[{"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1404.5084"}],"status":"public","date_created":"2018-12-11T11:55:27Z","_id":"2053","type":"conference","ec_funded":1,"conference":{"name":"CONCUR: Concurrency Theory","location":"Rome, Italy","end_date":"2014-09-05","start_date":"2014-09-02"},"author":[{"last_name":"Hermanns","first_name":"Holger","full_name":"Hermanns, Holger"},{"full_name":"Krčál, Jan","last_name":"Krčál","first_name":"Jan"},{"last_name":"Kretinsky","first_name":"Jan","orcid":"0000-0002-8122-2881","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","full_name":"Kretinsky, Jan"}],"project":[{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","grant_number":"S11402-N23","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","name":"Moderne Concurrency Paradigms"}],"oa_version":"Submitted Version","language":[{"iso":"eng"}],"volume":8704,"month":"09","acknowledgement":"This work is supported by the EU 7th Framework Programme under grant agreements 295261 (MEALS) and 318490 (SENSATION), Czech Science Foundation under grant agreement P202/12/G061, the DFG Transregional Collaborative Research Centre SFB/TR 14 AVACS, and by the CAS/SAFEA International Partnership Program for Creative Research Teams.","page":"249 - 265","year":"2014","day":"01","doi":"10.1007/978-3-662-44584-6_18","oa":1,"intvolume":" 8704","publist_id":"4993","publication":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","editor":[{"full_name":"Baldan, Paolo","last_name":"Baldan","first_name":"Paolo"},{"first_name":"Daniele","last_name":"Gorla","full_name":"Gorla, Daniele"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","alternative_title":["LNCS"],"date_updated":"2021-01-12T06:55:00Z","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"citation":{"mla":"Hermanns, Holger, et al. “Probabilistic Bisimulation: Naturally on Distributions.” Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Paolo Baldan and Daniele Gorla, vol. 8704, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014, pp. 249–65, doi:10.1007/978-3-662-44584-6_18.","short":"H. Hermanns, J. Krčál, J. Kretinsky, in:, P. Baldan, D. Gorla (Eds.), Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014, pp. 249–265.","ista":"Hermanns H, Krčál J, Kretinsky J. 2014. Probabilistic bisimulation: Naturally on distributions. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). CONCUR: Concurrency Theory, LNCS, vol. 8704, 249–265.","chicago":"Hermanns, Holger, Jan Krčál, and Jan Kretinsky. “Probabilistic Bisimulation: Naturally on Distributions.” In Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Paolo Baldan and Daniele Gorla, 8704:249–65. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014. https://doi.org/10.1007/978-3-662-44584-6_18.","ama":"Hermanns H, Krčál J, Kretinsky J. Probabilistic bisimulation: Naturally on distributions. In: Baldan P, Gorla D, eds. Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol 8704. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2014:249-265. doi:10.1007/978-3-662-44584-6_18","apa":"Hermanns, H., Krčál, J., & Kretinsky, J. (2014). Probabilistic bisimulation: Naturally on distributions. In P. Baldan & D. Gorla (Eds.), Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 8704, pp. 249–265). Rome, Italy: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.1007/978-3-662-44584-6_18","ieee":"H. Hermanns, J. Krčál, and J. Kretinsky, “Probabilistic bisimulation: Naturally on distributions,” in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Rome, Italy, 2014, vol. 8704, pp. 249–265."},"date_published":"2014-09-01T00:00:00Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","title":"Probabilistic bisimulation: Naturally on distributions","abstract":[{"lang":"eng","text":"In contrast to the usual understanding of probabilistic systems as stochastic processes, recently these systems have also been regarded as transformers of probabilities. In this paper, we give a natural definition of strong bisimulation for probabilistic systems corresponding to this view that treats probability distributions as first-class citizens. Our definition applies in the same way to discrete systems as well as to systems with uncountable state and action spaces. Several examples demonstrate that our definition refines the understanding of behavioural equivalences of probabilistic systems. In particular, it solves a longstanding open problem concerning the representation of memoryless continuous time by memoryfull continuous time. Finally, we give algorithms for computing this bisimulation not only for finite but also for classes of uncountably infinite systems."}],"publication_status":"published"},{"main_file_link":[{"url":"http://arxiv.org/abs/1303.4532","open_access":"1"}],"status":"public","type":"journal_article","_id":"2056","date_created":"2018-12-11T11:55:28Z","volume":69,"language":[{"iso":"eng"}],"issue":"3","month":"11","author":[{"full_name":"Ganguly, Arnab","last_name":"Ganguly","first_name":"Arnab"},{"last_name":"Petrov","first_name":"Tatjana","orcid":"0000-0002-9041-0905","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","full_name":"Petrov, Tatjana"},{"full_name":"Koeppl, Heinz","first_name":"Heinz","last_name":"Koeppl"}],"oa_version":"Submitted Version","quality_controlled":"1","publication":"Journal of Mathematical Biology","publist_id":"4990","intvolume":" 69","scopus_import":1,"page":"767 - 797","doi":"10.1007/s00285-013-0738-7","year":"2014","day":"20","acknowledgement":"T. Petrov is supported by SystemsX.ch—the Swiss Inititative for Systems Biology.","oa":1,"title":"Markov chain aggregation and its applications to combinatorial reaction networks","publisher":"Springer","date_published":"2014-11-20T00:00:00Z","publication_status":"published","abstract":[{"lang":"eng","text":"We consider a continuous-time Markov chain (CTMC) whose state space is partitioned into aggregates, and each aggregate is assigned a probability measure. A sufficient condition for defining a CTMC over the aggregates is presented as a variant of weak lumpability, which also characterizes that the measure over the original process can be recovered from that of the aggregated one. We show how the applicability of de-aggregation depends on the initial distribution. The application section is devoted to illustrate how the developed theory aids in reducing CTMC models of biochemical systems particularly in connection to protein-protein interactions. We assume that the model is written by a biologist in form of site-graph-rewrite rules. Site-graph-rewrite rules compactly express that, often, only a local context of a protein (instead of a full molecular species) needs to be in a certain configuration in order to trigger a reaction event. This observation leads to suitable aggregate Markov chains with smaller state spaces, thereby providing sufficient reduction in computational complexity. This is further exemplified in two case studies: simple unbounded polymerization and early EGFR/insulin crosstalk."}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Ganguly A, Petrov T, Koeppl H. 2014. Markov chain aggregation and its applications to combinatorial reaction networks. Journal of Mathematical Biology. 69(3), 767–797.","ama":"Ganguly A, Petrov T, Koeppl H. Markov chain aggregation and its applications to combinatorial reaction networks. Journal of Mathematical Biology. 2014;69(3):767-797. doi:10.1007/s00285-013-0738-7","chicago":"Ganguly, Arnab, Tatjana Petrov, and Heinz Koeppl. “Markov Chain Aggregation and Its Applications to Combinatorial Reaction Networks.” Journal of Mathematical Biology. Springer, 2014. https://doi.org/10.1007/s00285-013-0738-7.","apa":"Ganguly, A., Petrov, T., & Koeppl, H. (2014). Markov chain aggregation and its applications to combinatorial reaction networks. Journal of Mathematical Biology. Springer. https://doi.org/10.1007/s00285-013-0738-7","ieee":"A. Ganguly, T. Petrov, and H. Koeppl, “Markov chain aggregation and its applications to combinatorial reaction networks,” Journal of Mathematical Biology, vol. 69, no. 3. Springer, pp. 767–797, 2014.","short":"A. Ganguly, T. Petrov, H. Koeppl, Journal of Mathematical Biology 69 (2014) 767–797.","mla":"Ganguly, Arnab, et al. “Markov Chain Aggregation and Its Applications to Combinatorial Reaction Networks.” Journal of Mathematical Biology, vol. 69, no. 3, Springer, 2014, pp. 767–97, doi:10.1007/s00285-013-0738-7."},"department":[{"_id":"CaGu"},{"_id":"ToHe"}],"date_updated":"2021-01-12T06:55:01Z"},{"conference":{"location":"Joensuu, Finland","name":"IAPR: International Workshop on Structural, Syntactic, and Statistical Pattern Recognition","start_date":"2014-08-20","end_date":"2014-08-22"},"ec_funded":1,"date_created":"2018-12-11T11:55:28Z","_id":"2057","type":"conference","status":"public","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1404.7796"}],"month":"01","language":[{"iso":"eng"}],"volume":8621,"project":[{"call_identifier":"FP7","_id":"2532554C-B435-11E9-9278-68D0E5697425","grant_number":"308036","name":"Lifelong Learning of Visual Scene Understanding"}],"quality_controlled":"1","oa_version":"Preprint","author":[{"id":"4BAC2A72-F248-11E8-B48F-1D18A9856A87","full_name":"Morvant, Emilie","first_name":"Emilie","last_name":"Morvant","orcid":"0000-0002-8301-7240"},{"first_name":"Amaury","last_name":"Habrard","full_name":"Habrard, Amaury"},{"first_name":"Stéphane","last_name":"Ayache","full_name":"Ayache, Stéphane"}],"scopus_import":1,"publist_id":"4989","arxiv":1,"intvolume":" 8621","publication":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","oa":1,"page":"153 - 162","doi":"10.1007/978-3-662-44415-3_16","year":"2014","day":"01","publication_status":"published","abstract":[{"lang":"eng","text":"In the past few years, a lot of attention has been devoted to multimedia indexing by fusing multimodal informations. Two kinds of fusion schemes are generally considered: The early fusion and the late fusion. We focus on late classifier fusion, where one combines the scores of each modality at the decision level. To tackle this problem, we investigate a recent and elegant well-founded quadratic program named MinCq coming from the machine learning PAC-Bayesian theory. MinCq looks for the weighted combination, over a set of real-valued functions seen as voters, leading to the lowest misclassification rate, while maximizing the voters’ diversity. We propose an extension of MinCq tailored to multimedia indexing. Our method is based on an order-preserving pairwise loss adapted to ranking that allows us to improve Mean Averaged Precision measure while taking into account the diversity of the voters that we want to fuse. We provide evidence that this method is naturally adapted to late fusion procedures and confirm the good behavior of our approach on the challenging PASCAL VOC’07 benchmark."}],"publisher":"Springer","date_published":"2014-01-01T00:00:00Z","title":"Majority vote of diverse classifiers for late fusion","department":[{"_id":"ChLa"}],"date_updated":"2021-01-12T06:55:01Z","citation":{"short":"E. Morvant, A. Habrard, S. Ayache, in:, Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer, 2014, pp. 153–162.","mla":"Morvant, Emilie, et al. “Majority Vote of Diverse Classifiers for Late Fusion.” Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 8621, Springer, 2014, pp. 153–62, doi:10.1007/978-3-662-44415-3_16.","apa":"Morvant, E., Habrard, A., & Ayache, S. (2014). Majority vote of diverse classifiers for late fusion. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 8621, pp. 153–162). Joensuu, Finland: Springer. https://doi.org/10.1007/978-3-662-44415-3_16","chicago":"Morvant, Emilie, Amaury Habrard, and Stéphane Ayache. “Majority Vote of Diverse Classifiers for Late Fusion.” In Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 8621:153–62. Springer, 2014. https://doi.org/10.1007/978-3-662-44415-3_16.","ista":"Morvant E, Habrard A, Ayache S. 2014. Majority vote of diverse classifiers for late fusion. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). IAPR: International Workshop on Structural, Syntactic, and Statistical Pattern Recognition, LNCS, vol. 8621, 153–162.","ama":"Morvant E, Habrard A, Ayache S. Majority vote of diverse classifiers for late fusion. In: Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol 8621. Springer; 2014:153-162. doi:10.1007/978-3-662-44415-3_16","ieee":"E. Morvant, A. Habrard, and S. Ayache, “Majority vote of diverse classifiers for late fusion,” in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Joensuu, Finland, 2014, vol. 8621, pp. 153–162."},"alternative_title":["LNCS"],"external_id":{"arxiv":["1404.7796"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"has_accepted_license":"1","month":"07","issue":"4","article_number":"137","file":[{"access_level":"open_access","file_size":8387384,"checksum":"1752760a2e71e254537f31c0d10d9c6c","file_id":"4688","creator":"system","relation":"main_file","file_name":"IST-2016-606-v1+1_BlendingLiquids-Preprint.pdf","date_created":"2018-12-12T10:08:27Z","date_updated":"2020-07-14T12:45:27Z","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"article_processing_charge":"No","volume":33,"quality_controlled":"1","project":[{"name":"ROOTS Genome-wide Analysis of Root Traits","grant_number":"11-NSF-1070","_id":"25636330-B435-11E9-9278-68D0E5697425"}],"oa_version":"Submitted Version","author":[{"full_name":"Raveendran, Karthik","first_name":"Karthik","last_name":"Raveendran"},{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","full_name":"Wojtan, Christopher J","last_name":"Wojtan","first_name":"Christopher J","orcid":"0000-0001-6646-5546"},{"full_name":"Thuerey, Nils","last_name":"Thuerey","first_name":"Nils"},{"full_name":"Türk, Greg","last_name":"Türk","first_name":"Greg"}],"pubrep_id":"606","conference":{"end_date":"2014-08-14","start_date":"2014-08-10","name":"SIGGRAPH: International Conference and Exhibition on Computer Graphics and Interactive Techniques","location":"Vancouver, Canada"},"date_created":"2018-12-11T11:55:28Z","type":"conference","_id":"2058","status":"public","abstract":[{"lang":"eng","text":"We present a method for smoothly blending between existing liquid animations. We introduce a semi-automatic method for matching two existing liquid animations, which we use to create new fluid motion that plausibly interpolates the input. Our contributions include a new space-time non-rigid iterative closest point algorithm that incorporates user guidance, a subsampling technique for efficient registration of meshes with millions of vertices, and a fast surface extraction algorithm that produces 3D triangle meshes from a 4D space-time surface. Our technique can be used to instantly create hundreds of new simulations, or to interactively explore complex parameter spaces. Our method is guaranteed to produce output that does not deviate from the input animations, and it generalizes to multiple dimensions. Because our method runs at interactive rates after the initial precomputation step, it has potential applications in games and training simulations."}],"publication_status":"published","ddc":["000"],"publisher":"ACM","file_date_updated":"2020-07-14T12:45:27Z","date_published":"2014-07-01T00:00:00Z","title":"Blending liquids","date_updated":"2022-08-25T14:02:46Z","department":[{"_id":"ChWo"}],"citation":{"short":"K. Raveendran, C. Wojtan, N. Thuerey, G. Türk, in:, ACM Transactions on Graphics, ACM, 2014.","mla":"Raveendran, Karthik, et al. “Blending Liquids.” ACM Transactions on Graphics, vol. 33, no. 4, 137, ACM, 2014, doi:10.1145/2601097.2601126.","ieee":"K. Raveendran, C. Wojtan, N. Thuerey, and G. Türk, “Blending liquids,” in ACM Transactions on Graphics, Vancouver, Canada, 2014, vol. 33, no. 4.","chicago":"Raveendran, Karthik, Chris Wojtan, Nils Thuerey, and Greg Türk. “Blending Liquids.” In ACM Transactions on Graphics, Vol. 33. ACM, 2014. https://doi.org/10.1145/2601097.2601126.","ista":"Raveendran K, Wojtan C, Thuerey N, Türk G. 2014. Blending liquids. ACM Transactions on Graphics. SIGGRAPH: International Conference and Exhibition on Computer Graphics and Interactive Techniques vol. 33, 137.","ama":"Raveendran K, Wojtan C, Thuerey N, Türk G. Blending liquids. In: ACM Transactions on Graphics. Vol 33. ACM; 2014. doi:10.1145/2601097.2601126","apa":"Raveendran, K., Wojtan, C., Thuerey, N., & Türk, G. (2014). Blending liquids. In ACM Transactions on Graphics (Vol. 33). Vancouver, Canada: ACM. https://doi.org/10.1145/2601097.2601126"},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","intvolume":" 33","publist_id":"4988","publication":"ACM Transactions on Graphics","oa":1,"day":"01","doi":"10.1145/2601097.2601126","year":"2014"},{"acknowledgement":"The research was supported by the IPP PAS-IPGB SAS bilateral project (“Molecular analysis of auxin distribution in oilseed androgenic embryos”), IPP PAS-FWO VIB bilateral project (“Auxin as signaling molecule in doubled haploid production of rape (B. napus var. oleifera)”), individual national research project 2011/01/D/NZ9/02547, and VEGA 2-0090-14.","year":"2014","day":"20","page":"1077 - 1087","doi":"10.1007/s00709-014-0616-1","oa":1,"intvolume":" 251","publist_id":"4987","publication":"Protoplasma","scopus_import":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:55:02Z","department":[{"_id":"EvBe"}],"citation":{"mla":"Dubas, Ewa, et al. “The Influence of Heat Stress on Auxin Distribution in Transgenic B Napus Microspores and Microspore Derived Embryos.” Protoplasma, vol. 251, no. 5, Springer, 2014, pp. 1077–87, doi:10.1007/s00709-014-0616-1.","short":"E. Dubas, J. Moravčíková, J. Libantová, I. Matušíková, E. Benková, I. Zur, M. Krzewska, Protoplasma 251 (2014) 1077–1087.","apa":"Dubas, E., Moravčíková, J., Libantová, J., Matušíková, I., Benková, E., Zur, I., & Krzewska, M. (2014). The influence of heat stress on auxin distribution in transgenic B napus microspores and microspore derived embryos. Protoplasma. Springer. https://doi.org/10.1007/s00709-014-0616-1","ama":"Dubas E, Moravčíková J, Libantová J, et al. The influence of heat stress on auxin distribution in transgenic B napus microspores and microspore derived embryos. Protoplasma. 2014;251(5):1077-1087. doi:10.1007/s00709-014-0616-1","chicago":"Dubas, Ewa, Jana Moravčíková, Jana Libantová, Ildikó Matušíková, Eva Benková, Iwona Zur, and Monika Krzewska. “The Influence of Heat Stress on Auxin Distribution in Transgenic B Napus Microspores and Microspore Derived Embryos.” Protoplasma. Springer, 2014. https://doi.org/10.1007/s00709-014-0616-1.","ista":"Dubas E, Moravčíková J, Libantová J, Matušíková I, Benková E, Zur I, Krzewska M. 2014. The influence of heat stress on auxin distribution in transgenic B napus microspores and microspore derived embryos. Protoplasma. 251(5), 1077–1087.","ieee":"E. Dubas et al., “The influence of heat stress on auxin distribution in transgenic B napus microspores and microspore derived embryos,” Protoplasma, vol. 251, no. 5. Springer, pp. 1077–1087, 2014."},"file_date_updated":"2020-07-14T12:45:27Z","date_published":"2014-02-20T00:00:00Z","publisher":"Springer","title":"The influence of heat stress on auxin distribution in transgenic B napus microspores and microspore derived embryos","abstract":[{"lang":"eng","text":"Plant embryogenesis is regulated by differential distribution of the plant hormone auxin. However, the cells establishing these gradients during microspore embryogenesis remain to be identified. For the first time, we describe, using the DR5 or DR5rev reporter gene systems, the GFP- and GUS-based auxin biosensors to monitor auxin during Brassica napus androgenesis at cellular resolution in the initial stages. Our study provides evidence that the distribution of auxin changes during embryo development and depends on the temperature-inducible in vitro culture conditions. For this, microspores (mcs) were induced to embryogenesis by heat treatment and then subjected to genetic modification via Agrobacterium tumefaciens. The duration of high temperature treatment had a significant influence on auxin distribution in isolated and in vitro-cultured microspores and on microspore-derived embryo development. In the “mild” heat-treated (1 day at 32 °C) mcs, auxin localized in a polar way already at the uni-nucleate microspore, which was critical for the initiation of embryos with suspensor-like structure. Assuming a mean mcs radius of 20 μm, endogenous auxin content in a single cell corresponded to concentration of 1.01 μM. In mcs subjected to a prolonged heat (5 days at 32 °C), although auxin concentration increased dozen times, auxin polarization was set up at a few-celled pro-embryos without suspensor. Those embryos were enclosed in the outer wall called the exine. The exine rupture was accompanied by the auxin gradient polarization. Relative quantitative estimation of auxin, using time-lapse imaging, revealed that primordia possess up to 1.3-fold higher amounts than those found in the root apices of transgenic MDEs in the presence of exogenous auxin. Our results show, for the first time, which concentration of endogenous auxin coincides with the first cell division and how the high temperature interplays with auxin, by what affects delay early establishing microspore polarity. Moreover, we present how the local auxin accumulation demonstrates the apical–basal axis formation of the androgenic embryo and directs the axiality of the adult haploid plant."}],"publication_status":"published","ddc":["580"],"status":"public","date_created":"2018-12-11T11:55:29Z","type":"journal_article","_id":"2059","pubrep_id":"394","author":[{"last_name":"Dubas","first_name":"Ewa","full_name":"Dubas, Ewa"},{"full_name":"Moravčíková, Jana","last_name":"Moravčíková","first_name":"Jana"},{"first_name":"Jana","last_name":"Libantová","full_name":"Libantová, Jana"},{"full_name":"Matušíková, Ildikó","first_name":"Ildikó","last_name":"Matušíková"},{"first_name":"Eva","last_name":"Benková","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva"},{"full_name":"Zur, Iwona","last_name":"Zur","first_name":"Iwona"},{"full_name":"Krzewska, Monika","last_name":"Krzewska","first_name":"Monika"}],"quality_controlled":"1","oa_version":"Published Version","language":[{"iso":"eng"}],"volume":251,"has_accepted_license":"1","month":"02","issue":"5","file":[{"date_updated":"2020-07-14T12:45:27Z","date_created":"2018-12-12T10:18:31Z","content_type":"application/pdf","file_name":"IST-2015-394-v1+1_s00709-014-0616-1.pdf","relation":"main_file","file_size":6377990,"access_level":"open_access","creator":"system","checksum":"d570a6073765118fc0bb83c31d96fa53","file_id":"5353"}]},{"publication":"Science","publist_id":"4984","intvolume":" 345","scopus_import":1,"day":"01","year":"2014","doi":"10.1126/science.1255263","oa":1,"title":"Fast-spiking parvalbumin^+ GABAergic interneurons: From cellular design to microcircuit function","publisher":"American Association for the Advancement of Science","file_date_updated":"2020-07-14T12:45:27Z","date_published":"2014-08-01T00:00:00Z","ddc":["570"],"publication_status":"published","abstract":[{"text":"The success story of fast-spiking, parvalbumin-positive (PV+) GABAergic interneurons (GABA, γ-aminobutyric acid) in the mammalian central nervous system is noteworthy. In 1995, the properties of these interneurons were completely unknown. Twenty years later, thanks to the massive use of subcellular patch-clamp techniques, simultaneous multiple-cell recording, optogenetics, in vivo measurements, and computational approaches, our knowledge about PV+ interneurons became more extensive than for several types of pyramidal neurons. These findings have implications beyond the “small world” of basic research on GABAergic cells. For example, the results provide a first proof of principle that neuroscientists might be able to close the gaps between the molecular, cellular, network, and behavioral levels, representing one of the main challenges at the present time. Furthermore, the results may form the basis for PV+ interneurons as therapeutic targets for brain disease in the future. However, much needs to be learned about the basic function of these interneurons before clinical neuroscientists will be able to use PV+ interneurons for therapeutic purposes.","lang":"eng"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"H. Hu, J. Gan, and P. M. Jonas, “Fast-spiking parvalbumin^+ GABAergic interneurons: From cellular design to microcircuit function,” Science, vol. 345, no. 6196. American Association for the Advancement of Science, 2014.","ista":"Hu H, Gan J, Jonas PM. 2014. Fast-spiking parvalbumin^+ GABAergic interneurons: From cellular design to microcircuit function. Science. 345(6196), 1255263.","chicago":"Hu, Hua, Jian Gan, and Peter M Jonas. “Fast-Spiking Parvalbumin^+ GABAergic Interneurons: From Cellular Design to Microcircuit Function.” Science. American Association for the Advancement of Science, 2014. https://doi.org/10.1126/science.1255263.","ama":"Hu H, Gan J, Jonas PM. Fast-spiking parvalbumin^+ GABAergic interneurons: From cellular design to microcircuit function. Science. 2014;345(6196). doi:10.1126/science.1255263","apa":"Hu, H., Gan, J., & Jonas, P. M. (2014). Fast-spiking parvalbumin^+ GABAergic interneurons: From cellular design to microcircuit function. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1255263","mla":"Hu, Hua, et al. “Fast-Spiking Parvalbumin^+ GABAergic Interneurons: From Cellular Design to Microcircuit Function.” Science, vol. 345, no. 6196, 1255263, American Association for the Advancement of Science, 2014, doi:10.1126/science.1255263.","short":"H. Hu, J. Gan, P.M. Jonas, Science 345 (2014)."},"department":[{"_id":"PeJo"}],"date_updated":"2021-01-12T06:55:03Z","ec_funded":1,"pubrep_id":"821","status":"public","_id":"2062","type":"journal_article","date_created":"2018-12-11T11:55:29Z","volume":345,"language":[{"iso":"eng"}],"article_number":"1255263","file":[{"creator":"system","file_id":"5185","checksum":"a0036a589037d37e86364fa25cc0a82f","file_size":215514,"access_level":"open_access","relation":"main_file","file_name":"IST-2017-821-v1+1_1255263JonasPVReviewTextR_Final.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:45:27Z","date_created":"2018-12-12T10:16:00Z"},{"content_type":"application/pdf","date_updated":"2020-07-14T12:45:27Z","date_created":"2018-12-12T10:16:01Z","file_name":"IST-2017-821-v1+2_1255263JonasPVReviewFigures_Final.pdf","relation":"main_file","creator":"system","file_id":"5186","checksum":"e1f57d2713725449cb898fdcb8ef47b8","file_size":1732723,"access_level":"open_access"}],"issue":"6196","has_accepted_license":"1","month":"08","author":[{"first_name":"Hua","last_name":"Hu","id":"4AC0145C-F248-11E8-B48F-1D18A9856A87","full_name":"Hu, Hua"},{"full_name":"Gan, Jian","id":"3614E438-F248-11E8-B48F-1D18A9856A87","first_name":"Jian","last_name":"Gan"},{"orcid":"0000-0001-5001-4804","last_name":"Jonas","first_name":"Peter M","full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Submitted Version","project":[{"name":"Mechanisms of transmitter release at GABAergic synapses","grant_number":"P24909-B24","_id":"25C26B1E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"25C0F108-B435-11E9-9278-68D0E5697425","grant_number":"268548","name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons","call_identifier":"FP7"}],"quality_controlled":"1"},{"date_created":"2018-12-11T11:55:30Z","_id":"2064","type":"journal_article","status":"public","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4198489/"}],"quality_controlled":"1","oa_version":"Submitted Version","author":[{"last_name":"Rubio","first_name":"Maía","full_name":"Rubio, Maía"},{"last_name":"Fukazawa","first_name":"Yugo","full_name":"Fukazawa, Yugo"},{"full_name":"Kamasawa, Naomi","first_name":"Naomi","last_name":"Kamasawa"},{"last_name":"Clarkson","first_name":"Cheryl","full_name":"Clarkson, Cheryl"},{"full_name":"Molnár, Elek","first_name":"Elek","last_name":"Molnár"},{"orcid":"0000-0001-8761-9444","first_name":"Ryuichi","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"}],"month":"07","issue":"18","language":[{"iso":"eng"}],"volume":522,"oa":1,"acknowledgement":"National Institutes of Health (NIH) Grant Number: 1R01DC013048‐0; Biotechnology and Biological Sciences Research Council, UK Grant Number: BB/J015938/1\r\n","day":"29","doi":"10.1002/cne.23654","page":"4023 - 4042","year":"2014","scopus_import":1,"publist_id":"4974","intvolume":" 522","publication":"Journal of Comparative Neurology","department":[{"_id":"RySh"}],"date_updated":"2021-01-12T06:55:05Z","citation":{"short":"M. Rubio, Y. Fukazawa, N. Kamasawa, C. Clarkson, E. Molnár, R. Shigemoto, Journal of Comparative Neurology 522 (2014) 4023–4042.","mla":"Rubio, Maía, et al. “Target- and Input-Dependent Organization of AMPA and NMDA Receptors in Synaptic Connections of the Cochlear Nucleus.” Journal of Comparative Neurology, vol. 522, no. 18, Wiley-Blackwell, 2014, pp. 4023–42, doi:10.1002/cne.23654.","ieee":"M. Rubio, Y. Fukazawa, N. Kamasawa, C. Clarkson, E. Molnár, and R. Shigemoto, “Target- and input-dependent organization of AMPA and NMDA receptors in synaptic connections of the cochlear nucleus,” Journal of Comparative Neurology, vol. 522, no. 18. Wiley-Blackwell, pp. 4023–4042, 2014.","apa":"Rubio, M., Fukazawa, Y., Kamasawa, N., Clarkson, C., Molnár, E., & Shigemoto, R. (2014). Target- and input-dependent organization of AMPA and NMDA receptors in synaptic connections of the cochlear nucleus. Journal of Comparative Neurology. Wiley-Blackwell. https://doi.org/10.1002/cne.23654","chicago":"Rubio, Maía, Yugo Fukazawa, Naomi Kamasawa, Cheryl Clarkson, Elek Molnár, and Ryuichi Shigemoto. “Target- and Input-Dependent Organization of AMPA and NMDA Receptors in Synaptic Connections of the Cochlear Nucleus.” Journal of Comparative Neurology. Wiley-Blackwell, 2014. https://doi.org/10.1002/cne.23654.","ista":"Rubio M, Fukazawa Y, Kamasawa N, Clarkson C, Molnár E, Shigemoto R. 2014. Target- and input-dependent organization of AMPA and NMDA receptors in synaptic connections of the cochlear nucleus. Journal of Comparative Neurology. 522(18), 4023–4042.","ama":"Rubio M, Fukazawa Y, Kamasawa N, Clarkson C, Molnár E, Shigemoto R. Target- and input-dependent organization of AMPA and NMDA receptors in synaptic connections of the cochlear nucleus. Journal of Comparative Neurology. 2014;522(18):4023-4042. doi:10.1002/cne.23654"},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publication_status":"published","abstract":[{"lang":"eng","text":"We examined the synaptic structure, quantity, and distribution of α-amino-3-hydroxy-5-methylisoxazole-4-propionic acid (AMPA)- and N-methyl-D-aspartate (NMDA)-type glutamate receptors (AMPARs and NMDARs, respectively) in rat cochlear nuclei by a highly sensitive freeze-fracture replica labeling technique. Four excitatory synapses formed by two distinct inputs, auditory nerve (AN) and parallel fibers (PF), on different cell types were analyzed. These excitatory synapse types included AN synapses on bushy cells (AN-BC synapses) and fusiform cells (AN-FC synapses) and PF synapses on FC (PF-FC synapses) and cartwheel cell spines (PF-CwC synapses). Immunogold labeling revealed differences in synaptic structure as well as AMPAR and NMDAR number and/or density in both AN and PF synapses, indicating a target-dependent organization. The immunogold receptor labeling also identified differences in the synaptic organization of FCs based on AN or PF connections, indicating an input-dependent organization in FCs. Among the four excitatory synapse types, the AN-BC synapses were the smallest and had the most densely packed intramembrane particles (IMPs), whereas the PF-CwC synapses were the largest and had sparsely packed IMPs. All four synapse types showed positive correlations between the IMP-cluster area and the AMPAR number, indicating a common intrasynapse-type relationship for glutamatergic synapses. Immunogold particles for AMPARs were distributed over the entire area of individual AN synapses; PF synapses often showed synaptic areas devoid of labeling. The gold-labeling for NMDARs occurred in a mosaic fashion, with less positive correlations between the IMP-cluster area and the NMDAR number. Our observations reveal target- and input-dependent features in the structure, number, and organization of AMPARs and NMDARs in AN and PF synapses."}],"publisher":"Wiley-Blackwell","date_published":"2014-07-29T00:00:00Z","title":"Target- and input-dependent organization of AMPA and NMDA receptors in synaptic connections of the cochlear nucleus"},{"oa_version":"Submitted Version","project":[{"name":"Provable Security for Physical Cryptography","grant_number":"259668","_id":"258C570E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"quality_controlled":"1","author":[{"first_name":"Peter","last_name":"Gazi","id":"3E0BFE38-F248-11E8-B48F-1D18A9856A87","full_name":"Gazi, Peter"},{"orcid":"0000-0002-9139-1654","last_name":"Pietrzak","first_name":"Krzysztof Z","full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"},{"id":"2B3E3DE8-F248-11E8-B48F-1D18A9856A87","full_name":"Rybar, Michal","first_name":"Michal","last_name":"Rybar"}],"file":[{"relation":"main_file","file_id":"4999","checksum":"dab6ab36a5f6af94f2b597e6404ed11d","creator":"system","access_level":"open_access","file_size":492310,"content_type":"application/pdf","date_created":"2018-12-12T10:13:17Z","date_updated":"2020-07-14T12:45:28Z","file_name":"IST-2016-682-v1+1_578.pdf"}],"issue":"1","month":"01","has_accepted_license":"1","volume":8616,"language":[{"iso":"eng"}],"type":"conference","_id":"2082","date_created":"2018-12-11T11:55:36Z","status":"public","pubrep_id":"682","conference":{"name":"CRYPTO: International Cryptology Conference","location":"Santa Barbara, USA","start_date":"2014-08-17","end_date":"2014-08-21"},"ec_funded":1,"citation":{"mla":"Gazi, Peter, et al. The Exact PRF-Security of NMAC and HMAC. Edited by Juan Garay and Rosario Gennaro, vol. 8616, no. 1, Springer, 2014, pp. 113–30, doi:10.1007/978-3-662-44371-2_7.","short":"P. Gazi, K.Z. Pietrzak, M. Rybar, in:, J. Garay, R. Gennaro (Eds.), Springer, 2014, pp. 113–130.","ieee":"P. Gazi, K. Z. Pietrzak, and M. Rybar, “The exact PRF-security of NMAC and HMAC,” presented at the CRYPTO: International Cryptology Conference, Santa Barbara, USA, 2014, vol. 8616, no. 1, pp. 113–130.","chicago":"Gazi, Peter, Krzysztof Z Pietrzak, and Michal Rybar. “The Exact PRF-Security of NMAC and HMAC.” edited by Juan Garay and Rosario Gennaro, 8616:113–30. Springer, 2014. https://doi.org/10.1007/978-3-662-44371-2_7.","ama":"Gazi P, Pietrzak KZ, Rybar M. The exact PRF-security of NMAC and HMAC. In: Garay J, Gennaro R, eds. Vol 8616. Springer; 2014:113-130. doi:10.1007/978-3-662-44371-2_7","ista":"Gazi P, Pietrzak KZ, Rybar M. 2014. The exact PRF-security of NMAC and HMAC. CRYPTO: International Cryptology Conference, LNCS, vol. 8616, 113–130.","apa":"Gazi, P., Pietrzak, K. Z., & Rybar, M. (2014). The exact PRF-security of NMAC and HMAC. In J. Garay & R. Gennaro (Eds.) (Vol. 8616, pp. 113–130). Presented at the CRYPTO: International Cryptology Conference, Santa Barbara, USA: Springer. https://doi.org/10.1007/978-3-662-44371-2_7"},"department":[{"_id":"KrPi"}],"date_updated":"2023-09-07T12:02:27Z","alternative_title":["LNCS"],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","ddc":["000","004"],"publication_status":"published","abstract":[{"text":"NMAC is a mode of operation which turns a fixed input-length keyed hash function f into a variable input-length function. A practical single-key variant of NMAC called HMAC is a very popular and widely deployed message authentication code (MAC). Security proofs and attacks for NMAC can typically be lifted to HMAC. NMAC was introduced by Bellare, Canetti and Krawczyk [Crypto'96], who proved it to be a secure pseudorandom function (PRF), and thus also a MAC, assuming that (1) f is a PRF and (2) the function we get when cascading f is weakly collision-resistant. Unfortunately, HMAC is typically instantiated with cryptographic hash functions like MD5 or SHA-1 for which (2) has been found to be wrong. To restore the provable guarantees for NMAC, Bellare [Crypto'06] showed its security based solely on the assumption that f is a PRF, albeit via a non-uniform reduction. - Our first contribution is a simpler and uniform proof for this fact: If f is an ε-secure PRF (against q queries) and a δ-non-adaptively secure PRF (against q queries), then NMAC f is an (ε+ℓqδ)-secure PRF against q queries of length at most ℓ blocks each. - We then show that this ε+ℓqδ bound is basically tight. For the most interesting case where ℓqδ ≥ ε we prove this by constructing an f for which an attack with advantage ℓqδ exists. This also violates the bound O(ℓε) on the PRF-security of NMAC recently claimed by Koblitz and Menezes. - Finally, we analyze the PRF-security of a modification of NMAC called NI [An and Bellare, Crypto'99] that differs mainly by using a compression function with an additional keying input. This avoids the constant rekeying on multi-block messages in NMAC and allows for a security proof starting by the standard switch from a PRF to a random function, followed by an information-theoretic analysis. We carry out such an analysis, obtaining a tight ℓq2/2 c bound for this step, improving over the trivial bound of ℓ2q2/2c. The proof borrows combinatorial techniques originally developed for proving the security of CBC-MAC [Bellare et al., Crypto'05].","lang":"eng"}],"title":"The exact PRF-security of NMAC and HMAC","file_date_updated":"2020-07-14T12:45:28Z","date_published":"2014-01-01T00:00:00Z","publisher":"Springer","oa":1,"doi":"10.1007/978-3-662-44371-2_7","day":"01","year":"2014","page":"113 - 130","editor":[{"last_name":"Garay","first_name":"Juan","full_name":"Garay, Juan"},{"last_name":"Gennaro","first_name":"Rosario","full_name":"Gennaro, Rosario"}],"related_material":{"record":[{"status":"public","id":"838","relation":"dissertation_contains"}]},"publist_id":"4955","intvolume":" 8616"},{"publication":"Evolution","intvolume":" 68","publist_id":"4954","related_material":{"record":[{"status":"public","relation":"research_data","id":"9747"}]},"scopus_import":1,"day":"25","page":"2296 - 2305","year":"2014","doi":"10.1111/evo.12440","acknowledgement":"The authors are grateful to the Leverhulme Trust (F/00 215/AW) for funding this work.","oa":1,"title":"Role of sex and migration in adaptation to sink environments","date_published":"2014-04-25T00:00:00Z","file_date_updated":"2020-07-14T12:45:28Z","publisher":"Wiley","ddc":["570"],"abstract":[{"text":"Understanding the effects of sex and migration on adaptation to novel environments remains a key problem in evolutionary biology. Using a single-cell alga Chlamydomonas reinhardtii, we investigated how sex and migration affected rates of evolutionary rescue in a sink environment, and subsequent changes in fitness following evolutionary rescue. We show that sex and migration affect both the rate of evolutionary rescue and subsequent adaptation. However, their combined effects change as the populations adapt to a sink habitat. Both sex and migration independently increased rates of evolutionary rescue, but the effect of sex on subsequent fitness improvements, following initial rescue, changed with migration, as sex was beneficial in the absence of migration but constraining adaptation when combined with migration. These results suggest that sex and migration are beneficial during the initial stages of adaptation, but can become detrimental as the population adapts to its environment.","lang":"eng"}],"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Lagator, Mato, et al. “Role of Sex and Migration in Adaptation to Sink Environments.” Evolution, vol. 68, no. 8, Wiley, 2014, pp. 2296–305, doi:10.1111/evo.12440.","short":"M. Lagator, A. Morgan, P. Neve, N. Colegrave, Evolution 68 (2014) 2296–2305.","ieee":"M. Lagator, A. Morgan, P. Neve, and N. Colegrave, “Role of sex and migration in adaptation to sink environments,” Evolution, vol. 68, no. 8. Wiley, pp. 2296–2305, 2014.","apa":"Lagator, M., Morgan, A., Neve, P., & Colegrave, N. (2014). Role of sex and migration in adaptation to sink environments. Evolution. Wiley. https://doi.org/10.1111/evo.12440","ama":"Lagator M, Morgan A, Neve P, Colegrave N. Role of sex and migration in adaptation to sink environments. Evolution. 2014;68(8):2296-2305. doi:10.1111/evo.12440","chicago":"Lagator, Mato, Andrew Morgan, Paul Neve, and Nick Colegrave. “Role of Sex and Migration in Adaptation to Sink Environments.” Evolution. Wiley, 2014. https://doi.org/10.1111/evo.12440.","ista":"Lagator M, Morgan A, Neve P, Colegrave N. 2014. Role of sex and migration in adaptation to sink environments. Evolution. 68(8), 2296–2305."},"date_updated":"2023-02-23T14:06:51Z","department":[{"_id":"CaGu"}],"status":"public","type":"journal_article","_id":"2083","article_type":"original","date_created":"2018-12-11T11:55:36Z","article_processing_charge":"No","volume":68,"language":[{"iso":"eng"}],"issue":"8","file":[{"file_size":467254,"access_level":"open_access","creator":"dernst","file_id":"7845","checksum":"8d459b07e4a11bb5fde92d969184fe48","relation":"main_file","file_name":"2014_Evolution_Lagator.pdf","date_updated":"2020-07-14T12:45:28Z","date_created":"2020-05-14T16:40:31Z","content_type":"application/pdf"}],"has_accepted_license":"1","month":"04","author":[{"last_name":"Lagator","first_name":"Mato","full_name":"Lagator, Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Andrew","last_name":"Morgan","full_name":"Morgan, Andrew"},{"first_name":"Paul","last_name":"Neve","full_name":"Neve, Paul"},{"full_name":"Colegrave, Nick","first_name":"Nick","last_name":"Colegrave"}],"oa_version":"Published Version","quality_controlled":"1"},{"title":"Spatio-temporally precise activation of engineered receptor tyrosine kinases by light","date_published":"2014-07-01T00:00:00Z","publisher":"Wiley-Blackwell","abstract":[{"lang":"eng","text":"Receptor tyrosine kinases (RTKs) are a large family of cell surface receptors that sense growth factors and hormones and regulate a variety of cell behaviours in health and disease. Contactless activation of RTKs with spatial and temporal precision is currently not feasible. Here, we generated RTKs that are insensitive to endogenous ligands but can be selectively activated by low-intensity blue light. We screened light-oxygen-voltage (LOV)-sensing domains for their ability to activate RTKs by light-activated dimerization. Incorporation of LOV domains found in aureochrome photoreceptors of stramenopiles resulted in robust activation of the fibroblast growth factor receptor 1 (FGFR1), epidermal growth factor receptor (EGFR) and rearranged during transfection (RET). In human cancer and endothelial cells, light induced cellular signalling with spatial and temporal precision. Furthermore, light faithfully mimicked complex mitogenic and morphogenic cell behaviour induced by growth factors. RTKs under optical control (Opto-RTKs) provide a powerful optogenetic approach to actuate cellular signals and manipulate cell behaviour."}],"publication_status":"published","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"M. Grusch et al., “Spatio-temporally precise activation of engineered receptor tyrosine kinases by light,” EMBO Journal, vol. 33, no. 15. Wiley-Blackwell, pp. 1713–1726, 2014.","ista":"Grusch M, Schelch K, Riedler R, Gschaider-Reichhart E, Differ C, Berger W, Inglés Prieto Á, Janovjak HL. 2014. Spatio-temporally precise activation of engineered receptor tyrosine kinases by light. EMBO Journal. 33(15), 1713–1726.","chicago":"Grusch, Michael, Karin Schelch, Robert Riedler, Eva Gschaider-Reichhart, Christopher Differ, Walter Berger, Álvaro Inglés Prieto, and Harald L Janovjak. “Spatio-Temporally Precise Activation of Engineered Receptor Tyrosine Kinases by Light.” EMBO Journal. Wiley-Blackwell, 2014. https://doi.org/10.15252/embj.201387695.","ama":"Grusch M, Schelch K, Riedler R, et al. Spatio-temporally precise activation of engineered receptor tyrosine kinases by light. EMBO Journal. 2014;33(15):1713-1726. doi:10.15252/embj.201387695","apa":"Grusch, M., Schelch, K., Riedler, R., Gschaider-Reichhart, E., Differ, C., Berger, W., … Janovjak, H. L. (2014). Spatio-temporally precise activation of engineered receptor tyrosine kinases by light. EMBO Journal. Wiley-Blackwell. https://doi.org/10.15252/embj.201387695","mla":"Grusch, Michael, et al. “Spatio-Temporally Precise Activation of Engineered Receptor Tyrosine Kinases by Light.” EMBO Journal, vol. 33, no. 15, Wiley-Blackwell, 2014, pp. 1713–26, doi:10.15252/embj.201387695.","short":"M. Grusch, K. Schelch, R. Riedler, E. Gschaider-Reichhart, C. Differ, W. Berger, Á. Inglés Prieto, H.L. Janovjak, EMBO Journal 33 (2014) 1713–1726."},"date_updated":"2023-09-07T12:49:09Z","department":[{"_id":"HaJa"}],"publication":"EMBO Journal","intvolume":" 33","publist_id":"4953","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"418"}]},"scopus_import":1,"day":"01","year":"2014","page":"1713 - 1726","doi":"10.15252/embj.201387695","acknowledgement":"European Union Seventh Framework Programme; Human Frontier Science Program; Oesterreichische Nationalbank Anniversary Fund 14211; Austrian Research Promotion Agency; FemTech","oa":1,"volume":33,"language":[{"iso":"eng"}],"issue":"15","month":"07","author":[{"full_name":"Grusch, Michael","last_name":"Grusch","first_name":"Michael"},{"full_name":"Schelch, Karin","last_name":"Schelch","first_name":"Karin"},{"last_name":"Riedler","first_name":"Robert","full_name":"Riedler, Robert"},{"full_name":"Gschaider-Reichhart, Eva","id":"3FEE232A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7218-7738","last_name":"Gschaider-Reichhart","first_name":"Eva"},{"full_name":"Differ, Christopher","first_name":"Christopher","last_name":"Differ"},{"last_name":"Berger","first_name":"Walter","full_name":"Berger, Walter"},{"id":"2A9DB292-F248-11E8-B48F-1D18A9856A87","full_name":"Inglés Prieto, Álvaro","last_name":"Inglés Prieto","first_name":"Álvaro","orcid":"0000-0002-5409-8571"},{"id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","full_name":"Janovjak, Harald L","last_name":"Janovjak","first_name":"Harald L","orcid":"0000-0002-8023-9315"}],"oa_version":"Submitted Version","quality_controlled":"1","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4194103/","open_access":"1"}],"status":"public","_id":"2084","type":"journal_article","date_created":"2018-12-11T11:55:37Z"},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Wolf, Stephan, et al. “So near and yet so Far: Harmonic Radar Reveals Reduced Homing Ability of Nosema Infected Honeybees.” PLoS One, vol. 9, no. 8, e103989, Public Library of Science, 2014, doi:10.1371/journal.pone.0103989.","short":"S. Wolf, D. Mcmahon, K. Lim, C. Pull, S. Clark, R. Paxton, J. Osborne, PLoS One 9 (2014).","apa":"Wolf, S., Mcmahon, D., Lim, K., Pull, C., Clark, S., Paxton, R., & Osborne, J. (2014). So near and yet so far: Harmonic radar reveals reduced homing ability of Nosema infected honeybees. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0103989","ista":"Wolf S, Mcmahon D, Lim K, Pull C, Clark S, Paxton R, Osborne J. 2014. So near and yet so far: Harmonic radar reveals reduced homing ability of Nosema infected honeybees. PLoS One. 9(8), e103989.","chicago":"Wolf, Stephan, Dino Mcmahon, Ka Lim, Christopher Pull, Suzanne Clark, Robert Paxton, and Juliet Osborne. “So near and yet so Far: Harmonic Radar Reveals Reduced Homing Ability of Nosema Infected Honeybees.” PLoS One. Public Library of Science, 2014. https://doi.org/10.1371/journal.pone.0103989.","ama":"Wolf S, Mcmahon D, Lim K, et al. So near and yet so far: Harmonic radar reveals reduced homing ability of Nosema infected honeybees. PLoS One. 2014;9(8). doi:10.1371/journal.pone.0103989","ieee":"S. Wolf et al., “So near and yet so far: Harmonic radar reveals reduced homing ability of Nosema infected honeybees,” PLoS One, vol. 9, no. 8. Public Library of Science, 2014."},"department":[{"_id":"SyCr"}],"date_updated":"2023-02-23T14:11:56Z","title":"So near and yet so far: Harmonic radar reveals reduced homing ability of Nosema infected honeybees","publisher":"Public Library of Science","date_published":"2014-08-06T00:00:00Z","file_date_updated":"2020-07-14T12:45:28Z","ddc":["570"],"publication_status":"published","abstract":[{"text":"Pathogens may gain a fitness advantage through manipulation of the behaviour of their hosts. Likewise, host behavioural changes can be a defence mechanism, counteracting the impact of pathogens on host fitness. We apply harmonic radar technology to characterize the impact of an emerging pathogen - Nosema ceranae (Microsporidia) - on honeybee (Apis mellifera) flight and orientation performance in the field. Honeybees are the most important commercial pollinators. Emerging diseases have been proposed to play a prominent role in colony decline, partly through sub-lethal behavioural manipulation of their hosts. We found that homing success was significantly reduced in diseased (65.8%) versus healthy foragers (92.5%). Although lost bees had significantly reduced continuous flight times and prolonged resting times, other flight characteristics and navigational abilities showed no significant difference between infected and non-infected bees. Our results suggest that infected bees express normal flight characteristics but are constrained in their homing ability, potentially compromising the colony by reducing its resource inputs, but also counteracting the intra-colony spread of infection. We provide the first high-resolution analysis of sub-lethal effects of an emerging disease on insect flight behaviour. The potential causes and the implications for both host and parasite are discussed.","lang":"eng"}],"day":"06","year":"2014","doi":"10.1371/journal.pone.0103989","acknowledgement":"This study was funded jointly by a grant from BBSRC, Defra, NERC, the Scottish Government and the Wellcome Trust, under the Insect Pollinators Initiative (grant numbers BB/I00097/1 and BB/I000100/1). Rothamsted Research is a national institute of bioscience strategically funded by the UK Biotechnology and Biological Sciences Research Council (BBSRC).","oa":1,"publication":"PLoS One","publist_id":"4949","intvolume":" 9","scopus_import":1,"related_material":{"record":[{"status":"public","relation":"research_data","id":"9888"}]},"author":[{"last_name":"Wolf","first_name":"Stephan","full_name":"Wolf, Stephan"},{"full_name":"Mcmahon, Dino","last_name":"Mcmahon","first_name":"Dino"},{"full_name":"Lim, Ka","first_name":"Ka","last_name":"Lim"},{"last_name":"Pull","first_name":"Christopher","orcid":"0000-0003-1122-3982","id":"3C7F4840-F248-11E8-B48F-1D18A9856A87","full_name":"Pull, Christopher"},{"first_name":"Suzanne","last_name":"Clark","full_name":"Clark, Suzanne"},{"last_name":"Paxton","first_name":"Robert","full_name":"Paxton, Robert"},{"full_name":"Osborne, Juliet","last_name":"Osborne","first_name":"Juliet"}],"oa_version":"Published Version","quality_controlled":"1","volume":9,"language":[{"iso":"eng"}],"file":[{"file_name":"IST-2016-437-v1+1_journal.pone.0103989.pdf","date_updated":"2020-07-14T12:45:28Z","date_created":"2018-12-12T10:13:55Z","content_type":"application/pdf","file_size":1013386,"access_level":"open_access","creator":"system","checksum":"2fc62c6739eada4bddf026afbae669db","file_id":"5042","relation":"main_file"}],"article_number":"e103989","issue":"8","month":"08","has_accepted_license":"1","status":"public","type":"journal_article","_id":"2086","date_created":"2018-12-11T11:55:37Z","pubrep_id":"437"},{"_id":"2131","type":"journal_article","date_created":"2018-12-11T11:55:53Z","oa":1,"doi":"10.1002/cpa.21495","main_file_link":[{"url":"http://arxiv.org/abs/1202.3094 ","open_access":"1"}],"page":"776 - 870","day":"01","status":"public","year":"2014","acknowledgement":"JM is supported by Rubicon grant 680-50-0901 of the Netherlands Organisation for Scientific Research (NWO). MH is supported by EPSRC grant EP/D071593/1 and by the Royal Society through a Wolfson Research Merit Award. Both MH and HW are supported by the Le","publication":"Communications on Pure and Applied Mathematics","publist_id":"4902","intvolume":" 67","citation":{"ista":"Hairer M, Maas J, Weber H. 2014. Approximating Rough Stochastic PDEs. Communications on Pure and Applied Mathematics. 67(5), 776–870.","chicago":"Hairer, Martin, Jan Maas, and Hendrik Weber. “Approximating Rough Stochastic PDEs.” Communications on Pure and Applied Mathematics. Wiley-Blackwell, 2014. https://doi.org/10.1002/cpa.21495.","ama":"Hairer M, Maas J, Weber H. Approximating Rough Stochastic PDEs. Communications on Pure and Applied Mathematics. 2014;67(5):776-870. doi:10.1002/cpa.21495","apa":"Hairer, M., Maas, J., & Weber, H. (2014). Approximating Rough Stochastic PDEs. Communications on Pure and Applied Mathematics. Wiley-Blackwell. https://doi.org/10.1002/cpa.21495","ieee":"M. Hairer, J. Maas, and H. Weber, “Approximating Rough Stochastic PDEs,” Communications on Pure and Applied Mathematics, vol. 67, no. 5. Wiley-Blackwell, pp. 776–870, 2014.","mla":"Hairer, Martin, et al. “Approximating Rough Stochastic PDEs.” Communications on Pure and Applied Mathematics, vol. 67, no. 5, Wiley-Blackwell, 2014, pp. 776–870, doi:10.1002/cpa.21495.","short":"M. Hairer, J. Maas, H. Weber, Communications on Pure and Applied Mathematics 67 (2014) 776–870."},"extern":1,"quality_controlled":0,"date_updated":"2021-01-12T06:55:30Z","author":[{"full_name":"Hairer, Martin M","first_name":"Martin","last_name":"Hairer"},{"id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","full_name":"Jan Maas","last_name":"Maas","first_name":"Jan","orcid":"0000-0002-0845-1338"},{"full_name":"Weber, Hendrik","first_name":"Hendrik","last_name":"Weber"}],"issue":"5","month":"05","publication_status":"published","abstract":[{"text":"We study approximations to a class of vector-valued equations of Burgers type driven by a multiplicative space-time white noise. A solution theory for this class of equations has been developed recently in Probability Theory Related Fields by Hairer and Weber. The key idea was to use the theory of controlled rough paths to give definitions of weak/mild solutions and to set up a Picard iteration argument. In this article the limiting behavior of a rather large class of (spatial) approximations to these equations is studied. These approximations are shown to converge and convergence rates are given, but the limit may depend on the particular choice of approximation. This effect is a spatial analogue to the Itô-Stratonovich correction in the theory of stochastic ordinary differential equations, where it is well known that different approximation schemes may converge to different solutions.","lang":"eng"}],"title":"Approximating Rough Stochastic PDEs","volume":67,"publisher":"Wiley-Blackwell","date_published":"2014-05-01T00:00:00Z"},{"publication":"Discrete and Continuous Dynamical Systems- Series A","publist_id":"4903","intvolume":" 34","page":"1355 - 1374","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1212.1129"}],"doi":"10.3934/dcds.2014.34.1355 ","year":"2014","status":"public","day":"01","_id":"2132","type":"journal_article","oa":1,"date_created":"2018-12-11T11:55:54Z","volume":34,"title":"Gradient flow structures for discrete porous medium equations","date_published":"2014-04-01T00:00:00Z","publisher":"Southwest Missouri State University","issue":"4","month":"04","publication_status":"published","abstract":[{"lang":"eng","text":"We consider discrete porous medium equations of the form ∂tρt=Δϕ(ρt), where Δ is the generator of a reversible continuous time Markov chain on a finite set χ, and ϕ is an increasing function. We show that these equations arise as gradient flows of certain entropy functionals with respect to suitable non-local transportation metrics. This may be seen as a discrete analogue of the Wasserstein gradient flow structure for porous medium equations in ℝn discovered by Otto. We present a one-dimensional counterexample to geodesic convexity and discuss Gromov-Hausdorff convergence to the Wasserstein metric."}],"author":[{"last_name":"Erbar","first_name":"Matthias","full_name":"Erbar, Matthias"},{"id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","full_name":"Jan Maas","last_name":"Maas","first_name":"Jan","orcid":"0000-0002-0845-1338"}],"citation":{"mla":"Erbar, Matthias, and Jan Maas. “Gradient Flow Structures for Discrete Porous Medium Equations.” Discrete and Continuous Dynamical Systems- Series A, vol. 34, no. 4, Southwest Missouri State University, 2014, pp. 1355–74, doi:10.3934/dcds.2014.34.1355 .","short":"M. Erbar, J. Maas, Discrete and Continuous Dynamical Systems- Series A 34 (2014) 1355–1374.","ieee":"M. Erbar and J. Maas, “Gradient flow structures for discrete porous medium equations,” Discrete and Continuous Dynamical Systems- Series A, vol. 34, no. 4. Southwest Missouri State University, pp. 1355–1374, 2014.","apa":"Erbar, M., & Maas, J. (2014). Gradient flow structures for discrete porous medium equations. Discrete and Continuous Dynamical Systems- Series A. Southwest Missouri State University. https://doi.org/10.3934/dcds.2014.34.1355 ","ista":"Erbar M, Maas J. 2014. Gradient flow structures for discrete porous medium equations. Discrete and Continuous Dynamical Systems- Series A. 34(4), 1355–1374.","ama":"Erbar M, Maas J. Gradient flow structures for discrete porous medium equations. Discrete and Continuous Dynamical Systems- Series A. 2014;34(4):1355-1374. doi:10.3934/dcds.2014.34.1355 ","chicago":"Erbar, Matthias, and Jan Maas. “Gradient Flow Structures for Discrete Porous Medium Equations.” Discrete and Continuous Dynamical Systems- Series A. Southwest Missouri State University, 2014. https://doi.org/10.3934/dcds.2014.34.1355 ."},"quality_controlled":0,"extern":1,"date_updated":"2021-01-12T06:55:30Z"},{"year":"2014","day":"01","main_file_link":[{"url":"http://arxiv.org/abs/1203.5377 ","open_access":"1"}],"status":"public","page":"887 - 926","doi":"10.1007/s00220-014-2124-8","type":"journal_article","_id":"2133","date_created":"2018-12-11T11:55:54Z","oa":1,"publication":"Communications in Mathematical Physics","publist_id":"4901","intvolume":" 331","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Carlen","first_name":"Eric","full_name":"Carlen, Eric"},{"last_name":"Maas","first_name":"Jan","orcid":"0000-0002-0845-1338","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","full_name":"Maas, Jan"}],"oa_version":"Submitted Version","citation":{"ieee":"E. Carlen and J. Maas, “An analog of the 2-Wasserstein metric in non-commutative probability under which the fermionic Fokker-Planck equation is gradient flow for the entropy,” Communications in Mathematical Physics, vol. 331, no. 3. Springer, pp. 887–926, 2014.","ama":"Carlen E, Maas J. An analog of the 2-Wasserstein metric in non-commutative probability under which the fermionic Fokker-Planck equation is gradient flow for the entropy. Communications in Mathematical Physics. 2014;331(3):887-926. doi:10.1007/s00220-014-2124-8","ista":"Carlen E, Maas J. 2014. An analog of the 2-Wasserstein metric in non-commutative probability under which the fermionic Fokker-Planck equation is gradient flow for the entropy. Communications in Mathematical Physics. 331(3), 887–926.","chicago":"Carlen, Eric, and Jan Maas. “An Analog of the 2-Wasserstein Metric in Non-Commutative Probability under Which the Fermionic Fokker-Planck Equation Is Gradient Flow for the Entropy.” Communications in Mathematical Physics. Springer, 2014. https://doi.org/10.1007/s00220-014-2124-8.","apa":"Carlen, E., & Maas, J. (2014). An analog of the 2-Wasserstein metric in non-commutative probability under which the fermionic Fokker-Planck equation is gradient flow for the entropy. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-014-2124-8","mla":"Carlen, Eric, and Jan Maas. “An Analog of the 2-Wasserstein Metric in Non-Commutative Probability under Which the Fermionic Fokker-Planck Equation Is Gradient Flow for the Entropy.” Communications in Mathematical Physics, vol. 331, no. 3, Springer, 2014, pp. 887–926, doi:10.1007/s00220-014-2124-8.","short":"E. Carlen, J. Maas, Communications in Mathematical Physics 331 (2014) 887–926."},"extern":"1","quality_controlled":"1","date_updated":"2021-01-12T06:55:30Z","volume":331,"title":"An analog of the 2-Wasserstein metric in non-commutative probability under which the fermionic Fokker-Planck equation is gradient flow for the entropy","language":[{"iso":"eng"}],"publisher":"Springer","date_published":"2014-11-01T00:00:00Z","issue":"3","publication_status":"published","month":"11","abstract":[{"lang":"eng","text":"Let ℭ denote the Clifford algebra over ℝ𝑛, which is the von Neumann algebra generated by n self-adjoint operators Q j , j = 1,…,n satisfying the canonical anticommutation relations, Q i Q j + Q j Q i = 2δ ij I, and let τ denote the normalized trace on ℭ. This algebra arises in quantum mechanics as the algebra of observables generated by n fermionic degrees of freedom. Let 𝔓 denote the set of all positive operators 𝜌∈ℭ such that τ(ρ) = 1; these are the non-commutative analogs of probability densities in the non-commutative probability space (ℭ,𝜏). The fermionic Fokker–Planck equation is a quantum-mechanical analog of the classical Fokker–Planck equation with which it has much in common, such as the same optimal hypercontractivity properties. In this paper we construct a Riemannian metric on 𝔓 that we show to be a natural analog of the classical 2-Wasserstein metric, and we show that, in analogy with the classical case, the fermionic Fokker–Planck equation is gradient flow in this metric for the relative entropy with respect to the ground state. We derive a number of consequences of this, such as a sharp Talagrand inequality for this metric, and we prove a number of results pertaining to this metric. Several open problems are raised."}]},{"publisher":"American Physical Society","date_published":"2014-08-11T00:00:00Z","language":[{"iso":"eng"}],"volume":113,"title":"Dissipative preparation of spatial order in Rydberg-dressed Bose-Einstein condensates","abstract":[{"text":"We propose a technique for engineering momentum-dependent dissipation in Bose-Einstein condensates with non-local interactions. The scheme relies on the use of momentum-dependent dark-states in close analogy to velocity-selective coherent population trapping. During the short-time dissipative dynamics, the system is driven into a particular finite-momentum phonon mode, which in real space corresponds to an ordered structure with non-local density-density correlations. Dissipation-induced ordering can be observed and studied in present-day experiments using cold atoms with dipole-dipole or off-resonant Rydberg interactions. Due to its dissipative nature, the ordering does not require artificial breaking of translational symmetry by an opticallattice or harmonic trap. This opens up a perspective of direct cooling of quantum gases into strongly-interacting phases.","lang":"eng"}],"month":"08","publication_status":"published","issue":"7","article_number":"070401","author":[{"first_name":"Johannes","last_name":"Otterbach","full_name":"Otterbach, Johannes"},{"orcid":"0000-0002-6990-7802","first_name":"Mikhail","last_name":"Lemeshko","full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:55:33Z","extern":"1","citation":{"apa":"Otterbach, J., & Lemeshko, M. (2014). Dissipative preparation of spatial order in Rydberg-dressed Bose-Einstein condensates. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.113.070401","ista":"Otterbach J, Lemeshko M. 2014. Dissipative preparation of spatial order in Rydberg-dressed Bose-Einstein condensates. Physical Review Letters. 113(7), 070401.","chicago":"Otterbach, Johannes, and Mikhail Lemeshko. “Dissipative Preparation of Spatial Order in Rydberg-Dressed Bose-Einstein Condensates.” Physical Review Letters. American Physical Society, 2014. https://doi.org/10.1103/PhysRevLett.113.070401.","ama":"Otterbach J, Lemeshko M. Dissipative preparation of spatial order in Rydberg-dressed Bose-Einstein condensates. Physical Review Letters. 2014;113(7). doi:10.1103/PhysRevLett.113.070401","ieee":"J. Otterbach and M. Lemeshko, “Dissipative preparation of spatial order in Rydberg-dressed Bose-Einstein condensates,” Physical Review Letters, vol. 113, no. 7. American Physical Society, 2014.","short":"J. Otterbach, M. Lemeshko, Physical Review Letters 113 (2014).","mla":"Otterbach, Johannes, and Mikhail Lemeshko. “Dissipative Preparation of Spatial Order in Rydberg-Dressed Bose-Einstein Condensates.” Physical Review Letters, vol. 113, no. 7, 070401, American Physical Society, 2014, doi:10.1103/PhysRevLett.113.070401."},"oa_version":"Submitted Version","intvolume":" 113","publist_id":"4884","publication":"Physical Review Letters","acknowledgement":"This work was supported by NSF through a grant for the Institute for Theoretical Atomic, Molecular, and Optical Physics at Harvard University and Smithsonian Astrophysical Observatory as well as the Harvard Quantum Optics Center.","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1308.5905"}],"doi":"10.1103/PhysRevLett.113.070401","status":"public","year":"2014","day":"11","date_created":"2018-12-11T11:55:56Z","oa":1,"type":"journal_article","_id":"2140"},{"publication":"Journal of the ACM","intvolume":" 61","publist_id":"4883","related_material":{"record":[{"id":"3165","relation":"earlier_version","status":"public"}]},"scopus_import":"1","year":"2014","doi":"10.1145/2597631","day":"01","oa":1,"title":"Efficient and dynamic algorithms for alternating Büchi games and maximal end-component decomposition","publisher":"ACM","date_published":"2014-05-01T00:00:00Z","abstract":[{"text":"The computation of the winning set for Büchi objectives in alternating games on graphs is a central problem in computer-aided verification with a large number of applications. The long-standing best known upper bound for solving the problem is Õ(n ⋅ m), where n is the number of vertices and m is the number of edges in the graph. We are the first to break the Õ(n ⋅ m) boundary by presenting a new technique that reduces the running time to O(n2). This bound also leads to O(n2)-time algorithms for computing the set of almost-sure winning vertices for Büchi objectives (1) in alternating games with probabilistic transitions (improving an earlier bound of Õ(n ⋅ m)), (2) in concurrent graph games with constant actions (improving an earlier bound of O(n3)), and (3) in Markov decision processes (improving for m>n4/3 an earlier bound of O(m ⋅ √m)). We then show how to maintain the winning set for Büchi objectives in alternating games under a sequence of edge insertions or a sequence of edge deletions in O(n) amortized time per operation. Our algorithms are the first dynamic algorithms for this problem. We then consider another core graph theoretic problem in verification of probabilistic systems, namely computing the maximal end-component decomposition of a graph. We present two improved static algorithms for the maximal end-component decomposition problem. Our first algorithm is an O(m ⋅ √m)-time algorithm, and our second algorithm is an O(n2)-time algorithm which is obtained using the same technique as for alternating Büchi games. Thus, we obtain an O(min &lcu;m ⋅ √m,n2})-time algorithm improving the long-standing O(n ⋅ m) time bound. Finally, we show how to maintain the maximal end-component decomposition of a graph under a sequence of edge insertions or a sequence of edge deletions in O(n) amortized time per edge deletion, and O(m) worst-case time per edge insertion. Again, our algorithms are the first dynamic algorithms for this problem.","lang":"eng"}],"publication_status":"published","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"short":"K. Chatterjee, M.H. Henzinger, Journal of the ACM 61 (2014).","mla":"Chatterjee, Krishnendu, and Monika H. Henzinger. “Efficient and Dynamic Algorithms for Alternating Büchi Games and Maximal End-Component Decomposition.” Journal of the ACM, vol. 61, no. 3, a15, ACM, 2014, doi:10.1145/2597631.","apa":"Chatterjee, K., & Henzinger, M. H. (2014). Efficient and dynamic algorithms for alternating Büchi games and maximal end-component decomposition. Journal of the ACM. ACM. https://doi.org/10.1145/2597631","chicago":"Chatterjee, Krishnendu, and Monika H Henzinger. “Efficient and Dynamic Algorithms for Alternating Büchi Games and Maximal End-Component Decomposition.” Journal of the ACM. ACM, 2014. https://doi.org/10.1145/2597631.","ista":"Chatterjee K, Henzinger MH. 2014. Efficient and dynamic algorithms for alternating Büchi games and maximal end-component decomposition. Journal of the ACM. 61(3), a15.","ama":"Chatterjee K, Henzinger MH. Efficient and dynamic algorithms for alternating Büchi games and maximal end-component decomposition. Journal of the ACM. 2014;61(3). doi:10.1145/2597631","ieee":"K. Chatterjee and M. H. Henzinger, “Efficient and dynamic algorithms for alternating Büchi games and maximal end-component decomposition,” Journal of the ACM, vol. 61, no. 3. ACM, 2014."},"date_updated":"2025-06-02T08:53:48Z","department":[{"_id":"KrCh"}],"ec_funded":1,"status":"public","main_file_link":[{"open_access":"1","url":"https://eprints.cs.univie.ac.at/3933/"}],"_id":"2141","type":"journal_article","date_created":"2018-12-11T11:55:57Z","article_processing_charge":"No","volume":61,"language":[{"iso":"eng"}],"issue":"3","article_number":"a15","month":"05","author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"},{"last_name":"Henzinger","first_name":"Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H"}],"oa_version":"Submitted Version","quality_controlled":"1","project":[{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003"},{"call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory"},{"name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}]},{"oa_version":"Submitted Version","citation":{"short":"U. Bauer, M. Lesnick, in:, Proceedings of the Annual Symposium on Computational Geometry, ACM, 2014, pp. 355–364.","mla":"Bauer, Ulrich, and Michael Lesnick. “Induced Matchings of Barcodes and the Algebraic Stability of Persistence.” Proceedings of the Annual Symposium on Computational Geometry, ACM, 2014, pp. 355–64, doi:10.1145/2582112.2582168.","apa":"Bauer, U., & Lesnick, M. (2014). Induced matchings of barcodes and the algebraic stability of persistence. In Proceedings of the Annual Symposium on Computational Geometry (pp. 355–364). Kyoto, Japan: ACM. https://doi.org/10.1145/2582112.2582168","ista":"Bauer U, Lesnick M. 2014. Induced matchings of barcodes and the algebraic stability of persistence. Proceedings of the Annual Symposium on Computational Geometry. SoCG: Symposium on Computational Geometry, 355–364.","ama":"Bauer U, Lesnick M. Induced matchings of barcodes and the algebraic stability of persistence. In: Proceedings of the Annual Symposium on Computational Geometry. ACM; 2014:355-364. doi:10.1145/2582112.2582168","chicago":"Bauer, Ulrich, and Michael Lesnick. “Induced Matchings of Barcodes and the Algebraic Stability of Persistence.” In Proceedings of the Annual Symposium on Computational Geometry, 355–64. ACM, 2014. https://doi.org/10.1145/2582112.2582168.","ieee":"U. Bauer and M. Lesnick, “Induced matchings of barcodes and the algebraic stability of persistence,” in Proceedings of the Annual Symposium on Computational Geometry, Kyoto, Japan, 2014, pp. 355–364."},"project":[{"call_identifier":"FP7","grant_number":"318493","_id":"255D761E-B435-11E9-9278-68D0E5697425","name":"Topological Complex Systems"}],"quality_controlled":"1","department":[{"_id":"HeEd"}],"date_updated":"2021-01-12T06:55:38Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Bauer","first_name":"Ulrich","orcid":"0000-0002-9683-0724","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","full_name":"Bauer, Ulrich"},{"first_name":"Michael","last_name":"Lesnick","full_name":"Lesnick, Michael"}],"month":"06","publication_status":"published","abstract":[{"lang":"eng","text":"We define a simple, explicit map sending a morphism f : M → N of pointwise finite dimensional persistence modules to a matching between the barcodes of M and N. Our main result is that, in a precise sense, the quality of this matching is tightly controlled by the lengths of the longest intervals in the barcodes of ker f and coker f . As an immediate corollary, we obtain a new proof of the algebraic stability theorem for persistence barcodes [5, 9], a fundamental result in the theory of persistent homology. In contrast to previous proofs, ours shows explicitly how a δ-interleaving morphism between two persistence modules induces a δ-matching between the barcodes of the two modules. Our main result also specializes to a structure theorem for submodules and quotients of persistence modules. Copyright is held by the owner/author(s)."}],"title":"Induced matchings of barcodes and the algebraic stability of persistence","date_published":"2014-06-01T00:00:00Z","publisher":"ACM","language":[{"iso":"eng"}],"_id":"2153","type":"conference","date_created":"2018-12-11T11:56:01Z","oa":1,"page":"355 - 364","year":"2014","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1311.3681"}],"doi":"10.1145/2582112.2582168","day":"01","status":"public","scopus_import":1,"publication":"Proceedings of the Annual Symposium on Computational Geometry","publist_id":"4853","conference":{"location":"Kyoto, Japan","name":"SoCG: Symposium on Computational Geometry","end_date":"2014-06-11","start_date":"2014-06-08"},"ec_funded":1},{"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Matoušek, Jiří, and Uli Wagner. “On Gromov’s Method of Selecting Heavily Covered Points.” Discrete & Computational Geometry, vol. 52, no. 1, Springer, 2014, pp. 1–33, doi:10.1007/s00454-014-9584-7.","short":"J. Matoušek, U. Wagner, Discrete & Computational Geometry 52 (2014) 1–33.","ama":"Matoušek J, Wagner U. On Gromov’s method of selecting heavily covered points. Discrete & Computational Geometry. 2014;52(1):1-33. doi:10.1007/s00454-014-9584-7","ista":"Matoušek J, Wagner U. 2014. On Gromov’s method of selecting heavily covered points. Discrete & Computational Geometry. 52(1), 1–33.","chicago":"Matoušek, Jiří, and Uli Wagner. “On Gromov’s Method of Selecting Heavily Covered Points.” Discrete & Computational Geometry. Springer, 2014. https://doi.org/10.1007/s00454-014-9584-7.","apa":"Matoušek, J., & Wagner, U. (2014). On Gromov’s method of selecting heavily covered points. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-014-9584-7","ieee":"J. Matoušek and U. Wagner, “On Gromov’s method of selecting heavily covered points,” Discrete & Computational Geometry, vol. 52, no. 1. Springer, pp. 1–33, 2014."},"department":[{"_id":"UlWa"}],"date_updated":"2021-01-12T06:55:38Z","title":"On Gromov's method of selecting heavily covered points","publisher":"Springer","date_published":"2014-07-01T00:00:00Z","publication_status":"published","abstract":[{"text":"A result of Boros and Füredi (d = 2) and of Bárány (arbitrary d) asserts that for every d there exists cd > 0 such that for every n-point set P ⊂ ℝd, some point of ℝd is covered by at least (Formula presented.) of the d-simplices spanned by the points of P. The largest possible value of cd has been the subject of ongoing research. Recently Gromov improved the existing lower bounds considerably by introducing a new, topological proof method. We provide an exposition of the combinatorial component of Gromov's approach, in terms accessible to combinatorialists and discrete geometers, and we investigate the limits of his method. In particular, we give tighter bounds on the cofilling profiles for the (n - 1)-simplex. These bounds yield a minor improvement over Gromov's lower bounds on cd for large d, but they also show that the room for further improvement through the cofilling profiles alone is quite small. We also prove a slightly better lower bound for c3 by an approach using an additional structure besides the cofilling profiles. We formulate a combinatorial extremal problem whose solution might perhaps lead to a tight lower bound for cd.","lang":"eng"}],"day":"01","page":"1 - 33","doi":"10.1007/s00454-014-9584-7","year":"2014","acknowledgement":"Swiss National Science Foundation (SNF 200021-125309, 200020-138230, 200020-12507)","oa":1,"publication":"Discrete & Computational Geometry","publist_id":"4852","intvolume":" 52","scopus_import":1,"author":[{"full_name":"Matoušek, Jiří","last_name":"Matoušek","first_name":"Jiří"},{"orcid":"0000-0002-1494-0568","last_name":"Wagner","first_name":"Uli","full_name":"Wagner, Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Submitted Version","quality_controlled":"1","project":[{"_id":"25FA3206-B435-11E9-9278-68D0E5697425","grant_number":"PP00P2_138948","name":"Embeddings in Higher Dimensions: Algorithms and Combinatorics"}],"volume":52,"language":[{"iso":"eng"}],"issue":"1","month":"07","status":"public","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1102.3515"}],"type":"journal_article","_id":"2154","date_created":"2018-12-11T11:56:01Z"},{"conference":{"end_date":"2014-06-11","start_date":"2014-06-08","name":"SoCG: Symposium on Computational Geometry","location":"Kyoto, Japan"},"ec_funded":1,"status":"public","main_file_link":[{"url":"http://arxiv.org/abs/1312.1231","open_access":"1"}],"date_created":"2018-12-11T11:56:01Z","_id":"2155","type":"conference","language":[{"iso":"eng"}],"month":"06","author":[{"last_name":"Bauer","first_name":"Ulrich","orcid":"0000-0002-9683-0724","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","full_name":"Bauer, Ulrich"},{"orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","first_name":"Herbert","full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"}],"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Topological Complex Systems","_id":"255D761E-B435-11E9-9278-68D0E5697425","grant_number":"318493"}],"oa_version":"Submitted Version","publist_id":"4851","publication":"Proceedings of the Annual Symposium on Computational Geometry","scopus_import":1,"acknowledgement":"This research is partially supported by ESF under the ACAT Research Network Programme, and by the Russian Government under mega project 11.G34.31.0053","day":"01","page":"484 - 490","doi":"10.1145/2582112.2582167","year":"2014","oa":1,"publisher":"ACM","date_published":"2014-06-01T00:00:00Z","title":"The morse theory of Čech and Delaunay filtrations","publication_status":"published","abstract":[{"lang":"eng","text":"Given a finite set of points in Rn and a positive radius, we study the Čech, Delaunay-Čech, alpha, and wrap complexes as instances of a generalized discrete Morse theory. We prove that the latter three complexes are simple-homotopy equivalent. Our results have applications in topological data analysis and in the reconstruction of shapes from sampled data. Copyright is held by the owner/author(s)."}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"HeEd"}],"date_updated":"2021-01-12T06:55:38Z","citation":{"ieee":"U. Bauer and H. Edelsbrunner, “The morse theory of Čech and Delaunay filtrations,” in Proceedings of the Annual Symposium on Computational Geometry, Kyoto, Japan, 2014, pp. 484–490.","apa":"Bauer, U., & Edelsbrunner, H. (2014). The morse theory of Čech and Delaunay filtrations. In Proceedings of the Annual Symposium on Computational Geometry (pp. 484–490). Kyoto, Japan: ACM. https://doi.org/10.1145/2582112.2582167","ista":"Bauer U, Edelsbrunner H. 2014. The morse theory of Čech and Delaunay filtrations. Proceedings of the Annual Symposium on Computational Geometry. SoCG: Symposium on Computational Geometry, 484–490.","chicago":"Bauer, Ulrich, and Herbert Edelsbrunner. “The Morse Theory of Čech and Delaunay Filtrations.” In Proceedings of the Annual Symposium on Computational Geometry, 484–90. ACM, 2014. https://doi.org/10.1145/2582112.2582167.","ama":"Bauer U, Edelsbrunner H. The morse theory of Čech and Delaunay filtrations. In: Proceedings of the Annual Symposium on Computational Geometry. ACM; 2014:484-490. doi:10.1145/2582112.2582167","short":"U. Bauer, H. Edelsbrunner, in:, Proceedings of the Annual Symposium on Computational Geometry, ACM, 2014, pp. 484–490.","mla":"Bauer, Ulrich, and Herbert Edelsbrunner. “The Morse Theory of Čech and Delaunay Filtrations.” Proceedings of the Annual Symposium on Computational Geometry, ACM, 2014, pp. 484–90, doi:10.1145/2582112.2582167."}},{"language":[{"iso":"eng"}],"month":"06","author":[{"first_name":"Ulrich","last_name":"Bauer","orcid":"0000-0002-9683-0724","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","full_name":"Bauer, Ulrich"},{"last_name":"Ge","first_name":"Xiaoyin","full_name":"Ge, Xiaoyin"},{"full_name":"Wang, Yusu","first_name":"Yusu","last_name":"Wang"}],"project":[{"call_identifier":"FP7","_id":"255D761E-B435-11E9-9278-68D0E5697425","grant_number":"318493","name":"Topological Complex Systems"}],"quality_controlled":"1","oa_version":"Submitted Version","ec_funded":1,"conference":{"end_date":"2014-06-11","start_date":"2014-06-08","location":"Kyoto, Japan","name":"SoCG: Symposium on Computational Geometry"},"status":"public","main_file_link":[{"url":"http://arxiv.org/abs/1307.2839","open_access":"1"}],"date_created":"2018-12-11T11:56:02Z","_id":"2156","type":"conference","date_published":"2014-06-01T00:00:00Z","publisher":"ACM","title":"Measuring distance between Reeb graphs","abstract":[{"lang":"eng","text":"We propose a metric for Reeb graphs, called the functional distortion distance. Under this distance, the Reeb graph is stable against small changes of input functions. At the same time, it remains discriminative at differentiating input functions. In particular, the main result is that the functional distortion distance between two Reeb graphs is bounded from below by the bottleneck distance between both the ordinary and extended persistence diagrams for appropriate dimensions. As an application of our results, we analyze a natural simplification scheme for Reeb graphs, and show that persistent features in Reeb graph remains persistent under simplification. Understanding the stability of important features of the Reeb graph under simplification is an interesting problem on its own right, and critical to the practical usage of Reeb graphs. Copyright is held by the owner/author(s)."}],"publication_status":"published","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:55:39Z","department":[{"_id":"HeEd"}],"citation":{"ama":"Bauer U, Ge X, Wang Y. Measuring distance between Reeb graphs. In: Proceedings of the Annual Symposium on Computational Geometry. ACM; 2014:464-473. doi:10.1145/2582112.2582169","ista":"Bauer U, Ge X, Wang Y. 2014. Measuring distance between Reeb graphs. Proceedings of the Annual Symposium on Computational Geometry. SoCG: Symposium on Computational Geometry, 464–473.","chicago":"Bauer, Ulrich, Xiaoyin Ge, and Yusu Wang. “Measuring Distance between Reeb Graphs.” In Proceedings of the Annual Symposium on Computational Geometry, 464–73. ACM, 2014. https://doi.org/10.1145/2582112.2582169.","apa":"Bauer, U., Ge, X., & Wang, Y. (2014). Measuring distance between Reeb graphs. In Proceedings of the Annual Symposium on Computational Geometry (pp. 464–473). Kyoto, Japan: ACM. https://doi.org/10.1145/2582112.2582169","ieee":"U. Bauer, X. Ge, and Y. Wang, “Measuring distance between Reeb graphs,” in Proceedings of the Annual Symposium on Computational Geometry, Kyoto, Japan, 2014, pp. 464–473.","mla":"Bauer, Ulrich, et al. “Measuring Distance between Reeb Graphs.” Proceedings of the Annual Symposium on Computational Geometry, ACM, 2014, pp. 464–73, doi:10.1145/2582112.2582169.","short":"U. Bauer, X. Ge, Y. Wang, in:, Proceedings of the Annual Symposium on Computational Geometry, ACM, 2014, pp. 464–473."},"publist_id":"4850","publication":"Proceedings of the Annual Symposium on Computational Geometry","scopus_import":1,"acknowledgement":"National Science Foundation under grants CCF-1319406, CCF-1116258.","doi":"10.1145/2582112.2582169","year":"2014","page":"464 - 473","day":"01","oa":1}]