielsen J, eds. Vol 10212. Springer; 2017:33-62. doi:10.1007/978-3-319-56617-7_2","mla":"Alwen, Joel F., et al. Scrypt Is Maximally Memory Hard. Edited by Jean-Sébastien Coron and Jesper Buus Nielsen, vol. 10212, Springer, 2017, pp. 33–62, doi:10.1007/978-3-319-56617-7_2.","ista":"Alwen JF, Chen B, Pietrzak KZ, Reyzin L, Tessaro S. 2017. Scrypt is maximally memory hard. EUROCRYPT: Theory and Applications of Cryptographic Techniques, LNCS, vol. 10212, 33–62.","chicago":"Alwen, Joel F, Binchi Chen, Krzysztof Z Pietrzak, Leonid Reyzin, and Stefano Tessaro. “Scrypt Is Maximally Memory Hard.” edited by Jean-Sébastien Coron and Jesper Buus Nielsen, 10212:33–62. Springer, 2017. https://doi.org/10.1007/978-3-319-56617-7_2."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publisher":"Springer","quality_controlled":"1","oa":1,"page":"33 - 62","doi":"10.1007/978-3-319-56617-7_2","date_published":"2017-01-01T00:00:00Z","date_created":"2018-12-11T11:47:37Z","year":"2017","day":"01","type":"conference","conference":{"start_date":"2017-04-30","location":"Paris, France","end_date":"2017-05-04","name":"EUROCRYPT: Theory and Applications of Cryptographic Techniques"},"status":"public","_id":"635","department":[{"_id":"KrPi"}],"date_updated":"2021-01-12T08:07:10Z","alternative_title":["LNCS"],"scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2016/989"}],"month":"01","intvolume":" 10212","abstract":[{"text":"Memory-hard functions (MHFs) are hash algorithms whose evaluation cost is dominated by memory cost. As memory, unlike computation, costs about the same across different platforms, MHFs cannot be evaluated at significantly lower cost on dedicated hardware like ASICs. MHFs have found widespread applications including password hashing, key derivation, and proofs-of-work. This paper focuses on scrypt, a simple candidate MHF designed by Percival, and described in RFC 7914. It has been used within a number of cryptocurrencies (e.g., Litecoin and Dogecoin) and has been an inspiration for Argon2d, one of the winners of the recent password-hashing competition. Despite its popularity, no rigorous lower bounds on its memory complexity are known. We prove that scrypt is optimally memory-hard, i.e., its cumulative memory complexity (cmc) in the parallel random oracle model is Ω(n2w), where w and n are the output length and number of invocations of the underlying hash function, respectively. High cmc is a strong security target for MHFs introduced by Alwen and Serbinenko (STOC’15) which implies high memory cost even for adversaries who can amortize the cost over many evaluations and evaluate the underlying hash functions many times in parallel. Our proof is the first showing optimal memory-hardness for any MHF. Our result improves both quantitatively and qualitatively upon the recent work by Alwen et al. (EUROCRYPT’16) who proved a weaker lower bound of Ω(n2w/ log2 n) for a restricted class of adversaries.","lang":"eng"}],"oa_version":"Submitted Version","volume":10212,"ec_funded":1,"publication_identifier":{"isbn":["978-331956616-0"]},"publication_status":"published","language":[{"iso":"eng"}]},{"month":"08","intvolume":" 10419","scopus_import":1,"alternative_title":["LNCS"],"main_file_link":[{"url":"https://hal.archives-ouvertes.fr/hal-01552132","open_access":"1"}],"oa_version":"Submitted Version","abstract":[{"text":"Signal regular expressions can specify sequential properties of real-valued signals based on threshold conditions, regular operations, and duration constraints. In this paper we endow them with a quantitative semantics which indicates how robustly a signal matches or does not match a given expression. First, we show that this semantics is a safe approximation of a distance between the signal and the language defined by the expression. Then, we consider the robust matching problem, that is, computing the quantitative semantics of every segment of a given signal relative to an expression. We present an algorithm that solves this problem for piecewise-constant and piecewise-linear signals and show that for such signals the robustness map is a piecewise-linear function. The availability of an indicator describing how robustly a signal segment matches some regular pattern provides a general framework for quantitative monitoring of cyber-physical systems.","lang":"eng"}],"volume":10419,"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-331965764-6"]},"publication_status":"published","status":"public","type":"conference","conference":{"name":"FORMATS: Formal Modelling and Analysis of Timed Systems","start_date":"2017-09-05","end_date":"2017-09-07","location":"Berlin, Germany"},"_id":"636","department":[{"_id":"ToHe"}],"date_updated":"2021-01-12T08:07:14Z","quality_controlled":"1","publisher":"Springer","oa":1,"date_published":"2017-08-03T00:00:00Z","doi":"10.1007/978-3-319-65765-3_11","date_created":"2018-12-11T11:47:38Z","page":"189 - 206","day":"03","year":"2017","project":[{"_id":"25F5A88A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S11402-N23","name":"Moderne Concurrency Paradigms"},{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","grant_number":"Z211"}],"editor":[{"full_name":"Abate, Alessandro","last_name":"Abate","first_name":"Alessandro"},{"first_name":"Gilles","last_name":"Geeraerts","full_name":"Geeraerts, Gilles"}],"title":"On the quantitative semantics of regular expressions over real-valued signals","publist_id":"7152","author":[{"first_name":"Alexey","full_name":"Bakhirkin, Alexey","last_name":"Bakhirkin"},{"id":"40960E6E-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","orcid":"0000-0001-5199-3143","full_name":"Ferrere, Thomas","last_name":"Ferrere"},{"last_name":"Maler","full_name":"Maler, Oded","first_name":"Oded"},{"first_name":"Dogan","full_name":"Ulus, Dogan","last_name":"Ulus"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Bakhirkin, Alexey, et al. On the Quantitative Semantics of Regular Expressions over Real-Valued Signals. Edited by Alessandro Abate and Gilles Geeraerts, vol. 10419, Springer, 2017, pp. 189–206, doi:10.1007/978-3-319-65765-3_11.","ama":"Bakhirkin A, Ferrere T, Maler O, Ulus D. On the quantitative semantics of regular expressions over real-valued signals. In: Abate A, Geeraerts G, eds. Vol 10419. Springer; 2017:189-206. doi:10.1007/978-3-319-65765-3_11","apa":"Bakhirkin, A., Ferrere, T., Maler, O., & Ulus, D. (2017). On the quantitative semantics of regular expressions over real-valued signals. In A. Abate & G. Geeraerts (Eds.) (Vol. 10419, pp. 189–206). Presented at the FORMATS: Formal Modelling and Analysis of Timed Systems, Berlin, Germany: Springer. https://doi.org/10.1007/978-3-319-65765-3_11","ieee":"A. Bakhirkin, T. Ferrere, O. Maler, and D. Ulus, “On the quantitative semantics of regular expressions over real-valued signals,” presented at the FORMATS: Formal Modelling and Analysis of Timed Systems, Berlin, Germany, 2017, vol. 10419, pp. 189–206.","short":"A. Bakhirkin, T. Ferrere, O. Maler, D. Ulus, in:, A. Abate, G. Geeraerts (Eds.), Springer, 2017, pp. 189–206.","chicago":"Bakhirkin, Alexey, Thomas Ferrere, Oded Maler, and Dogan Ulus. “On the Quantitative Semantics of Regular Expressions over Real-Valued Signals.” edited by Alessandro Abate and Gilles Geeraerts, 10419:189–206. Springer, 2017. https://doi.org/10.1007/978-3-319-65765-3_11.","ista":"Bakhirkin A, Ferrere T, Maler O, Ulus D. 2017. On the quantitative semantics of regular expressions over real-valued signals. FORMATS: Formal Modelling and Analysis of Timed Systems, LNCS, vol. 10419, 189–206."}}]