[{"citation":{"ista":"Henzinger MH, Krinninger S, Nanongkai D. 2015. Improved algorithms for decremental single-source reachability on directed graphs. 42nd International Colloquium on Automata, Languages and Programming. ICALP: International Colloquium on Automata, Languages, and Programming, LNCS, vol. 9134, 725–736.","chicago":"Henzinger, Monika H, Sebastian Krinninger, and Danupon Nanongkai. “Improved Algorithms for Decremental Single-Source Reachability on Directed Graphs.” In 42nd International Colloquium on Automata, Languages and Programming, 9134:725–36. Springer Nature, 2015. https://doi.org/10.1007/978-3-662-47672-7_59.","apa":"Henzinger, M. H., Krinninger, S., & Nanongkai, D. (2015). Improved algorithms for decremental single-source reachability on directed graphs. In 42nd International Colloquium on Automata, Languages and Programming (Vol. 9134, pp. 725–736). Kyoto, Japan: Springer Nature. https://doi.org/10.1007/978-3-662-47672-7_59","ama":"Henzinger MH, Krinninger S, Nanongkai D. Improved algorithms for decremental single-source reachability on directed graphs. In: 42nd International Colloquium on Automata, Languages and Programming. Vol 9134. Springer Nature; 2015:725-736. doi:10.1007/978-3-662-47672-7_59","short":"M.H. Henzinger, S. Krinninger, D. Nanongkai, in:, 42nd International Colloquium on Automata, Languages and Programming, Springer Nature, 2015, pp. 725–736.","ieee":"M. H. Henzinger, S. Krinninger, and D. Nanongkai, “Improved algorithms for decremental single-source reachability on directed graphs,” in 42nd International Colloquium on Automata, Languages and Programming, Kyoto, Japan, 2015, vol. 9134, pp. 725–736.","mla":"Henzinger, Monika H., et al. “Improved Algorithms for Decremental Single-Source Reachability on Directed Graphs.” 42nd International Colloquium on Automata, Languages and Programming, vol. 9134, Springer Nature, 2015, pp. 725–36, doi:10.1007/978-3-662-47672-7_59."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","last_name":"Henzinger"},{"last_name":"Krinninger","full_name":"Krinninger, Sebastian","first_name":"Sebastian"},{"full_name":"Nanongkai, Danupon","last_name":"Nanongkai","first_name":"Danupon"}],"external_id":{"arxiv":["1612.03856"]},"article_processing_charge":"No","title":"Improved algorithms for decremental single-source reachability on directed graphs","year":"2015","day":"01","publication":"42nd International Colloquium on Automata, Languages and Programming","page":"725 - 736","doi":"10.1007/978-3-662-47672-7_59","date_published":"2015-01-01T00:00:00Z","date_created":"2022-08-11T08:51:32Z","publisher":"Springer Nature","quality_controlled":"1","oa":1,"date_updated":"2023-02-10T09:10:26Z","extern":"1","_id":"11785","type":"conference","conference":{"name":"ICALP: International Colloquium on Automata, Languages, and Programming","start_date":"2015-07-06","end_date":"2015-07-10","location":"Kyoto, Japan"},"status":"public","publication_identifier":{"isbn":["9783662476710"],"issn":["0302-9743"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":9134,"abstract":[{"text":"Recently we presented the first algorithm for maintaining the set of nodes reachable from a source node in a directed graph that is modified by edge deletions with 𝑜(𝑚𝑛) total update time, where 𝑚 is the number of edges and 𝑛 is the number of nodes in the graph [Henzinger et al. STOC 2014]. The algorithm is a combination of several different algorithms, each for a different 𝑚 vs. 𝑛 trade-off. For the case of 𝑚=Θ(𝑛1.5) the running time is 𝑂(𝑛2.47), just barely below 𝑚𝑛=Θ(𝑛2.5). In this paper we simplify the previous algorithm using new algorithmic ideas and achieve an improved running time of 𝑂̃ (min(𝑚7/6𝑛2/3,𝑚3/4𝑛5/4+𝑜(1),𝑚2/3𝑛4/3+𝑜(1)+𝑚3/7𝑛12/7+𝑜(1))). This gives, e.g., 𝑂(𝑛2.36) for the notorious case 𝑚=Θ(𝑛1.5). We obtain the same upper bounds for the problem of maintaining the strongly connected components of a directed graph undergoing edge deletions. Our algorithms are correct with high probabililty against an oblivious adversary.","lang":"eng"}],"oa_version":"Preprint","scopus_import":"1","alternative_title":["LNCS"],"main_file_link":[{"url":"https://arxiv.org/abs/1612.03856","open_access":"1"}],"month":"01","intvolume":" 9134"},{"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0302-9743"],"isbn":["9783662476710"]},"volume":9134,"oa_version":"Preprint","abstract":[{"text":"We present faster algorithms for computing the 2-edge and 2-vertex strongly connected components of a directed graph. While in undirected graphs the 2-edge and 2-vertex connected components can be found in linear time, in directed graphs with m edges and n vertices only rather simple O(m n)-time algorithms were known. We use a hierarchical sparsification technique to obtain algorithms that run in time 𝑂(𝑛2). For 2-edge strongly connected components our algorithm gives the first running time improvement in 20 years. Additionally we present an 𝑂(𝑚2/log𝑛)-time algorithm for 2-edge strongly connected components, and thus improve over the O(m n) running time also when 𝑚=𝑂(𝑛). Our approach extends to k-edge and k-vertex strongly connected components for any constant k with a running time of 𝑂(𝑛2log𝑛) for k-edge-connectivity and 𝑂(𝑛3) for k-vertex-connectivity.","lang":"eng"}],"intvolume":" 9134","month":"07","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1412.6466"}],"scopus_import":"1","alternative_title":["LNCS"],"extern":"1","date_updated":"2023-02-10T09:21:47Z","_id":"11787","status":"public","conference":{"name":"ICALP: International Colloquium on Automata, Languages, and Programming","start_date":"2015-07-06","location":"Kyoto, Japan","end_date":"2015-07-10"},"type":"conference","publication":"2nd International Colloquium on Automata, Languages and Programming","day":"06","year":"2015","date_created":"2022-08-11T09:38:34Z","date_published":"2015-07-06T00:00:00Z","doi":"10.1007/978-3-662-47672-7_58","page":"713 - 724","oa":1,"quality_controlled":"1","publisher":"Springer Nature","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Henzinger MH, Krinninger S, Loitzenbauer V. 2015. Finding 2-edge and 2-vertex strongly connected components in quadratic time. 2nd International Colloquium on Automata, Languages and Programming. ICALP: International Colloquium on Automata, Languages, and Programming, LNCS, vol. 9134, 713–724.","chicago":"Henzinger, Monika H, Sebastian Krinninger, and Veronika Loitzenbauer. “Finding 2-Edge and 2-Vertex Strongly Connected Components in Quadratic Time.” In 2nd International Colloquium on Automata, Languages and Programming, 9134:713–24. Springer Nature, 2015. https://doi.org/10.1007/978-3-662-47672-7_58.","short":"M.H. Henzinger, S. Krinninger, V. Loitzenbauer, in:, 2nd International Colloquium on Automata, Languages and Programming, Springer Nature, 2015, pp. 713–724.","ieee":"M. H. Henzinger, S. Krinninger, and V. Loitzenbauer, “Finding 2-edge and 2-vertex strongly connected components in quadratic time,” in 2nd International Colloquium on Automata, Languages and Programming, Kyoto, Japan, 2015, vol. 9134, pp. 713–724.","ama":"Henzinger MH, Krinninger S, Loitzenbauer V. Finding 2-edge and 2-vertex strongly connected components in quadratic time. In: 2nd International Colloquium on Automata, Languages and Programming. Vol 9134. Springer Nature; 2015:713-724. doi:10.1007/978-3-662-47672-7_58","apa":"Henzinger, M. H., Krinninger, S., & Loitzenbauer, V. (2015). Finding 2-edge and 2-vertex strongly connected components in quadratic time. In 2nd International Colloquium on Automata, Languages and Programming (Vol. 9134, pp. 713–724). Kyoto, Japan: Springer Nature. https://doi.org/10.1007/978-3-662-47672-7_58","mla":"Henzinger, Monika H., et al. “Finding 2-Edge and 2-Vertex Strongly Connected Components in Quadratic Time.” 2nd International Colloquium on Automata, Languages and Programming, vol. 9134, Springer Nature, 2015, pp. 713–24, doi:10.1007/978-3-662-47672-7_58."},"title":"Finding 2-edge and 2-vertex strongly connected components in quadratic time","external_id":{"arxiv":["1412.6466"]},"article_processing_charge":"No","author":[{"last_name":"Henzinger","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H"},{"last_name":"Krinninger","full_name":"Krinninger, Sebastian","first_name":"Sebastian"},{"full_name":"Loitzenbauer, Veronika","last_name":"Loitzenbauer","first_name":"Veronika"}]},{"author":[{"first_name":"Wolfgang","last_name":"Dvořák","full_name":"Dvořák, Wolfgang"},{"first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H"}],"article_processing_charge":"No","external_id":{"arxiv":["1604.05603"]},"title":"Online ad assignment with an ad exchange","citation":{"ista":"Dvořák W, Henzinger MH. 2015. Online ad assignment with an ad exchange. 12th International Workshop of Approximation and Online Algorithms. WAOA: International Workshop on Approximation and Online Algorithms, LNCS, vol. 8952, 156–167.","chicago":"Dvořák, Wolfgang, and Monika H Henzinger. “Online Ad Assignment with an Ad Exchange.” In 12th International Workshop of Approximation and Online Algorithms, 8952:156–167. Springer Nature, 2015. https://doi.org/10.1007/978-3-319-18263-6_14.","ieee":"W. Dvořák and M. H. Henzinger, “Online ad assignment with an ad exchange,” in 12th International Workshop of Approximation and Online Algorithms, Wroclaw, Poland, 2015, vol. 8952, pp. 156–167.","short":"W. Dvořák, M.H. Henzinger, in:, 12th International Workshop of Approximation and Online Algorithms, Springer Nature, 2015, pp. 156–167.","apa":"Dvořák, W., & Henzinger, M. H. (2015). Online ad assignment with an ad exchange. In 12th International Workshop of Approximation and Online Algorithms (Vol. 8952, pp. 156–167). Wroclaw, Poland: Springer Nature. https://doi.org/10.1007/978-3-319-18263-6_14","ama":"Dvořák W, Henzinger MH. Online ad assignment with an ad exchange. In: 12th International Workshop of Approximation and Online Algorithms. Vol 8952. Springer Nature; 2015:156–167. doi:10.1007/978-3-319-18263-6_14","mla":"Dvořák, Wolfgang, and Monika H. Henzinger. “Online Ad Assignment with an Ad Exchange.” 12th International Workshop of Approximation and Online Algorithms, vol. 8952, Springer Nature, 2015, pp. 156–167, doi:10.1007/978-3-319-18263-6_14."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"156–167","date_published":"2015-01-01T00:00:00Z","doi":"10.1007/978-3-319-18263-6_14","date_created":"2022-08-11T09:43:32Z","year":"2015","day":"01","publication":"12th International Workshop of Approximation and Online Algorithms","quality_controlled":"1","publisher":"Springer Nature","oa":1,"date_updated":"2023-02-10T09:26:06Z","extern":"1","type":"conference","conference":{"end_date":"2014-09-12","location":"Wroclaw, Poland","start_date":"2014-09-11","name":"WAOA: International Workshop on Approximation and Online Algorithms"},"status":"public","_id":"11788","volume":8952,"publication_identifier":{"issn":["0302-9743"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","alternative_title":["LNCS"],"main_file_link":[{"url":"https://arxiv.org/abs/1604.05603","open_access":"1"}],"month":"01","intvolume":" 8952","abstract":[{"text":"Ad exchanges are becoming an increasingly popular way to sell advertisement slots on the internet. An ad exchange is basically a spot market for ad impressions. A publisher who has already signed contracts reserving advertisement impressions on his pages can choose between assigning a new ad impression for a new page view to a contracted advertiser or to sell it at an ad exchange. This leads to an online revenue maximization problem for the publisher. Given a new impression to sell decide whether (a) to assign it to a contracted advertiser and if so to which one or (b) to sell it at the ad exchange and if so at which reserve price. We make no assumptions about the distribution of the advertiser valuations that participate in the ad exchange and show that there exists a simple primal-dual based online algorithm, whose lower bound for the revenue converges to 𝑅𝐴𝐷𝑋+𝑅𝐴(1−1/𝑒), where 𝑅𝐴𝐷𝑋 is the revenue that the optimum algorithm achieves from the ad exchange and 𝑅𝐴 is the revenue that the optimum algorithm achieves from the contracted advertisers.","lang":"eng"}],"oa_version":"Preprint"},{"type":"conference","conference":{"start_date":"2015-07-06","end_date":"2015-07-10","location":"Kyoto, Japan","name":"ICALP: International Colloquium on Automata, Languages, and Programming"},"status":"public","_id":"11786","date_updated":"2023-02-10T09:13:31Z","extern":"1","alternative_title":["LNCS"],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1604.05337"}],"month":"01","intvolume":" 9134","abstract":[{"lang":"eng","text":"In this paper, we develop a dynamic version of the primal-dual method for optimization problems, and apply it to obtain the following results. (1) For the dynamic set-cover problem, we maintain an 𝑂(𝑓2)-approximately optimal solution in 𝑂(𝑓⋅log(𝑚+𝑛)) amortized update time, where 𝑓 is the maximum “frequency” of an element, 𝑛 is the number of sets, and 𝑚 is the maximum number of elements in the universe at any point in time. (2) For the dynamic 𝑏-matching problem, we maintain an 𝑂(1)-approximately optimal solution in 𝑂(log3𝑛) amortized update time, where 𝑛 is the number of nodes in the graph."}],"oa_version":"Preprint","volume":9134,"publication_identifier":{"isbn":["9783662476710"],"issn":["0302-9743"]},"publication_status":"published","language":[{"iso":"eng"}],"author":[{"full_name":"Bhattacharya, Sayan","last_name":"Bhattacharya","first_name":"Sayan"},{"last_name":"Henzinger","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H"},{"full_name":"Italiano, Giuseppe F.","last_name":"Italiano","first_name":"Giuseppe F."}],"external_id":{"arxiv":["1604.05337"]},"article_processing_charge":"No","title":"Design of dynamic algorithms via primal-dual method","citation":{"ista":"Bhattacharya S, Henzinger MH, Italiano GF. 2015. Design of dynamic algorithms via primal-dual method. 42nd International Colloquium on Automata, Languages and Programming. ICALP: International Colloquium on Automata, Languages, and Programming, LNCS, vol. 9134, 206–218.","chicago":"Bhattacharya, Sayan, Monika H Henzinger, and Giuseppe F. Italiano. “Design of Dynamic Algorithms via Primal-Dual Method.” In 42nd International Colloquium on Automata, Languages and Programming, 9134:206–18. Springer Nature, 2015. https://doi.org/10.1007/978-3-662-47672-7_17.","ieee":"S. Bhattacharya, M. H. Henzinger, and G. F. Italiano, “Design of dynamic algorithms via primal-dual method,” in 42nd International Colloquium on Automata, Languages and Programming, Kyoto, Japan, 2015, vol. 9134, pp. 206–218.","short":"S. Bhattacharya, M.H. Henzinger, G.F. Italiano, in:, 42nd International Colloquium on Automata, Languages and Programming, Springer Nature, 2015, pp. 206–218.","apa":"Bhattacharya, S., Henzinger, M. H., & Italiano, G. F. (2015). Design of dynamic algorithms via primal-dual method. In 42nd International Colloquium on Automata, Languages and Programming (Vol. 9134, pp. 206–218). Kyoto, Japan: Springer Nature. https://doi.org/10.1007/978-3-662-47672-7_17","ama":"Bhattacharya S, Henzinger MH, Italiano GF. Design of dynamic algorithms via primal-dual method. In: 42nd International Colloquium on Automata, Languages and Programming. Vol 9134. Springer Nature; 2015:206-218. doi:10.1007/978-3-662-47672-7_17","mla":"Bhattacharya, Sayan, et al. “Design of Dynamic Algorithms via Primal-Dual Method.” 42nd International Colloquium on Automata, Languages and Programming, vol. 9134, Springer Nature, 2015, pp. 206–18, doi:10.1007/978-3-662-47672-7_17."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publisher":"Springer Nature","oa":1,"page":"206 - 218","date_published":"2015-01-01T00:00:00Z","doi":"10.1007/978-3-662-47672-7_17","date_created":"2022-08-11T09:28:49Z","year":"2015","day":"01","publication":"42nd International Colloquium on Automata, Languages and Programming"},{"type":"journal_article","article_type":"original","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","_id":"11845","file_date_updated":"2022-08-16T06:52:53Z","date_updated":"2023-02-17T09:30:08Z","extern":"1","ddc":["570"],"scopus_import":"1","month":"01","intvolume":" 6","abstract":[{"text":"Phylogenetic diversity (PD) is a measure of biodiversity based on the evolutionary history of species. Here, we discuss several optimization problems related to the use of PD, and the more general measure split diversity (SD), in conservation prioritization.\r\nDepending on the conservation goal and the information available about species, one can construct optimization routines that incorporate various conservation constraints. We demonstrate how this information can be used to select sets of species for conservation action. Specifically, we discuss the use of species' geographic distributions, the choice of candidates under economic pressure, and the use of predator–prey interactions between the species in a community to define viability constraints.\r\nDespite such optimization problems falling into the area of NP hard problems, it is possible to solve them in a reasonable amount of time using integer programming. We apply integer linear programming to a variety of models for conservation prioritization that incorporate the SD measure.\r\nWe exemplarily show the results for two data sets: the Cape region of South Africa and a Caribbean coral reef community. Finally, we provide user-friendly software at http://www.cibiv.at/software/pda.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"volume":6,"issue":"1","license":"https://creativecommons.org/licenses/by/4.0/","publication_identifier":{"eissn":["2041-210X"]},"publication_status":"published","file":[{"file_name":"2015_MethodsInEcologyAndEvolutionChernomor.pdf","date_created":"2022-08-16T06:52:53Z","creator":"asandaue","file_size":411415,"date_updated":"2022-08-16T06:52:53Z","success":1,"checksum":"880e78f09f0ac99cb351c48dc97623b6","file_id":"11846","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"author":[{"first_name":"Olga","last_name":"Chernomor","full_name":"Chernomor, Olga"},{"first_name":"Bui Quang","full_name":"Minh, Bui Quang","last_name":"Minh"},{"last_name":"Forest","full_name":"Forest, Félix","first_name":"Félix"},{"first_name":"Steffen","full_name":"Klaere, Steffen","last_name":"Klaere"},{"last_name":"Ingram","full_name":"Ingram, Travis","first_name":"Travis"},{"orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H"},{"last_name":"von Haeseler","full_name":"von Haeseler, Arndt","first_name":"Arndt"}],"article_processing_charge":"No","external_id":{"pmid":["25893087"]},"title":"Split diversity in constrained conservation prioritization using integer linear programming","citation":{"ista":"Chernomor O, Minh BQ, Forest F, Klaere S, Ingram T, Henzinger MH, von Haeseler A. 2015. Split diversity in constrained conservation prioritization using integer linear programming. Methods in Ecology and Evolution. 6(1), 83–91.","chicago":"Chernomor, Olga, Bui Quang Minh, Félix Forest, Steffen Klaere, Travis Ingram, Monika H Henzinger, and Arndt von Haeseler. “Split Diversity in Constrained Conservation Prioritization Using Integer Linear Programming.” Methods in Ecology and Evolution. Wiley, 2015. https://doi.org/10.1111/2041-210x.12299.","short":"O. Chernomor, B.Q. Minh, F. Forest, S. Klaere, T. Ingram, M.H. Henzinger, A. von Haeseler, Methods in Ecology and Evolution 6 (2015) 83–91.","ieee":"O. Chernomor et al., “Split diversity in constrained conservation prioritization using integer linear programming,” Methods in Ecology and Evolution, vol. 6, no. 1. Wiley, pp. 83–91, 2015.","ama":"Chernomor O, Minh BQ, Forest F, et al. Split diversity in constrained conservation prioritization using integer linear programming. Methods in Ecology and Evolution. 2015;6(1):83-91. doi:10.1111/2041-210x.12299","apa":"Chernomor, O., Minh, B. Q., Forest, F., Klaere, S., Ingram, T., Henzinger, M. H., & von Haeseler, A. (2015). Split diversity in constrained conservation prioritization using integer linear programming. Methods in Ecology and Evolution. Wiley. https://doi.org/10.1111/2041-210x.12299","mla":"Chernomor, Olga, et al. “Split Diversity in Constrained Conservation Prioritization Using Integer Linear Programming.” Methods in Ecology and Evolution, vol. 6, no. 1, Wiley, 2015, pp. 83–91, doi:10.1111/2041-210x.12299."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publisher":"Wiley","oa":1,"page":"83-91","doi":"10.1111/2041-210x.12299","date_published":"2015-01-01T00:00:00Z","date_created":"2022-08-16T06:43:49Z","has_accepted_license":"1","year":"2015","day":"01","publication":"Methods in Ecology and Evolution"},{"status":"public","type":"conference","conference":{"start_date":"2015-06-14","end_date":"2015-06-17","location":"Portland, OR, United States","name":"STOC: Symposium on Theory of Computing"},"article_number":"21-30","_id":"11868","title":"Unifying and strengthening hardness for dynamic problems via the online matrix-vector multiplication conjecture","author":[{"orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","last_name":"Henzinger","first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"first_name":"Sebastian","last_name":"Krinninger","full_name":"Krinninger, Sebastian"},{"first_name":"Danupon","last_name":"Nanongkai","full_name":"Nanongkai, Danupon"},{"last_name":"Saranurak","full_name":"Saranurak, Thatchaphol","first_name":"Thatchaphol"}],"article_processing_charge":"No","external_id":{"arxiv":["1511.06773"]},"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Henzinger, Monika H, Sebastian Krinninger, Danupon Nanongkai, and Thatchaphol Saranurak. “Unifying and Strengthening Hardness for Dynamic Problems via the Online Matrix-Vector Multiplication Conjecture.” In 47th Annual ACM Symposium on Theory of Computing. Association for Computing Machinery, 2015. https://doi.org/10.1145/2746539.2746609.","ista":"Henzinger MH, Krinninger S, Nanongkai D, Saranurak T. 2015. Unifying and strengthening hardness for dynamic problems via the online matrix-vector multiplication conjecture. 47th Annual ACM Symposium on Theory of Computing. STOC: Symposium on Theory of Computing, 21–30.","mla":"Henzinger, Monika H., et al. “Unifying and Strengthening Hardness for Dynamic Problems via the Online Matrix-Vector Multiplication Conjecture.” 47th Annual ACM Symposium on Theory of Computing, 21–30, Association for Computing Machinery, 2015, doi:10.1145/2746539.2746609.","ieee":"M. H. Henzinger, S. Krinninger, D. Nanongkai, and T. Saranurak, “Unifying and strengthening hardness for dynamic problems via the online matrix-vector multiplication conjecture,” in 47th Annual ACM Symposium on Theory of Computing, Portland, OR, United States, 2015.","short":"M.H. Henzinger, S. Krinninger, D. Nanongkai, T. Saranurak, in:, 47th Annual ACM Symposium on Theory of Computing, Association for Computing Machinery, 2015.","apa":"Henzinger, M. H., Krinninger, S., Nanongkai, D., & Saranurak, T. (2015). Unifying and strengthening hardness for dynamic problems via the online matrix-vector multiplication conjecture. In 47th Annual ACM Symposium on Theory of Computing. Portland, OR, United States: Association for Computing Machinery. https://doi.org/10.1145/2746539.2746609","ama":"Henzinger MH, Krinninger S, Nanongkai D, Saranurak T. Unifying and strengthening hardness for dynamic problems via the online matrix-vector multiplication conjecture. In: 47th Annual ACM Symposium on Theory of Computing. Association for Computing Machinery; 2015. doi:10.1145/2746539.2746609"},"date_updated":"2023-02-17T11:09:54Z","month":"06","publisher":"Association for Computing Machinery","scopus_import":"1","quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1511.06773"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Consider the following Online Boolean Matrix-Vector Multiplication problem: We are given an n x n matrix M and will receive n column-vectors of size n, denoted by v1, ..., vn, one by one. After seeing each vector vi, we have to output the product Mvi before we can see the next vector. A naive algorithm can solve this problem using O(n3) time in total, and its running time can be slightly improved to O(n3/log2 n) [Williams SODA'07]. We show that a conjecture that there is no truly subcubic (O(n3-ε)) time algorithm for this problem can be used to exhibit the underlying polynomial time hardness shared by many dynamic problems. For a number of problems, such as subgraph connectivity, Pagh's problem, d-failure connectivity, decremental single-source shortest paths, and decremental transitive closure, this conjecture implies tight hardness results. Thus, proving or disproving this conjecture will be very interesting as it will either imply several tight unconditional lower bounds or break through a common barrier that blocks progress with these problems. This conjecture might also be considered as strong evidence against any further improvement for these problems since refuting it will imply a major breakthrough for combinatorial Boolean matrix multiplication and other long-standing problems if the term \"combinatorial algorithms\" is interpreted as \"Strassen-like algorithms\" [Ballard et al. SPAA'11].\r\n\r\nThe conjecture also leads to hardness results for problems that were previously based on diverse problems and conjectures -- such as 3SUM, combinatorial Boolean matrix multiplication, triangle detection, and multiphase -- thus providing a uniform way to prove polynomial hardness results for dynamic algorithms; some of the new proofs are also simpler or even become trivial. The conjecture also leads to stronger and new, non-trivial, hardness results, e.g., for the fully-dynamic densest subgraph and diameter problems."}],"doi":"10.1145/2746539.2746609","date_published":"2015-06-14T00:00:00Z","date_created":"2022-08-16T09:31:21Z","day":"14","language":[{"iso":"eng"}],"publication":"47th Annual ACM Symposium on Theory of Computing","publication_identifier":{"isbn":["978-145033536-2"],"issn":["0737.8017"]},"publication_status":"published","year":"2015"},{"status":"public","conference":{"end_date":"2015-06-17","location":"Portland, OR, United States","start_date":"2015-06-14","name":"STOC: Symposium on Theory of Computing"},"type":"conference","_id":"11869","title":"Space- and time-efficient algorithm for maintaining dense subgraphs on one-pass dynamic streams","article_processing_charge":"No","external_id":{"arxiv":["1504.02268"]},"author":[{"first_name":"Sayan","last_name":"Bhattacharya","full_name":"Bhattacharya, Sayan"},{"orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H"},{"last_name":"Nanongkai","full_name":"Nanongkai, Danupon","first_name":"Danupon"},{"first_name":"Charalampos","last_name":"Tsourakakis","full_name":"Tsourakakis, Charalampos"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","date_updated":"2023-02-17T11:17:03Z","citation":{"ama":"Bhattacharya S, Henzinger MH, Nanongkai D, Tsourakakis C. Space- and time-efficient algorithm for maintaining dense subgraphs on one-pass dynamic streams. In: 47th Annual ACM Symposium on Theory of Computing. Association for Computing Machinery; 2015:173-182. doi:10.1145/2746539.2746592","apa":"Bhattacharya, S., Henzinger, M. H., Nanongkai, D., & Tsourakakis, C. (2015). Space- and time-efficient algorithm for maintaining dense subgraphs on one-pass dynamic streams. In 47th Annual ACM Symposium on Theory of Computing (pp. 173–182). Portland, OR, United States: Association for Computing Machinery. https://doi.org/10.1145/2746539.2746592","short":"S. Bhattacharya, M.H. Henzinger, D. Nanongkai, C. Tsourakakis, in:, 47th Annual ACM Symposium on Theory of Computing, Association for Computing Machinery, 2015, pp. 173–182.","ieee":"S. Bhattacharya, M. H. Henzinger, D. Nanongkai, and C. Tsourakakis, “Space- and time-efficient algorithm for maintaining dense subgraphs on one-pass dynamic streams,” in 47th Annual ACM Symposium on Theory of Computing, Portland, OR, United States, 2015, pp. 173–182.","mla":"Bhattacharya, Sayan, et al. “Space- and Time-Efficient Algorithm for Maintaining Dense Subgraphs on One-Pass Dynamic Streams.” 47th Annual ACM Symposium on Theory of Computing, Association for Computing Machinery, 2015, pp. 173–82, doi:10.1145/2746539.2746592.","ista":"Bhattacharya S, Henzinger MH, Nanongkai D, Tsourakakis C. 2015. Space- and time-efficient algorithm for maintaining dense subgraphs on one-pass dynamic streams. 47th Annual ACM Symposium on Theory of Computing. STOC: Symposium on Theory of Computing, 173–182.","chicago":"Bhattacharya, Sayan, Monika H Henzinger, Danupon Nanongkai, and Charalampos Tsourakakis. “Space- and Time-Efficient Algorithm for Maintaining Dense Subgraphs on One-Pass Dynamic Streams.” In 47th Annual ACM Symposium on Theory of Computing, 173–82. Association for Computing Machinery, 2015. https://doi.org/10.1145/2746539.2746592."},"month":"06","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1504.02268"}],"quality_controlled":"1","scopus_import":"1","publisher":"Association for Computing Machinery","oa_version":"Preprint","abstract":[{"lang":"eng","text":"While in many graph mining applications it is crucial to handle a stream of updates efficiently in terms of both time and space, not much was known about achieving such type of algorithm. In this paper we study this issue for a problem which lies at the core of many graph mining applications called densest subgraph problem. We develop an algorithm that achieves time- and space-efficiency for this problem simultaneously. It is one of the first of its kind for graph problems to the best of our knowledge.\r\n\r\nGiven an input graph, the densest subgraph is the subgraph that maximizes the ratio between the number of edges and the number of nodes. For any ε>0, our algorithm can, with high probability, maintain a (4+ε)-approximate solution under edge insertions and deletions using ~O(n) space and ~O(1) amortized time per update; here, $n$ is the number of nodes in the graph and ~O hides the O(polylog_{1+ε} n) term. The approximation ratio can be improved to (2+ε) with more time. It can be extended to a (2+ε)-approximation sublinear-time algorithm and a distributed-streaming algorithm. Our algorithm is the first streaming algorithm that can maintain the densest subgraph in one pass. Prior to this, no algorithm could do so even in the special case of an incremental stream and even when there is no time restriction. The previously best algorithm in this setting required O(log n) passes [BahmaniKV12]. The space required by our algorithm is tight up to a polylogarithmic factor."}],"date_created":"2022-08-16T09:36:48Z","date_published":"2015-06-01T00:00:00Z","doi":"10.1145/2746539.2746592","page":"173 - 182","publication":"47th Annual ACM Symposium on Theory of Computing","language":[{"iso":"eng"}],"day":"01","year":"2015","publication_status":"published","publication_identifier":{"isbn":["978-145033536-2"],"issn":["0737-8017"]}},{"citation":{"mla":"Bhattacharya, Sayan, et al. “Welfare Maximization with Friends-of-Friends Network Externalities.” 32nd International Symposium on Theoretical Aspects of Computer Science, vol. 30, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 90–102, doi:10.4230/LIPICS.STACS.2015.90.","apa":"Bhattacharya, S., Dvorák, W., Henzinger, M. H., & Starnberger, Martin. (2015). Welfare maximization with friends-of-friends network externalities. In 32nd International Symposium on Theoretical Aspects of Computer Science (Vol. 30, pp. 90–102). Garching, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.STACS.2015.90","ama":"Bhattacharya S, Dvorák W, Henzinger MH, Starnberger Martin. Welfare maximization with friends-of-friends network externalities. In: 32nd International Symposium on Theoretical Aspects of Computer Science. Vol 30. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2015:90-102. doi:10.4230/LIPICS.STACS.2015.90","short":"S. Bhattacharya, W. Dvorák, M.H. Henzinger, Martin Starnberger, in:, 32nd International Symposium on Theoretical Aspects of Computer Science, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 90–102.","ieee":"S. Bhattacharya, W. Dvorák, M. H. Henzinger, and Martin Starnberger, “Welfare maximization with friends-of-friends network externalities,” in 32nd International Symposium on Theoretical Aspects of Computer Science, Garching, Germany, 2015, vol. 30, pp. 90–102.","chicago":"Bhattacharya, Sayan, Wolfgang Dvorák, Monika H Henzinger, and Martin Starnberger. “Welfare Maximization with Friends-of-Friends Network Externalities.” In 32nd International Symposium on Theoretical Aspects of Computer Science, 30:90–102. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015. https://doi.org/10.4230/LIPICS.STACS.2015.90.","ista":"Bhattacharya S, Dvorák W, Henzinger MH, Starnberger Martin. 2015. Welfare maximization with friends-of-friends network externalities. 32nd International Symposium on Theoretical Aspects of Computer Science. STACS: Symposium on Theoretical Aspects of Computer Science, LIPIcs, vol. 30, 90–102."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Bhattacharya, Sayan","last_name":"Bhattacharya","first_name":"Sayan"},{"first_name":"Wolfgang","last_name":"Dvorák","full_name":"Dvorák, Wolfgang"},{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H","last_name":"Henzinger","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530"},{"full_name":"Starnberger, Martin","last_name":"Starnberger","first_name":" Martin"}],"article_processing_charge":"No","title":"Welfare maximization with friends-of-friends network externalities","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","oa":1,"year":"2015","day":"26","publication":"32nd International Symposium on Theoretical Aspects of Computer Science","page":"90-102","doi":"10.4230/LIPICS.STACS.2015.90","date_published":"2015-02-26T00:00:00Z","date_created":"2022-08-12T11:39:40Z","_id":"11837","type":"conference","conference":{"end_date":"2015-03-07","location":"Garching, Germany","start_date":"2015-03-04","name":"STACS: Symposium on Theoretical Aspects of Computer Science"},"status":"public","date_updated":"2023-02-21T16:32:37Z","extern":"1","abstract":[{"lang":"eng","text":"Online social networks allow the collection of large amounts of data about the influence between users connected by a friendship-like relationship. When distributing items among agents forming a social network, this information allows us to exploit network externalities that each agent receives from his neighbors that get the same item. In this paper we consider Friends-of-Friends (2-hop) network externalities, i.e., externalities that not only depend on the neighbors that get the same item but also on neighbors of neighbors. For these externalities we study a setting where multiple different items are assigned to unit-demand agents. Specifically, we study the problem of welfare maximization under different types of externality functions. Let n be the number of agents and m be the number of items. Our contributions are the following: (1) We show that welfare maximization is APX-hard; we show that even for step functions with 2-hop (and also with 1-hop) externalities it is NP-hard to approximate social welfare better than (1-1/e). (2) On the positive side we present (i) an O(sqrt n)-approximation algorithm for general concave externality functions,\r\n(ii) an O(\\log m)-approximation algorithm for linear externality functions, and (iii) an (1-1/e)\\frac{1}{6}-approximation algorithm for 2-hop step function externalities. We also improve the result from [6] for 1-hop step function externalities by giving a (1-1/e)/2-approximation algorithm."}],"oa_version":"Published Version","scopus_import":"1","alternative_title":["LIPIcs"],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.4230/LIPICS.STACS.2015.90"}],"month":"02","intvolume":" 30","publication_identifier":{"isbn":["978-3-939897-78-1"],"issn":["1868-8969"]},"publication_status":"published","language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"later_version","id":"11903","status":"public"}]},"volume":30},{"year":"2015","publication":"Theoretical Computer Science","day":"30","page":"1-15","date_created":"2022-08-17T09:06:53Z","doi":"10.1016/j.tcs.2015.01.033","date_published":"2015-03-30T00:00:00Z","oa":1,"publisher":"Elsevier","quality_controlled":"1","citation":{"apa":"Henzinger, M. H., & Loitzenbauer, V. (2015). Truthful unit-demand auctions with budgets revisited. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2015.01.033","ama":"Henzinger MH, Loitzenbauer V. Truthful unit-demand auctions with budgets revisited. Theoretical Computer Science. 2015;573:1-15. doi:10.1016/j.tcs.2015.01.033","short":"M.H. Henzinger, V. Loitzenbauer, Theoretical Computer Science 573 (2015) 1–15.","ieee":"M. H. Henzinger and V. Loitzenbauer, “Truthful unit-demand auctions with budgets revisited,” Theoretical Computer Science, vol. 573. Elsevier, pp. 1–15, 2015.","mla":"Henzinger, Monika H., and Veronika Loitzenbauer. “Truthful Unit-Demand Auctions with Budgets Revisited.” Theoretical Computer Science, vol. 573, Elsevier, 2015, pp. 1–15, doi:10.1016/j.tcs.2015.01.033.","ista":"Henzinger MH, Loitzenbauer V. 2015. Truthful unit-demand auctions with budgets revisited. Theoretical Computer Science. 573, 1–15.","chicago":"Henzinger, Monika H, and Veronika Loitzenbauer. “Truthful Unit-Demand Auctions with Budgets Revisited.” Theoretical Computer Science. Elsevier, 2015. https://doi.org/10.1016/j.tcs.2015.01.033."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","last_name":"Henzinger"},{"first_name":"Veronika","last_name":"Loitzenbauer","full_name":"Loitzenbauer, Veronika"}],"title":"Truthful unit-demand auctions with budgets revisited","publication_status":"published","publication_identifier":{"issn":["0304-3975"]},"language":[{"iso":"eng"}],"volume":573,"abstract":[{"lang":"eng","text":"We consider auctions of indivisible items to unit-demand bidders with budgets. This setting was suggested as an expressive model for single sponsored search auctions. Prior work presented mechanisms that compute bidder-optimal outcomes and are truthful for a restricted set of inputs, i.e., inputs in so-called general position. This condition is easily violated. We provide the first mechanism that is truthful in expectation for all inputs and achieves for each bidder no worse utility than the bidder-optimal outcome. Additionally we give a complete characterization for which inputs mechanisms that compute bidder-optimal outcomes are truthful."}],"oa_version":"None","main_file_link":[{"url":"https://doi.org/10.1016/j.tcs.2015.01.033","open_access":"1"}],"scopus_import":"1","intvolume":" 573","month":"03","date_updated":"2023-02-17T14:50:04Z","extern":"1","_id":"11901","type":"journal_article","article_type":"original","status":"public"},{"day":"09","publication":"Chemistry - A European Journal","year":"2015","date_published":"2015-03-09T00:00:00Z","doi":"10.1002/chem.201406439","date_created":"2022-08-24T11:11:10Z","page":"4368-4376","quality_controlled":"1","publisher":"Wiley","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Pieber, Bartholomäus, Toma Glasnov, and C. Oliver Kappe. “Continuous Flow Reduction of Artemisinic Acid Utilizing Multi-Injection Strategies-Closing the Gap towards a Fully Continuous Synthesis of Antimalarial Drugs.” Chemistry - A European Journal. Wiley, 2015. https://doi.org/10.1002/chem.201406439.","ista":"Pieber B, Glasnov T, Kappe CO. 2015. Continuous flow reduction of artemisinic acid utilizing multi-injection strategies-closing the gap towards a fully continuous synthesis of antimalarial drugs. Chemistry - A European Journal. 21(11), 4368–4376.","mla":"Pieber, Bartholomäus, et al. “Continuous Flow Reduction of Artemisinic Acid Utilizing Multi-Injection Strategies-Closing the Gap towards a Fully Continuous Synthesis of Antimalarial Drugs.” Chemistry - A European Journal, vol. 21, no. 11, Wiley, 2015, pp. 4368–76, doi:10.1002/chem.201406439.","ieee":"B. Pieber, T. Glasnov, and C. O. Kappe, “Continuous flow reduction of artemisinic acid utilizing multi-injection strategies-closing the gap towards a fully continuous synthesis of antimalarial drugs,” Chemistry - A European Journal, vol. 21, no. 11. Wiley, pp. 4368–4376, 2015.","short":"B. Pieber, T. Glasnov, C.O. Kappe, Chemistry - A European Journal 21 (2015) 4368–4376.","apa":"Pieber, B., Glasnov, T., & Kappe, C. O. (2015). Continuous flow reduction of artemisinic acid utilizing multi-injection strategies-closing the gap towards a fully continuous synthesis of antimalarial drugs. Chemistry - A European Journal. Wiley. https://doi.org/10.1002/chem.201406439","ama":"Pieber B, Glasnov T, Kappe CO. Continuous flow reduction of artemisinic acid utilizing multi-injection strategies-closing the gap towards a fully continuous synthesis of antimalarial drugs. Chemistry - A European Journal. 2015;21(11):4368-4376. doi:10.1002/chem.201406439"},"title":"Continuous flow reduction of artemisinic acid utilizing multi-injection strategies-closing the gap towards a fully continuous synthesis of antimalarial drugs","author":[{"first_name":"Bartholomäus","id":"93e5e5b2-0da6-11ed-8a41-af589a024726","last_name":"Pieber","orcid":"0000-0001-8689-388X","full_name":"Pieber, Bartholomäus"},{"full_name":"Glasnov, Toma","last_name":"Glasnov","first_name":"Toma"},{"last_name":"Kappe","full_name":"Kappe, C. Oliver","first_name":"C. Oliver"}],"article_processing_charge":"No","external_id":{"pmid":["25655090"]},"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1521-3765"],"issn":["0947-6539"]},"publication_status":"published","issue":"11","volume":21,"oa_version":"None","pmid":1,"abstract":[{"text":"One of the rare alternative reagents for the reduction of carbon–carbon double bonds is diimide (HNNH), which can be generated in situ from hydrazine hydrate (N2H4⋅H2O) and O2. Although this selective method is extremely clean and powerful, it is rarely used, as the rate-determining oxidation of hydrazine in the absence of a catalyst is relatively slow using conventional batch protocols. A continuous high-temperature/high-pressure methodology dramatically enhances the initial oxidation step, at the same time allowing for a safe and scalable processing of the hazardous reaction mixture. Simple alkenes can be selectively reduced within 10–20 min at 100–120 °C and 20 bar O2 pressure. The development of a multi-injection reactor platform for the periodic addition of N2H4⋅H2O enables the reduction of less reactive olefins even at lower reaction temperatures. This concept was utilized for the highly selective reduction of artemisinic acid to dihydroartemisinic acid, the precursor molecule for the semisynthesis of the antimalarial drug artemisinin. The industrially relevant reduction was achieved by using four consecutive liquid feeds (of N2H4⋅H2O) and residence time units resulting in a highly selective reduction within approximately 40 min at 60 °C and 20 bar O2 pressure, providing dihydroartemisinic acid in ≥93 % yield and ≥95 % selectivity.","lang":"eng"}],"month":"03","intvolume":" 21","scopus_import":"1","extern":"1","date_updated":"2023-02-21T10:09:30Z","_id":"11962","status":"public","article_type":"original","type":"journal_article"},{"publication_identifier":{"eissn":["1520-6904"],"issn":["0022-3263"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"9","volume":80,"abstract":[{"text":"The development of a continuous flow multistep strategy for the synthesis of linear peptoids and their subsequent macrocyclization via Click chemistry is described. The central transformation of this process is an Ugi four-component reaction generating the peptidomimetic core structure. In order to avoid exposure to the often toxic and malodorous isocyanide building blocks, the continuous approach was telescoped by the dehydration of the corresponding formamide. In a concurrent operation, the highly energetic azide moiety required for the subsequent intramolecular copper-catalyzed azide–alkyne cycloaddition (Click reaction) was installed by nucleophilic substitution from a bromide precursor. All steps yielding to the linear core structures can be conveniently coupled without the need for purification steps resulting in a single process generating the desired peptidomimetics in good to excellent yields within a 25 min reaction time. The following macrocyclization was realized in a coil reactor made of copper without any additional additive. A careful process intensification study demonstrated that this transformation occurs quantitatively within 25 min at 140 °C. Depending on the resulting ring strain, either a dimeric or a monomeric form of the cyclic product was obtained.","lang":"eng"}],"pmid":1,"oa_version":"None","scopus_import":"1","month":"05","intvolume":" 80","date_updated":"2023-02-21T10:10:04Z","extern":"1","_id":"11977","article_type":"original","type":"journal_article","status":"public","year":"2015","day":"01","publication":"The Journal of Organic Chemistry","page":"4590-4602","doi":"10.1021/acs.joc.5b00445","date_published":"2015-05-01T00:00:00Z","date_created":"2022-08-25T10:52:24Z","quality_controlled":"1","publisher":"American Chemical Society","citation":{"mla":"Salvador, Carlos Eduardo M., et al. “A Sequential Ugi Multicomponent/Cu-Catalyzed Azide–Alkyne Cycloaddition Approach for the Continuous Flow Generation of Cyclic Peptoids.” The Journal of Organic Chemistry, vol. 80, no. 9, American Chemical Society, 2015, pp. 4590–602, doi:10.1021/acs.joc.5b00445.","ama":"Salvador CEM, Pieber B, Neu PM, Torvisco A, Kleber Z. Andrade C, Kappe CO. A sequential Ugi multicomponent/Cu-catalyzed azide–alkyne cycloaddition approach for the continuous flow generation of cyclic peptoids. The Journal of Organic Chemistry. 2015;80(9):4590-4602. doi:10.1021/acs.joc.5b00445","apa":"Salvador, C. E. M., Pieber, B., Neu, P. M., Torvisco, A., Kleber Z. Andrade, C., & Kappe, C. O. (2015). A sequential Ugi multicomponent/Cu-catalyzed azide–alkyne cycloaddition approach for the continuous flow generation of cyclic peptoids. The Journal of Organic Chemistry. American Chemical Society. https://doi.org/10.1021/acs.joc.5b00445","short":"C.E.M. Salvador, B. Pieber, P.M. Neu, A. Torvisco, C. Kleber Z. Andrade, C.O. Kappe, The Journal of Organic Chemistry 80 (2015) 4590–4602.","ieee":"C. E. M. Salvador, B. Pieber, P. M. Neu, A. Torvisco, C. Kleber Z. Andrade, and C. O. Kappe, “A sequential Ugi multicomponent/Cu-catalyzed azide–alkyne cycloaddition approach for the continuous flow generation of cyclic peptoids,” The Journal of Organic Chemistry, vol. 80, no. 9. American Chemical Society, pp. 4590–4602, 2015.","chicago":"Salvador, Carlos Eduardo M., Bartholomäus Pieber, Philipp M. Neu, Ana Torvisco, Carlos Kleber Z. Andrade, and C. Oliver Kappe. “A Sequential Ugi Multicomponent/Cu-Catalyzed Azide–Alkyne Cycloaddition Approach for the Continuous Flow Generation of Cyclic Peptoids.” The Journal of Organic Chemistry. American Chemical Society, 2015. https://doi.org/10.1021/acs.joc.5b00445.","ista":"Salvador CEM, Pieber B, Neu PM, Torvisco A, Kleber Z. Andrade C, Kappe CO. 2015. A sequential Ugi multicomponent/Cu-catalyzed azide–alkyne cycloaddition approach for the continuous flow generation of cyclic peptoids. The Journal of Organic Chemistry. 80(9), 4590–4602."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Salvador","full_name":"Salvador, Carlos Eduardo M.","first_name":"Carlos Eduardo M."},{"last_name":"Pieber","full_name":"Pieber, Bartholomäus","orcid":"0000-0001-8689-388X","id":"93e5e5b2-0da6-11ed-8a41-af589a024726","first_name":"Bartholomäus"},{"first_name":"Philipp M.","last_name":"Neu","full_name":"Neu, Philipp M."},{"first_name":"Ana","last_name":"Torvisco","full_name":"Torvisco, Ana"},{"full_name":"Kleber Z. Andrade, Carlos","last_name":"Kleber Z. Andrade","first_name":"Carlos"},{"last_name":"Kappe","full_name":"Kappe, C. Oliver","first_name":"C. Oliver"}],"external_id":{"pmid":["25842982"]},"article_processing_charge":"No","title":"A sequential Ugi multicomponent/Cu-catalyzed azide–alkyne cycloaddition approach for the continuous flow generation of cyclic peptoids"},{"editor":[{"first_name":"Timothy","last_name":"Noël","full_name":"Noël, Timothy"}],"title":"Aerobic oxidations in continuous flow","article_processing_charge":"No","author":[{"last_name":"Pieber","full_name":"Pieber, Bartholomäus","orcid":"0000-0001-8689-388X","first_name":"Bartholomäus","id":"93e5e5b2-0da6-11ed-8a41-af589a024726"},{"full_name":"Kappe, C. Oliver","last_name":"Kappe","first_name":"C. Oliver"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"B. Pieber and C. O. Kappe, “Aerobic oxidations in continuous flow,” in Organometallic Flow Chemistry, 1st ed., vol. 57, T. Noël, Ed. Cham: Springer Nature, 2015, pp. 97–136.","short":"B. Pieber, C.O. Kappe, in:, T. Noël (Ed.), Organometallic Flow Chemistry, 1st ed., Springer Nature, Cham, 2015, pp. 97–136.","apa":"Pieber, B., & Kappe, C. O. (2015). Aerobic oxidations in continuous flow. In T. Noël (Ed.), Organometallic Flow Chemistry (1st ed., Vol. 57, pp. 97–136). Cham: Springer Nature. https://doi.org/10.1007/3418_2015_133","ama":"Pieber B, Kappe CO. Aerobic oxidations in continuous flow. In: Noël T, ed. Organometallic Flow Chemistry. Vol 57. 1st ed. TOPORGAN. Cham: Springer Nature; 2015:97–136. doi:10.1007/3418_2015_133","mla":"Pieber, Bartholomäus, and C. Oliver Kappe. “Aerobic Oxidations in Continuous Flow.” Organometallic Flow Chemistry, edited by Timothy Noël, 1st ed., vol. 57, Springer Nature, 2015, pp. 97–136, doi:10.1007/3418_2015_133.","ista":"Pieber B, Kappe CO. 2015.Aerobic oxidations in continuous flow. In: Organometallic Flow Chemistry. Topics in Organometallic Chemistry, vol. 57, 97–136.","chicago":"Pieber, Bartholomäus, and C. Oliver Kappe. “Aerobic Oxidations in Continuous Flow.” In Organometallic Flow Chemistry, edited by Timothy Noël, 1st ed., 57:97–136. TOPORGAN. Cham: Springer Nature, 2015. https://doi.org/10.1007/3418_2015_133."},"date_created":"2022-08-25T11:58:38Z","date_published":"2015-06-10T00:00:00Z","doi":"10.1007/3418_2015_133","page":"97–136","publication":"Organometallic Flow Chemistry","day":"10","year":"2015","edition":"1","quality_controlled":"1","publisher":"Springer Nature","extern":"1","date_updated":"2023-02-21T10:10:35Z","status":"public","type":"book_chapter","_id":"11989","series_title":"TOPORGAN","volume":57,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eisbn":["9783319332437"],"issn":["1436-6002"],"eissn":["1616-8534"],"isbn":["9783319332413"]},"intvolume":" 57","month":"06","place":"Cham","scopus_import":"1","alternative_title":["Topics in Organometallic Chemistry"],"oa_version":"None","abstract":[{"text":"In recent years, the high demand for sustainable processes resulted in the development of highly attractive oxidation protocols utilizing molecular oxygen or even air instead of more uneconomic and often toxic reagents. The application of these sustainable, gaseous oxidants in conventional batch reactors is often associated with severe safety risks and process challenges especially on larger scales. Continuous flow technology offers the possibility to minimize these safety hazards and concurrently allows working in high-temperature/high-pressure regimes to access highly efficient oxidation protocols. This review article critically discusses recent literature examples of flow methodologies for selective aerobic oxidations of organic compounds. Several technologies and reactor designs for biphasic gas/liquid as well as supercritical reaction media are presented in detail. © Springer International Publishing Switzerland 2015.","lang":"eng"}]},{"publist_id":"7934","author":[{"last_name":"Lee","full_name":"Lee, Victor","first_name":"Victor"},{"orcid":"0000-0002-2299-3176","full_name":"Waitukaitis, Scott R","last_name":"Waitukaitis","first_name":"Scott R","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Miskin","full_name":"Miskin, Marc","first_name":"Marc"},{"last_name":"Jaeger","full_name":"Jaeger, Heinrich","first_name":"Heinrich"}],"title":"Direct observation of particle interactions and clustering in charged granular streams","citation":{"short":"V. Lee, S.R. Waitukaitis, M. Miskin, H. Jaeger, Nature Physics 11 (2015) 733–737.","ieee":"V. Lee, S. R. Waitukaitis, M. Miskin, and H. Jaeger, “Direct observation of particle interactions and clustering in charged granular streams,” Nature Physics, vol. 11, no. 9. Nature Publishing Group, pp. 733–737, 2015.","apa":"Lee, V., Waitukaitis, S. R., Miskin, M., & Jaeger, H. (2015). Direct observation of particle interactions and clustering in charged granular streams. Nature Physics. Nature Publishing Group. https://doi.org/10.1038/nphys3396","ama":"Lee V, Waitukaitis SR, Miskin M, Jaeger H. Direct observation of particle interactions and clustering in charged granular streams. Nature Physics. 2015;11(9):733-737. doi:10.1038/nphys3396","mla":"Lee, Victor, et al. “Direct Observation of Particle Interactions and Clustering in Charged Granular Streams.” Nature Physics, vol. 11, no. 9, Nature Publishing Group, 2015, pp. 733–37, doi:10.1038/nphys3396.","ista":"Lee V, Waitukaitis SR, Miskin M, Jaeger H. 2015. Direct observation of particle interactions and clustering in charged granular streams. Nature Physics. 11(9), 733–737.","chicago":"Lee, Victor, Scott R Waitukaitis, Marc Miskin, and Heinrich Jaeger. “Direct Observation of Particle Interactions and Clustering in Charged Granular Streams.” Nature Physics. Nature Publishing Group, 2015. https://doi.org/10.1038/nphys3396."},"date_updated":"2021-01-12T06:49:02Z","extern":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","type":"journal_article","status":"public","_id":"120","page":"733 - 737","date_published":"2015-07-13T00:00:00Z","volume":11,"doi":"10.1038/nphys3396","issue":"9","date_created":"2018-12-11T11:44:44Z","year":"2015","publication_status":"published","day":"13","publication":"Nature Physics","language":[{"iso":"eng"}],"quality_controlled":"1","publisher":"Nature Publishing Group","month":"07","intvolume":" 11","abstract":[{"lang":"eng","text":"Clustering of fine particles is of crucial importance in settings ranging from the early stages of planet formation to the coagulation of industrial powders and airborne pollutants. Models of such clustering typically focus on inelastic deformation and cohesion. However, even in charge-neutral particle systems comprising grains of the same dielectric material, tribocharging can generate large amounts of net positive or negative charge on individual particles, resulting in long-range electrostatic forces. The effects of such forces on cluster formation are not well understood and have so far not been studied in situ. Here we report the first observations of individual collide-and-capture events between charged submillimetre particles, including Kepler-like orbits. Charged particles can become trapped in their mutual electrostatic energy well and aggregate via multiple bounces. This enables the initiation of clustering at relative velocities much larger than the upper limit for sticking after a head-on collision, a long-standing issue known from pre-planetary dust aggregation. Moreover, Coulomb interactions together with dielectric polarization are found to stabilize characteristic molecule-like configurations, providing new insights for the modelling of clustering dynamics in a wide range of microscopic dielectric systems, such as charged polarizable ions, biomolecules and colloids."}],"oa_version":"None","acknowledgement":"This research was supported by NSF through DMR-1309611. The Chicago MRSEC, supported by NSF DMR-1420709, is gratefully acknowledged for access to its shared experimental facilities."},{"_id":"121","status":"public","type":"journal_article","extern":"1","date_updated":"2021-01-12T06:49:07Z","oa_version":"Preprint","abstract":[{"text":"We show that the simplest building blocks of origami-based materials - rigid, degree-four vertices - are generically multistable. The existence of two distinct branches of folding motion emerging from the flat state suggests at least bistability, but we show how nonlinearities in the folding motions allow generic vertex geometries to have as many as five stable states. In special geometries with collinear folds and symmetry, more branches emerge leading to as many as six stable states. Tuning the fold energy parameters, we show how monostability is also possible. Finally, we show how to program the stability features of a single vertex into a periodic fold tessellation. The resulting metasheets provide a previously unanticipated functionality - tunable and switchable shape and size via multistability.","lang":"eng"}],"month":"02","intvolume":" 114","main_file_link":[{"url":"https://arxiv.org/abs/1408.1607","open_access":"1"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":114,"issue":"5","article_number":"055503","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Waitukaitis, Scott R, Rémi Menaut, Bryan Chen, and Martin Van Hecke. “Origami Multistability: From Single Vertices to Metasheets.” APS Physics, Physical Review Letters. American Physical Society, 2015. https://doi.org/10.1103/PhysRevLett.114.055503.","ista":"Waitukaitis SR, Menaut R, Chen B, Van Hecke M. 2015. Origami multistability: From single vertices to metasheets. APS Physics, Physical Review Letters. 114(5), 055503.","mla":"Waitukaitis, Scott R., et al. “Origami Multistability: From Single Vertices to Metasheets.” APS Physics, Physical Review Letters, vol. 114, no. 5, 055503, American Physical Society, 2015, doi:10.1103/PhysRevLett.114.055503.","short":"S.R. Waitukaitis, R. Menaut, B. Chen, M. Van Hecke, APS Physics, Physical Review Letters 114 (2015).","ieee":"S. R. Waitukaitis, R. Menaut, B. Chen, and M. Van Hecke, “Origami multistability: From single vertices to metasheets,” APS Physics, Physical Review Letters, vol. 114, no. 5. American Physical Society, 2015.","ama":"Waitukaitis SR, Menaut R, Chen B, Van Hecke M. Origami multistability: From single vertices to metasheets. APS Physics, Physical Review Letters. 2015;114(5). doi:10.1103/PhysRevLett.114.055503","apa":"Waitukaitis, S. R., Menaut, R., Chen, B., & Van Hecke, M. (2015). Origami multistability: From single vertices to metasheets. APS Physics, Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.114.055503"},"title":"Origami multistability: From single vertices to metasheets","author":[{"first_name":"Scott R","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","last_name":"Waitukaitis","full_name":"Waitukaitis, Scott R","orcid":"0000-0002-2299-3176"},{"full_name":"Menaut, Rémi","last_name":"Menaut","first_name":"Rémi"},{"first_name":"Bryan","full_name":"Chen, Bryan","last_name":"Chen"},{"first_name":"Martin","full_name":"Van Hecke, Martin","last_name":"Van Hecke"}],"publist_id":"7933","external_id":{"arxiv":["1408.1607"]},"acknowledgement":"B. G. C. acknowledges support from FOM, and S. W. and M. v. H. acknowledge support from NWO.","publisher":"American Physical Society","quality_controlled":"1","oa":1,"day":"04","publication":"APS Physics, Physical Review Letters","year":"2015","doi":"10.1103/PhysRevLett.114.055503","date_published":"2015-02-04T00:00:00Z","date_created":"2018-12-11T11:44:44Z"},{"extern":1,"citation":{"apa":"Fischer, J. L., & Grün, G. (2015). Finite speed of propagation and waiting times for the stochastic porous medium equation: A unifying approach. SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics . https://doi.org/10.1137/140960578","ama":"Fischer JL, Grün G. Finite speed of propagation and waiting times for the stochastic porous medium equation: A unifying approach. SIAM Journal on Mathematical Analysis. 2015;47(1):825-854. doi:10.1137/140960578","ieee":"J. L. Fischer and G. Grün, “Finite speed of propagation and waiting times for the stochastic porous medium equation: A unifying approach,” SIAM Journal on Mathematical Analysis, vol. 47, no. 1. Society for Industrial and Applied Mathematics , pp. 825–854, 2015.","short":"J.L. Fischer, G. Grün, SIAM Journal on Mathematical Analysis 47 (2015) 825–854.","mla":"Fischer, Julian L., and Günther Grün. “Finite Speed of Propagation and Waiting Times for the Stochastic Porous Medium Equation: A Unifying Approach.” SIAM Journal on Mathematical Analysis, vol. 47, no. 1, Society for Industrial and Applied Mathematics , 2015, pp. 825–54, doi:10.1137/140960578.","ista":"Fischer JL, Grün G. 2015. Finite speed of propagation and waiting times for the stochastic porous medium equation: A unifying approach. SIAM Journal on Mathematical Analysis. 47(1), 825–854.","chicago":"Fischer, Julian L, and Günther Grün. “Finite Speed of Propagation and Waiting Times for the Stochastic Porous Medium Equation: A Unifying Approach.” SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics , 2015. https://doi.org/10.1137/140960578."},"date_updated":"2021-01-12T06:49:48Z","title":"Finite speed of propagation and waiting times for the stochastic porous medium equation: A unifying approach","publist_id":"5958","author":[{"full_name":"Julian Fischer","orcid":"0000-0002-0479-558X","last_name":"Fischer","first_name":"Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Grün, Günther","last_name":"Grün","first_name":"Günther"}],"_id":"1311","status":"public","type":"journal_article","publication":"SIAM Journal on Mathematical Analysis","day":"01","year":"2015","publication_status":"published","date_created":"2018-12-11T11:51:18Z","volume":47,"doi":"10.1137/140960578","issue":"1","date_published":"2015-01-01T00:00:00Z","page":"825 - 854","acknowledgement":"The first author has been supported by the Lithuanian-Swiss co- operation program under the project agreement No. CH-SMM-01/0.","abstract":[{"lang":"eng","text":"In this paper, we develop an energy method to study finite speed of propagation and waiting time phenomena for the stochastic porous media equation with linear multiplicative noise in up to three spatial dimensions. Based on a novel iteration technique and on stochastic counterparts of weighted integral estimates used in the deterministic setting, we formulate a sufficient criterion on the growth of initial data which locally guarantees a waiting time phenomenon to occur almost surely. Up to a logarithmic factor, this criterion coincides with the optimal criterion known from the deterministic setting. Our technique can be modified to prove finite speed of propagation as well."}],"intvolume":" 47","month":"01","quality_controlled":0,"publisher":"Society for Industrial and Applied Mathematics "},{"date_created":"2018-12-11T11:51:19Z","date_published":"2015-01-01T00:00:00Z","doi":"10.1137/140966654","volume":53,"issue":"5","page":"2178 - 2205","publication":"SIAM Journal on Numerical Analysis","language":[{"iso":"eng"}],"day":"01","year":"2015","publication_status":"published","intvolume":" 53","month":"01","quality_controlled":"1","publisher":"Society for Industrial and Applied Mathematics ","acknowledgement":"The research of the author was supported by the Lithuanian-Swiss cooperation program under the project agreement CH-SMM-01/0.","oa_version":"None","abstract":[{"text":"We derive a posteriori estimates for the modeling error caused by the assumption of perfect incompressibility in the incompressible Navier-Stokes equation: Real fluids are never perfectly incompressible but always feature at least some low amount of compressibility. Thus, their behavior is described by the compressible Navier-Stokes equation, the pressure being a steep function of the density. We rigorously estimate the difference between an approximate solution to the incompressible Navier-Stokes equation and any weak solution to the compressible Navier-Stokes equation in the sense of Lions (without assuming any additional regularity of solutions). Heuristics and numerical results suggest that our error estimates are of optimal order in the case of "well-behaved" flows and divergence-free approximations of the velocity field. Thus, we expect our estimates to justify the idealization of fluids as perfectly incompressible also in practical situations.","lang":"eng"}],"title":"A posteriori modeling error estimates for the assumption of perfect incompressibility in the Navier-Stokes equation","author":[{"id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","first_name":"Julian L","orcid":"0000-0002-0479-558X","full_name":"Fischer, Julian L","last_name":"Fischer"}],"publist_id":"5957","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","date_updated":"2021-01-12T06:49:49Z","citation":{"chicago":"Fischer, Julian L. “A Posteriori Modeling Error Estimates for the Assumption of Perfect Incompressibility in the Navier-Stokes Equation.” SIAM Journal on Numerical Analysis. Society for Industrial and Applied Mathematics , 2015. https://doi.org/10.1137/140966654.","ista":"Fischer JL. 2015. A posteriori modeling error estimates for the assumption of perfect incompressibility in the Navier-Stokes equation. SIAM Journal on Numerical Analysis. 53(5), 2178–2205.","mla":"Fischer, Julian L. “A Posteriori Modeling Error Estimates for the Assumption of Perfect Incompressibility in the Navier-Stokes Equation.” SIAM Journal on Numerical Analysis, vol. 53, no. 5, Society for Industrial and Applied Mathematics , 2015, pp. 2178–205, doi:10.1137/140966654.","apa":"Fischer, J. L. (2015). A posteriori modeling error estimates for the assumption of perfect incompressibility in the Navier-Stokes equation. SIAM Journal on Numerical Analysis. Society for Industrial and Applied Mathematics . https://doi.org/10.1137/140966654","ama":"Fischer JL. A posteriori modeling error estimates for the assumption of perfect incompressibility in the Navier-Stokes equation. SIAM Journal on Numerical Analysis. 2015;53(5):2178-2205. doi:10.1137/140966654","ieee":"J. L. Fischer, “A posteriori modeling error estimates for the assumption of perfect incompressibility in the Navier-Stokes equation,” SIAM Journal on Numerical Analysis, vol. 53, no. 5. Society for Industrial and Applied Mathematics , pp. 2178–2205, 2015.","short":"J.L. Fischer, SIAM Journal on Numerical Analysis 53 (2015) 2178–2205."},"status":"public","type":"journal_article","_id":"1314"},{"title":"Estimates on front propagation for nonlinear higher-order parabolic equations: An algorithmic approach","author":[{"id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","first_name":"Julian L","orcid":"0000-0002-0479-558X","full_name":"Julian Fischer","last_name":"Fischer"}],"publist_id":"5956","extern":1,"citation":{"chicago":"Fischer, Julian L. “Estimates on Front Propagation for Nonlinear Higher-Order Parabolic Equations: An Algorithmic Approach.” Interfaces and Free Boundaries. European Mathematical Society Publishing House, 2015. https://doi.org/10.4171/IFB/331.","ista":"Fischer JL. 2015. Estimates on front propagation for nonlinear higher-order parabolic equations: An algorithmic approach. Interfaces and Free Boundaries. 17(1), 1–20.","mla":"Fischer, Julian L. “Estimates on Front Propagation for Nonlinear Higher-Order Parabolic Equations: An Algorithmic Approach.” Interfaces and Free Boundaries, vol. 17, no. 1, European Mathematical Society Publishing House, 2015, pp. 1–20, doi:10.4171/IFB/331.","ieee":"J. L. Fischer, “Estimates on front propagation for nonlinear higher-order parabolic equations: An algorithmic approach,” Interfaces and Free Boundaries, vol. 17, no. 1. European Mathematical Society Publishing House, pp. 1–20, 2015.","short":"J.L. Fischer, Interfaces and Free Boundaries 17 (2015) 1–20.","apa":"Fischer, J. L. (2015). Estimates on front propagation for nonlinear higher-order parabolic equations: An algorithmic approach. Interfaces and Free Boundaries. European Mathematical Society Publishing House. https://doi.org/10.4171/IFB/331","ama":"Fischer JL. Estimates on front propagation for nonlinear higher-order parabolic equations: An algorithmic approach. Interfaces and Free Boundaries. 2015;17(1):1-20. doi:10.4171/IFB/331"},"date_updated":"2021-01-12T06:49:48Z","status":"public","type":"journal_article","_id":"1313","date_created":"2018-12-11T11:51:19Z","doi":"10.4171/IFB/331","issue":"1","volume":17,"date_published":"2015-01-01T00:00:00Z","page":"1 - 20","publication":"Interfaces and Free Boundaries","day":"01","publication_status":"published","year":"2015","intvolume":" 17","month":"01","publisher":"European Mathematical Society Publishing House","quality_controlled":0,"acknowledgement":"This research was supported by the Lithuanian-Swiss cooperation program under the project agreement No. CH-SMM-01/0.","abstract":[{"text":"We present an algorithm for the derivation of lower bounds on support propagation for a certain class of nonlinear parabolic equations. We proceed by combining the ideas in some recent papers by the author with the algorithmic construction of entropies due to Jüngel and Matthes, reducing the problem to a quantifier elimination problem. Due to its complexity, the quantifier elimination problem cannot be solved by present exact algorithms. However, by tackling the quantifier elimination problem numerically, in the case of the thin-film equation we are able to improve recent results by the author in the regime of strong slippage n ∈ (1, 2). For certain second-order doubly nonlinear parabolic equations, we are able to extend the known lower bounds on free boundary propagation to the case of irregular oscillatory initial data. Finally, we apply our method to a sixth-order quantum drift-diffusion equation, resulting in an upper bound on the time which it takes for the support to reach every point in the domain.","lang":"eng"}]},{"publication":"Archive for Rational Mechanics and Analysis","day":"01","publication_status":"published","year":"2015","date_created":"2018-12-11T11:51:20Z","volume":218,"issue":"1","date_published":"2015-10-01T00:00:00Z","doi":"10.1007/s00205-015-0866-x","page":"553 - 587","acknowledgement":"This research was supported by the Lithuanian-Swiss cooperation program under the project agreement No. CH-SMM-01/0.","abstract":[{"lang":"eng","text":"In the present work we introduce the notion of a renormalized solution for reaction–diffusion systems with entropy-dissipating reactions. We establish the global existence of renormalized solutions. In the case of integrable reaction terms our notion of a renormalized solution reduces to the usual notion of a weak solution. Our existence result in particular covers all reaction–diffusion systems involving a single reversible reaction with mass-action kinetics and (possibly species-dependent) Fick-law diffusion; more generally, it covers the case of systems of reversible reactions with mass-action kinetics which satisfy the detailed balance condition. For such equations the existence of any kind of solution in general was an open problem, thereby motivating the study of renormalized solutions."}],"intvolume":" 218","month":"10","quality_controlled":0,"publisher":"Springer","extern":1,"date_updated":"2021-01-12T06:49:50Z","citation":{"ieee":"J. L. Fischer, “Global existence of renormalized solutions to entropy-dissipating reaction–diffusion systems,” Archive for Rational Mechanics and Analysis, vol. 218, no. 1. Springer, pp. 553–587, 2015.","short":"J.L. Fischer, Archive for Rational Mechanics and Analysis 218 (2015) 553–587.","ama":"Fischer JL. Global existence of renormalized solutions to entropy-dissipating reaction–diffusion systems. Archive for Rational Mechanics and Analysis. 2015;218(1):553-587. doi:10.1007/s00205-015-0866-x","apa":"Fischer, J. L. (2015). Global existence of renormalized solutions to entropy-dissipating reaction–diffusion systems. Archive for Rational Mechanics and Analysis. Springer. https://doi.org/10.1007/s00205-015-0866-x","mla":"Fischer, Julian L. “Global Existence of Renormalized Solutions to Entropy-Dissipating Reaction–Diffusion Systems.” Archive for Rational Mechanics and Analysis, vol. 218, no. 1, Springer, 2015, pp. 553–87, doi:10.1007/s00205-015-0866-x.","ista":"Fischer JL. 2015. Global existence of renormalized solutions to entropy-dissipating reaction–diffusion systems. Archive for Rational Mechanics and Analysis. 218(1), 553–587.","chicago":"Fischer, Julian L. “Global Existence of Renormalized Solutions to Entropy-Dissipating Reaction–Diffusion Systems.” Archive for Rational Mechanics and Analysis. Springer, 2015. https://doi.org/10.1007/s00205-015-0866-x."},"title":"Global existence of renormalized solutions to entropy-dissipating reaction–diffusion systems","publist_id":"5955","author":[{"id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","first_name":"Julian L","full_name":"Julian Fischer","orcid":"0000-0002-0479-558X","last_name":"Fischer"}],"_id":"1316","status":"public","type":"journal_article"},{"type":"journal_article","article_type":"original","status":"public","_id":"1383","department":[{"_id":"JiFr"}],"date_updated":"2021-01-12T06:50:18Z","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4905525/","open_access":"1"}],"scopus_import":1,"intvolume":" 1","month":"07","abstract":[{"lang":"eng","text":"In plants, vacuolar H+-ATPase (V-ATPase) activity acidifies both the trans-Golgi network/early endosome (TGN/EE) and the vacuole. This dual V-ATPase function has impeded our understanding of how the pH homeostasis within the plant TGN/EE controls exo- and endocytosis. Here, we show that the weak V-ATPase mutant deetiolated3 (det3) displayed a pH increase in the TGN/EE, but not in the vacuole, strongly impairing secretion and recycling of the brassinosteroid receptor and the cellulose synthase complexes to the plasma membrane, in contrast to mutants lacking tonoplast-localized V-ATPase activity only. The brassinosteroid insensitivity and the cellulose deficiency defects in det3 were tightly correlated with reduced Golgi and TGN/EE motility. Thus, our results provide strong evidence that acidification of the TGN/EE, but not of the vacuole, is indispensable for functional secretion and recycling in plants."}],"pmid":1,"oa_version":"Submitted Version","volume":1,"issue":"7","publication_status":"published","language":[{"iso":"eng"}],"article_number":"15094","external_id":{"pmid":["27250258"]},"article_processing_charge":"No","publist_id":"5827","author":[{"full_name":"Yu, Luo","last_name":"Yu","first_name":"Luo"},{"last_name":"Scholl","full_name":"Scholl, Stefan","first_name":"Stefan"},{"first_name":"Anett","last_name":"Doering","full_name":"Doering, Anett"},{"full_name":"Yi, Zhang","last_name":"Yi","first_name":"Zhang"},{"full_name":"Irani, Niloufer","last_name":"Irani","first_name":"Niloufer"},{"first_name":"Simone","last_name":"Di Rubbo","full_name":"Di Rubbo, Simone"},{"last_name":"Neumetzler","full_name":"Neumetzler, Lutz","first_name":"Lutz"},{"first_name":"Praveen","last_name":"Krishnamoorthy","full_name":"Krishnamoorthy, Praveen"},{"full_name":"Van Houtte, Isabelle","last_name":"Van Houtte","first_name":"Isabelle"},{"full_name":"Mylle, Evelien","last_name":"Mylle","first_name":"Evelien"},{"full_name":"Bischoff, Volker","last_name":"Bischoff","first_name":"Volker"},{"full_name":"Vernhettes, Samantha","last_name":"Vernhettes","first_name":"Samantha"},{"full_name":"Winne, Johan","last_name":"Winne","first_name":"Johan"},{"last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"York","full_name":"Stierhof, York","last_name":"Stierhof"},{"first_name":"Karin","full_name":"Schumacher, Karin","last_name":"Schumacher"},{"last_name":"Persson","full_name":"Persson, Staffan","first_name":"Staffan"},{"first_name":"Eugenia","full_name":"Russinova, Eugenia","last_name":"Russinova"}],"title":"V-ATPase activity in the TGN/EE is required for exocytosis and recycling in Arabidopsis","citation":{"mla":"Yu, Luo, et al. “V-ATPase Activity in the TGN/EE Is Required for Exocytosis and Recycling in Arabidopsis.” Nature Plants, vol. 1, no. 7, 15094, Nature Publishing Group, 2015, doi:10.1038/nplants.2015.94.","ama":"Yu L, Scholl S, Doering A, et al. V-ATPase activity in the TGN/EE is required for exocytosis and recycling in Arabidopsis. Nature Plants. 2015;1(7). doi:10.1038/nplants.2015.94","apa":"Yu, L., Scholl, S., Doering, A., Yi, Z., Irani, N., Di Rubbo, S., … Russinova, E. (2015). V-ATPase activity in the TGN/EE is required for exocytosis and recycling in Arabidopsis. Nature Plants. Nature Publishing Group. https://doi.org/10.1038/nplants.2015.94","short":"L. Yu, S. Scholl, A. Doering, Z. Yi, N. Irani, S. Di Rubbo, L. Neumetzler, P. Krishnamoorthy, I. Van Houtte, E. Mylle, V. Bischoff, S. Vernhettes, J. Winne, J. Friml, Y. Stierhof, K. Schumacher, S. Persson, E. Russinova, Nature Plants 1 (2015).","ieee":"L. Yu et al., “V-ATPase activity in the TGN/EE is required for exocytosis and recycling in Arabidopsis,” Nature Plants, vol. 1, no. 7. Nature Publishing Group, 2015.","chicago":"Yu, Luo, Stefan Scholl, Anett Doering, Zhang Yi, Niloufer Irani, Simone Di Rubbo, Lutz Neumetzler, et al. “V-ATPase Activity in the TGN/EE Is Required for Exocytosis and Recycling in Arabidopsis.” Nature Plants. Nature Publishing Group, 2015. https://doi.org/10.1038/nplants.2015.94.","ista":"Yu L, Scholl S, Doering A, Yi Z, Irani N, Di Rubbo S, Neumetzler L, Krishnamoorthy P, Van Houtte I, Mylle E, Bischoff V, Vernhettes S, Winne J, Friml J, Stierhof Y, Schumacher K, Persson S, Russinova E. 2015. V-ATPase activity in the TGN/EE is required for exocytosis and recycling in Arabidopsis. Nature Plants. 1(7), 15094."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"publisher":"Nature Publishing Group","quality_controlled":"1","date_created":"2018-12-11T11:51:42Z","doi":"10.1038/nplants.2015.94","date_published":"2015-07-06T00:00:00Z","year":"2015","publication":"Nature Plants","day":"06"},{"language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"volume":2015,"oa_version":"None","abstract":[{"lang":"eng","text":"In this work we aim at extending the theoretical foundations of lifelong learning. Previous work analyzing this scenario is based on the assumption that learning tasks are sampled i.i.d. from a task environment or limited to strongly constrained data distributions. Instead, we study two scenarios when lifelong learning is possible, even though the observed tasks do not form an i.i.d. sample: first, when they are sampled from the same environment, but possibly with dependencies, and second, when the task environment is allowed to change over time in a consistent way. In the first case we prove a PAC-Bayesian theorem that can be seen as a direct generalization of the analogous previous result for the i.i.d. case. For the second scenario we propose to learn an inductive bias in form of a transfer procedure. We present a generalization bound and show on a toy example how it can be used to identify a beneficial transfer algorithm."}],"intvolume":" 2015","month":"01","main_file_link":[{"url":"http://papers.nips.cc/paper/6007-lifelong-learning-with-non-iid-tasks","open_access":"1"}],"scopus_import":1,"alternative_title":["Advances in Neural Information Processing Systems"],"date_updated":"2021-01-12T06:50:39Z","department":[{"_id":"ChLa"}],"_id":"1425","status":"public","conference":{"name":"NIPS: Neural Information Processing Systems","start_date":"2015-12-07","location":"Montreal, Canada","end_date":"2015-12-12"},"type":"conference","day":"01","year":"2015","date_created":"2018-12-11T11:51:57Z","date_published":"2015-01-01T00:00:00Z","page":"1540 - 1548","oa":1,"publisher":"Neural Information Processing Systems","quality_controlled":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Pentina, Anastasia, and Christoph Lampert. “Lifelong Learning with Non-i.i.d. Tasks,” 2015:1540–48. Neural Information Processing Systems, 2015.","ista":"Pentina A, Lampert C. 2015. Lifelong learning with non-i.i.d. tasks. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 2015, 1540–1548.","mla":"Pentina, Anastasia, and Christoph Lampert. Lifelong Learning with Non-i.i.d. Tasks. Vol. 2015, Neural Information Processing Systems, 2015, pp. 1540–48.","ama":"Pentina A, Lampert C. Lifelong learning with non-i.i.d. tasks. In: Vol 2015. Neural Information Processing Systems; 2015:1540-1548.","apa":"Pentina, A., & Lampert, C. (2015). Lifelong learning with non-i.i.d. tasks (Vol. 2015, pp. 1540–1548). Presented at the NIPS: Neural Information Processing Systems, Montreal, Canada: Neural Information Processing Systems.","ieee":"A. Pentina and C. Lampert, “Lifelong learning with non-i.i.d. tasks,” presented at the NIPS: Neural Information Processing Systems, Montreal, Canada, 2015, vol. 2015, pp. 1540–1548.","short":"A. Pentina, C. Lampert, in:, Neural Information Processing Systems, 2015, pp. 1540–1548."},"title":"Lifelong learning with non-i.i.d. tasks","author":[{"first_name":"Anastasia","id":"42E87FC6-F248-11E8-B48F-1D18A9856A87","last_name":"Pentina","full_name":"Pentina, Anastasia"},{"first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887"}],"publist_id":"5781","project":[{"name":"Lifelong Learning of Visual Scene Understanding","grant_number":"308036","_id":"2532554C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}]},{"oa_version":"Submitted Version","acknowledgement":"This work was partially supported by the Austrian Science FUnd, project no. KLI 00012.","abstract":[{"lang":"eng","text":"We consider the problem of statistical computations with persistence diagrams, a summary representation of topological features in data. These diagrams encode persistent homology, a widely used invariant in topological data analysis. While several avenues towards a statistical treatment of the diagrams have been explored recently, we follow an alternative route that is motivated by the success of methods based on the embedding of probability measures into reproducing kernel Hilbert spaces. In fact, a positive definite kernel on persistence diagrams has recently been proposed, connecting persistent homology to popular kernel-based learning techniques such as support vector machines. However, important properties of that kernel enabling a principled use in the context of probability measure embeddings remain to be explored. Our contribution is to close this gap by proving universality of a variant of the original kernel, and to demonstrate its effective use in twosample hypothesis testing on synthetic as well as real-world data."}],"month":"12","intvolume":" 28","publisher":"Neural Information Processing Systems","quality_controlled":"1","alternative_title":["Advances in Neural Information Processing Systems"],"main_file_link":[{"url":"https://papers.nips.cc/paper/5887-statistical-topological-data-analysis-a-kernel-perspective","open_access":"1"}],"oa":1,"day":"01","language":[{"iso":"eng"}],"publication_status":"published","year":"2015","volume":28,"date_published":"2015-12-01T00:00:00Z","date_created":"2018-12-11T11:51:56Z","page":"3070 - 3078","_id":"1424","status":"public","type":"conference","conference":{"name":"NIPS: Neural Information Processing Systems","start_date":"2015-12-07","end_date":"2015-12-12","location":"Montreal, Canada"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:50:38Z","citation":{"ista":"Kwitt R, Huber S, Niethammer M, Lin W, Bauer U. 2015. Statistical topological data analysis-A kernel perspective. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 28, 3070–3078.","chicago":"Kwitt, Roland, Stefan Huber, Marc Niethammer, Weili Lin, and Ulrich Bauer. “Statistical Topological Data Analysis-A Kernel Perspective,” 28:3070–78. Neural Information Processing Systems, 2015.","apa":"Kwitt, R., Huber, S., Niethammer, M., Lin, W., & Bauer, U. (2015). Statistical topological data analysis-A kernel perspective (Vol. 28, pp. 3070–3078). Presented at the NIPS: Neural Information Processing Systems, Montreal, Canada: Neural Information Processing Systems.","ama":"Kwitt R, Huber S, Niethammer M, Lin W, Bauer U. Statistical topological data analysis-A kernel perspective. In: Vol 28. Neural Information Processing Systems; 2015:3070-3078.","short":"R. Kwitt, S. Huber, M. Niethammer, W. Lin, U. Bauer, in:, Neural Information Processing Systems, 2015, pp. 3070–3078.","ieee":"R. Kwitt, S. Huber, M. Niethammer, W. Lin, and U. Bauer, “Statistical topological data analysis-A kernel perspective,” presented at the NIPS: Neural Information Processing Systems, Montreal, Canada, 2015, vol. 28, pp. 3070–3078.","mla":"Kwitt, Roland, et al. Statistical Topological Data Analysis-A Kernel Perspective. Vol. 28, Neural Information Processing Systems, 2015, pp. 3070–78."},"department":[{"_id":"HeEd"}],"title":"Statistical topological data analysis-A kernel perspective","author":[{"last_name":"Kwitt","full_name":"Kwitt, Roland","first_name":"Roland"},{"orcid":"0000-0002-8871-5814","full_name":"Huber, Stefan","last_name":"Huber","id":"4700A070-F248-11E8-B48F-1D18A9856A87","first_name":"Stefan"},{"first_name":"Marc","full_name":"Niethammer, Marc","last_name":"Niethammer"},{"last_name":"Lin","full_name":"Lin, Weili","first_name":"Weili"},{"orcid":"0000-0002-9683-0724","full_name":"Bauer, Ulrich","last_name":"Bauer","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","first_name":"Ulrich"}],"publist_id":"5782"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Paixao T, Sudholt D, Heredia J, Trubenova B. 2015. First steps towards a runtime comparison of natural and artificial evolution. Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation. GECCO: Genetic and evolutionary computation conference, 1455–1462.","chicago":"Paixao, Tiago, Dirk Sudholt, Jorge Heredia, and Barbora Trubenova. “First Steps towards a Runtime Comparison of Natural and Artificial Evolution.” In Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation, 1455–62. ACM, 2015. https://doi.org/10.1145/2739480.2754758.","apa":"Paixao, T., Sudholt, D., Heredia, J., & Trubenova, B. (2015). First steps towards a runtime comparison of natural and artificial evolution. In Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation (pp. 1455–1462). Madrid, Spain: ACM. https://doi.org/10.1145/2739480.2754758","ama":"Paixao T, Sudholt D, Heredia J, Trubenova B. First steps towards a runtime comparison of natural and artificial evolution. In: Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation. ACM; 2015:1455-1462. doi:10.1145/2739480.2754758","ieee":"T. Paixao, D. Sudholt, J. Heredia, and B. Trubenova, “First steps towards a runtime comparison of natural and artificial evolution,” in Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation, Madrid, Spain, 2015, pp. 1455–1462.","short":"T. Paixao, D. Sudholt, J. Heredia, B. Trubenova, in:, Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation, ACM, 2015, pp. 1455–1462.","mla":"Paixao, Tiago, et al. “First Steps towards a Runtime Comparison of Natural and Artificial Evolution.” Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation, ACM, 2015, pp. 1455–62, doi:10.1145/2739480.2754758."},"date_updated":"2021-01-12T06:50:41Z","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"title":"First steps towards a runtime comparison of natural and artificial evolution","author":[{"full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953","last_name":"Paixao","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","first_name":"Tiago"},{"last_name":"Sudholt","full_name":"Sudholt, Dirk","first_name":"Dirk"},{"full_name":"Heredia, Jorge","last_name":"Heredia","first_name":"Jorge"},{"id":"42302D54-F248-11E8-B48F-1D18A9856A87","first_name":"Barbora","full_name":"Trubenova, Barbora","orcid":"0000-0002-6873-2967","last_name":"Trubenova"}],"publist_id":"5768","_id":"1430","status":"public","project":[{"_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"618091","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation"}],"type":"conference","conference":{"start_date":"2015-07-11","location":"Madrid, Spain","end_date":"2015-07-15","name":"GECCO: Genetic and evolutionary computation conference"},"day":"11","publication":"Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation","language":[{"iso":"eng"}],"year":"2015","publication_status":"published","date_published":"2015-07-11T00:00:00Z","doi":"10.1145/2739480.2754758","date_created":"2018-12-11T11:51:58Z","ec_funded":1,"page":"1455 - 1462","oa_version":"Preprint","abstract":[{"text":"Evolutionary algorithms (EAs) form a popular optimisation paradigm inspired by natural evolution. In recent years the field of evolutionary computation has developed a rigorous analytical theory to analyse their runtime on many illustrative problems. Here we apply this theory to a simple model of natural evolution. In the Strong Selection Weak Mutation (SSWM) evolutionary regime the time between occurrence of new mutations is much longer than the time it takes for a new beneficial mutation to take over the population. In this situation, the population only contains copies of one genotype and evolution can be modelled as a (1+1)-type process where the probability of accepting a new genotype (improvements or worsenings) depends on the change in fitness. We present an initial runtime analysis of SSWM, quantifying its performance for various parameters and investigating differences to the (1+1) EA. We show that SSWM can have a moderate advantage over the (1+1) EA at crossing fitness valleys and study an example where SSWM outperforms the (1+1) EA by taking advantage of information on the fitness gradient.","lang":"eng"}],"month":"07","scopus_import":1,"publisher":"ACM","quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1504.06260"}]},{"project":[{"_id":"258C570E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"259668","name":"Provable Security for Physical Cryptography"}],"status":"public","type":"conference","conference":{"name":"CSF: Computer Security Foundations","end_date":"2015-07-17","location":"Verona, Italy","start_date":"2015-07-13"},"_id":"1474","title":"Policy privacy in cryptographic access control","department":[{"_id":"KrPi"}],"author":[{"first_name":"Anna","last_name":"Ferrara","full_name":"Ferrara, Anna"},{"full_name":"Fuchsbauer, Georg","last_name":"Fuchsbauer","id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","first_name":"Georg"},{"full_name":"Liu, Bin","last_name":"Liu","first_name":"Bin"},{"first_name":"Bogdan","last_name":"Warinschi","full_name":"Warinschi, Bogdan"}],"publist_id":"5722","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Ferrara, A., Fuchsbauer, G., Liu, B., & Warinschi, B. (2015). Policy privacy in cryptographic access control (pp. 46–60). Presented at the CSF: Computer Security Foundations, Verona, Italy: IEEE. https://doi.org/10.1109/CSF.2015.11","ama":"Ferrara A, Fuchsbauer G, Liu B, Warinschi B. Policy privacy in cryptographic access control. In: IEEE; 2015:46-60. doi:10.1109/CSF.2015.11","short":"A. Ferrara, G. Fuchsbauer, B. Liu, B. Warinschi, in:, IEEE, 2015, pp. 46–60.","ieee":"A. Ferrara, G. Fuchsbauer, B. Liu, and B. Warinschi, “Policy privacy in cryptographic access control,” presented at the CSF: Computer Security Foundations, Verona, Italy, 2015, pp. 46–60.","mla":"Ferrara, Anna, et al. Policy Privacy in Cryptographic Access Control. IEEE, 2015, pp. 46–60, doi:10.1109/CSF.2015.11.","ista":"Ferrara A, Fuchsbauer G, Liu B, Warinschi B. 2015. Policy privacy in cryptographic access control. CSF: Computer Security Foundations, 46–60.","chicago":"Ferrara, Anna, Georg Fuchsbauer, Bin Liu, and Bogdan Warinschi. “Policy Privacy in Cryptographic Access Control,” 46–60. IEEE, 2015. https://doi.org/10.1109/CSF.2015.11."},"date_updated":"2021-01-12T06:50:59Z","month":"09","quality_controlled":"1","publisher":"IEEE","oa":1,"main_file_link":[{"open_access":"1","url":"http://epubs.surrey.ac.uk/808055/"}],"oa_version":"Submitted Version","abstract":[{"text":"Cryptographic access control offers selective access to encrypted data via a combination of key management and functionality-rich cryptographic schemes, such as attribute-based encryption. Using this approach, publicly available meta-data may inadvertently leak information on the access policy that is enforced by cryptography, which renders cryptographic access control unusable in settings where this information is highly sensitive. We begin to address this problem by presenting rigorous definitions for policy privacy in cryptographic access control. For concreteness we set our results in the model of Role-Based Access Control (RBAC), where we identify and formalize several different flavors of privacy, however, our framework should serve as inspiration for other models of access control. Based on our insights we propose a new system which significantly improves on the privacy properties of state-of-the-art constructions. Our design is based on a novel type of privacy-preserving attribute-based encryption, which we introduce and show how to instantiate. We present our results in the context of a cryptographic RBAC system by Ferrara et al. (CSF'13), which uses cryptography to control read access to files, while write access is still delegated to trusted monitors. We give an extension of the construction that permits cryptographic control over write access. Our construction assumes that key management uses out-of-band channels between the policy enforcer and the users but eliminates completely the need for monitoring read/write access to the data.","lang":"eng"}],"date_published":"2015-09-04T00:00:00Z","doi":"10.1109/CSF.2015.11","date_created":"2018-12-11T11:52:14Z","ec_funded":1,"page":"46-60","day":"04","language":[{"iso":"eng"}],"year":"2015","publication_status":"published"},{"day":"01","publication":"Asterisque","publication_status":"published","year":"2015","issue":"370","date_published":"2015-01-01T00:00:00Z","volume":2015,"date_created":"2018-12-11T11:52:13Z","page":"113 - 156","abstract":[{"lang":"eng","text":"In this paper we survey geometric and arithmetic techniques to study the cohomology of semiprojective hyperkähler manifolds including toric hyperkähler varieties, Nakajima quiver varieties and moduli spaces of Higgs bundles on Riemann surfaces. The resulting formulae for their Poincaré polynomials are combinatorial and representation theoretical in nature. In particular we will look at their Betti numbers and will establish some results and state some expectations on their asymptotic shape."}],"month":"01","intvolume":" 2015","publisher":"Societe Mathematique de France","quality_controlled":0,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1309.4914"}],"oa":1,"extern":1,"date_updated":"2021-01-12T06:50:59Z","citation":{"mla":"Hausel, Tamás, and Fernando Rodríguez Villegas. “Cohomology of Large Semiprojective Hyperkähler Varieties.” Asterisque, vol. 2015, no. 370, Societe Mathematique de France, 2015, pp. 113–56.","ieee":"T. Hausel and F. Rodríguez Villegas, “Cohomology of large semiprojective hyperkähler varieties,” Asterisque, vol. 2015, no. 370. Societe Mathematique de France, pp. 113–156, 2015.","short":"T. Hausel, F. Rodríguez Villegas, Asterisque 2015 (2015) 113–156.","apa":"Hausel, T., & Rodríguez Villegas, F. (2015). Cohomology of large semiprojective hyperkähler varieties. Asterisque. Societe Mathematique de France.","ama":"Hausel T, Rodríguez Villegas F. Cohomology of large semiprojective hyperkähler varieties. Asterisque. 2015;2015(370):113-156.","chicago":"Hausel, Tamás, and Fernando Rodríguez Villegas. “Cohomology of Large Semiprojective Hyperkähler Varieties.” Asterisque. Societe Mathematique de France, 2015.","ista":"Hausel T, Rodríguez Villegas F. 2015. Cohomology of large semiprojective hyperkähler varieties. Asterisque. 2015(370), 113–156."},"title":"Cohomology of large semiprojective hyperkähler varieties","author":[{"first_name":"Tamas","id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","last_name":"Hausel","full_name":"Tamas Hausel"},{"last_name":"Rodríguez Villegas","full_name":"Rodríguez Villegas, Fernando","first_name":"Fernando"}],"publist_id":"5723","_id":"1473","status":"public","type":"review"},{"status":"public","conference":{"name":"CVPR: Computer Vision and Pattern Recognition","end_date":"2015-06-12","location":"Boston, MA, USA","start_date":"2015-06-07"},"type":"conference","_id":"1483","title":"A stable multi-scale kernel for topological machine learning","department":[{"_id":"HeEd"}],"publist_id":"5709","author":[{"last_name":"Reininghaus","full_name":"Reininghaus, Jan","first_name":"Jan","id":"4505473A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Huber","orcid":"0000-0002-8871-5814","full_name":"Huber, Stefan","first_name":"Stefan","id":"4700A070-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ulrich","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","last_name":"Bauer","orcid":"0000-0002-9683-0724","full_name":"Bauer, Ulrich"},{"full_name":"Kwitt, Roland","last_name":"Kwitt","first_name":"Roland"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Reininghaus, Jan, Stefan Huber, Ulrich Bauer, and Roland Kwitt. “A Stable Multi-Scale Kernel for Topological Machine Learning,” 4741–48. IEEE, 2015. https://doi.org/10.1109/CVPR.2015.7299106.","ista":"Reininghaus J, Huber S, Bauer U, Kwitt R. 2015. A stable multi-scale kernel for topological machine learning. CVPR: Computer Vision and Pattern Recognition, 4741–4748.","mla":"Reininghaus, Jan, et al. A Stable Multi-Scale Kernel for Topological Machine Learning. IEEE, 2015, pp. 4741–48, doi:10.1109/CVPR.2015.7299106.","ieee":"J. Reininghaus, S. Huber, U. Bauer, and R. Kwitt, “A stable multi-scale kernel for topological machine learning,” presented at the CVPR: Computer Vision and Pattern Recognition, Boston, MA, USA, 2015, pp. 4741–4748.","short":"J. Reininghaus, S. Huber, U. Bauer, R. Kwitt, in:, IEEE, 2015, pp. 4741–4748.","ama":"Reininghaus J, Huber S, Bauer U, Kwitt R. A stable multi-scale kernel for topological machine learning. In: IEEE; 2015:4741-4748. doi:10.1109/CVPR.2015.7299106","apa":"Reininghaus, J., Huber, S., Bauer, U., & Kwitt, R. (2015). A stable multi-scale kernel for topological machine learning (pp. 4741–4748). Presented at the CVPR: Computer Vision and Pattern Recognition, Boston, MA, USA: IEEE. https://doi.org/10.1109/CVPR.2015.7299106"},"date_updated":"2021-01-12T06:51:03Z","month":"10","oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1412.6821"}],"scopus_import":1,"publisher":"IEEE","oa_version":"Preprint","abstract":[{"text":"Topological data analysis offers a rich source of valuable information to study vision problems. Yet, so far we lack a theoretically sound connection to popular kernel-based learning techniques, such as kernel SVMs or kernel PCA. In this work, we establish such a connection by designing a multi-scale kernel for persistence diagrams, a stable summary representation of topological features in data. We show that this kernel is positive definite and prove its stability with respect to the 1-Wasserstein distance. Experiments on two benchmark datasets for 3D shape classification/retrieval and texture recognition show considerable performance gains of the proposed method compared to an alternative approach that is based on the recently introduced persistence landscapes.","lang":"eng"}],"date_created":"2018-12-11T11:52:17Z","doi":"10.1109/CVPR.2015.7299106","date_published":"2015-10-14T00:00:00Z","page":"4741 - 4748","language":[{"iso":"eng"}],"day":"14","year":"2015","publication_status":"published","publication_identifier":{"eisbn":["978-1-4673-6964-0 "]}},{"oa":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","year":"2015","has_accepted_license":"1","day":"01","page":"90 - 102","date_created":"2018-12-11T11:52:22Z","date_published":"2015-01-01T00:00:00Z","doi":"10.4230/LIPIcs.SNAPL.2015.90","project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"267989","name":"Quantitative Reactive Modeling"},{"grant_number":"S11402-N23","name":"Moderne Concurrency Paradigms","call_identifier":"FWF","_id":"25F5A88A-B435-11E9-9278-68D0E5697425"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z211","name":"The Wittgenstein Prize"}],"citation":{"ieee":"C. Dragoi, T. A. Henzinger, and D. Zufferey, “The need for language support for fault-tolerant distributed systems,” vol. 32. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, pp. 90–102, 2015.","short":"C. Dragoi, T.A. Henzinger, D. Zufferey, 32 (2015) 90–102.","ama":"Dragoi C, Henzinger TA, Zufferey D. The need for language support for fault-tolerant distributed systems. 2015;32:90-102. doi:10.4230/LIPIcs.SNAPL.2015.90","apa":"Dragoi, C., Henzinger, T. A., & Zufferey, D. (2015). The need for language support for fault-tolerant distributed systems. Presented at the SNAPL: Summit oN Advances in Programming Languages, Asilomar, CA, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SNAPL.2015.90","mla":"Dragoi, Cezara, et al. The Need for Language Support for Fault-Tolerant Distributed Systems. Vol. 32, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 90–102, doi:10.4230/LIPIcs.SNAPL.2015.90.","ista":"Dragoi C, Henzinger TA, Zufferey D. 2015. The need for language support for fault-tolerant distributed systems. 32, 90–102.","chicago":"Dragoi, Cezara, Thomas A Henzinger, and Damien Zufferey. “The Need for Language Support for Fault-Tolerant Distributed Systems.” Leibniz International Proceedings in Informatics. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015. https://doi.org/10.4230/LIPIcs.SNAPL.2015.90."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Cezara","id":"2B2B5ED0-F248-11E8-B48F-1D18A9856A87","full_name":"Dragoi, Cezara","last_name":"Dragoi"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"id":"4397AC76-F248-11E8-B48F-1D18A9856A87","first_name":"Damien","full_name":"Zufferey, Damien","orcid":"0000-0002-3197-8736","last_name":"Zufferey"}],"publist_id":"5681","title":"The need for language support for fault-tolerant distributed systems","abstract":[{"lang":"eng","text":"Fault-tolerant distributed algorithms play an important role in many critical/high-availability applications. These algorithms are notoriously difficult to implement correctly, due to asynchronous communication and the occurrence of faults, such as the network dropping messages or computers crashing. Nonetheless there is surprisingly little language and verification support to build distributed systems based on fault-tolerant algorithms. In this paper, we present some of the challenges that a designer has to overcome to implement a fault-tolerant distributed system. Then we review different models that have been proposed to reason about distributed algorithms and sketch how such a model can form the basis for a domain-specific programming language. Adopting a high-level programming model can simplify the programmer's life and make the code amenable to automated verification, while still compiling to efficiently executable code. We conclude by summarizing the current status of an ongoing language design and implementation project that is based on this idea."}],"oa_version":"Published Version","scopus_import":1,"alternative_title":["LIPIcs"],"intvolume":" 32","month":"01","publication_status":"published","publication_identifier":{"isbn":["978-3-939897-80-4 "]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5050","checksum":"cf5e94baa89a2dc4c5de01abc676eda8","file_size":489362,"date_updated":"2020-07-14T12:44:58Z","creator":"system","file_name":"IST-2016-499-v1+1_9.pdf","date_created":"2018-12-12T10:14:02Z"}],"ec_funded":1,"volume":32,"series_title":"Leibniz International Proceedings in Informatics","_id":"1498","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":"SNAPL: Summit oN Advances in Programming Languages","location":"Asilomar, CA, United States","end_date":"2015-05-06","start_date":"2015-05-03"},"type":"conference","pubrep_id":"499","status":"public","date_updated":"2020-08-11T10:09:14Z","ddc":["005"],"department":[{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:44:58Z"},{"publication":"Nucleic Acids Research","day":"21","year":"2015","has_accepted_license":"1","date_created":"2018-12-11T11:52:22Z","date_published":"2015-07-21T00:00:00Z","doi":"10.1093/nar/gkv727","acknowledgement":"Austrian Science Fund [FWF P25185-B22, FWF F4302- B09, FWFW1207-B09]. Funding for open access charge: Austrian Science Fund.\r\nWe thank Florian Breitwieser for advice during the early stages of this project. High-throughput sequencing was conducted by the Biomedical Sequencing Facility (BSF) at CeMM in Vienna.","oa":1,"publisher":"Oxford University Press","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Andergassen D, Dotter C, Kulinski T, Guenzl P, Bammer P, Barlow D, Pauler F, Hudson Q. 2015. Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data. Nucleic Acids Research. 43(21), e146.","chicago":"Andergassen, Daniel, Christoph Dotter, Tomasz Kulinski, Philipp Guenzl, Philipp Bammer, Denise Barlow, Florian Pauler, and Quanah Hudson. “Allelome.PRO, a Pipeline to Define Allele-Specific Genomic Features from High-Throughput Sequencing Data.” Nucleic Acids Research. Oxford University Press, 2015. https://doi.org/10.1093/nar/gkv727.","ama":"Andergassen D, Dotter C, Kulinski T, et al. Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data. Nucleic Acids Research. 2015;43(21). doi:10.1093/nar/gkv727","apa":"Andergassen, D., Dotter, C., Kulinski, T., Guenzl, P., Bammer, P., Barlow, D., … Hudson, Q. (2015). Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data. Nucleic Acids Research. Oxford University Press. https://doi.org/10.1093/nar/gkv727","short":"D. Andergassen, C. Dotter, T. Kulinski, P. Guenzl, P. Bammer, D. Barlow, F. Pauler, Q. Hudson, Nucleic Acids Research 43 (2015).","ieee":"D. Andergassen et al., “Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data,” Nucleic Acids Research, vol. 43, no. 21. Oxford University Press, 2015.","mla":"Andergassen, Daniel, et al. “Allelome.PRO, a Pipeline to Define Allele-Specific Genomic Features from High-Throughput Sequencing Data.” Nucleic Acids Research, vol. 43, no. 21, e146, Oxford University Press, 2015, doi:10.1093/nar/gkv727."},"title":"Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data","publist_id":"5682","author":[{"first_name":"Daniel","last_name":"Andergassen","full_name":"Andergassen, Daniel"},{"first_name":"Christoph","id":"4C66542E-F248-11E8-B48F-1D18A9856A87","last_name":"Dotter","full_name":"Dotter, Christoph"},{"full_name":"Kulinski, Tomasz","last_name":"Kulinski","first_name":"Tomasz"},{"last_name":"Guenzl","full_name":"Guenzl, Philipp","first_name":"Philipp"},{"first_name":"Philipp","last_name":"Bammer","full_name":"Bammer, Philipp"},{"last_name":"Barlow","full_name":"Barlow, Denise","first_name":"Denise"},{"full_name":"Pauler, Florian","last_name":"Pauler","first_name":"Florian"},{"first_name":"Quanah","full_name":"Hudson, Quanah","last_name":"Hudson"}],"article_number":"e146","language":[{"iso":"eng"}],"file":[{"checksum":"385b83854fd0eb2e4f386867da2823e2","file_id":"5768","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2015_NucleicAcidsRes_Andergassen.pdf","date_created":"2018-12-20T14:18:57Z","creator":"dernst","file_size":6863297,"date_updated":"2020-07-14T12:44:58Z"}],"publication_status":"published","issue":"21","volume":43,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Detecting allelic biases from high-throughput sequencing data requires an approach that maximises sensitivity while minimizing false positives. Here, we present Allelome.PRO, an automated user-friendly bioinformatics pipeline, which uses high-throughput sequencing data from reciprocal crosses of two genetically distinct mouse strains to detect allele-specific expression and chromatin modifications. Allelome.PRO extends approaches used in previous studies that exclusively analyzed imprinted expression to give a complete picture of the ‘allelome’ by automatically categorising the allelic expression of all genes in a given cell type into imprinted, strain-biased, biallelic or non-informative. Allelome.PRO offers increased sensitivity to analyze lowly expressed transcripts, together with a robust false discovery rate empirically calculated from variation in the sequencing data. We used RNA-seq data from mouse embryonic fibroblasts from F1 reciprocal crosses to determine a biologically relevant allelic ratio cutoff, and define for the first time an entire allelome. Furthermore, we show that Allelome.PRO detects differential enrichment of H3K4me3 over promoters from ChIP-seq data validating the RNA-seq results. This approach can be easily extended to analyze histone marks of active enhancers, or transcription factor binding sites and therefore provides a powerful tool to identify candidate cis regulatory elements genome wide."}],"intvolume":" 43","month":"07","scopus_import":1,"ddc":["570"],"date_updated":"2021-01-12T06:51:09Z","file_date_updated":"2020-07-14T12:44:58Z","department":[{"_id":"GaNo"}],"_id":"1497","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"},{"alternative_title":["LIPIcs"],"scopus_import":1,"intvolume":" 42","month":"01","abstract":[{"text":"We consider weighted automata with both positive and negative integer weights on edges and\r\nstudy the problem of synchronization using adaptive strategies that may only observe whether\r\nthe current weight-level is negative or nonnegative. We show that the synchronization problem is decidable in polynomial time for deterministic weighted automata.","lang":"eng"}],"oa_version":"Published Version","ec_funded":1,"volume":42,"publication_status":"published","language":[{"iso":"eng"}],"file":[{"checksum":"49eb5021caafaabe5356c65b9c5f8c9c","file_id":"4672","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:08:12Z","file_name":"IST-2016-498-v1+1_32.pdf","date_updated":"2020-07-14T12:44:58Z","file_size":623563,"creator":"system"}],"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":"CONCUR: Concurrency Theory","end_date":"2015-09-04","location":"Madrid, Spain","start_date":"2015-09-01"},"type":"conference","pubrep_id":"498","status":"public","_id":"1499","file_date_updated":"2020-07-14T12:44:58Z","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"date_updated":"2021-01-12T06:51:10Z","ddc":["000","003"],"oa":1,"quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","acknowledgement":"The research leading to these results has received funding from the European Union Seventh Framework Programme (FP7/2007-2013) under grant agreement 601148 (CASSTING), EU FP7 FET project SENSATION, Sino-Danish Basic Research Center IDAE4CPS, the European Research Council (ERC) under grant agreement 267989 (QUAREM), the Austrian Science Fund (FWF) project S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award), the Czech Science Foundation under grant agreement P202/12/G061, and People Programme (Marie Curie Actions) of the European Union’s Seventh Framework\r\nProgramme (FP7/2007-2013) REA Grant No 291734.","page":"142 - 154","date_created":"2018-12-11T11:52:22Z","doi":"10.4230/LIPIcs.CONCUR.2015.142","date_published":"2015-01-01T00:00:00Z","year":"2015","has_accepted_license":"1","day":"01","project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize"},{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"author":[{"last_name":"Kretinsky","full_name":"Kretinsky, Jan","orcid":"0000-0002-8122-2881","first_name":"Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Kim","last_name":"Larsen","full_name":"Larsen, Kim"},{"first_name":"Simon","last_name":"Laursen","full_name":"Laursen, Simon"},{"first_name":"Jiří","last_name":"Srba","full_name":"Srba, Jiří"}],"publist_id":"5680","title":"Polynomial time decidability of weighted synchronization under partial observability","citation":{"ieee":"J. Kretinsky, K. Larsen, S. Laursen, and J. Srba, “Polynomial time decidability of weighted synchronization under partial observability,” presented at the CONCUR: Concurrency Theory, Madrid, Spain, 2015, vol. 42, pp. 142–154.","short":"J. Kretinsky, K. Larsen, S. Laursen, J. Srba, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 142–154.","apa":"Kretinsky, J., Larsen, K., Laursen, S., & Srba, J. (2015). Polynomial time decidability of weighted synchronization under partial observability (Vol. 42, pp. 142–154). Presented at the CONCUR: Concurrency Theory, Madrid, Spain: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2015.142","ama":"Kretinsky J, Larsen K, Laursen S, Srba J. Polynomial time decidability of weighted synchronization under partial observability. In: Vol 42. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2015:142-154. doi:10.4230/LIPIcs.CONCUR.2015.142","mla":"Kretinsky, Jan, et al. Polynomial Time Decidability of Weighted Synchronization under Partial Observability. Vol. 42, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 142–54, doi:10.4230/LIPIcs.CONCUR.2015.142.","ista":"Kretinsky J, Larsen K, Laursen S, Srba J. 2015. Polynomial time decidability of weighted synchronization under partial observability. CONCUR: Concurrency Theory, LIPIcs, vol. 42, 142–154.","chicago":"Kretinsky, Jan, Kim Larsen, Simon Laursen, and Jiří Srba. “Polynomial Time Decidability of Weighted Synchronization under Partial Observability,” 42:142–54. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015. https://doi.org/10.4230/LIPIcs.CONCUR.2015.142."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"abstract":[{"text":"Motivated by biological questions, we study configurations of equal-sized disks in the Euclidean plane that neither pack nor cover. Measuring the quality by the probability that a random point lies in exactly one disk, we show that the regular hexagonal grid gives the maximum among lattice configurations. ","lang":"eng"}],"oa_version":"Submitted Version","scopus_import":1,"quality_controlled":"1","publisher":"Queen's University","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1505.03402","open_access":"1"}],"month":"08","year":"2015","publication_status":"published","day":"01","language":[{"iso":"eng"}],"publication":"Proceedings of the 27th Canadian Conference on Computational Geometry","page":"128-135","volume":"2015-August","date_published":"2015-08-01T00:00:00Z","ec_funded":1,"date_created":"2018-12-11T11:52:21Z","_id":"1495","type":"conference","conference":{"start_date":"2015-08-10","end_date":"2015-08-12","location":"Ontario, Canada","name":"CCCG: Canadian Conference on Computational Geometry"},"status":"public","project":[{"name":"Topological Complex Systems","grant_number":"318493","call_identifier":"FP7","_id":"255D761E-B435-11E9-9278-68D0E5697425"}],"citation":{"chicago":"Edelsbrunner, Herbert, Mabel Iglesias Ham, and Vitaliy Kurlin. “Relaxed Disk Packing.” In Proceedings of the 27th Canadian Conference on Computational Geometry, 2015–August:128–35. Queen’s University, 2015.","ista":"Edelsbrunner H, Iglesias Ham M, Kurlin V. 2015. Relaxed disk packing. Proceedings of the 27th Canadian Conference on Computational Geometry. CCCG: Canadian Conference on Computational Geometry vol. 2015–August, 128–135.","mla":"Edelsbrunner, Herbert, et al. “Relaxed Disk Packing.” Proceedings of the 27th Canadian Conference on Computational Geometry, vol. 2015–August, Queen’s University, 2015, pp. 128–35.","ieee":"H. Edelsbrunner, M. Iglesias Ham, and V. Kurlin, “Relaxed disk packing,” in Proceedings of the 27th Canadian Conference on Computational Geometry, Ontario, Canada, 2015, vol. 2015–August, pp. 128–135.","short":"H. Edelsbrunner, M. Iglesias Ham, V. Kurlin, in:, Proceedings of the 27th Canadian Conference on Computational Geometry, Queen’s University, 2015, pp. 128–135.","ama":"Edelsbrunner H, Iglesias Ham M, Kurlin V. Relaxed disk packing. In: Proceedings of the 27th Canadian Conference on Computational Geometry. Vol 2015-August. Queen’s University; 2015:128-135.","apa":"Edelsbrunner, H., Iglesias Ham, M., & Kurlin, V. (2015). Relaxed disk packing. In Proceedings of the 27th Canadian Conference on Computational Geometry (Vol. 2015–August, pp. 128–135). Ontario, Canada: Queen’s University."},"date_updated":"2021-01-12T06:51:09Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"5684","author":[{"last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert"},{"id":"41B58C0C-F248-11E8-B48F-1D18A9856A87","first_name":"Mabel","last_name":"Iglesias Ham","full_name":"Iglesias Ham, Mabel"},{"last_name":"Kurlin","full_name":"Kurlin, Vitaliy","first_name":"Vitaliy"}],"department":[{"_id":"HeEd"}],"title":"Relaxed disk packing"},{"publist_id":"5674","author":[{"id":"442E6A6C-F248-11E8-B48F-1D18A9856A87","first_name":"Zhigang","full_name":"Bao, Zhigang","orcid":"0000-0003-3036-1475","last_name":"Bao"},{"first_name":"Liang","last_name":"Lin","full_name":"Lin, Liang"},{"full_name":"Pan, Guangming","last_name":"Pan","first_name":"Guangming"},{"first_name":"Wang","last_name":"Zhou","full_name":"Zhou, Wang"}],"title":"Spectral statistics of large dimensional spearman s rank correlation matrix and its application","citation":{"ista":"Bao Z, Lin L, Pan G, Zhou W. 2015. Spectral statistics of large dimensional spearman s rank correlation matrix and its application. Annals of Statistics. 43(6), 2588–2623.","chicago":"Bao, Zhigang, Liang Lin, Guangming Pan, and Wang Zhou. “Spectral Statistics of Large Dimensional Spearman s Rank Correlation Matrix and Its Application.” Annals of Statistics. Institute of Mathematical Statistics, 2015. https://doi.org/10.1214/15-AOS1353.","apa":"Bao, Z., Lin, L., Pan, G., & Zhou, W. (2015). Spectral statistics of large dimensional spearman s rank correlation matrix and its application. Annals of Statistics. Institute of Mathematical Statistics. https://doi.org/10.1214/15-AOS1353","ama":"Bao Z, Lin L, Pan G, Zhou W. Spectral statistics of large dimensional spearman s rank correlation matrix and its application. Annals of Statistics. 2015;43(6):2588-2623. doi:10.1214/15-AOS1353","short":"Z. Bao, L. Lin, G. Pan, W. Zhou, Annals of Statistics 43 (2015) 2588–2623.","ieee":"Z. Bao, L. Lin, G. Pan, and W. Zhou, “Spectral statistics of large dimensional spearman s rank correlation matrix and its application,” Annals of Statistics, vol. 43, no. 6. Institute of Mathematical Statistics, pp. 2588–2623, 2015.","mla":"Bao, Zhigang, et al. “Spectral Statistics of Large Dimensional Spearman s Rank Correlation Matrix and Its Application.” Annals of Statistics, vol. 43, no. 6, Institute of Mathematical Statistics, 2015, pp. 2588–623, doi:10.1214/15-AOS1353."},"date_updated":"2021-01-12T06:51:14Z","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","status":"public","_id":"1504","page":"2588 - 2623","issue":"6","volume":43,"doi":"10.1214/15-AOS1353","date_published":"2015-12-01T00:00:00Z","date_created":"2018-12-11T11:52:24Z","year":"2015","publication_status":"published","day":"01","language":[{"iso":"eng"}],"publication":"Annals of Statistics","publisher":"Institute of Mathematical Statistics","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1312.5119","open_access":"1"}],"oa":1,"month":"12","intvolume":" 43","abstract":[{"lang":"eng","text":"Let Q = (Q1, . . . , Qn) be a random vector drawn from the uniform distribution on the set of all n! permutations of {1, 2, . . . , n}. Let Z = (Z1, . . . , Zn), where Zj is the mean zero variance one random variable obtained by centralizing and normalizing Qj , j = 1, . . . , n. Assume that Xi , i = 1, . . . ,p are i.i.d. copies of 1/√ p Z and X = Xp,n is the p × n random matrix with Xi as its ith row. Then Sn = XX is called the p × n Spearman's rank correlation matrix which can be regarded as a high dimensional extension of the classical nonparametric statistic Spearman's rank correlation coefficient between two independent random variables. In this paper, we establish a CLT for the linear spectral statistics of this nonparametric random matrix model in the scenario of high dimension, namely, p = p(n) and p/n→c ∈ (0,∞) as n→∞.We propose a novel evaluation scheme to estimate the core quantity in Anderson and Zeitouni's cumulant method in [Ann. Statist. 36 (2008) 2553-2576] to bypass the so-called joint cumulant summability. In addition, we raise a two-step comparison approach to obtain the explicit formulae for the mean and covariance functions in the CLT. Relying on this CLT, we then construct a distribution-free statistic to test complete independence for components of random vectors. Owing to the nonparametric property, we can use this test on generally distributed random variables including the heavy-tailed ones."}],"oa_version":"Published Version"},{"abstract":[{"lang":"eng","text":"In this poster, we present methods for randomly generating hybrid automata with affine differential equations, invariants, guards, and assignments. Selecting an arbitrary affine function from the set of all affine functions results in a low likelihood of generating hybrid automata with diverse and interesting behaviors, as there are an uncountable number of elements in the set of all affine functions. Instead, we partition the set of all affine functions into potentially interesting classes and randomly select elements from these classes. For example, we partition the set of all affine differential equations by using restrictions on eigenvalues such as those that yield stable, unstable, etc. equilibrium points. We partition the components describing discrete behavior (guards, assignments, and invariants) to allow either time-dependent or state-dependent switching, and in particular provide the ability to generate subclasses of piecewise-affine hybrid automata. Our preliminary experimental results with a prototype tool called HyRG (Hybrid Random Generator) illustrate the feasibility of this generation method to automatically create standard hybrid automaton examples like the bouncing ball and thermostat."}],"publisher":"Springer","alternative_title":["18th ACM International Conference on Hybrid Systems: Computation and Control, HSCC 2015"],"quality_controlled":0,"month":"04","publication_status":"published","year":"2015","day":"14","publication":"HSCC: Hybrid Systems - Computation and Control","page":"289 - 290","date_published":"2015-04-14T00:00:00Z","doi":"10.1145/2728606.2728650","date_created":"2018-12-11T11:52:23Z","_id":"1500","type":"conference_poster","status":"public","date_updated":"2019-04-26T07:22:03Z","citation":{"ista":"Nguyen L, Schilling C, Bogomolov S, Johnson T. 2015. Poster: HyRG: A random generation tool for affine hybrid automata, Springer,p.","chicago":"Nguyen, Luan, Christian Schilling, Sergiy Bogomolov, and Taylor Johnson. Poster: HyRG: A Random Generation Tool for Affine Hybrid Automata. HSCC: Hybrid Systems - Computation and Control. Springer, 2015. https://doi.org/10.1145/2728606.2728650.","ieee":"L. Nguyen, C. Schilling, S. Bogomolov, and T. Johnson, Poster: HyRG: A random generation tool for affine hybrid automata. Springer, 2015, pp. 289–290.","short":"L. Nguyen, C. Schilling, S. Bogomolov, T. Johnson, Poster: HyRG: A Random Generation Tool for Affine Hybrid Automata, Springer, 2015.","ama":"Nguyen L, Schilling C, Bogomolov S, Johnson T. Poster: HyRG: A Random Generation Tool for Affine Hybrid Automata. Springer; 2015:289-290. doi:10.1145/2728606.2728650","apa":"Nguyen, L., Schilling, C., Bogomolov, S., & Johnson, T. (2015). Poster: HyRG: A random generation tool for affine hybrid automata. HSCC: Hybrid Systems - Computation and Control (pp. 289–290). Springer. https://doi.org/10.1145/2728606.2728650","mla":"Nguyen, Luan, et al. “Poster: HyRG: A Random Generation Tool for Affine Hybrid Automata.” HSCC: Hybrid Systems - Computation and Control, Springer, 2015, pp. 289–90, doi:10.1145/2728606.2728650."},"extern":1,"publist_id":"5678","author":[{"full_name":"Nguyen, Luan V","last_name":"Nguyen","first_name":"Luan"},{"full_name":"Christian Schilling","orcid":"0000-0003-3658-1065","last_name":"Schilling","first_name":"Christian","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Bogomolov","full_name":"Sergiy Bogomolov","orcid":"0000-0002-0686-0365","first_name":"Sergiy","id":"369D9A44-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Taylor","full_name":"Johnson, Taylor T","last_name":"Johnson"}],"title":"Poster: HyRG: A random generation tool for affine hybrid automata"},{"title":"A Herman-Avila-Bochi formula for higher-dimensional pseudo-unitary and Hermitian-symplectic-cocycles","publist_id":"5675","author":[{"last_name":"Sadel","full_name":"Sadel, Christian","orcid":"0000-0001-8255-3968","first_name":"Christian","id":"4760E9F8-F248-11E8-B48F-1D18A9856A87"}],"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Sadel, C. (2015). A Herman-Avila-Bochi formula for higher-dimensional pseudo-unitary and Hermitian-symplectic-cocycles. Ergodic Theory and Dynamical Systems. Cambridge University Press. https://doi.org/10.1017/etds.2013.103","ama":"Sadel C. A Herman-Avila-Bochi formula for higher-dimensional pseudo-unitary and Hermitian-symplectic-cocycles. Ergodic Theory and Dynamical Systems. 2015;35(5):1582-1591. doi:10.1017/etds.2013.103","short":"C. Sadel, Ergodic Theory and Dynamical Systems 35 (2015) 1582–1591.","ieee":"C. Sadel, “A Herman-Avila-Bochi formula for higher-dimensional pseudo-unitary and Hermitian-symplectic-cocycles,” Ergodic Theory and Dynamical Systems, vol. 35, no. 5. Cambridge University Press, pp. 1582–1591, 2015.","mla":"Sadel, Christian. “A Herman-Avila-Bochi Formula for Higher-Dimensional Pseudo-Unitary and Hermitian-Symplectic-Cocycles.” Ergodic Theory and Dynamical Systems, vol. 35, no. 5, Cambridge University Press, 2015, pp. 1582–91, doi:10.1017/etds.2013.103.","ista":"Sadel C. 2015. A Herman-Avila-Bochi formula for higher-dimensional pseudo-unitary and Hermitian-symplectic-cocycles. Ergodic Theory and Dynamical Systems. 35(5), 1582–1591.","chicago":"Sadel, Christian. “A Herman-Avila-Bochi Formula for Higher-Dimensional Pseudo-Unitary and Hermitian-Symplectic-Cocycles.” Ergodic Theory and Dynamical Systems. Cambridge University Press, 2015. https://doi.org/10.1017/etds.2013.103."},"date_updated":"2021-01-12T06:51:13Z","status":"public","type":"journal_article","_id":"1503","doi":"10.1017/etds.2013.103","issue":"5","date_published":"2015-03-14T00:00:00Z","volume":35,"date_created":"2018-12-11T11:52:24Z","page":"1582 - 1591","day":"14","language":[{"iso":"eng"}],"publication":"Ergodic Theory and Dynamical Systems","publication_status":"published","year":"2015","month":"03","intvolume":" 35","publisher":"Cambridge University Press","quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1307.8414","open_access":"1"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"A Herman-Avila-Bochi type formula is obtained for the average sum of the top d Lyapunov exponents over a one-parameter family of double-struck G-cocycles, where double-struck G is the group that leaves a certain, non-degenerate Hermitian form of signature (c, d) invariant. The generic example of such a group is the pseudo-unitary group U(c, d) or, in the case c = d, the Hermitian-symplectic group HSp(2d) which naturally appears for cocycles related to Schrödinger operators. In the case d = 1, the formula for HSp(2d) cocycles reduces to the Herman-Avila-Bochi formula for SL(2, ℝ) cocycles."}]},{"abstract":[{"text":"The concept of well group in a special but important case captures homological properties of the zero set of a continuous map f from K to R^n on a compact space K that are invariant with respect to perturbations of f. The perturbations are arbitrary continuous maps within L_infty distance r from f for a given r > 0. The main drawback of the approach is that the computability of well groups was shown only when dim K = n or n = 1. Our contribution to the theory of well groups is twofold: on the one hand we improve on the computability issue, but on the other hand we present a range of examples where the well groups are incomplete invariants, that is, fail to capture certain important robust properties of the zero set. For the first part, we identify a computable subgroup of the well group that is obtained by cap product with the pullback of the orientation of R^n by f. In other words, well groups can be algorithmically approximated from below. When f is smooth and dim K < 2n-2, our approximation of the (dim K-n)th well group is exact. For the second part, we find examples of maps f, f' from K to R^n with all well groups isomorphic but whose perturbations have different zero sets. We discuss on a possible replacement of the well groups of vector valued maps by an invariant of a better descriptive power and computability status. ","lang":"eng"}],"oa_version":"Published Version","scopus_import":1,"alternative_title":["LIPIcs"],"month":"06","intvolume":" 34","publication_status":"published","file":[{"checksum":"49eb5021caafaabe5356c65b9c5f8c9c","file_id":"5001","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2016-503-v1+1_32.pdf","date_created":"2018-12-12T10:13:19Z","creator":"system","file_size":623563,"date_updated":"2020-07-14T12:44:59Z"}],"language":[{"iso":"eng"}],"volume":34,"related_material":{"record":[{"status":"public","id":"1408","relation":"later_version"}]},"ec_funded":1,"_id":"1510","type":"conference","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":{"start_date":"2015-06-22","end_date":"2015-06-25","location":"Eindhoven, Netherlands","name":"SoCG: Symposium on Computational Geometry"},"status":"public","pubrep_id":"503","date_updated":"2023-02-21T17:02:57Z","ddc":["510"],"department":[{"_id":"UlWa"},{"_id":"HeEd"}],"file_date_updated":"2020-07-14T12:44:59Z","quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","oa":1,"has_accepted_license":"1","year":"2015","day":"11","page":"842 - 856","doi":"10.4230/LIPIcs.SOCG.2015.842","date_published":"2015-06-11T00:00:00Z","date_created":"2018-12-11T11:52:26Z","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"citation":{"chicago":"Franek, Peter, and Marek Krcál. “On Computability and Triviality of Well Groups,” 34:842–56. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015. https://doi.org/10.4230/LIPIcs.SOCG.2015.842.","ista":"Franek P, Krcál M. 2015. On computability and triviality of well groups. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 34, 842–856.","mla":"Franek, Peter, and Marek Krcál. On Computability and Triviality of Well Groups. Vol. 34, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 842–56, doi:10.4230/LIPIcs.SOCG.2015.842.","ama":"Franek P, Krcál M. On computability and triviality of well groups. In: Vol 34. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2015:842-856. doi:10.4230/LIPIcs.SOCG.2015.842","apa":"Franek, P., & Krcál, M. (2015). On computability and triviality of well groups (Vol. 34, pp. 842–856). Presented at the SoCG: Symposium on Computational Geometry, Eindhoven, Netherlands: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SOCG.2015.842","ieee":"P. Franek and M. Krcál, “On computability and triviality of well groups,” presented at the SoCG: Symposium on Computational Geometry, Eindhoven, Netherlands, 2015, vol. 34, pp. 842–856.","short":"P. Franek, M. Krcál, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 842–856."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Peter","id":"473294AE-F248-11E8-B48F-1D18A9856A87","full_name":"Franek, Peter","last_name":"Franek"},{"last_name":"Krcál","full_name":"Krcál, Marek","id":"33E21118-F248-11E8-B48F-1D18A9856A87","first_name":"Marek"}],"publist_id":"5667","title":"On computability and triviality of well groups"},{"year":"2015","publication_status":"published","day":"01","language":[{"iso":"eng"}],"publication":"Annals of Statistics","page":"382 - 421","doi":"10.1214/14-AOS1281","volume":43,"date_published":"2015-02-01T00:00:00Z","issue":"1","date_created":"2018-12-11T11:52:25Z","abstract":[{"text":"This paper is aimed at deriving the universality of the largest eigenvalue of a class of high-dimensional real or complex sample covariance matrices of the form W N =Σ 1/2XX∗Σ 1/2 . Here, X = (xij )M,N is an M× N random matrix with independent entries xij , 1 ≤ i M,≤ 1 ≤ j ≤ N such that Exij = 0, E|xij |2 = 1/N . On dimensionality, we assume that M = M(N) and N/M → d ε (0, ∞) as N ∞→. For a class of general deterministic positive-definite M × M matrices Σ , under some additional assumptions on the distribution of xij 's, we show that the limiting behavior of the largest eigenvalue of W N is universal, via pursuing a Green function comparison strategy raised in [Probab. Theory Related Fields 154 (2012) 341-407, Adv. Math. 229 (2012) 1435-1515] by Erd″os, Yau and Yin for Wigner matrices and extended by Pillai and Yin [Ann. Appl. Probab. 24 (2014) 935-1001] to sample covariance matrices in the null case (&Epsi = I ). Consequently, in the standard complex case (Ex2 ij = 0), combing this universality property and the results known for Gaussian matrices obtained by El Karoui in [Ann. Probab. 35 (2007) 663-714] (nonsingular case) and Onatski in [Ann. Appl. Probab. 18 (2008) 470-490] (singular case), we show that after an appropriate normalization the largest eigenvalue of W N converges weakly to the type 2 Tracy-Widom distribution TW2 . Moreover, in the real case, we show that whenΣ is spiked with a fixed number of subcritical spikes, the type 1 Tracy-Widom limit TW1 holds for the normalized largest eigenvalue of W N , which extends a result of Féral and Péché in [J. Math. Phys. 50 (2009) 073302] to the scenario of nondiagonal Σ and more generally distributed X . In summary, we establish the Tracy-Widom type universality for the largest eigenvalue of generally distributed sample covariance matrices under quite light assumptions on &Sigma . Applications of these limiting results to statistical signal detection and structure recognition of separable covariance matrices are also discussed.","lang":"eng"}],"oa_version":"Preprint","acknowledgement":"B.Z. was supported in part by NSFC Grant 11071213, ZJNSF Grant R6090034 and SRFDP Grant 20100101110001. P.G. was supported in part by the Ministry of Education, Singapore, under Grant ARC 14/11. Z.W. was supported in part by the Ministry of Education, Singapore, under Grant ARC 14/11, and by a Grant R-155-000-131-112 at the National University of Singapore\r\n","publisher":"Institute of Mathematical Statistics","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1304.5690","open_access":"1"}],"oa":1,"month":"02","intvolume":" 43","date_updated":"2021-01-12T06:51:14Z","citation":{"mla":"Bao, Zhigang, et al. “Universality for the Largest Eigenvalue of Sample Covariance Matrices with General Population.” Annals of Statistics, vol. 43, no. 1, Institute of Mathematical Statistics, 2015, pp. 382–421, doi:10.1214/14-AOS1281.","ama":"Bao Z, Pan G, Zhou W. Universality for the largest eigenvalue of sample covariance matrices with general population. Annals of Statistics. 2015;43(1):382-421. doi:10.1214/14-AOS1281","apa":"Bao, Z., Pan, G., & Zhou, W. (2015). Universality for the largest eigenvalue of sample covariance matrices with general population. Annals of Statistics. Institute of Mathematical Statistics. https://doi.org/10.1214/14-AOS1281","ieee":"Z. Bao, G. Pan, and W. Zhou, “Universality for the largest eigenvalue of sample covariance matrices with general population,” Annals of Statistics, vol. 43, no. 1. Institute of Mathematical Statistics, pp. 382–421, 2015.","short":"Z. Bao, G. Pan, W. Zhou, Annals of Statistics 43 (2015) 382–421.","chicago":"Bao, Zhigang, Guangming Pan, and Wang Zhou. “Universality for the Largest Eigenvalue of Sample Covariance Matrices with General Population.” Annals of Statistics. Institute of Mathematical Statistics, 2015. https://doi.org/10.1214/14-AOS1281.","ista":"Bao Z, Pan G, Zhou W. 2015. Universality for the largest eigenvalue of sample covariance matrices with general population. Annals of Statistics. 43(1), 382–421."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"442E6A6C-F248-11E8-B48F-1D18A9856A87","first_name":"Zhigang","last_name":"Bao","full_name":"Bao, Zhigang","orcid":"0000-0003-3036-1475"},{"last_name":"Pan","full_name":"Pan, Guangming","first_name":"Guangming"},{"full_name":"Zhou, Wang","last_name":"Zhou","first_name":"Wang"}],"publist_id":"5672","title":"Universality for the largest eigenvalue of sample covariance matrices with general population","department":[{"_id":"LaEr"}],"_id":"1505","type":"journal_article","status":"public"},{"date_created":"2018-12-11T11:52:26Z","issue":"8","date_published":"2015-08-01T00:00:00Z","volume":17,"doi":"10.4171/JEMS/548","page":"1927 - 2036","publication":"Journal of the European Mathematical Society","language":[{"iso":"eng"}],"day":"01","year":"2015","publication_status":"published","intvolume":" 17","month":"08","oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1211.3786"}],"publisher":"European Mathematical Society","quality_controlled":"1","scopus_import":1,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We consider generalized Wigner ensembles and general β-ensembles with analytic potentials for any β ≥ 1. The recent universality results in particular assert that the local averages of consecutive eigenvalue gaps in the bulk of the spectrum are universal in the sense that they coincide with those of the corresponding Gaussian β-ensembles. In this article, we show that local averaging is not necessary for this result, i.e. we prove that the single gap distributions in the bulk are universal. In fact, with an additional step, our result can be extended to any C4(ℝ) potential."}],"title":"Gap universality of generalized Wigner and β ensembles","department":[{"_id":"LaEr"}],"publist_id":"5669","author":[{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","orcid":"0000-0001-5366-9603","full_name":"Erdös, László","last_name":"Erdös"},{"full_name":"Yau, Horng","last_name":"Yau","first_name":"Horng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:51:15Z","citation":{"ama":"Erdös L, Yau H. Gap universality of generalized Wigner and β ensembles. Journal of the European Mathematical Society. 2015;17(8):1927-2036. doi:10.4171/JEMS/548","apa":"Erdös, L., & Yau, H. (2015). Gap universality of generalized Wigner and β ensembles. Journal of the European Mathematical Society. European Mathematical Society. https://doi.org/10.4171/JEMS/548","ieee":"L. Erdös and H. Yau, “Gap universality of generalized Wigner and β ensembles,” Journal of the European Mathematical Society, vol. 17, no. 8. European Mathematical Society, pp. 1927–2036, 2015.","short":"L. Erdös, H. Yau, Journal of the European Mathematical Society 17 (2015) 1927–2036.","mla":"Erdös, László, and Horng Yau. “Gap Universality of Generalized Wigner and β Ensembles.” Journal of the European Mathematical Society, vol. 17, no. 8, European Mathematical Society, 2015, pp. 1927–2036, doi:10.4171/JEMS/548.","ista":"Erdös L, Yau H. 2015. Gap universality of generalized Wigner and β ensembles. Journal of the European Mathematical Society. 17(8), 1927–2036.","chicago":"Erdös, László, and Horng Yau. “Gap Universality of Generalized Wigner and β Ensembles.” Journal of the European Mathematical Society. European Mathematical Society, 2015. https://doi.org/10.4171/JEMS/548."},"status":"public","type":"journal_article","_id":"1508"},{"oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1208.5823","open_access":"1"}],"quality_controlled":"1","publisher":"Bernoulli Society for Mathematical Statistics and Probability","intvolume":" 21","month":"08","abstract":[{"text":"Consider the square random matrix An = (aij)n,n, where {aij:= a(n)ij , i, j = 1, . . . , n} is a collection of independent real random variables with means zero and variances one. Under the additional moment condition supn max1≤i,j ≤n Ea4ij <∞, we prove Girko's logarithmic law of det An in the sense that as n→∞ log | detAn| ? (1/2) log(n-1)! d/→√(1/2) log n N(0, 1).","lang":"eng"}],"oa_version":"Preprint","page":"1600 - 1628","date_created":"2018-12-11T11:52:25Z","doi":"10.3150/14-BEJ615","date_published":"2015-08-01T00:00:00Z","volume":21,"issue":"3","publication_status":"published","year":"2015","publication":"Bernoulli","language":[{"iso":"eng"}],"day":"01","type":"journal_article","status":"public","_id":"1506","author":[{"id":"442E6A6C-F248-11E8-B48F-1D18A9856A87","first_name":"Zhigang","last_name":"Bao","full_name":"Bao, Zhigang","orcid":"0000-0003-3036-1475"},{"last_name":"Pan","full_name":"Pan, Guangming","first_name":"Guangming"},{"first_name":"Wang","full_name":"Zhou, Wang","last_name":"Zhou"}],"publist_id":"5671","department":[{"_id":"LaEr"}],"title":"The logarithmic law of random determinant","citation":{"mla":"Bao, Zhigang, et al. “The Logarithmic Law of Random Determinant.” Bernoulli, vol. 21, no. 3, Bernoulli Society for Mathematical Statistics and Probability, 2015, pp. 1600–28, doi:10.3150/14-BEJ615.","short":"Z. Bao, G. Pan, W. Zhou, Bernoulli 21 (2015) 1600–1628.","ieee":"Z. Bao, G. Pan, and W. Zhou, “The logarithmic law of random determinant,” Bernoulli, vol. 21, no. 3. Bernoulli Society for Mathematical Statistics and Probability, pp. 1600–1628, 2015.","ama":"Bao Z, Pan G, Zhou W. The logarithmic law of random determinant. Bernoulli. 2015;21(3):1600-1628. doi:10.3150/14-BEJ615","apa":"Bao, Z., Pan, G., & Zhou, W. (2015). The logarithmic law of random determinant. Bernoulli. Bernoulli Society for Mathematical Statistics and Probability. https://doi.org/10.3150/14-BEJ615","chicago":"Bao, Zhigang, Guangming Pan, and Wang Zhou. “The Logarithmic Law of Random Determinant.” Bernoulli. Bernoulli Society for Mathematical Statistics and Probability, 2015. https://doi.org/10.3150/14-BEJ615.","ista":"Bao Z, Pan G, Zhou W. 2015. The logarithmic law of random determinant. Bernoulli. 21(3), 1600–1628."},"date_updated":"2021-01-12T06:51:14Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"citation":{"mla":"Pal, Arka, and Beatriz Vicoso. “The X Chromosome of Hemipteran Insects: Conservation, Dosage Compensation and Sex-Biased Expression.” Genome Biology and Evolution, vol. 7, no. 12, Oxford University Press, 2015, pp. 3259–68, doi:10.1093/gbe/evv215.","ama":"Pal A, Vicoso B. The X chromosome of hemipteran insects: Conservation, dosage compensation and sex-biased expression. Genome Biology and Evolution. 2015;7(12):3259-3268. doi:10.1093/gbe/evv215","apa":"Pal, A., & Vicoso, B. (2015). The X chromosome of hemipteran insects: Conservation, dosage compensation and sex-biased expression. Genome Biology and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evv215","short":"A. Pal, B. Vicoso, Genome Biology and Evolution 7 (2015) 3259–3268.","ieee":"A. Pal and B. Vicoso, “The X chromosome of hemipteran insects: Conservation, dosage compensation and sex-biased expression,” Genome Biology and Evolution, vol. 7, no. 12. Oxford University Press, pp. 3259–3268, 2015.","chicago":"Pal, Arka, and Beatriz Vicoso. “The X Chromosome of Hemipteran Insects: Conservation, Dosage Compensation and Sex-Biased Expression.” Genome Biology and Evolution. Oxford University Press, 2015. https://doi.org/10.1093/gbe/evv215.","ista":"Pal A, Vicoso B. 2015. The X chromosome of hemipteran insects: Conservation, dosage compensation and sex-biased expression. Genome Biology and Evolution. 7(12), 3259–3268."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"first_name":"Arka","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","full_name":"Pal, Arka","last_name":"Pal"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","last_name":"Vicoso"}],"publist_id":"5664","title":"The X chromosome of hemipteran insects: Conservation, dosage compensation and sex-biased expression","oa":1,"publisher":"Oxford University Press","quality_controlled":"1","year":"2015","has_accepted_license":"1","publication":"Genome Biology and Evolution","day":"01","page":"3259 - 3268","date_created":"2018-12-11T11:52:27Z","date_published":"2015-12-01T00:00:00Z","doi":"10.1093/gbe/evv215","_id":"1513","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":"496","status":"public","date_updated":"2021-01-12T06:51:18Z","ddc":["570"],"department":[{"_id":"BeVi"}],"file_date_updated":"2020-07-14T12:45:00Z","abstract":[{"text":"Insects of the order Hemiptera (true bugs) use a wide range of mechanisms of sex determination, including genetic sex determination, paternal genome elimination, and haplodiploidy. Genetic sex determination, the prevalent mode, is generally controlled by a pair of XY sex chromosomes or by an XX/X0 system, but different configurations that include additional sex chromosomes are also present. Although this diversity of sex determining systems has been extensively studied at the cytogenetic level, only the X chromosome of the model pea aphid Acyrthosiphon pisum has been analyzed at the genomic level, and little is known about X chromosome biology in the rest of the order.\r\n\r\nIn this study, we take advantage of published DNA- and RNA-seq data from three additional Hemiptera species to perform a comparative analysis of the gene content and expression of the X chromosome throughout this clade. We find that, despite showing evidence of dosage compensation, the X chromosomes of these species show female-biased expression, and a deficit of male-biased genes, in direct contrast to the pea aphid X. We further detect an excess of shared gene content between these very distant species, suggesting that despite the diversity of sex determining systems, the same chromosomal element is used as the X throughout a large portion of the order. ","lang":"eng"}],"oa_version":"Published Version","scopus_import":1,"intvolume":" 7","month":"12","publication_status":"published","language":[{"iso":"eng"}],"file":[{"checksum":"2b56b8c2e2a1d4cc3c9cb8daba26dd9b","file_id":"5284","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:17:29Z","file_name":"IST-2016-496-v1+1_Genome_Biol_Evol-2015-Pal-3259-68.pdf","creator":"system","date_updated":"2020-07-14T12:45:00Z","file_size":858027}],"ec_funded":1,"volume":7,"issue":"12"},{"date_updated":"2021-01-12T06:51:19Z","ddc":["519"],"file_date_updated":"2020-07-14T12:45:00Z","department":[{"_id":"JaMa"}],"_id":"1517","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":"494","status":"public","publication_status":"published","language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"4828","checksum":"135741c17d3e1547ca696b6fbdcd559c","creator":"system","date_updated":"2020-07-14T12:45:00Z","file_size":230525,"date_created":"2018-12-12T10:10:39Z","file_name":"IST-2016-494-v1+1_4315-23820-1-PB.pdf"}],"volume":20,"abstract":[{"lang":"eng","text":"We study the large deviation rate functional for the empirical distribution of independent Brownian particles with drift. In one dimension, it has been shown by Adams, Dirr, Peletier and Zimmer that this functional is asymptotically equivalent (in the sense of Γ-convergence) to the Jordan-Kinderlehrer-Otto functional arising in the Wasserstein gradient flow structure of the Fokker-Planck equation. In higher dimensions, part of this statement (the lower bound) has been recently proved by Duong, Laschos and Renger, but the upper bound remained open, since the proof of Duong et al relies on regularity properties of optimal transport maps that are restricted to one dimension. In this note we present a new proof of the upper bound, thereby generalising the result of Adams et al to arbitrary dimensions.\r\n"}],"oa_version":"Published Version","scopus_import":1,"intvolume":" 20","month":"11","citation":{"mla":"Erbar, Matthias, et al. “From Large Deviations to Wasserstein Gradient Flows in Multiple Dimensions.” Electronic Communications in Probability, vol. 20, 89, Institute of Mathematical Statistics, 2015, doi:10.1214/ECP.v20-4315.","ama":"Erbar M, Maas J, Renger M. From large deviations to Wasserstein gradient flows in multiple dimensions. Electronic Communications in Probability. 2015;20. doi:10.1214/ECP.v20-4315","apa":"Erbar, M., Maas, J., & Renger, M. (2015). From large deviations to Wasserstein gradient flows in multiple dimensions. Electronic Communications in Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/ECP.v20-4315","ieee":"M. Erbar, J. Maas, and M. Renger, “From large deviations to Wasserstein gradient flows in multiple dimensions,” Electronic Communications in Probability, vol. 20. Institute of Mathematical Statistics, 2015.","short":"M. Erbar, J. Maas, M. Renger, Electronic Communications in Probability 20 (2015).","chicago":"Erbar, Matthias, Jan Maas, and Michiel Renger. “From Large Deviations to Wasserstein Gradient Flows in Multiple Dimensions.” Electronic Communications in Probability. Institute of Mathematical Statistics, 2015. https://doi.org/10.1214/ECP.v20-4315.","ista":"Erbar M, Maas J, Renger M. 2015. From large deviations to Wasserstein gradient flows in multiple dimensions. Electronic Communications in Probability. 20, 89."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"5660","author":[{"first_name":"Matthias","full_name":"Erbar, Matthias","last_name":"Erbar"},{"last_name":"Maas","full_name":"Maas, Jan","orcid":"0000-0002-0845-1338","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"},{"first_name":"Michiel","last_name":"Renger","full_name":"Renger, Michiel"}],"title":"From large deviations to Wasserstein gradient flows in multiple dimensions","article_number":"89","year":"2015","has_accepted_license":"1","publication":"Electronic Communications in Probability","day":"29","date_created":"2018-12-11T11:52:29Z","doi":"10.1214/ECP.v20-4315","date_published":"2015-11-29T00:00:00Z","oa":1,"publisher":"Institute of Mathematical Statistics","quality_controlled":"1"},{"day":"01","publication":"European Journal of Neuroscience","publication_status":"published","year":"2015","volume":41,"doi":"10.1111/ejn.12779","date_published":"2015-01-01T00:00:00Z","issue":"2","date_created":"2018-12-11T11:52:28Z","page":"157 - 167","acknowledgement":"This work was supported by the Austrian Science Fund (FWF) (project W012060-10 to F.F.), The Japan Society for the Promotion of Science (JSPS) (to R.S.) and Agence Nationale de la Recherche (ANR-11-BSV4-018-03, DELTAPLAN), Région Languedoc-Roussillon (Chercheur d’Avenir) (to J.P.). The authors thank S. Schönherr for excellent technical support and Dr Furuichi for kindly providing anti-Homer3 antibodies.","abstract":[{"text":"Type 1 metabotropic glutamate (mGlu1) receptors play a pivotal role in different forms of synaptic plasticity in the cerebellar cortex, e.g. long-term depression at glutamatergic synapses and rebound potentiation at GABAergic synapses. These various forms of plasticity might depend on the subsynaptic arrangement of the receptor in Purkinje cells that can be regulated by protein-protein interactions. This study investigated, by means of the freeze-fracture replica immunogold labelling method, the subcellular localization of mGlu1 receptors in the rodent cerebellum and whether Homer proteins regulate their subsynaptic distribution. We observed a widespread extrasynaptic localization of mGlu1 receptors and confirmed their peri-synaptic enrichment at glutamatergic synapses. Conversely, we detected mGlu1 receptors within the main body of GABAergic synapses onto Purkinje cell dendrites. Although Homer proteins are known to interact with the mGlu1 receptor C-terminus, we could not detect Homer3, the most abundant Homer protein in the cerebellar cortex, at GABAergic synapses by pre-embedding and post-embedding immunoelectron microscopy. We then hypothesized a critical role for Homer proteins in the peri-junctional localization of mGlu1 receptors at glutamatergic synapses. To disrupt Homer-associated protein complexes, mice were tail-vein injected with the membrane-permeable dominant-negative TAT-Homer1a. Freeze-fracture replica immunogold labelling analysis showed no significant alteration in the mGlu1 receptor distribution pattern at parallel fibre-Purkinje cell synapses, suggesting that other scaffolding proteins are involved in the peri-synaptic confinement. The identification of interactors that regulate the subsynaptic localization of the mGlu1 receptor at neurochemically distinct synapses may offer new insight into its trafficking and intracellular signalling.","lang":"eng"}],"month":"01","intvolume":" 41","quality_controlled":0,"publisher":"Wiley-Blackwell","extern":1,"citation":{"chicago":"Mansouri, Mahnaz, Yu Kasugai, Yugo Fukazawa, Federica Bertaso, Fabrice Raynaud, Julie Perroy, Laurent Fagni, et al. “Distinct Subsynaptic Localization of Type 1 Metabotropic Glutamate Receptors at Glutamatergic and GABAergic Synapses in the Rodent Cerebellar Cortex.” European Journal of Neuroscience. Wiley-Blackwell, 2015. https://doi.org/10.1111/ejn.12779.","ista":"Mansouri M, Kasugai Y, Fukazawa Y, Bertaso F, Raynaud F, Perroy J, Fagni L, Kaufmann W, Watanabe M, Shigemoto R, Ferraguti F. 2015. Distinct subsynaptic localization of type 1 metabotropic glutamate receptors at glutamatergic and GABAergic synapses in the rodent cerebellar cortex. European Journal of Neuroscience. 41(2), 157–167.","mla":"Mansouri, Mahnaz, et al. “Distinct Subsynaptic Localization of Type 1 Metabotropic Glutamate Receptors at Glutamatergic and GABAergic Synapses in the Rodent Cerebellar Cortex.” European Journal of Neuroscience, vol. 41, no. 2, Wiley-Blackwell, 2015, pp. 157–67, doi:10.1111/ejn.12779.","ama":"Mansouri M, Kasugai Y, Fukazawa Y, et al. Distinct subsynaptic localization of type 1 metabotropic glutamate receptors at glutamatergic and GABAergic synapses in the rodent cerebellar cortex. European Journal of Neuroscience. 2015;41(2):157-167. doi:10.1111/ejn.12779","apa":"Mansouri, M., Kasugai, Y., Fukazawa, Y., Bertaso, F., Raynaud, F., Perroy, J., … Ferraguti, F. (2015). Distinct subsynaptic localization of type 1 metabotropic glutamate receptors at glutamatergic and GABAergic synapses in the rodent cerebellar cortex. European Journal of Neuroscience. Wiley-Blackwell. https://doi.org/10.1111/ejn.12779","short":"M. Mansouri, Y. Kasugai, Y. Fukazawa, F. Bertaso, F. Raynaud, J. Perroy, L. Fagni, W. Kaufmann, M. Watanabe, R. Shigemoto, F. Ferraguti, European Journal of Neuroscience 41 (2015) 157–167.","ieee":"M. Mansouri et al., “Distinct subsynaptic localization of type 1 metabotropic glutamate receptors at glutamatergic and GABAergic synapses in the rodent cerebellar cortex,” European Journal of Neuroscience, vol. 41, no. 2. Wiley-Blackwell, pp. 157–167, 2015."},"date_updated":"2023-02-23T10:02:24Z","title":"Distinct subsynaptic localization of type 1 metabotropic glutamate receptors at glutamatergic and GABAergic synapses in the rodent cerebellar cortex","publist_id":"5662","author":[{"first_name":"Mahnaz","last_name":"Mansouri","full_name":"Mansouri, Mahnaz"},{"last_name":"Kasugai","full_name":"Kasugai, Yu","first_name":"Yu"},{"first_name":"Yugo","full_name":"Fukazawa, Yugo","last_name":"Fukazawa"},{"full_name":"Bertaso, Federica","last_name":"Bertaso","first_name":"Federica"},{"first_name":"Fabrice","full_name":"Raynaud, Fabrice","last_name":"Raynaud"},{"last_name":"Perroy","full_name":"Perroy, Julie","first_name":"Julie"},{"full_name":"Fagni, Laurent","last_name":"Fagni","first_name":"Laurent"},{"orcid":"0000-0001-9735-5315","full_name":"Walter Kaufmann","last_name":"Kaufmann","first_name":"Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Masahiko","last_name":"Watanabe","full_name":"Watanabe, Masahiko"},{"orcid":"0000-0001-8761-9444","full_name":"Ryuichi Shigemoto","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi"},{"full_name":"Ferraguti, Francesco","last_name":"Ferraguti","first_name":"Francesco"}],"_id":"1515","status":"public","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)"}},{"day":"10","publication":"Cerebral Cortex","year":"2015","publication_status":"published","volume":25,"doi":"10.1093/cercor/bhu231","date_published":"2015-10-10T00:00:00Z","issue":"10","date_created":"2018-12-11T11:52:27Z","page":"3699 - 3712","acknowledgement":"This work was supported by grants from Ministerio de Economia y Competitividad, Spain (MINECO; BFU2010-15832), European Union (HEALTH-F2-2007-202167), and Cajal Blue Brain to A.A. Grants from Spain (MINECO; BFU-2009-08404 and\nCSD2008-00005) to R.L. Grants from Spain (MINECO; Consolider, CSD2010-00045; Ramón y Cajal Program, RYC-2012-12014; and BFU2013-47265) to G.P. We thank Dr Atsu Aiba (Animal Resources, Center for Disease Biology and Integrative Medicine, Faculty of Medicine, University of Tokyo) for the donation of the mGluR1b rescue mice.","abstract":[{"lang":"eng","text":"Endocannabinoids (eCBs) play key roles in brain function, acting as modulatory signals in synaptic transmission and plasticity. They are recognized as retrograde messengers that mediate long-term synaptic depression (LTD), but their ability to induce long-term potentiation (LTP) is poorly known. We show that eCBs induce the long-term enhancement of transmitter release at single hippocampal synapses through stimulation of astrocytes when coincident with postsynaptic activity. This LTP requires the coordinated activity of the 3 elements of the tripartite synapse: 1) eCB-evoked astrocyte calcium signal that stimulates glutamate release; 2) postsynaptic nitric oxide production; and 3) activation of protein kinase C and presynaptic group I metabotropic glutamate receptors, whose location at presynaptic sites was confirmed by immunoelectron microscopy. Hence, while eCBs act as retrograde signals to depress homoneuronal synapses, they serve as lateral messengers to induce LTP in distant heteroneuronal synapses through stimulation of astrocytes. Therefore, eCBs can trigger LTP through stimulation of astrocyte-neuron signaling, revealing novel cellular mechanisms of eCB effects on synaptic plasticity."}],"month":"10","intvolume":" 25","quality_controlled":0,"publisher":"Oxford University Press","extern":1,"date_updated":"2021-01-12T06:51:18Z","citation":{"ama":"Gómez Gonzalo M, Navarrete M, Perea G, et al. Endocannabinoids induce lateral long term potentiation of transmitter release by stimulation of gliotransmission. Cerebral Cortex. 2015;25(10):3699-3712. doi:10.1093/cercor/bhu231","apa":"Gómez Gonzalo, M., Navarrete, M., Perea, G., Covelo, A., Martín Fernández, M., Shigemoto, R., … Araque, A. (2015). Endocannabinoids induce lateral long term potentiation of transmitter release by stimulation of gliotransmission. Cerebral Cortex. Oxford University Press. https://doi.org/10.1093/cercor/bhu231","ieee":"M. Gómez Gonzalo et al., “Endocannabinoids induce lateral long term potentiation of transmitter release by stimulation of gliotransmission,” Cerebral Cortex, vol. 25, no. 10. Oxford University Press, pp. 3699–3712, 2015.","short":"M. Gómez Gonzalo, M. Navarrete, G. Perea, A. Covelo, M. Martín Fernández, R. Shigemoto, R. Luján, A. Araque, Cerebral Cortex 25 (2015) 3699–3712.","mla":"Gómez Gonzalo, Marta, et al. “Endocannabinoids Induce Lateral Long Term Potentiation of Transmitter Release by Stimulation of Gliotransmission.” Cerebral Cortex, vol. 25, no. 10, Oxford University Press, 2015, pp. 3699–712, doi:10.1093/cercor/bhu231.","ista":"Gómez Gonzalo M, Navarrete M, Perea G, Covelo A, Martín Fernández M, Shigemoto R, Luján R, Araque A. 2015. Endocannabinoids induce lateral long term potentiation of transmitter release by stimulation of gliotransmission. Cerebral Cortex. 25(10), 3699–3712.","chicago":"Gómez Gonzalo, Marta, Marta Navarrete, Gertrudis Perea, Ana Covelo, Mario Martín Fernández, Ryuichi Shigemoto, Rafael Luján, and Alfonso Araque. “Endocannabinoids Induce Lateral Long Term Potentiation of Transmitter Release by Stimulation of Gliotransmission.” Cerebral Cortex. Oxford University Press, 2015. https://doi.org/10.1093/cercor/bhu231."},"title":"Endocannabinoids induce lateral long term potentiation of transmitter release by stimulation of gliotransmission","author":[{"last_name":"Gómez Gonzalo","full_name":"Gómez-Gonzalo, Marta","first_name":"Marta"},{"first_name":"Marta","full_name":"Navarrete, Marta","last_name":"Navarrete"},{"last_name":"Perea","full_name":"Perea, Gertrudis","first_name":"Gertrudis"},{"first_name":"Ana","last_name":"Covelo","full_name":"Covelo, Ana"},{"first_name":"Mario","full_name":"Martín-Fernández, Mario","last_name":"Martín Fernández"},{"last_name":"Shigemoto","full_name":"Ryuichi Shigemoto","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi"},{"first_name":"Rafael","full_name":"Luján, Rafael","last_name":"Luján"},{"first_name":"Alfonso","full_name":"Araque, Alfonso","last_name":"Araque"}],"publist_id":"5663","_id":"1514","status":"public","type":"journal_article"},{"has_accepted_license":"1","year":"2015","day":"19","publication":"Evolution","page":"1101 - 1112","doi":"10.1111/evo.12641","date_published":"2015-03-19T00:00:00Z","date_created":"2018-12-11T11:52:29Z","quality_controlled":"1","publisher":"Wiley","oa":1,"citation":{"ista":"Barton NH, Servedio M. 2015. The interpretation of selection coefficients. Evolution. 69(5), 1101–1112.","chicago":"Barton, Nicholas H, and Maria Servedio. “The Interpretation of Selection Coefficients.” Evolution. Wiley, 2015. https://doi.org/10.1111/evo.12641.","ama":"Barton NH, Servedio M. The interpretation of selection coefficients. Evolution. 2015;69(5):1101-1112. doi:10.1111/evo.12641","apa":"Barton, N. H., & Servedio, M. (2015). The interpretation of selection coefficients. Evolution. Wiley. https://doi.org/10.1111/evo.12641","ieee":"N. H. Barton and M. Servedio, “The interpretation of selection coefficients,” Evolution, vol. 69, no. 5. Wiley, pp. 1101–1112, 2015.","short":"N.H. Barton, M. Servedio, Evolution 69 (2015) 1101–1112.","mla":"Barton, Nicholas H., and Maria Servedio. “The Interpretation of Selection Coefficients.” Evolution, vol. 69, no. 5, Wiley, 2015, pp. 1101–12, doi:10.1111/evo.12641."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"first_name":"Maria","last_name":"Servedio","full_name":"Servedio, Maria"}],"publist_id":"5656","title":"The interpretation of selection coefficients","project":[{"name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","file":[{"date_updated":"2020-07-14T12:45:00Z","file_size":188872,"creator":"system","date_created":"2018-12-12T10:10:34Z","file_name":"IST-2016-560-v1+1_Interpreting_ML_coefficients_11.2.15_App.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"fd8d23f476bc194419929b72ca265c02","file_id":"4822"},{"date_created":"2018-12-12T10:10:35Z","file_name":"IST-2016-560-v1+2_Interpreting_ML_coefficients_11.2.15_mainText.pdf","creator":"system","date_updated":"2020-07-14T12:45:00Z","file_size":577415,"file_id":"4823","checksum":"b774911e70044641d556e258efcb52ef","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"volume":69,"issue":"5","ec_funded":1,"abstract":[{"lang":"eng","text":"Evolutionary biologists have an array of powerful theoretical techniques that can accurately predict changes in the genetic composition of populations. Changes in gene frequencies and genetic associations between loci can be tracked as they respond to a wide variety of evolutionary forces. However, it is often less clear how to decompose these various forces into components that accurately reflect the underlying biology. Here, we present several issues that arise in the definition and interpretation of selection and selection coefficients, focusing on insights gained through the examination of selection coefficients in multilocus notation. Using this notation, we discuss how its flexibility-which allows different biological units to be identified as targets of selection-is reflected in the interpretation of the coefficients that the notation generates. In many situations, it can be difficult to agree on whether loci can be considered to be under "direct" versus "indirect" selection, or to quantify this selection. We present arguments for what the terms direct and indirect selection might best encompass, considering a range of issues, from viability and sexual selection to kin selection. We show how multilocus notation can discriminate between direct and indirect selection, and describe when it can do so."}],"oa_version":"Submitted Version","scopus_import":1,"month":"03","intvolume":" 69","date_updated":"2021-01-12T06:51:20Z","ddc":["570"],"department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:45:00Z","_id":"1519","type":"journal_article","status":"public","pubrep_id":"560"},{"author":[{"full_name":"Bauer, Bruno","last_name":"Bauer","first_name":"Bruno"},{"last_name":"Blechl","full_name":"Blechl, Guido","first_name":"Guido"},{"full_name":"Bock, Christoph","last_name":"Bock","first_name":"Christoph"},{"first_name":"Patrick","id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","full_name":"Danowski, Patrick","orcid":"0000-0002-6026-4409","last_name":"Danowski"},{"full_name":"Ferus, Andreas","last_name":"Ferus","first_name":"Andreas"},{"first_name":"Anton","last_name":"Graschopf","full_name":"Graschopf, Anton"},{"first_name":"Thomas","full_name":"König, Thomas","last_name":"König"},{"full_name":"Mayer, Katja","last_name":"Mayer","first_name":"Katja"},{"first_name":"Falk","full_name":"Reckling, Falk","last_name":"Reckling"},{"last_name":"Rieck","full_name":"Rieck, Katharina","first_name":"Katharina"},{"first_name":"Peter","last_name":"Seitz","full_name":"Seitz, Peter"},{"full_name":"Stöger, Herwig","last_name":"Stöger","first_name":"Herwig"},{"last_name":"Welzig","full_name":"Welzig, Elvira","first_name":"Elvira"}],"publist_id":"5648","article_processing_charge":"No","title":"Arbeitsgruppe „Nationale Strategie“ des Open Access Network Austria OANA","citation":{"mla":"Bauer, Bruno, et al. “Arbeitsgruppe „Nationale Strategie“ Des Open Access Network Austria OANA.” VÖB Mitteilungen, vol. 68, no. 3, Verein Österreichischer Bibliothekare, 2015, pp. 580–607, doi:10.5281/zenodo.33178.","ieee":"B. Bauer et al., “Arbeitsgruppe „Nationale Strategie“ des Open Access Network Austria OANA,” VÖB Mitteilungen, vol. 68, no. 3. Verein Österreichischer Bibliothekare, pp. 580–607, 2015.","short":"B. Bauer, G. Blechl, C. Bock, P. Danowski, A. Ferus, A. Graschopf, T. König, K. Mayer, F. Reckling, K. Rieck, P. Seitz, H. Stöger, E. Welzig, VÖB Mitteilungen 68 (2015) 580–607.","apa":"Bauer, B., Blechl, G., Bock, C., Danowski, P., Ferus, A., Graschopf, A., … Welzig, E. (2015). Arbeitsgruppe „Nationale Strategie“ des Open Access Network Austria OANA. VÖB Mitteilungen. Verein Österreichischer Bibliothekare. https://doi.org/10.5281/zenodo.33178","ama":"Bauer B, Blechl G, Bock C, et al. Arbeitsgruppe „Nationale Strategie“ des Open Access Network Austria OANA. VÖB Mitteilungen. 2015;68(3):580-607. doi:10.5281/zenodo.33178","chicago":"Bauer, Bruno, Guido Blechl, Christoph Bock, Patrick Danowski, Andreas Ferus, Anton Graschopf, Thomas König, et al. “Arbeitsgruppe „Nationale Strategie“ Des Open Access Network Austria OANA.” VÖB Mitteilungen. Verein Österreichischer Bibliothekare, 2015. https://doi.org/10.5281/zenodo.33178.","ista":"Bauer B, Blechl G, Bock C, Danowski P, Ferus A, Graschopf A, König T, Mayer K, Reckling F, Rieck K, Seitz P, Stöger H, Welzig E. 2015. Arbeitsgruppe „Nationale Strategie“ des Open Access Network Austria OANA. VÖB Mitteilungen. 68(3), 580–607."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"580 - 607","doi":"10.5281/zenodo.33178","date_published":"2015-11-12T00:00:00Z","date_created":"2018-12-11T11:52:31Z","has_accepted_license":"1","year":"2015","day":"12","publication":"VÖB Mitteilungen","quality_controlled":"1","publisher":"Verein Österreichischer Bibliothekare","oa":1,"file_date_updated":"2020-07-14T12:45:00Z","department":[{"_id":"E-Lib"}],"date_updated":"2021-01-12T06:51:22Z","ddc":["020"],"type":"journal_article","article_type":"original","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":"720","_id":"1525","volume":68,"issue":"3","publication_status":"published","file":[{"creator":"system","date_updated":"2020-07-14T12:45:00Z","file_size":931707,"date_created":"2018-12-12T10:17:59Z","file_name":"IST-2016-720-v1+1_OANA_OA-Empfehlungen_12-11-2015.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"5317","checksum":"a495fe253bbc7615b1d60e9e85c94408"}],"language":[{"iso":"eng"}],"scopus_import":1,"month":"11","intvolume":" 68","abstract":[{"text":"Based on 16 recommendations, efforts should be made to achieve the following goal: By 2025, all scholarly publication activity in Austria should be Open Access. In other words, the final versions of all scholarly publications resulting from the support of public resources must be freely accessible on the Internet without delay (Gold Open Access). The resources required to meet this obligation shall be provided to the authors, or the cost of the publication venues shall be borne directly by the research organisations.","lang":"eng"}],"oa_version":"Published Version"},{"publication_status":"published","year":"2015","publication_identifier":{"isbn":["978-1-4503-3496-9"]},"language":[{"iso":"eng"}],"day":"01","page":"93 - 100","date_created":"2018-12-11T11:52:30Z","doi":"10.1145/2786784.2786803","date_published":"2015-08-01T00:00:00Z","abstract":[{"lang":"eng","text":"Creating mechanical automata that can walk in stable and pleasing manners is a challenging task that requires both skill and expertise. We propose to use computational design to offset the technical difficulties of this process. A simple drag-and-drop interface allows casual users to create personalized walking toys from a library of pre-defined template mechanisms. Provided with this input, our method leverages physical simulation and evolutionary optimization to refine the mechanical designs such that the resulting toys are able to walk. The optimization process is guided by an intuitive set of objectives that measure the quality of the walking motions. We demonstrate our approach on a set of simulated mechanical toys with different numbers of legs and various distinct gaits. Two fabricated prototypes showcase the feasibility of our designs."}],"oa_version":"None","publisher":"ACM","quality_controlled":"1","scopus_import":1,"month":"08","date_updated":"2021-01-12T06:51:21Z","citation":{"ieee":"G. Bharaj, S. Coros, B. Thomaszewski, J. Tompkin, B. Bickel, and H. Pfister, “Computational design of walking automata,” presented at the SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation, Los Angeles, CA, United States, 2015, pp. 93–100.","short":"G. Bharaj, S. Coros, B. Thomaszewski, J. Tompkin, B. Bickel, H. Pfister, in:, ACM, 2015, pp. 93–100.","ama":"Bharaj G, Coros S, Thomaszewski B, Tompkin J, Bickel B, Pfister H. Computational design of walking automata. In: ACM; 2015:93-100. doi:10.1145/2786784.2786803","apa":"Bharaj, G., Coros, S., Thomaszewski, B., Tompkin, J., Bickel, B., & Pfister, H. (2015). Computational design of walking automata (pp. 93–100). Presented at the SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation, Los Angeles, CA, United States: ACM. https://doi.org/10.1145/2786784.2786803","mla":"Bharaj, Gaurav, et al. Computational Design of Walking Automata. ACM, 2015, pp. 93–100, doi:10.1145/2786784.2786803.","ista":"Bharaj G, Coros S, Thomaszewski B, Tompkin J, Bickel B, Pfister H. 2015. Computational design of walking automata. SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation, 93–100.","chicago":"Bharaj, Gaurav, Stelian Coros, Bernhard Thomaszewski, James Tompkin, Bernd Bickel, and Hanspeter Pfister. “Computational Design of Walking Automata,” 93–100. ACM, 2015. https://doi.org/10.1145/2786784.2786803."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"5655","author":[{"last_name":"Bharaj","full_name":"Bharaj, Gaurav","first_name":"Gaurav"},{"full_name":"Coros, Stelian","last_name":"Coros","first_name":"Stelian"},{"first_name":"Bernhard","full_name":"Thomaszewski, Bernhard","last_name":"Thomaszewski"},{"full_name":"Tompkin, James","last_name":"Tompkin","first_name":"James"},{"first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","last_name":"Bickel"},{"last_name":"Pfister","full_name":"Pfister, Hanspeter","first_name":"Hanspeter"}],"department":[{"_id":"BeBi"}],"title":"Computational design of walking automata","_id":"1520","conference":{"name":"SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation","start_date":"2015-08-07","end_date":"2015-08-09","location":"Los Angeles, CA, United States"},"type":"conference","status":"public"},{"publication":"Functional Plant Biology","day":"01","year":"2015","date_created":"2018-12-11T11:52:34Z","date_published":"2015-03-01T00:00:00Z","doi":"10.1071/FP14171","page":"239 - 251","quality_controlled":"1","publisher":"CSIRO","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Yang, Huaiyu, Jenny Von Der Fecht Bartenbach, Jiří Friml, Jan Lohmann, Benjamin Neuhäuser, and Uwe Ludewig. “Auxin-Modulated Root Growth Inhibition in Arabidopsis Thaliana Seedlings with Ammonium as the Sole Nitrogen Source.” Functional Plant Biology. CSIRO, 2015. https://doi.org/10.1071/FP14171.","ista":"Yang H, Von Der Fecht Bartenbach J, Friml J, Lohmann J, Neuhäuser B, Ludewig U. 2015. Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with ammonium as the sole nitrogen source. Functional Plant Biology. 42(3), 239–251.","mla":"Yang, Huaiyu, et al. “Auxin-Modulated Root Growth Inhibition in Arabidopsis Thaliana Seedlings with Ammonium as the Sole Nitrogen Source.” Functional Plant Biology, vol. 42, no. 3, CSIRO, 2015, pp. 239–51, doi:10.1071/FP14171.","ieee":"H. Yang, J. Von Der Fecht Bartenbach, J. Friml, J. Lohmann, B. Neuhäuser, and U. Ludewig, “Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with ammonium as the sole nitrogen source,” Functional Plant Biology, vol. 42, no. 3. CSIRO, pp. 239–251, 2015.","short":"H. Yang, J. Von Der Fecht Bartenbach, J. Friml, J. Lohmann, B. Neuhäuser, U. Ludewig, Functional Plant Biology 42 (2015) 239–251.","ama":"Yang H, Von Der Fecht Bartenbach J, Friml J, Lohmann J, Neuhäuser B, Ludewig U. Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with ammonium as the sole nitrogen source. Functional Plant Biology. 2015;42(3):239-251. doi:10.1071/FP14171","apa":"Yang, H., Von Der Fecht Bartenbach, J., Friml, J., Lohmann, J., Neuhäuser, B., & Ludewig, U. (2015). Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with ammonium as the sole nitrogen source. Functional Plant Biology. CSIRO. https://doi.org/10.1071/FP14171"},"title":"Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with ammonium as the sole nitrogen source","external_id":{"pmid":["32480670"]},"article_processing_charge":"No","publist_id":"5639","author":[{"last_name":"Yang","full_name":"Yang, Huaiyu","first_name":"Huaiyu"},{"full_name":"Von Der Fecht Bartenbach, Jenny","last_name":"Von Der Fecht Bartenbach","first_name":"Jenny"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"},{"first_name":"Jan","last_name":"Lohmann","full_name":"Lohmann, Jan"},{"last_name":"Neuhäuser","full_name":"Neuhäuser, Benjamin","first_name":"Benjamin"},{"full_name":"Ludewig, Uwe","last_name":"Ludewig","first_name":"Uwe"}],"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["1445-4408"]},"issue":"3","volume":42,"pmid":1,"oa_version":"None","abstract":[{"text":"Ammonium is the major nitrogen source in some plant ecosystems but is toxic at high concentrations, especially when available as the exclusive nitrogen source. Ammonium stress rapidly leads to various metabolic and hormonal imbalances that ultimately inhibit root and shoot growth in many plant species, including Arabidopsis thaliana (L.) Heynh. To identify molecular and genetic factors involved in seedling survival with prolonged exclusive NH4+ nutrition, a transcriptomic analysis with microarrays was used. Substantial transcriptional differences were most pronounced in (NH4)2SO4-grown seedlings, compared with plants grown on KNO3 or NH4NO3. Consistent with previous physiological analyses, major differences in the expression modules of photosynthesis-related genes, an altered mitochondrial metabolism, differential expression of the primary NH4+ assimilation, alteration of transporter gene expression and crucial changes in cell wall biosynthesis were found. A major difference in plant hormone responses, particularly of auxin but not cytokinin, was striking. The activity of the DR5::GUS reporter revealed a dramatically decreased auxin response in (NH4)2SO4-grown primary roots. The impaired root growth on (NH4)2SO4 was partially rescued by exogenous auxin or in specific mutants in the auxin pathway. The data suggest that NH4+-induced nutritional and metabolic imbalances can be partially overcome by elevated auxin levels.","lang":"eng"}],"intvolume":" 42","month":"03","scopus_import":"1","date_updated":"2022-05-24T09:02:24Z","department":[{"_id":"JiFr"}],"_id":"1532","status":"public","article_type":"original","type":"journal_article"},{"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"isbn":["978-3-319-15089-5"]},"volume":40,"oa_version":"None","abstract":[{"text":"The Heat Kernel Signature (HKS) is a scalar quantity which is derived from the heat kernel of a given shape. Due to its robustness, isometry invariance, and multiscale nature, it has been successfully applied in many geometric applications. From a more general point of view, the HKS can be considered as a descriptor of the metric of a Riemannian manifold. Given a symmetric positive definite tensor field we may interpret it as the metric of some Riemannian manifold and thereby apply the HKS to visualize and analyze the given tensor data. In this paper, we propose a generalization of this approach that enables the treatment of indefinite tensor fields, like the stress tensor, by interpreting them as a generator of a positive definite tensor field. To investigate the usefulness of this approach we consider the stress tensor from the two-point-load model example and from a mechanical work piece.","lang":"eng"}],"intvolume":" 40","month":"01","alternative_title":["Mathematics and Visualization"],"scopus_import":"1","date_updated":"2022-06-10T09:50:14Z","department":[{"_id":"HeEd"}],"_id":"1531","status":"public","type":"book_chapter","publication":"Visualization and Processing of Higher Order Descriptors for Multi-Valued Data","day":"01","year":"2015","date_created":"2018-12-11T11:52:33Z","doi":"10.1007/978-3-319-15090-1_13","date_published":"2015-01-01T00:00:00Z","page":"257 - 267","edition":"1","quality_controlled":"1","publisher":"Springer","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Zobel, V., Reininghaus, J., & Hotz, I. (2015). Visualizing symmetric indefinite 2D tensor fields using The Heat Kernel Signature. In I. Hotz & T. Schultz (Eds.), Visualization and Processing of Higher Order Descriptors for Multi-Valued Data (1st ed., Vol. 40, pp. 257–267). Springer. https://doi.org/10.1007/978-3-319-15090-1_13","ama":"Zobel V, Reininghaus J, Hotz I. Visualizing symmetric indefinite 2D tensor fields using The Heat Kernel Signature. In: Hotz I, Schultz T, eds. Visualization and Processing of Higher Order Descriptors for Multi-Valued Data. Vol 40. 1st ed. Springer; 2015:257-267. doi:10.1007/978-3-319-15090-1_13","ieee":"V. Zobel, J. Reininghaus, and I. Hotz, “Visualizing symmetric indefinite 2D tensor fields using The Heat Kernel Signature,” in Visualization and Processing of Higher Order Descriptors for Multi-Valued Data, 1st ed., vol. 40, I. Hotz and T. Schultz, Eds. Springer, 2015, pp. 257–267.","short":"V. Zobel, J. Reininghaus, I. Hotz, in:, I. Hotz, T. Schultz (Eds.), Visualization and Processing of Higher Order Descriptors for Multi-Valued Data, 1st ed., Springer, 2015, pp. 257–267.","mla":"Zobel, Valentin, et al. “Visualizing Symmetric Indefinite 2D Tensor Fields Using The Heat Kernel Signature.” Visualization and Processing of Higher Order Descriptors for Multi-Valued Data, edited by Ingrid Hotz and Thomas Schultz, 1st ed., vol. 40, Springer, 2015, pp. 257–67, doi:10.1007/978-3-319-15090-1_13.","ista":"Zobel V, Reininghaus J, Hotz I. 2015.Visualizing symmetric indefinite 2D tensor fields using The Heat Kernel Signature. In: Visualization and Processing of Higher Order Descriptors for Multi-Valued Data. Mathematics and Visualization, vol. 40, 257–267.","chicago":"Zobel, Valentin, Jan Reininghaus, and Ingrid Hotz. “Visualizing Symmetric Indefinite 2D Tensor Fields Using The Heat Kernel Signature.” In Visualization and Processing of Higher Order Descriptors for Multi-Valued Data, edited by Ingrid Hotz and Thomas Schultz, 1st ed., 40:257–67. Springer, 2015. https://doi.org/10.1007/978-3-319-15090-1_13."},"editor":[{"last_name":"Hotz","full_name":"Hotz, Ingrid","first_name":"Ingrid"},{"full_name":"Schultz, Thomas","last_name":"Schultz","first_name":"Thomas"}],"title":"Visualizing symmetric indefinite 2D tensor fields using The Heat Kernel Signature","article_processing_charge":"No","publist_id":"5640","author":[{"first_name":"Valentin","full_name":"Zobel, Valentin","last_name":"Zobel"},{"last_name":"Reininghaus","full_name":"Reininghaus, Jan","first_name":"Jan","id":"4505473A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ingrid","full_name":"Hotz, Ingrid","last_name":"Hotz"}]},{"status":"public","type":"journal_article","article_number":"066003","_id":"1530","department":[{"_id":"MiSi"}],"title":"Impact of the cell division cycle on gene circuits","publist_id":"5641","author":[{"first_name":"Veronika","id":"3FD04378-F248-11E8-B48F-1D18A9856A87","last_name":"Bierbaum","full_name":"Bierbaum, Veronika"},{"first_name":"Stefan","last_name":"Klumpp","full_name":"Klumpp, Stefan"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:51:25Z","citation":{"ista":"Bierbaum V, Klumpp S. 2015. Impact of the cell division cycle on gene circuits. Physical Biology. 12(6), 066003.","chicago":"Bierbaum, Veronika, and Stefan Klumpp. “Impact of the Cell Division Cycle on Gene Circuits.” Physical Biology. IOP Publishing Ltd., 2015. https://doi.org/10.1088/1478-3975/12/6/066003.","ieee":"V. Bierbaum and S. Klumpp, “Impact of the cell division cycle on gene circuits,” Physical Biology, vol. 12, no. 6. IOP Publishing Ltd., 2015.","short":"V. Bierbaum, S. Klumpp, Physical Biology 12 (2015).","ama":"Bierbaum V, Klumpp S. Impact of the cell division cycle on gene circuits. Physical Biology. 2015;12(6). doi:10.1088/1478-3975/12/6/066003","apa":"Bierbaum, V., & Klumpp, S. (2015). Impact of the cell division cycle on gene circuits. Physical Biology. IOP Publishing Ltd. https://doi.org/10.1088/1478-3975/12/6/066003","mla":"Bierbaum, Veronika, and Stefan Klumpp. “Impact of the Cell Division Cycle on Gene Circuits.” Physical Biology, vol. 12, no. 6, 066003, IOP Publishing Ltd., 2015, doi:10.1088/1478-3975/12/6/066003."},"intvolume":" 12","month":"09","publisher":"IOP Publishing Ltd.","quality_controlled":"1","scopus_import":1,"oa_version":"None","abstract":[{"text":"In growing cells, protein synthesis and cell growth are typically not synchronous, and, thus, protein concentrations vary over the cell division cycle. We have developed a theoretical description of genetic regulatory systems in bacteria that explicitly considers the cell division cycle to investigate its impact on gene expression. We calculate the cell-to-cell variations arising from cells being at different stages in the division cycle for unregulated genes and for basic regulatory mechanisms. These variations contribute to the extrinsic noise observed in single-cell experiments, and are most significant for proteins with short lifetimes. Negative autoregulation buffers against variation of protein concentration over the division cycle, but the effect is found to be relatively weak. Stronger buffering is achieved by an increased protein lifetime. Positive autoregulation can strongly amplify such variation if the parameters are set to values that lead to resonance-like behaviour. For cooperative positive autoregulation, the concentration variation over the division cycle diminishes the parameter region of bistability and modulates the switching times between the two stable states. The same effects are seen for a two-gene mutual-repression toggle switch. By contrast, an oscillatory circuit, the repressilator, is only weakly affected by the division cycle.","lang":"eng"}],"date_created":"2018-12-11T11:52:33Z","date_published":"2015-09-25T00:00:00Z","doi":"10.1088/1478-3975/12/6/066003","issue":"6","volume":12,"language":[{"iso":"eng"}],"publication":"Physical Biology","day":"25","publication_status":"published","year":"2015"},{"scopus_import":1,"intvolume":" 143","month":"12","abstract":[{"lang":"eng","text":"Many stochastic models of biochemical reaction networks contain some chemical species for which the number of molecules that are present in the system can only be finite (for instance due to conservation laws), but also other species that can be present in arbitrarily large amounts. The prime example of such networks are models of gene expression, which typically contain a small and finite number of possible states for the promoter but an infinite number of possible states for the amount of mRNA and protein. One of the main approaches to analyze such models is through the use of equations for the time evolution of moments of the chemical species. Recently, a new approach based on conditional moments of the species with infinite state space given all the different possible states of the finite species has been proposed. It was argued that this approach allows one to capture more details about the full underlying probability distribution with a smaller number of equations. Here, I show that the result that less moments provide more information can only stem from an unnecessarily complicated description of the system in the classical formulation. The foundation of this argument will be the derivation of moment equations that describe the complete probability distribution over the finite state space but only low-order moments over the infinite state space. I will show that the number of equations that is needed is always less than what was previously claimed and always less than the number of conditional moment equations up to the same order. To support these arguments, a symbolic algorithm is provided that can be used to derive minimal systems of unconditional moment equations for models with partially finite state space. "}],"oa_version":"Published Version","ec_funded":1,"issue":"24","volume":143,"publication_status":"published","language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"838657118ae286463a2b7737319f35ce","file_id":"4641","creator":"system","date_updated":"2020-07-14T12:45:01Z","file_size":605355,"date_created":"2018-12-12T10:07:43Z","file_name":"IST-2016-593-v1+1_Minimal_moment_equations.pdf"}],"type":"journal_article","pubrep_id":"593","status":"public","_id":"1539","department":[{"_id":"ToHe"},{"_id":"GaTk"}],"file_date_updated":"2020-07-14T12:45:01Z","date_updated":"2021-01-12T06:51:28Z","ddc":["000"],"oa":1,"quality_controlled":"1","publisher":"American Institute of Physics","date_created":"2018-12-11T11:52:36Z","doi":"10.1063/1.4937937","date_published":"2015-12-22T00:00:00Z","year":"2015","has_accepted_license":"1","publication":"Journal of Chemical Physics","day":"22","project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"267989","name":"Quantitative Reactive Modeling"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"name":"The Wittgenstein Prize","grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"article_number":"244103","publist_id":"5632","author":[{"last_name":"Ruess","full_name":"Ruess, Jakob","orcid":"0000-0003-1615-3282","first_name":"Jakob","id":"4A245D00-F248-11E8-B48F-1D18A9856A87"}],"title":"Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space","citation":{"mla":"Ruess, Jakob. “Minimal Moment Equations for Stochastic Models of Biochemical Reaction Networks with Partially Finite State Space.” Journal of Chemical Physics, vol. 143, no. 24, 244103, American Institute of Physics, 2015, doi:10.1063/1.4937937.","ama":"Ruess J. Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space. Journal of Chemical Physics. 2015;143(24). doi:10.1063/1.4937937","apa":"Ruess, J. (2015). Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space. Journal of Chemical Physics. American Institute of Physics. https://doi.org/10.1063/1.4937937","ieee":"J. Ruess, “Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space,” Journal of Chemical Physics, vol. 143, no. 24. American Institute of Physics, 2015.","short":"J. Ruess, Journal of Chemical Physics 143 (2015).","chicago":"Ruess, Jakob. “Minimal Moment Equations for Stochastic Models of Biochemical Reaction Networks with Partially Finite State Space.” Journal of Chemical Physics. American Institute of Physics, 2015. https://doi.org/10.1063/1.4937937.","ista":"Ruess J. 2015. Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space. Journal of Chemical Physics. 143(24), 244103."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"282300","name":"Polarity and subcellular dynamics in plants"}],"article_number":"8822","title":"Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism","author":[{"first_name":"Hongzhe","last_name":"Wang","full_name":"Wang, Hongzhe"},{"full_name":"Yang, Kezhen","last_name":"Yang","first_name":"Kezhen"},{"last_name":"Zou","full_name":"Zou, Junjie","first_name":"Junjie"},{"full_name":"Zhu, Lingling","last_name":"Zhu","first_name":"Lingling"},{"first_name":"Zidian","last_name":"Xie","full_name":"Xie, Zidian"},{"first_name":"Miyoterao","full_name":"Morita, Miyoterao","last_name":"Morita"},{"last_name":"Tasaka","full_name":"Tasaka, Masao","first_name":"Masao"},{"last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Erich","last_name":"Grotewold","full_name":"Grotewold, Erich"},{"full_name":"Beeckman, Tom","last_name":"Beeckman","first_name":"Tom"},{"full_name":"Vanneste, Steffen","last_name":"Vanneste","first_name":"Steffen"},{"first_name":"Fred","last_name":"Sack","full_name":"Sack, Fred"},{"full_name":"Le, Jie","last_name":"Le","first_name":"Jie"}],"publist_id":"5637","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Wang, Hongzhe, et al. “Transcriptional Regulation of PIN Genes by FOUR LIPS and MYB88 during Arabidopsis Root Gravitropism.” Nature Communications, vol. 6, 8822, Nature Publishing Group, 2015, doi:10.1038/ncomms9822.","short":"H. Wang, K. Yang, J. Zou, L. Zhu, Z. Xie, M. Morita, M. Tasaka, J. Friml, E. Grotewold, T. Beeckman, S. Vanneste, F. Sack, J. Le, Nature Communications 6 (2015).","ieee":"H. Wang et al., “Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism,” Nature Communications, vol. 6. Nature Publishing Group, 2015.","apa":"Wang, H., Yang, K., Zou, J., Zhu, L., Xie, Z., Morita, M., … Le, J. (2015). Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms9822","ama":"Wang H, Yang K, Zou J, et al. Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism. Nature Communications. 2015;6. doi:10.1038/ncomms9822","chicago":"Wang, Hongzhe, Kezhen Yang, Junjie Zou, Lingling Zhu, Zidian Xie, Miyoterao Morita, Masao Tasaka, et al. “Transcriptional Regulation of PIN Genes by FOUR LIPS and MYB88 during Arabidopsis Root Gravitropism.” Nature Communications. Nature Publishing Group, 2015. https://doi.org/10.1038/ncomms9822.","ista":"Wang H, Yang K, Zou J, Zhu L, Xie Z, Morita M, Tasaka M, Friml J, Grotewold E, Beeckman T, Vanneste S, Sack F, Le J. 2015. Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism. Nature Communications. 6, 8822."},"oa":1,"quality_controlled":"1","publisher":"Nature Publishing Group","date_created":"2018-12-11T11:52:34Z","doi":"10.1038/ncomms9822","date_published":"2015-11-18T00:00:00Z","publication":"Nature Communications","day":"18","year":"2015","has_accepted_license":"1","pubrep_id":"485","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":"1534","department":[{"_id":"JiFr"}],"file_date_updated":"2020-07-14T12:45:01Z","ddc":["570"],"date_updated":"2021-01-12T06:51:26Z","intvolume":" 6","month":"11","scopus_import":1,"oa_version":"Published Version","abstract":[{"text":"PIN proteins are auxin export carriers that direct intercellular auxin flow and in turn regulate many aspects of plant growth and development including responses to environmental changes. The Arabidopsis R2R3-MYB transcription factor FOUR LIPS (FLP) and its paralogue MYB88 regulate terminal divisions during stomatal development, as well as female reproductive development and stress responses. Here we show that FLP and MYB88 act redundantly but differentially in regulating the transcription of PIN3 and PIN7 in gravity-sensing cells of primary and lateral roots. On the one hand, FLP is involved in responses to gravity stimulation in primary roots, whereas on the other, FLP and MYB88 function complementarily in establishing the gravitropic set-point angles of lateral roots. Our results support a model in which FLP and MYB88 expression specifically determines the temporal-spatial patterns of PIN3 and PIN7 transcription that are closely associated with their preferential functions during root responses to gravity.","lang":"eng"}],"ec_funded":1,"volume":6,"language":[{"iso":"eng"}],"file":[{"creator":"system","date_updated":"2020-07-14T12:45:01Z","file_size":1852268,"date_created":"2018-12-12T10:17:07Z","file_name":"IST-2016-485-v1+1_ncomms9822.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"5259","checksum":"3c06735fc7cd7e482ca830cbd26001bf"}],"publication_status":"published"},{"oa_version":"Submitted Version","pmid":1,"abstract":[{"text":"Systems biology rests on the idea that biological complexity can be better unraveled through the interplay of modeling and experimentation. However, the success of this approach depends critically on the informativeness of the chosen experiments, which is usually unknown a priori. Here, we propose a systematic scheme based on iterations of optimal experiment design, flow cytometry experiments, and Bayesian parameter inference to guide the discovery process in the case of stochastic biochemical reaction networks. To illustrate the benefit of our methodology, we apply it to the characterization of an engineered light-inducible gene expression circuit in yeast and compare the performance of the resulting model with models identified from nonoptimal experiments. In particular, we compare the parameter posterior distributions and the precision to which the outcome of future experiments can be predicted. Moreover, we illustrate how the identified stochastic model can be used to determine light induction patterns that make either the average amount of protein or the variability in a population of cells follow a desired profile. Our results show that optimal experiment design allows one to derive models that are accurate enough to precisely predict and regulate the protein expression in heterogeneous cell populations over extended periods of time.","lang":"eng"}],"month":"06","intvolume":" 112","scopus_import":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4491780/","open_access":"1"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":112,"issue":"26","ec_funded":1,"_id":"1538","status":"public","type":"journal_article","date_updated":"2021-01-12T06:51:27Z","department":[{"_id":"ToHe"},{"_id":"GaTk"}],"acknowledgement":"J.R., F.P., and J.L. acknowledge support from the European Commission under the Network of Excellence HYCON2 (highly-complex and networked control systems) and SystemsX.ch under the SignalX Project. J.R. acknowledges support from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme FP7/2007-2013 under REA (Research Executive Agency) Grant 291734. M.K. acknowledges support from Human Frontier Science Program Grant RP0061/2011 (www.hfsp.org). ","quality_controlled":"1","publisher":"National Academy of Sciences","oa":1,"day":"30","publication":"PNAS","year":"2015","doi":"10.1073/pnas.1423947112","date_published":"2015-06-30T00:00:00Z","date_created":"2018-12-11T11:52:36Z","page":"8148 - 8153","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Ruess, Jakob, et al. “Iterative Experiment Design Guides the Characterization of a Light-Inducible Gene Expression Circuit.” PNAS, vol. 112, no. 26, National Academy of Sciences, 2015, pp. 8148–53, doi:10.1073/pnas.1423947112.","apa":"Ruess, J., Parise, F., Milias Argeitis, A., Khammash, M., & Lygeros, J. (2015). Iterative experiment design guides the characterization of a light-inducible gene expression circuit. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1423947112","ama":"Ruess J, Parise F, Milias Argeitis A, Khammash M, Lygeros J. Iterative experiment design guides the characterization of a light-inducible gene expression circuit. PNAS. 2015;112(26):8148-8153. doi:10.1073/pnas.1423947112","ieee":"J. Ruess, F. Parise, A. Milias Argeitis, M. Khammash, and J. Lygeros, “Iterative experiment design guides the characterization of a light-inducible gene expression circuit,” PNAS, vol. 112, no. 26. National Academy of Sciences, pp. 8148–8153, 2015.","short":"J. Ruess, F. Parise, A. Milias Argeitis, M. Khammash, J. Lygeros, PNAS 112 (2015) 8148–8153.","chicago":"Ruess, Jakob, Francesca Parise, Andreas Milias Argeitis, Mustafa Khammash, and John Lygeros. “Iterative Experiment Design Guides the Characterization of a Light-Inducible Gene Expression Circuit.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1423947112.","ista":"Ruess J, Parise F, Milias Argeitis A, Khammash M, Lygeros J. 2015. Iterative experiment design guides the characterization of a light-inducible gene expression circuit. PNAS. 112(26), 8148–8153."},"title":"Iterative experiment design guides the characterization of a light-inducible gene expression circuit","author":[{"last_name":"Ruess","full_name":"Ruess, Jakob","orcid":"0000-0003-1615-3282","id":"4A245D00-F248-11E8-B48F-1D18A9856A87","first_name":"Jakob"},{"full_name":"Parise, Francesca","last_name":"Parise","first_name":"Francesca"},{"full_name":"Milias Argeitis, Andreas","last_name":"Milias Argeitis","first_name":"Andreas"},{"first_name":"Mustafa","last_name":"Khammash","full_name":"Khammash, Mustafa"},{"first_name":"John","full_name":"Lygeros, John","last_name":"Lygeros"}],"publist_id":"5633","external_id":{"pmid":["26085136"]}},{"year":"2015","day":"01","publication":"Current Molecular Pharmacology","page":"149 - 161","doi":"10.2174/1874467208666150507105443","date_published":"2015-10-01T00:00:00Z","date_created":"2018-12-11T11:52:35Z","acknowledgement":"This work was supported by the Italian MIUR (PRIN 2010/2011 project 2010JFYFY2) and the University of Torino.","publisher":"Bentham Science Publishers","quality_controlled":"1","oa":1,"citation":{"chicago":"Vandael, David H, Andrea Marcantoni, and Emilio Carbone. “Cav1.3 Channels as Key Regulators of Neuron-like Firings and Catecholamine Release in Chromaffin Cells.” Current Molecular Pharmacology. Bentham Science Publishers, 2015. https://doi.org/10.2174/1874467208666150507105443.","ista":"Vandael DH, Marcantoni A, Carbone E. 2015. Cav1.3 channels as key regulators of neuron-like firings and catecholamine release in chromaffin cells. Current Molecular Pharmacology. 8(2), 149–161.","mla":"Vandael, David H., et al. “Cav1.3 Channels as Key Regulators of Neuron-like Firings and Catecholamine Release in Chromaffin Cells.” Current Molecular Pharmacology, vol. 8, no. 2, Bentham Science Publishers, 2015, pp. 149–61, doi:10.2174/1874467208666150507105443.","ieee":"D. H. Vandael, A. Marcantoni, and E. Carbone, “Cav1.3 channels as key regulators of neuron-like firings and catecholamine release in chromaffin cells,” Current Molecular Pharmacology, vol. 8, no. 2. Bentham Science Publishers, pp. 149–161, 2015.","short":"D.H. Vandael, A. Marcantoni, E. Carbone, Current Molecular Pharmacology 8 (2015) 149–161.","ama":"Vandael DH, Marcantoni A, Carbone E. Cav1.3 channels as key regulators of neuron-like firings and catecholamine release in chromaffin cells. Current Molecular Pharmacology. 2015;8(2):149-161. doi:10.2174/1874467208666150507105443","apa":"Vandael, D. H., Marcantoni, A., & Carbone, E. (2015). Cav1.3 channels as key regulators of neuron-like firings and catecholamine release in chromaffin cells. Current Molecular Pharmacology. Bentham Science Publishers. https://doi.org/10.2174/1874467208666150507105443"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Vandael","full_name":"Vandael, David H","orcid":"0000-0001-7577-1676","first_name":"David H","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Andrea","last_name":"Marcantoni","full_name":"Marcantoni, Andrea"},{"last_name":"Carbone","full_name":"Carbone, Emilio","first_name":"Emilio"}],"publist_id":"5636","article_processing_charge":"No","external_id":{"pmid":["25966692"]},"title":"Cav1.3 channels as key regulators of neuron-like firings and catecholamine release in chromaffin cells","publication_status":"published","language":[{"iso":"eng"}],"volume":8,"issue":"2","abstract":[{"text":"Neuronal and neuroendocrine L-type calcium channels (Cav1.2, Cav1.3) open readily at relatively low membrane potentials and allow Ca2+ to enter the cells near resting potentials. In this way, Cav1.2 and Cav1.3 shape the action potential waveform, contribute to gene expression, synaptic plasticity, neuronal differentiation, hormone secretion and pacemaker activity. In the chromaffin cells (CCs) of the adrenal medulla, Cav1.3 is highly expressed and is shown to support most of the pacemaking current that sustains action potential (AP) firings and part of the catecholamine secretion. Cav1.3 forms Ca2+-nanodomains with the fast inactivating BK channels and drives the resting SK currents. These latter set the inter-spike interval duration between consecutive spikes during spontaneous firing and the rate of spike adaptation during sustained depolarizations. Cav1.3 plays also a primary role in the switch from “tonic” to “burst” firing that occurs in mouse CCs when either the availability of voltage-gated Na channels (Nav) is reduced or the β2 subunit featuring the fast inactivating BK channels is deleted. Here, we discuss the functional role of these “neuronlike” firing modes in CCs and how Cav1.3 contributes to them. The open issue is to understand how these novel firing patterns are adapted to regulate the quantity of circulating catecholamines during resting condition or in response to acute and chronic stress.","lang":"eng"}],"oa_version":"Submitted Version","pmid":1,"scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5384372/"}],"month":"10","intvolume":" 8","date_updated":"2021-01-12T06:51:26Z","department":[{"_id":"PeJo"}],"_id":"1535","type":"journal_article","article_type":"original","status":"public"},{"date_created":"2018-12-11T11:52:35Z","date_published":"2015-02-12T00:00:00Z","doi":"10.1016/j.cub.2015.01.015","volume":25,"issue":"5","page":"647 - 655","language":[{"iso":"eng"}],"publication":"Current Biology","day":"12","publication_status":"published","year":"2015","intvolume":" 25","month":"02","scopus_import":1,"quality_controlled":"1","publisher":"Cell Press","acknowledgement":"This work was funded by a grant of the Swiss National Foundation to E.M.\r\nWe thank Dr. José María Mateos (University of Zurich) for providing us with the vibratome, Prof. Dolf Weijers (Wageningen University, the Netherlands) for shipping us his set of ligation-independent cloning vectors, Prof. Bruno Humbel (University of Lausanne) for suggestions on GFP-PDR1 detection, and Dr. Undine Krügel (University of Zurich) and Prof. Michal Jasinski (Polish Academy of Science) for hints on protein quantification.","oa_version":"None","abstract":[{"lang":"eng","text":"Strigolactones, first discovered as germination stimulants for parasitic weeds [1], are carotenoid-derived phytohormones that play major roles in inhibiting lateral bud outgrowth and promoting plant-mycorrhizal symbiosis [2-4]. Furthermore, strigolactones are involved in the regulation of lateral and adventitious root development, root cell division [5, 6], secondary growth [7], and leaf senescence [8]. Recently, we discovered the strigolactone transporter Petunia axillaris PLEIOTROPIC DRUG RESISTANCE 1 (PaPDR1), which is required for efficient mycorrhizal colonization and inhibition of lateral bud outgrowth [9]. However, how strigolactones are transported through the plant remained unknown. Here we show that PaPDR1 exhibits a cell-type-specific asymmetric localization in different root tissues. In root tips, PaPDR1 is co-expressed with the strigolactone biosynthetic gene DAD1 (CCD8), and it is localized at the apical membrane of root hypodermal cells, presumably mediating the shootward transport of strigolactone. Above the root tip, in the hypodermal passage cells that form gates for the entry of mycorrhizal fungi, PaPDR1 is present in the outer-lateral membrane, compatible with its postulated function as strigolactone exporter from root to soil. Transport studies are in line with our localization studies since (1) a papdr1 mutant displays impaired transport of strigolactones out of the root tip to the shoot as well as into the rhizosphere and (2) DAD1 expression and PIN1/PIN2 levels change in plants deregulated for PDR1 expression, suggestive of variations in endogenous strigolactone contents. In conclusion, our results indicate that the polar localizations of PaPDR1 mediate directional shootward strigolactone transport as well as localized exudation into the soil."}],"title":"Asymmetric localizations of the ABC transporter PaPDR1 trace paths of directional strigolactone transport","department":[{"_id":"JiFr"}],"author":[{"full_name":"Sasse, Joëlle","last_name":"Sasse","first_name":"Joëlle"},{"orcid":"0000-0002-1998-6741","full_name":"Simon, Sibu","last_name":"Simon","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","first_name":"Sibu"},{"full_name":"Gübeli, Christian","last_name":"Gübeli","first_name":"Christian"},{"last_name":"Liu","full_name":"Liu, Guowei","first_name":"Guowei"},{"first_name":"Xi","last_name":"Cheng","full_name":"Cheng, Xi"},{"last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"},{"last_name":"Bouwmeester","full_name":"Bouwmeester, Harro","first_name":"Harro"},{"first_name":"Enrico","last_name":"Martinoia","full_name":"Martinoia, Enrico"},{"last_name":"Borghi","full_name":"Borghi, Lorenzo","first_name":"Lorenzo"}],"publist_id":"5635","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:51:27Z","citation":{"chicago":"Sasse, Joëlle, Sibu Simon, Christian Gübeli, Guowei Liu, Xi Cheng, Jiří Friml, Harro Bouwmeester, Enrico Martinoia, and Lorenzo Borghi. “Asymmetric Localizations of the ABC Transporter PaPDR1 Trace Paths of Directional Strigolactone Transport.” Current Biology. Cell Press, 2015. https://doi.org/10.1016/j.cub.2015.01.015.","ista":"Sasse J, Simon S, Gübeli C, Liu G, Cheng X, Friml J, Bouwmeester H, Martinoia E, Borghi L. 2015. Asymmetric localizations of the ABC transporter PaPDR1 trace paths of directional strigolactone transport. Current Biology. 25(5), 647–655.","mla":"Sasse, Joëlle, et al. “Asymmetric Localizations of the ABC Transporter PaPDR1 Trace Paths of Directional Strigolactone Transport.” Current Biology, vol. 25, no. 5, Cell Press, 2015, pp. 647–55, doi:10.1016/j.cub.2015.01.015.","ieee":"J. Sasse et al., “Asymmetric localizations of the ABC transporter PaPDR1 trace paths of directional strigolactone transport,” Current Biology, vol. 25, no. 5. Cell Press, pp. 647–655, 2015.","short":"J. Sasse, S. Simon, C. Gübeli, G. Liu, X. Cheng, J. Friml, H. Bouwmeester, E. Martinoia, L. Borghi, Current Biology 25 (2015) 647–655.","apa":"Sasse, J., Simon, S., Gübeli, C., Liu, G., Cheng, X., Friml, J., … Borghi, L. (2015). Asymmetric localizations of the ABC transporter PaPDR1 trace paths of directional strigolactone transport. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2015.01.015","ama":"Sasse J, Simon S, Gübeli C, et al. Asymmetric localizations of the ABC transporter PaPDR1 trace paths of directional strigolactone transport. Current Biology. 2015;25(5):647-655. doi:10.1016/j.cub.2015.01.015"},"status":"public","type":"journal_article","_id":"1536"},{"date_created":"2018-12-11T11:52:34Z","date_published":"2015-08-01T00:00:00Z","doi":"10.1109/TCSVT.2014.2379972","issue":"8","volume":25,"page":"1295 - 1308","language":[{"iso":"eng"}],"publication":"IEEE Transactions on Circuits and Systems for Video Technology","day":"01","year":"2015","publication_status":"published","intvolume":" 25","month":"08","scopus_import":1,"quality_controlled":"1","publisher":"IEEE","oa_version":"None","abstract":[{"text":"This paper addresses the problem of semantic segmentation, where the possible class labels are from a predefined set. We exploit top-down guidance, i.e., the coarse localization of the objects and their class labels provided by object detectors. For each detected bounding box, figure-ground segmentation is performed and the final result is achieved by merging the figure-ground segmentations. The main idea of the proposed approach, which is presented in our preliminary work, is to reformulate the figure-ground segmentation problem as sparse reconstruction pursuing the object mask in a nonparametric manner. The latent segmentation mask should be coherent subject to sparse error caused by intra-category diversity; thus, the object mask is inferred by making use of sparse representations over the training set. To handle local spatial deformations, local patch-level masks are also considered and inferred by sparse representations over the spatially nearby patches. The sparse reconstruction coefficients and the latent mask are alternately optimized by applying the Lasso algorithm and the accelerated proximal gradient method. The proposed formulation results in a convex optimization problem; thus, the global optimal solution is achieved. In this paper, we provide theoretical analysis of the convergence and optimality. We also give an extended numerical analysis of the proposed algorithm and a comprehensive comparison with the related semantic segmentation methods on the challenging PASCAL visual object class object segmentation datasets and the Weizmann horse dataset. The experimental results demonstrate that the proposed algorithm achieves a competitive performance when compared with the state of the arts.","lang":"eng"}],"department":[{"_id":"ChLa"}],"title":"Segmentation over detection via optimal sparse reconstructions","publist_id":"5638","author":[{"first_name":"Wei","full_name":"Xia, Wei","last_name":"Xia"},{"id":"492DACF8-F248-11E8-B48F-1D18A9856A87","first_name":"Csaba","last_name":"Domokos","full_name":"Domokos, Csaba"},{"first_name":"Junjun","full_name":"Xiong, Junjun","last_name":"Xiong"},{"first_name":"Loongfah","last_name":"Cheong","full_name":"Cheong, Loongfah"},{"first_name":"Shuicheng","last_name":"Yan","full_name":"Yan, Shuicheng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:51:26Z","citation":{"ista":"Xia W, Domokos C, Xiong J, Cheong L, Yan S. 2015. Segmentation over detection via optimal sparse reconstructions. IEEE Transactions on Circuits and Systems for Video Technology. 25(8), 1295–1308.","chicago":"Xia, Wei, Csaba Domokos, Junjun Xiong, Loongfah Cheong, and Shuicheng Yan. “Segmentation over Detection via Optimal Sparse Reconstructions.” IEEE Transactions on Circuits and Systems for Video Technology. IEEE, 2015. https://doi.org/10.1109/TCSVT.2014.2379972.","short":"W. Xia, C. Domokos, J. Xiong, L. Cheong, S. Yan, IEEE Transactions on Circuits and Systems for Video Technology 25 (2015) 1295–1308.","ieee":"W. Xia, C. Domokos, J. Xiong, L. Cheong, and S. Yan, “Segmentation over detection via optimal sparse reconstructions,” IEEE Transactions on Circuits and Systems for Video Technology, vol. 25, no. 8. IEEE, pp. 1295–1308, 2015.","apa":"Xia, W., Domokos, C., Xiong, J., Cheong, L., & Yan, S. (2015). Segmentation over detection via optimal sparse reconstructions. IEEE Transactions on Circuits and Systems for Video Technology. IEEE. https://doi.org/10.1109/TCSVT.2014.2379972","ama":"Xia W, Domokos C, Xiong J, Cheong L, Yan S. Segmentation over detection via optimal sparse reconstructions. IEEE Transactions on Circuits and Systems for Video Technology. 2015;25(8):1295-1308. doi:10.1109/TCSVT.2014.2379972","mla":"Xia, Wei, et al. “Segmentation over Detection via Optimal Sparse Reconstructions.” IEEE Transactions on Circuits and Systems for Video Technology, vol. 25, no. 8, IEEE, 2015, pp. 1295–308, doi:10.1109/TCSVT.2014.2379972."},"status":"public","type":"journal_article","_id":"1533"},{"department":[{"_id":"NiBa"},{"_id":"CaGu"}],"file_date_updated":"2020-07-14T12:45:01Z","date_updated":"2021-01-12T06:51:29Z","ddc":["570"],"tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"type":"journal_article","pubrep_id":"483","status":"public","_id":"1542","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","ec_funded":1,"volume":383,"publication_status":"published","language":[{"iso":"eng"}],"file":[{"creator":"system","date_updated":"2020-07-14T12:45:01Z","file_size":595307,"date_created":"2018-12-12T10:16:53Z","file_name":"IST-2016-483-v1+1_1-s2.0-S0022519315003409-main.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"33b60ecfea60764756a9ee9df5eb65ca","file_id":"5244"}],"scopus_import":1,"intvolume":" 383","month":"10","abstract":[{"lang":"eng","text":"The theory of population genetics and evolutionary computation have been evolving separately for nearly 30 years. Many results have been independently obtained in both fields and many others are unique to its respective field. We aim to bridge this gap by developing a unifying framework for evolutionary processes that allows both evolutionary algorithms and population genetics models to be cast in the same formal framework. The framework we present here decomposes the evolutionary process into its several components in order to facilitate the identification of similarities between different models. In particular, we propose a classification of evolutionary operators based on the defining properties of the different components. We cast several commonly used operators from both fields into this common framework. Using this, we map different evolutionary and genetic algorithms to different evolutionary regimes and identify candidates with the most potential for the translation of results between the fields. This provides a unified description of evolutionary processes and represents a stepping stone towards new tools and results to both fields. "}],"oa_version":"Published Version","author":[{"last_name":"Paixao","full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953","first_name":"Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Badkobeh","full_name":"Badkobeh, Golnaz","first_name":"Golnaz"},{"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":"Doğan","full_name":"Çörüş, Doğan","last_name":"Çörüş"},{"full_name":"Dang, Duccuong","last_name":"Dang","first_name":"Duccuong"},{"first_name":"Tobias","full_name":"Friedrich, Tobias","last_name":"Friedrich"},{"full_name":"Lehre, Per","last_name":"Lehre","first_name":"Per"},{"first_name":"Dirk","full_name":"Sudholt, Dirk","last_name":"Sudholt"},{"first_name":"Andrew","last_name":"Sutton","full_name":"Sutton, Andrew"},{"first_name":"Barbora","id":"42302D54-F248-11E8-B48F-1D18A9856A87","last_name":"Trubenova","full_name":"Trubenova, Barbora","orcid":"0000-0002-6873-2967"}],"publist_id":"5629","title":"Toward a unifying framework for evolutionary processes","citation":{"chicago":"Paixao, Tiago, Golnaz Badkobeh, Nicholas H Barton, Doğan Çörüş, Duccuong Dang, Tobias Friedrich, Per Lehre, Dirk Sudholt, Andrew Sutton, and Barbora Trubenova. “Toward a Unifying Framework for Evolutionary Processes.” Journal of Theoretical Biology. Elsevier, 2015. https://doi.org/10.1016/j.jtbi.2015.07.011.","ista":"Paixao T, Badkobeh G, Barton NH, Çörüş D, Dang D, Friedrich T, Lehre P, Sudholt D, Sutton A, Trubenova B. 2015. Toward a unifying framework for evolutionary processes. Journal of Theoretical Biology. 383, 28–43.","mla":"Paixao, Tiago, et al. “Toward a Unifying Framework for Evolutionary Processes.” Journal of Theoretical Biology, vol. 383, Elsevier, 2015, pp. 28–43, doi:10.1016/j.jtbi.2015.07.011.","ieee":"T. Paixao et al., “Toward a unifying framework for evolutionary processes,” Journal of Theoretical Biology, vol. 383. Elsevier, pp. 28–43, 2015.","short":"T. Paixao, G. Badkobeh, N.H. Barton, D. Çörüş, D. Dang, T. Friedrich, P. Lehre, D. Sudholt, A. Sutton, B. Trubenova, Journal of Theoretical Biology 383 (2015) 28–43.","ama":"Paixao T, Badkobeh G, Barton NH, et al. Toward a unifying framework for evolutionary processes. Journal of Theoretical Biology. 2015;383:28-43. doi:10.1016/j.jtbi.2015.07.011","apa":"Paixao, T., Badkobeh, G., Barton, N. H., Çörüş, D., Dang, D., Friedrich, T., … Trubenova, B. (2015). Toward a unifying framework for evolutionary processes. Journal of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2015.07.011"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","grant_number":"618091"},{"_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"}],"page":"28 - 43","date_created":"2018-12-11T11:52:37Z","doi":"10.1016/j.jtbi.2015.07.011","date_published":"2015-10-21T00:00:00Z","year":"2015","has_accepted_license":"1","publication":" Journal of Theoretical Biology","day":"21","oa":1,"quality_controlled":"1","publisher":"Elsevier"},{"publisher":"Elsevier","quality_controlled":"1","oa":1,"acknowledgement":"This work was supported by the Core Research for Evolutional Science and Technology (CREST) of Japan Science and Technology Agency to T.T. and R.S.; by the funding provided by Okinawa Institute of Science and Technology (OIST) to T.T. and Y.N.; by JSPS Core-to-Core Program, A. Advanced Networks to T.T.; by the Grant-in-Aid for Young Scientists from the Japanese Ministry of Education, Culture, Sports, Science and Technology (#23700474) to Y.N.; by the Centre National de la Recherche Scientifique through the Actions Thematiques et Initatives sur Programme, Fondation Fyssen, Fondation pour la Recherche Medicale, Federation pour la Recherche sur le Cerveau, Agence Nationale de la Recherche (ANR-2007-Neuro-008-01 and ANR-2010-BLAN-1411-01) to D.D. and Y.N.; and by the European Commission Coordination Action ENINET (LSHM-CT-2005-19063) to D.D. and R.A.S. R.A.S. and J.S.R. were funded by Wellcome Trust Senior (064413) and Principal (095667) Research Fellowship and an ERC advance grant (294667) to RAS.","date_published":"2015-01-07T00:00:00Z","doi":"10.1016/j.neuron.2014.11.019","date_created":"2018-12-11T11:52:39Z","page":"145 - 158","day":"07","publication":"Neuron","has_accepted_license":"1","year":"2015","title":"Nanoscale distribution of presynaptic Ca2+ channels and its impact on vesicular release during development","publist_id":"5625","author":[{"last_name":"Nakamura","full_name":"Nakamura, Yukihiro","first_name":"Yukihiro"},{"orcid":"0000-0001-7429-7896","full_name":"Harada, Harumi","last_name":"Harada","first_name":"Harumi","id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kamasawa","full_name":"Kamasawa, Naomi","first_name":"Naomi"},{"first_name":"Ko","last_name":"Matsui","full_name":"Matsui, Ko"},{"full_name":"Rothman, Jason","last_name":"Rothman","first_name":"Jason"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444"},{"last_name":"Silver","full_name":"Silver, R Angus","first_name":"R Angus"},{"full_name":"Digregorio, David","last_name":"Digregorio","first_name":"David"},{"full_name":"Takahashi, Tomoyuki","last_name":"Takahashi","first_name":"Tomoyuki"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Nakamura Y, Harada H, Kamasawa N, et al. Nanoscale distribution of presynaptic Ca2+ channels and its impact on vesicular release during development. Neuron. 2015;85(1):145-158. doi:10.1016/j.neuron.2014.11.019","apa":"Nakamura, Y., Harada, H., Kamasawa, N., Matsui, K., Rothman, J., Shigemoto, R., … Takahashi, T. (2015). Nanoscale distribution of presynaptic Ca2+ channels and its impact on vesicular release during development. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2014.11.019","short":"Y. Nakamura, H. Harada, N. Kamasawa, K. Matsui, J. Rothman, R. Shigemoto, R.A. Silver, D. Digregorio, T. Takahashi, Neuron 85 (2015) 145–158.","ieee":"Y. Nakamura et al., “Nanoscale distribution of presynaptic Ca2+ channels and its impact on vesicular release during development,” Neuron, vol. 85, no. 1. Elsevier, pp. 145–158, 2015.","mla":"Nakamura, Yukihiro, et al. “Nanoscale Distribution of Presynaptic Ca2+ Channels and Its Impact on Vesicular Release during Development.” Neuron, vol. 85, no. 1, Elsevier, 2015, pp. 145–58, doi:10.1016/j.neuron.2014.11.019.","ista":"Nakamura Y, Harada H, Kamasawa N, Matsui K, Rothman J, Shigemoto R, Silver RA, Digregorio D, Takahashi T. 2015. Nanoscale distribution of presynaptic Ca2+ channels and its impact on vesicular release during development. Neuron. 85(1), 145–158.","chicago":"Nakamura, Yukihiro, Harumi Harada, Naomi Kamasawa, Ko Matsui, Jason Rothman, Ryuichi Shigemoto, R Angus Silver, David Digregorio, and Tomoyuki Takahashi. “Nanoscale Distribution of Presynaptic Ca2+ Channels and Its Impact on Vesicular Release during Development.” Neuron. Elsevier, 2015. https://doi.org/10.1016/j.neuron.2014.11.019."},"month":"01","intvolume":" 85","scopus_import":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Synaptic efficacy and precision are influenced by the coupling of voltage-gated Ca2+ channels (VGCCs) to vesicles. But because the topography of VGCCs and their proximity to vesicles is unknown, a quantitative understanding of the determinants of vesicular release at nanometer scale is lacking. To investigate this, we combined freeze-fracture replica immunogold labeling of Cav2.1 channels, local [Ca2+] imaging, and patch pipette perfusion of EGTA at the calyx of Held. Between postnatal day 7 and 21, VGCCs formed variable sized clusters and vesicular release became less sensitive to EGTA, whereas fixed Ca2+ buffer properties remained constant. Experimentally constrained reaction-diffusion simulations suggest that Ca2+ sensors for vesicular release are located at the perimeter of VGCC clusters (<30nm) and predict that VGCC number per cluster determines vesicular release probability without altering release time course. This "perimeter release model" provides a unifying framework accounting for developmental changes in both synaptic efficacy and time course."}],"volume":85,"issue":"1","file":[{"date_created":"2018-12-12T10:15:47Z","file_name":"IST-2016-482-v1+1_1-s2.0-S0896627314010472-main.pdf","date_updated":"2020-07-14T12:45:01Z","file_size":3080111,"creator":"system","file_id":"5170","checksum":"725f4d5be2dbb44b283ce722645ef37d","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"publication_status":"published","status":"public","pubrep_id":"482","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":"1546","file_date_updated":"2020-07-14T12:45:01Z","department":[{"_id":"RySh"}],"ddc":["570"],"date_updated":"2021-01-12T06:51:31Z"},{"date_created":"2018-12-11T11:52:37Z","date_published":"2015-11-28T00:00:00Z","doi":"10.1007/978-3-319-26287-1_1","page":"3 - 18","day":"28","year":"2015","quality_controlled":"1","publisher":"Springer","acknowledgement":"This work was supported in part by the European Research Council (ERC) under grant 267989 (QUAREM) and by the Austrian Science Fund (FWF) under grants S11402-N23, S11405-N23 and S11412-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award).","title":"XSpeed: Accelerating reachability analysis on multi-core processors","publist_id":"5630","author":[{"full_name":"Ray, Rajarshi","last_name":"Ray","first_name":"Rajarshi"},{"first_name":"Amit","full_name":"Gurung, Amit","last_name":"Gurung"},{"first_name":"Binayak","last_name":"Das","full_name":"Das, Binayak"},{"first_name":"Ezio","full_name":"Bartocci, Ezio","last_name":"Bartocci"},{"last_name":"Bogomolov","orcid":"0000-0002-0686-0365","full_name":"Bogomolov, Sergiy","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","first_name":"Sergiy"},{"full_name":"Grosu, Radu","last_name":"Grosu","first_name":"Radu"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Ray, Rajarshi, Amit Gurung, Binayak Das, Ezio Bartocci, Sergiy Bogomolov, and Radu Grosu. “XSpeed: Accelerating Reachability Analysis on Multi-Core Processors.” Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-319-26287-1_1.","ista":"Ray R, Gurung A, Das B, Bartocci E, Bogomolov S, Grosu R. 2015. XSpeed: Accelerating reachability analysis on multi-core processors. 9434, 3–18.","mla":"Ray, Rajarshi, et al. XSpeed: Accelerating Reachability Analysis on Multi-Core Processors. Vol. 9434, Springer, 2015, pp. 3–18, doi:10.1007/978-3-319-26287-1_1.","apa":"Ray, R., Gurung, A., Das, B., Bartocci, E., Bogomolov, S., & Grosu, R. (2015). XSpeed: Accelerating reachability analysis on multi-core processors. Presented at the HVC: Haifa Verification Conference, Haifa, Israel: Springer. https://doi.org/10.1007/978-3-319-26287-1_1","ama":"Ray R, Gurung A, Das B, Bartocci E, Bogomolov S, Grosu R. XSpeed: Accelerating reachability analysis on multi-core processors. 2015;9434:3-18. doi:10.1007/978-3-319-26287-1_1","short":"R. Ray, A. Gurung, B. Das, E. Bartocci, S. Bogomolov, R. Grosu, 9434 (2015) 3–18.","ieee":"R. Ray, A. Gurung, B. Das, E. Bartocci, S. Bogomolov, and R. Grosu, “XSpeed: Accelerating reachability analysis on multi-core processors,” vol. 9434. Springer, pp. 3–18, 2015."},"project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"267989","name":"Quantitative Reactive Modeling"},{"grant_number":"S11402-N23","name":"Moderne Concurrency Paradigms","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","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"}],"ec_funded":1,"volume":9434,"language":[{"iso":"eng"}],"publication_status":"published","intvolume":" 9434","month":"11","alternative_title":["LNCS"],"scopus_import":1,"oa_version":"None","abstract":[{"text":"We present XSpeed a parallel state-space exploration algorithm for continuous systems with linear dynamics and nondeterministic inputs. The motivation of having parallel algorithms is to exploit the computational power of multi-core processors to speed-up performance. The parallelization is achieved on two fronts. First, we propose a parallel implementation of the support function algorithm by sampling functions in parallel. Second, we propose a parallel state-space exploration by slicing the time horizon and computing the reachable states in the time slices in parallel. The second method can be however applied only to a class of linear systems with invertible dynamics and fixed input. A GP-GPU implementation is also presented following a lazy evaluation strategy on support functions. The parallel algorithms are implemented in the tool XSpeed. We evaluated the performance on two benchmarks including an 28 dimension Helicopter model. Comparison with the sequential counterpart shows a maximum speed-up of almost 7× on a 6 core, 12 thread Intel Xeon CPU E5-2420 processor. Our GP-GPU implementation shows a maximum speed-up of 12× over the sequential implementation and 53× over SpaceEx (LGG scenario), the state of the art tool for reachability analysis of linear hybrid systems. Experiments illustrate that our parallel algorithm with time slicing not only speeds-up performance but also improves precision.","lang":"eng"}],"department":[{"_id":"ToHe"}],"date_updated":"2020-08-11T10:09:17Z","status":"public","conference":{"name":"HVC: Haifa Verification Conference","location":"Haifa, Israel","end_date":"2015-11-19","start_date":"2015-11-17"},"type":"conference","_id":"1541","series_title":"Lecture Notes in Computer Science"},{"title":"A conserved core of programmed cell death indicator genes discriminates developmentally and environmentally induced programmed cell death in plants","department":[{"_id":"JiFr"}],"publist_id":"5628","author":[{"first_name":"Yadira","last_name":"Olvera Carrillo","full_name":"Olvera Carrillo, Yadira"},{"first_name":"Michiel","full_name":"Van Bel, Michiel","last_name":"Van Bel"},{"first_name":"Tom","full_name":"Van Hautegem, Tom","last_name":"Van Hautegem"},{"id":"43905548-F248-11E8-B48F-1D18A9856A87","first_name":"Matyas","orcid":"0000-0002-9767-8699","full_name":"Fendrych, Matyas","last_name":"Fendrych"},{"first_name":"Marlies","full_name":"Huysmans, Marlies","last_name":"Huysmans"},{"first_name":"Mária","full_name":"Šimášková, Mária","last_name":"Šimášková"},{"first_name":"Matthias","full_name":"Van Durme, Matthias","last_name":"Van Durme"},{"first_name":"Pierre","last_name":"Buscaill","full_name":"Buscaill, Pierre"},{"first_name":"Susana","last_name":"Rivas","full_name":"Rivas, Susana"},{"full_name":"Coll, Núria","last_name":"Coll","first_name":"Núria"},{"first_name":"Frederik","last_name":"Coppens","full_name":"Coppens, Frederik"},{"first_name":"Steven","last_name":"Maere","full_name":"Maere, Steven"},{"last_name":"Nowack","full_name":"Nowack, Moritz","first_name":"Moritz"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"Y. Olvera Carrillo, M. Van Bel, T. Van Hautegem, M. Fendrych, M. Huysmans, M. Šimášková, M. Van Durme, P. Buscaill, S. Rivas, N. Coll, F. Coppens, S. Maere, M. Nowack, Plant Physiology 169 (2015) 2684–2699.","ieee":"Y. Olvera Carrillo et al., “A conserved core of programmed cell death indicator genes discriminates developmentally and environmentally induced programmed cell death in plants,” Plant Physiology, vol. 169, no. 4. American Society of Plant Biologists, pp. 2684–2699, 2015.","apa":"Olvera Carrillo, Y., Van Bel, M., Van Hautegem, T., Fendrych, M., Huysmans, M., Šimášková, M., … Nowack, M. (2015). A conserved core of programmed cell death indicator genes discriminates developmentally and environmentally induced programmed cell death in plants. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1104/pp.15.00769","ama":"Olvera Carrillo Y, Van Bel M, Van Hautegem T, et al. A conserved core of programmed cell death indicator genes discriminates developmentally and environmentally induced programmed cell death in plants. Plant Physiology. 2015;169(4):2684-2699. doi:10.1104/pp.15.00769","mla":"Olvera Carrillo, Yadira, et al. “A Conserved Core of Programmed Cell Death Indicator Genes Discriminates Developmentally and Environmentally Induced Programmed Cell Death in Plants.” Plant Physiology, vol. 169, no. 4, American Society of Plant Biologists, 2015, pp. 2684–99, doi:10.1104/pp.15.00769.","ista":"Olvera Carrillo Y, Van Bel M, Van Hautegem T, Fendrych M, Huysmans M, Šimášková M, Van Durme M, Buscaill P, Rivas S, Coll N, Coppens F, Maere S, Nowack M. 2015. A conserved core of programmed cell death indicator genes discriminates developmentally and environmentally induced programmed cell death in plants. Plant Physiology. 169(4), 2684–2699.","chicago":"Olvera Carrillo, Yadira, Michiel Van Bel, Tom Van Hautegem, Matyas Fendrych, Marlies Huysmans, Mária Šimášková, Matthias Van Durme, et al. “A Conserved Core of Programmed Cell Death Indicator Genes Discriminates Developmentally and Environmentally Induced Programmed Cell Death in Plants.” Plant Physiology. American Society of Plant Biologists, 2015. https://doi.org/10.1104/pp.15.00769."},"date_updated":"2021-01-12T06:51:30Z","status":"public","type":"journal_article","_id":"1543","doi":"10.1104/pp.15.00769","issue":"4","volume":169,"date_published":"2015-12-01T00:00:00Z","date_created":"2018-12-11T11:52:38Z","page":"2684 - 2699","day":"01","publication":"Plant Physiology","language":[{"iso":"eng"}],"publication_status":"published","year":"2015","month":"12","intvolume":" 169","scopus_import":1,"publisher":"American Society of Plant Biologists","oa_version":"None","abstract":[{"text":"A plethora of diverse programmed cell death (PCD) processes has been described in living organisms. In animals and plants, different forms of PCD play crucial roles in development, immunity, and responses to the environment. While the molecular control of some animal PCD forms such as apoptosis is known in great detail, we still know comparatively little about the regulation of the diverse types of plant PCD. In part, this deficiency in molecular understanding is caused by the lack of reliable reporters to detect PCD processes. Here, we addressed this issue by using a combination of bioinformatics approaches to identify commonly regulated genes during diverse plant PCD processes in Arabidopsis (Arabidopsis thaliana). Our results indicate that the transcriptional signatures of developmentally controlled cell death are largely distinct from the ones associated with environmentally induced cell death. Moreover, different cases of developmental PCD share a set of cell death-associated genes. Most of these genes are evolutionary conserved within the green plant lineage, arguing for an evolutionary conserved core machinery of developmental PCD. Based on this information, we established an array of specific promoter-reporter lines for developmental PCD in Arabidopsis. These PCD indicators represent a powerful resource that can be used in addition to established morphological and biochemical methods to detect and analyze PCD processes in vivo and in planta.","lang":"eng"}]},{"_id":"1544","type":"book_chapter","status":"public","date_updated":"2021-01-12T06:51:30Z","department":[{"_id":"MaLo"}],"abstract":[{"lang":"eng","text":"Cell division in prokaryotes and eukaryotes is commonly initiated by the well-controlled binding of proteins to the cytoplasmic side of the cell membrane. However, a precise characterization of the spatiotemporal dynamics of membrane-bound proteins is often difficult to achieve in vivo. Here, we present protocols for the use of supported lipid bilayers to rebuild the cytokinetic machineries of cells with greatly different dimensions: the bacterium Escherichia coli and eggs of the vertebrate Xenopus laevis. Combined with total internal reflection fluorescence microscopy, these experimental setups allow for precise quantitative analyses of membrane-bound proteins. The protocols described to obtain glass-supported membranes from bacterial and vertebrate lipids can be used as starting points for other reconstitution experiments. We believe that similar biochemical assays will be instrumental to study the biochemistry and biophysics underlying a variety of complex cellular tasks, such as signaling, vesicle trafficking, and cell motility."}],"oa_version":"Submitted Version","pmid":1,"scopus_import":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4578691/","open_access":"1"}],"month":"04","intvolume":" 128","publication_status":"published","language":[{"iso":"eng"}],"volume":128,"citation":{"ista":"Nguyen P, Field C, Groen A, Mitchison T, Loose M. 2015.Using supported bilayers to study the spatiotemporal organization of membrane-bound proteins. In: Building a Cell from its Components Parts. vol. 128, 223–241.","chicago":"Nguyen, Phuong, Christine Field, Aaron Groen, Timothy Mitchison, and Martin Loose. “Using Supported Bilayers to Study the Spatiotemporal Organization of Membrane-Bound Proteins.” In Building a Cell from Its Components Parts, 128:223–41. Academic Press, 2015. https://doi.org/10.1016/bs.mcb.2015.01.007.","ama":"Nguyen P, Field C, Groen A, Mitchison T, Loose M. Using supported bilayers to study the spatiotemporal organization of membrane-bound proteins. In: Building a Cell from Its Components Parts. Vol 128. Academic Press; 2015:223-241. doi:10.1016/bs.mcb.2015.01.007","apa":"Nguyen, P., Field, C., Groen, A., Mitchison, T., & Loose, M. (2015). Using supported bilayers to study the spatiotemporal organization of membrane-bound proteins. In Building a Cell from its Components Parts (Vol. 128, pp. 223–241). Academic Press. https://doi.org/10.1016/bs.mcb.2015.01.007","short":"P. Nguyen, C. Field, A. Groen, T. Mitchison, M. Loose, in:, Building a Cell from Its Components Parts, Academic Press, 2015, pp. 223–241.","ieee":"P. Nguyen, C. Field, A. Groen, T. Mitchison, and M. Loose, “Using supported bilayers to study the spatiotemporal organization of membrane-bound proteins,” in Building a Cell from its Components Parts, vol. 128, Academic Press, 2015, pp. 223–241.","mla":"Nguyen, Phuong, et al. “Using Supported Bilayers to Study the Spatiotemporal Organization of Membrane-Bound Proteins.” Building a Cell from Its Components Parts, vol. 128, Academic Press, 2015, pp. 223–41, doi:10.1016/bs.mcb.2015.01.007."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Nguyen, Phuong","last_name":"Nguyen","first_name":"Phuong"},{"last_name":"Field","full_name":"Field, Christine","first_name":"Christine"},{"first_name":"Aaron","full_name":"Groen, Aaron","last_name":"Groen"},{"first_name":"Timothy","last_name":"Mitchison","full_name":"Mitchison, Timothy"},{"full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","last_name":"Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"}],"publist_id":"5627","external_id":{"pmid":["25997350"]},"title":"Using supported bilayers to study the spatiotemporal organization of membrane-bound proteins","publisher":"Academic Press","quality_controlled":"1","oa":1,"year":"2015","day":"08","publication":"Building a Cell from its Components Parts","page":"223 - 241","doi":"10.1016/bs.mcb.2015.01.007","date_published":"2015-04-08T00:00:00Z","date_created":"2018-12-11T11:52:38Z"},{"status":"public","type":"journal_article","_id":"1540","department":[{"_id":"EvBe"}],"title":"The importance of localized auxin production for morphogenesis of reproductive organs and embryos in Arabidopsis","author":[{"full_name":"Robert, Hélène","last_name":"Robert","first_name":"Hélène"},{"first_name":"Lucie","full_name":"Crhák Khaitová, Lucie","last_name":"Crhák Khaitová"},{"first_name":"Souad","full_name":"Mroue, Souad","last_name":"Mroue"},{"full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","last_name":"Benková","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5631","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:51:29Z","citation":{"mla":"Robert, Hélène, et al. “The Importance of Localized Auxin Production for Morphogenesis of Reproductive Organs and Embryos in Arabidopsis.” Journal of Experimental Botany, vol. 66, no. 16, Oxford University Press, 2015, pp. 5029–42, doi:10.1093/jxb/erv256.","apa":"Robert, H., Crhák Khaitová, L., Mroue, S., & Benková, E. (2015). The importance of localized auxin production for morphogenesis of reproductive organs and embryos in Arabidopsis. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/erv256","ama":"Robert H, Crhák Khaitová L, Mroue S, Benková E. The importance of localized auxin production for morphogenesis of reproductive organs and embryos in Arabidopsis. Journal of Experimental Botany. 2015;66(16):5029-5042. doi:10.1093/jxb/erv256","ieee":"H. Robert, L. Crhák Khaitová, S. Mroue, and E. Benková, “The importance of localized auxin production for morphogenesis of reproductive organs and embryos in Arabidopsis,” Journal of Experimental Botany, vol. 66, no. 16. Oxford University Press, pp. 5029–5042, 2015.","short":"H. Robert, L. Crhák Khaitová, S. Mroue, E. Benková, Journal of Experimental Botany 66 (2015) 5029–5042.","chicago":"Robert, Hélène, Lucie Crhák Khaitová, Souad Mroue, and Eva Benková. “The Importance of Localized Auxin Production for Morphogenesis of Reproductive Organs and Embryos in Arabidopsis.” Journal of Experimental Botany. Oxford University Press, 2015. https://doi.org/10.1093/jxb/erv256.","ista":"Robert H, Crhák Khaitová L, Mroue S, Benková E. 2015. The importance of localized auxin production for morphogenesis of reproductive organs and embryos in Arabidopsis. Journal of Experimental Botany. 66(16), 5029–5042."},"intvolume":" 66","month":"05","scopus_import":1,"quality_controlled":"1","publisher":"Oxford University Press","acknowledgement":"The work was supported by grants from: the Employment of Best Young Scientists for International Cooperation Empowerment/OPVKII programme (CZ.1.07/2.3.00/30.0037) to HSR and LCK; the Czech Science Foundation (GA13-39982S) to EB, LCK and SM; and the SoMoPro II programme (3SGA5602), cofinanced by the South-Moravian Region and the EU (FP7/2007–2013 People Programme), to HSR.","oa_version":"None","abstract":[{"text":"Plant sexual reproduction involves highly structured and specialized organs: stamens (male) and gynoecia (female, containing ovules). These organs synchronously develop within protective flower buds, until anthesis, via tightly coordinated mechanisms that are essential for effective fertilization and production of viable seeds. The phytohormone auxin is one of the key endogenous signalling molecules controlling initiation and development of these, and other, plant organs. In particular, its uneven distribution, resulting from tightly controlled production, metabolism and directional transport, is an important morphogenic factor. In this review we discuss how developmentally controlled and localized auxin biosynthesis and transport contribute to the coordinated development of plants' reproductive organs, and their fertilized derivatives (embryos) via the regulation of auxin levels and distribution within and around them. Current understanding of the links between de novo local auxin biosynthesis, auxin transport and/or signalling is presented to highlight the importance of the non-cell autonomous action of auxin production on development and morphogenesis of reproductive organs and embryos. An overview of transcription factor families, which spatiotemporally define local auxin production by controlling key auxin biosynthetic enzymes, is also presented.","lang":"eng"}],"date_created":"2018-12-11T11:52:36Z","volume":66,"issue":"16","date_published":"2015-05-05T00:00:00Z","doi":"10.1093/jxb/erv256","page":"5029 - 5042","language":[{"iso":"eng"}],"publication":"Journal of Experimental Botany","day":"05","publication_status":"published","year":"2015"},{"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"citation":{"mla":"El Masri, Leila, et al. “Host–Pathogen Coevolution: The Selective Advantage of Bacillus Thuringiensis Virulence and Its Cry Toxin Genes.” PLoS Biology, vol. 13, no. 6, Public Library of Science, 2015, pp. 1–30, doi:10.1371/journal.pbio.1002169.","ama":"El Masri L, Branca A, Sheppard A, et al. Host–pathogen coevolution: The selective advantage of Bacillus thuringiensis virulence and its cry toxin genes. PLoS Biology. 2015;13(6):1-30. doi:10.1371/journal.pbio.1002169","apa":"El Masri, L., Branca, A., Sheppard, A., Papkou, A., Laehnemann, D., Guenther, P., … Schulenburg, H. (2015). Host–pathogen coevolution: The selective advantage of Bacillus thuringiensis virulence and its cry toxin genes. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.1002169","ieee":"L. El Masri et al., “Host–pathogen coevolution: The selective advantage of Bacillus thuringiensis virulence and its cry toxin genes,” PLoS Biology, vol. 13, no. 6. Public Library of Science, pp. 1–30, 2015.","short":"L. El Masri, A. Branca, A. Sheppard, A. Papkou, D. Laehnemann, P. Guenther, S. Prahl, M. Saebelfeld, J. Hollensteiner, H. Liesegang, E. Brzuszkiewicz, R. Daniel, N. Michiels, R. Schulte, J. Kurtz, P. Rosenstiel, A. Telschow, E. Bornberg Bauer, H. Schulenburg, PLoS Biology 13 (2015) 1–30.","chicago":"El Masri, Leila, Antoine Branca, Anna Sheppard, Andrei Papkou, David Laehnemann, Patrick Guenther, Swantje Prahl, et al. “Host–Pathogen Coevolution: The Selective Advantage of Bacillus Thuringiensis Virulence and Its Cry Toxin Genes.” PLoS Biology. Public Library of Science, 2015. https://doi.org/10.1371/journal.pbio.1002169.","ista":"El Masri L, Branca A, Sheppard A, Papkou A, Laehnemann D, Guenther P, Prahl S, Saebelfeld M, Hollensteiner J, Liesegang H, Brzuszkiewicz E, Daniel R, Michiels N, Schulte R, Kurtz J, Rosenstiel P, Telschow A, Bornberg Bauer E, Schulenburg H. 2015. Host–pathogen coevolution: The selective advantage of Bacillus thuringiensis virulence and its cry toxin genes. PLoS Biology. 13(6), 1–30."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"El Masri, Leila","last_name":"El Masri","id":"349A6E66-F248-11E8-B48F-1D18A9856A87","first_name":"Leila"},{"last_name":"Branca","full_name":"Branca, Antoine","first_name":"Antoine"},{"last_name":"Sheppard","full_name":"Sheppard, Anna","first_name":"Anna"},{"full_name":"Papkou, Andrei","last_name":"Papkou","first_name":"Andrei"},{"full_name":"Laehnemann, David","last_name":"Laehnemann","first_name":"David"},{"last_name":"Guenther","full_name":"Guenther, Patrick","first_name":"Patrick"},{"last_name":"Prahl","full_name":"Prahl, Swantje","first_name":"Swantje"},{"full_name":"Saebelfeld, Manja","last_name":"Saebelfeld","first_name":"Manja"},{"full_name":"Hollensteiner, Jacqueline","last_name":"Hollensteiner","first_name":"Jacqueline"},{"full_name":"Liesegang, Heiko","last_name":"Liesegang","first_name":"Heiko"},{"last_name":"Brzuszkiewicz","full_name":"Brzuszkiewicz, Elzbieta","first_name":"Elzbieta"},{"full_name":"Daniel, Rolf","last_name":"Daniel","first_name":"Rolf"},{"full_name":"Michiels, Nico","last_name":"Michiels","first_name":"Nico"},{"last_name":"Schulte","full_name":"Schulte, Rebecca","first_name":"Rebecca"},{"full_name":"Kurtz, Joachim","last_name":"Kurtz","first_name":"Joachim"},{"last_name":"Rosenstiel","full_name":"Rosenstiel, Philip","first_name":"Philip"},{"last_name":"Telschow","full_name":"Telschow, Arndt","first_name":"Arndt"},{"first_name":"Erich","full_name":"Bornberg Bauer, Erich","last_name":"Bornberg Bauer"},{"first_name":"Hinrich","full_name":"Schulenburg, Hinrich","last_name":"Schulenburg"}],"publist_id":"5620","title":"Host–pathogen coevolution: The selective advantage of Bacillus thuringiensis virulence and its cry toxin genes","acknowledgement":"We are very grateful for funding from the German Science Foundation (DFG) to HS (SCHU 1415/8, SCHU 1415/9), PR (RO 2994/3), EBB (BO 2544/7), HL (LI 1690/2), AT (TE 976/2), RDS (SCHU 2522/1), JK (KU 1929/4); from the Kiel Excellence Cluster Inflammation at Interfaces to HS and PR; and from the ISTFELLOW program (Co-fund Marie Curie Actions of the European Commission) to LM.","publisher":"Public Library of Science","quality_controlled":"1","oa":1,"has_accepted_license":"1","year":"2015","day":"04","publication":"PLoS Biology","page":"1 - 30","doi":"10.1371/journal.pbio.1002169","date_published":"2015-06-04T00:00:00Z","date_created":"2018-12-11T11:52:40Z","_id":"1551","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":"481","date_updated":"2021-01-12T06:51:33Z","ddc":["570"],"department":[{"_id":"SyCr"}],"file_date_updated":"2020-07-14T12:45:02Z","abstract":[{"text":"Reciprocal coevolution between host and pathogen is widely seen as a major driver of evolution and biological innovation. Yet, to date, the underlying genetic mechanisms and associated trait functions that are unique to rapid coevolutionary change are generally unknown. We here combined experimental evolution of the bacterial biocontrol agent Bacillus thuringiensis and its nematode host Caenorhabditis elegans with large-scale phenotyping, whole genome analysis, and functional genetics to demonstrate the selective benefit of pathogen virulence and the underlying toxin genes during the adaptation process. We show that: (i) high virulence was specifically favoured during pathogen–host coevolution rather than pathogen one-sided adaptation to a nonchanging host or to an environment without host; (ii) the pathogen genotype BT-679 with known nematocidal toxin genes and high virulence specifically swept to fixation in all of the independent replicate populations under coevolution but only some under one-sided adaptation; (iii) high virulence in the BT-679-dominated populations correlated with elevated copy numbers of the plasmid containing the nematocidal toxin genes; (iv) loss of virulence in a toxin-plasmid lacking BT-679 isolate was reconstituted by genetic reintroduction or external addition of the toxins.We conclude that sustained coevolution is distinct from unidirectional selection in shaping the pathogen's genome and life history characteristics. To our knowledge, this study is the first to characterize the pathogen genes involved in coevolutionary adaptation in an animal host–pathogen interaction system.","lang":"eng"}],"oa_version":"Published Version","scopus_import":1,"month":"06","intvolume":" 13","publication_status":"published","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"30dee7a2c11ed09f2f5634655c0146f8","file_id":"5063","creator":"system","date_updated":"2020-07-14T12:45:02Z","file_size":3468956,"date_created":"2018-12-12T10:14:13Z","file_name":"IST-2016-481-v1+1_journal.pbio.1002169.pdf"}],"language":[{"iso":"eng"}],"volume":13,"issue":"6","ec_funded":1},{"oa":1,"quality_controlled":"1","publisher":"Springer","date_created":"2018-12-11T11:52:39Z","doi":"10.1007/978-1-4939-2845-3_6","date_published":"2015-09-18T00:00:00Z","page":"101 - 117","publication":"Novel chemical tools to study ion channel biology","day":"18","year":"2015","has_accepted_license":"1","title":"Flipping the photoswitch: Ion channels under light control","author":[{"first_name":"Catherine","id":"3EEDE19A-F248-11E8-B48F-1D18A9856A87","full_name":"Mckenzie, Catherine","last_name":"Mckenzie"},{"full_name":"Sanchez Romero, Inmaculada","last_name":"Sanchez Romero","id":"3D9C5D30-F248-11E8-B48F-1D18A9856A87","first_name":"Inmaculada"},{"id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","first_name":"Harald L","orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L","last_name":"Janovjak"}],"publist_id":"5622","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Mckenzie, Catherine, et al. “Flipping the Photoswitch: Ion Channels under Light Control.” Novel Chemical Tools to Study Ion Channel Biology, vol. 869, Springer, 2015, pp. 101–17, doi:10.1007/978-1-4939-2845-3_6.","ama":"Mckenzie C, Sanchez-Romero I, Janovjak HL. Flipping the photoswitch: Ion channels under light control. In: Novel Chemical Tools to Study Ion Channel Biology. Vol 869. Advances in Experimental Medicine and Biology. Springer; 2015:101-117. doi:10.1007/978-1-4939-2845-3_6","apa":"Mckenzie, C., Sanchez-Romero, I., & Janovjak, H. L. (2015). Flipping the photoswitch: Ion channels under light control. In Novel chemical tools to study ion channel biology (Vol. 869, pp. 101–117). Springer. https://doi.org/10.1007/978-1-4939-2845-3_6","short":"C. Mckenzie, I. Sanchez-Romero, H.L. Janovjak, in:, Novel Chemical Tools to Study Ion Channel Biology, Springer, 2015, pp. 101–117.","ieee":"C. Mckenzie, I. Sanchez-Romero, and H. L. Janovjak, “Flipping the photoswitch: Ion channels under light control,” in Novel chemical tools to study ion channel biology, vol. 869, Springer, 2015, pp. 101–117.","chicago":"Mckenzie, Catherine, Inmaculada Sanchez-Romero, and Harald L Janovjak. “Flipping the Photoswitch: Ion Channels under Light Control.” In Novel Chemical Tools to Study Ion Channel Biology, 869:101–17. Advances in Experimental Medicine and Biology. Springer, 2015. https://doi.org/10.1007/978-1-4939-2845-3_6.","ista":"Mckenzie C, Sanchez-Romero I, Janovjak HL. 2015.Flipping the photoswitch: Ion channels under light control. In: Novel chemical tools to study ion channel biology. vol. 869, 101–117."},"intvolume":" 869","month":"09","scopus_import":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Nature has incorporated small photochromic molecules, colloquially termed 'photoswitches', in photoreceptor proteins to sense optical cues in photo-taxis and vision. While Nature's ability to employ light-responsive functionalities has long been recognized, it was not until recently that scientists designed, synthesized and applied synthetic photochromes to manipulate many of which open rapidly and locally in their native cell types, biological processes with the temporal and spatial resolution of light. Ion channels in particular have come to the forefront of proteins that can be put under the designer control of synthetic photochromes. Photochromic ion channel controllers are comprised of three classes, photochromic soluble ligands (PCLs), photochromic tethered ligands (PTLs) and photochromic crosslinkers (PXs), and in each class ion channel functionality is controlled through reversible changes in photochrome structure. By acting as light-dependent ion channel agonists, antagonist or modulators, photochromic controllers effectively converted a wide range of ion channels, including voltage-gated ion channels, 'leak channels', tri-, tetra- and pentameric ligand-gated ion channels, and temperaturesensitive ion channels, into man-made photoreceptors. Control by photochromes can be reversible, unlike in the case of 'caged' compounds, and non-invasive with high spatial precision, unlike pharmacology and electrical manipulation. Here, we introduce design principles of emerging photochromic molecules that act on ion channels and discuss the impact that these molecules are beginning to have on ion channel biophysics and neuronal physiology."}],"volume":869,"language":[{"iso":"eng"}],"file":[{"creator":"system","file_size":1919655,"date_updated":"2020-07-14T12:45:01Z","file_name":"IST-2017-839-v1+1_mckenzie.pdf","date_created":"2018-12-12T10:11:02Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"4854","checksum":"bd1bfdf2423a0c3b6e7cabfa8b44bc0f"}],"publication_status":"published","publication_identifier":{"isbn":["978-1-4939-2844-6"]},"pubrep_id":"839","status":"public","type":"book_chapter","_id":"1549","series_title":"Advances in Experimental Medicine and Biology","file_date_updated":"2020-07-14T12:45:01Z","department":[{"_id":"HaJa"}],"ddc":["571","576"],"date_updated":"2021-01-12T06:51:32Z"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Milutinovic, Barbara, et al. “Infection of Tribolium Castaneum with Bacillus Thuringiensis: Quantification of Bacterial Replication within Cadavers, Transmission via Cannibalism, and Inhibition of Spore Germination.” Applied and Environmental Microbiology, vol. 81, no. 23, American Society for Microbiology, 2015, pp. 8135–44, doi:10.1128/AEM.02051-15.","ieee":"B. Milutinovic, C. Höfling, M. Futo, J. Scharsack, and J. Kurtz, “Infection of Tribolium castaneum with Bacillus thuringiensis: Quantification of bacterial replication within cadavers, transmission via cannibalism, and inhibition of spore germination,” Applied and Environmental Microbiology, vol. 81, no. 23. American Society for Microbiology, pp. 8135–8144, 2015.","short":"B. Milutinovic, C. Höfling, M. Futo, J. Scharsack, J. Kurtz, Applied and Environmental Microbiology 81 (2015) 8135–8144.","apa":"Milutinovic, B., Höfling, C., Futo, M., Scharsack, J., & Kurtz, J. (2015). Infection of Tribolium castaneum with Bacillus thuringiensis: Quantification of bacterial replication within cadavers, transmission via cannibalism, and inhibition of spore germination. Applied and Environmental Microbiology. American Society for Microbiology. https://doi.org/10.1128/AEM.02051-15","ama":"Milutinovic B, Höfling C, Futo M, Scharsack J, Kurtz J. Infection of Tribolium castaneum with Bacillus thuringiensis: Quantification of bacterial replication within cadavers, transmission via cannibalism, and inhibition of spore germination. Applied and Environmental Microbiology. 2015;81(23):8135-8144. doi:10.1128/AEM.02051-15","chicago":"Milutinovic, Barbara, Christina Höfling, Momir Futo, Jörn Scharsack, and Joachim Kurtz. “Infection of Tribolium Castaneum with Bacillus Thuringiensis: Quantification of Bacterial Replication within Cadavers, Transmission via Cannibalism, and Inhibition of Spore Germination.” Applied and Environmental Microbiology. American Society for Microbiology, 2015. https://doi.org/10.1128/AEM.02051-15.","ista":"Milutinovic B, Höfling C, Futo M, Scharsack J, Kurtz J. 2015. Infection of Tribolium castaneum with Bacillus thuringiensis: Quantification of bacterial replication within cadavers, transmission via cannibalism, and inhibition of spore germination. Applied and Environmental Microbiology. 81(23), 8135–8144."},"title":"Infection of Tribolium castaneum with Bacillus thuringiensis: Quantification of bacterial replication within cadavers, transmission via cannibalism, and inhibition of spore germination","external_id":{"pmid":["26386058"]},"author":[{"first_name":"Barbara","id":"2CDC32B8-F248-11E8-B48F-1D18A9856A87","last_name":"Milutinovic","orcid":"0000-0002-8214-4758","full_name":"Milutinovic, Barbara"},{"last_name":"Höfling","full_name":"Höfling, Christina","first_name":"Christina"},{"last_name":"Futo","full_name":"Futo, Momir","first_name":"Momir"},{"first_name":"Jörn","last_name":"Scharsack","full_name":"Scharsack, Jörn"},{"first_name":"Joachim","last_name":"Kurtz","full_name":"Kurtz, Joachim"}],"publist_id":"5623","publication":"Applied and Environmental Microbiology","day":"01","year":"2015","date_created":"2018-12-11T11:52:39Z","date_published":"2015-12-01T00:00:00Z","doi":"10.1128/AEM.02051-15","page":"8135 - 8144","oa":1,"publisher":"American Society for Microbiology","quality_controlled":"1","date_updated":"2021-01-12T06:51:31Z","department":[{"_id":"SyCr"}],"_id":"1548","status":"public","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","volume":81,"issue":"23","oa_version":"Submitted Version","pmid":1,"abstract":[{"text":"Reproduction within a host and transmission to the next host are crucial for the virulence and fitness of pathogens. Nevertheless, basic knowledge about such parameters is often missing from the literature, even for well-studied bacteria, such as Bacillus thuringiensis, an endospore-forming insect pathogen, which infects its hosts via the oral route. To characterize bacterial replication success, we made use of an experimental oral infection system for the red flour beetle Tribolium castaneum and developed a flow cytometric assay for the quantification of both spore ingestion by the individual beetle larvae and the resulting spore load after bacterial replication and resporulation within cadavers. On average, spore numbers increased 460-fold, showing that Bacillus thuringiensis grows and replicates successfully in insect cadavers. By inoculating cadaver-derived spores and spores from bacterial stock cultures into nutrient medium, we next investigated outgrowth characteristics of vegetative cells and found that cadaver- derived bacteria showed reduced growth compared to bacteria from the stock cultures. Interestingly, this reduced growth was a consequence of inhibited spore germination, probably originating from the host and resulting in reduced host mortality in subsequent infections by cadaver-derived spores. Nevertheless, we further showed that Bacillus thuringiensis transmission was possible via larval cannibalism when no other food was offered. These results contribute to our understanding of the ecology of Bacillus thuringiensis as an insect pathogen.","lang":"eng"}],"intvolume":" 81","month":"12","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4651099/"}],"scopus_import":1},{"title":"Actin flows mediate a universal coupling between cell speed and cell persistence","department":[{"_id":"MiSi"},{"_id":"CaHe"}],"publist_id":"5618","author":[{"first_name":"Paolo","last_name":"Maiuri","full_name":"Maiuri, Paolo"},{"full_name":"Rupprecht, Jean","last_name":"Rupprecht","first_name":"Jean"},{"last_name":"Wieser","orcid":"0000-0002-2670-2217","full_name":"Wieser, Stefan","first_name":"Stefan","id":"355AA5A0-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Verena","id":"4D71A03A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4088-8633","full_name":"Ruprecht, Verena","last_name":"Ruprecht"},{"first_name":"Olivier","full_name":"Bénichou, Olivier","last_name":"Bénichou"},{"first_name":"Nicolas","full_name":"Carpi, Nicolas","last_name":"Carpi"},{"full_name":"Coppey, Mathieu","last_name":"Coppey","first_name":"Mathieu"},{"first_name":"Simon","last_name":"De Beco","full_name":"De Beco, Simon"},{"first_name":"Nir","full_name":"Gov, Nir","last_name":"Gov"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566"},{"first_name":"Carolina","last_name":"Lage Crespo","full_name":"Lage Crespo, Carolina"},{"last_name":"Lautenschlaeger","full_name":"Lautenschlaeger, Franziska","first_name":"Franziska"},{"first_name":"Maël","full_name":"Le Berre, Maël","last_name":"Le Berre"},{"first_name":"Ana","last_name":"Lennon Duménil","full_name":"Lennon Duménil, Ana"},{"last_name":"Raab","full_name":"Raab, Matthew","first_name":"Matthew"},{"full_name":"Thiam, Hawa","last_name":"Thiam","first_name":"Hawa"},{"full_name":"Piel, Matthieu","last_name":"Piel","first_name":"Matthieu"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"},{"first_name":"Raphaël","full_name":"Voituriez, Raphaël","last_name":"Voituriez"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:51:33Z","citation":{"chicago":"Maiuri, Paolo, Jean Rupprecht, Stefan Wieser, Verena Ruprecht, Olivier Bénichou, Nicolas Carpi, Mathieu Coppey, et al. “Actin Flows Mediate a Universal Coupling between Cell Speed and Cell Persistence.” Cell. Cell Press, 2015. https://doi.org/10.1016/j.cell.2015.01.056.","ista":"Maiuri P, Rupprecht J, Wieser S, Ruprecht V, Bénichou O, Carpi N, Coppey M, De Beco S, Gov N, Heisenberg C-PJ, Lage Crespo C, Lautenschlaeger F, Le Berre M, Lennon Duménil A, Raab M, Thiam H, Piel M, Sixt MK, Voituriez R. 2015. Actin flows mediate a universal coupling between cell speed and cell persistence. Cell. 161(2), 374–386.","mla":"Maiuri, Paolo, et al. “Actin Flows Mediate a Universal Coupling between Cell Speed and Cell Persistence.” Cell, vol. 161, no. 2, Cell Press, 2015, pp. 374–86, doi:10.1016/j.cell.2015.01.056.","ieee":"P. Maiuri et al., “Actin flows mediate a universal coupling between cell speed and cell persistence,” Cell, vol. 161, no. 2. Cell Press, pp. 374–386, 2015.","short":"P. Maiuri, J. Rupprecht, S. Wieser, V. Ruprecht, O. Bénichou, N. Carpi, M. Coppey, S. De Beco, N. Gov, C.-P.J. Heisenberg, C. Lage Crespo, F. Lautenschlaeger, M. Le Berre, A. Lennon Duménil, M. Raab, H. Thiam, M. Piel, M.K. Sixt, R. Voituriez, Cell 161 (2015) 374–386.","apa":"Maiuri, P., Rupprecht, J., Wieser, S., Ruprecht, V., Bénichou, O., Carpi, N., … Voituriez, R. (2015). Actin flows mediate a universal coupling between cell speed and cell persistence. Cell. Cell Press. https://doi.org/10.1016/j.cell.2015.01.056","ama":"Maiuri P, Rupprecht J, Wieser S, et al. Actin flows mediate a universal coupling between cell speed and cell persistence. Cell. 2015;161(2):374-386. doi:10.1016/j.cell.2015.01.056"},"project":[{"name":"Cell- and Tissue Mechanics in Zebrafish Germ Layer Formation","grant_number":"T 560-B17","_id":"2529486C-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"281556","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)","_id":"25A603A2-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"RGP0058/2011","name":"Cell migration in complex environments: from in vivo experiments to theoretical models","_id":"25ABD200-B435-11E9-9278-68D0E5697425"}],"status":"public","type":"journal_article","_id":"1553","date_published":"2015-04-09T00:00:00Z","issue":"2","doi":"10.1016/j.cell.2015.01.056","volume":161,"ec_funded":1,"date_created":"2018-12-11T11:52:41Z","page":"374 - 386","day":"09","publication":"Cell","language":[{"iso":"eng"}],"year":"2015","publication_status":"published","month":"04","intvolume":" 161","quality_controlled":"1","publisher":"Cell Press","scopus_import":1,"oa_version":"None","abstract":[{"lang":"eng","text":"Cell movement has essential functions in development, immunity, and cancer. Various cell migration patterns have been reported, but no general rule has emerged so far. Here, we show on the basis of experimental data in vitro and in vivo that cell persistence, which quantifies the straightness of trajectories, is robustly coupled to cell migration speed. We suggest that this universal coupling constitutes a generic law of cell migration, which originates in the advection of polarity cues by an actin cytoskeleton undergoing flows at the cellular scale. Our analysis relies on a theoretical model that we validate by measuring the persistence of cells upon modulation of actin flow speeds and upon optogenetic manipulation of the binding of an actin regulator to actin filaments. Beyond the quantitative prediction of the coupling, the model yields a generic phase diagram of cellular trajectories, which recapitulates the full range of observed migration patterns."}]},{"issue":"5","volume":87,"language":[{"iso":"eng"}],"publication_status":"published","month":"09","intvolume":" 87","scopus_import":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4560602/","open_access":"1"}],"oa_version":"Submitted Version","pmid":1,"abstract":[{"text":"The medial ganglionic eminence (MGE) gives rise to the majority of mouse forebrain interneurons. Here, we examine the lineage relationship among MGE-derived interneurons using a replication-defective retroviral library containing a highly diverse set of DNA barcodes. Recovering the barcodes from the mature progeny of infected progenitor cells enabled us to unambiguously determine their respective lineal relationship. We found that clonal dispersion occurs across large areas of the brain and is not restricted by anatomical divisions. As such, sibling interneurons can populate the cortex, hippocampus striatum, and globus pallidus. The majority of interneurons appeared to be generated from asymmetric divisions of MGE progenitor cells, followed by symmetric divisions within the subventricular zone. Altogether, our findings uncover that lineage relationships do not appear to determine interneuron allocation to particular regions. As such, it is likely that clonally related interneurons have considerable flexibility as to the particular forebrain circuits to which they can contribute.","lang":"eng"}],"department":[{"_id":"SiHi"}],"date_updated":"2021-01-12T06:51:32Z","status":"public","type":"journal_article","_id":"1550","date_published":"2015-09-02T00:00:00Z","doi":"10.1016/j.neuron.2015.07.011","date_created":"2018-12-11T11:52:40Z","page":"989 - 998","day":"02","publication":"Neuron","year":"2015","quality_controlled":"1","publisher":"Elsevier","oa":1,"acknowledgement":"Research in the G.F. laboratory is supported by NIH (NS 081297, MH095147, and P01NS074972) and the Simons Foundation. Research in the S.H. laboratory is supported by the European Union (FP7-CIG618444). C.M. is supported by EMBO ALTF (1295-2012). X.H.J. is supported by EMBO (ALTF 303-2010) and HFSP (LT000078/2011-L).\r\n\r\n","title":"Clonally related forebrain interneurons disperse broadly across both functional areas and structural boundaries","author":[{"first_name":"Christian","last_name":"Mayer","full_name":"Mayer, Christian"},{"first_name":"Xavier","last_name":"Jaglin","full_name":"Jaglin, Xavier"},{"full_name":"Cobbs, Lucy","last_name":"Cobbs","first_name":"Lucy"},{"first_name":"Rachel","last_name":"Bandler","full_name":"Bandler, Rachel"},{"full_name":"Streicher, Carmen","last_name":"Streicher","first_name":"Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Constance","last_name":"Cepko","full_name":"Cepko, Constance"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061"},{"last_name":"Fishell","full_name":"Fishell, Gord","first_name":"Gord"}],"publist_id":"5621","external_id":{"pmid":["26299473"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Mayer C, Jaglin X, Cobbs L, et al. Clonally related forebrain interneurons disperse broadly across both functional areas and structural boundaries. Neuron. 2015;87(5):989-998. doi:10.1016/j.neuron.2015.07.011","apa":"Mayer, C., Jaglin, X., Cobbs, L., Bandler, R., Streicher, C., Cepko, C., … Fishell, G. (2015). Clonally related forebrain interneurons disperse broadly across both functional areas and structural boundaries. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2015.07.011","ieee":"C. Mayer et al., “Clonally related forebrain interneurons disperse broadly across both functional areas and structural boundaries,” Neuron, vol. 87, no. 5. Elsevier, pp. 989–998, 2015.","short":"C. Mayer, X. Jaglin, L. Cobbs, R. Bandler, C. Streicher, C. Cepko, S. Hippenmeyer, G. Fishell, Neuron 87 (2015) 989–998.","mla":"Mayer, Christian, et al. “Clonally Related Forebrain Interneurons Disperse Broadly across Both Functional Areas and Structural Boundaries.” Neuron, vol. 87, no. 5, Elsevier, 2015, pp. 989–98, doi:10.1016/j.neuron.2015.07.011.","ista":"Mayer C, Jaglin X, Cobbs L, Bandler R, Streicher C, Cepko C, Hippenmeyer S, Fishell G. 2015. Clonally related forebrain interneurons disperse broadly across both functional areas and structural boundaries. Neuron. 87(5), 989–998.","chicago":"Mayer, Christian, Xavier Jaglin, Lucy Cobbs, Rachel Bandler, Carmen Streicher, Constance Cepko, Simon Hippenmeyer, and Gord Fishell. “Clonally Related Forebrain Interneurons Disperse Broadly across Both Functional Areas and Structural Boundaries.” Neuron. Elsevier, 2015. https://doi.org/10.1016/j.neuron.2015.07.011."}},{"abstract":[{"text":"Let G be a graph on the vertex set V(G) = {x1,…,xn} with the edge set E(G), and let R = K[x1,…, xn] be the polynomial ring over a field K. Two monomial ideals are associated to G, the edge ideal I(G) generated by all monomials xixj with {xi,xj} ∈ E(G), and the vertex cover ideal IG generated by monomials ∏xi∈Cxi for all minimal vertex covers C of G. A minimal vertex cover of G is a subset C ⊂ V(G) such that each edge has at least one vertex in C and no proper subset of C has the same property. Indeed, the vertex cover ideal of G is the Alexander dual of the edge ideal of G. In this paper, for an unmixed bipartite graph G we consider the lattice of vertex covers LG and we explicitly describe the minimal free resolution of the ideal associated to LG which is exactly the vertex cover ideal of G. Then we compute depth, projective dimension, regularity and extremal Betti numbers of R/I(G) in terms of the associated lattice.","lang":"eng"}],"oa_version":"Preprint","scopus_import":1,"main_file_link":[{"url":"http://arxiv.org/abs/0901.3015","open_access":"1"}],"month":"05","intvolume":" 52","publication_identifier":{"eissn":["2234-3016"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":52,"issue":"3","_id":"1547","type":"journal_article","status":"public","date_updated":"2021-01-12T06:51:31Z","department":[{"_id":"CaUh"}],"quality_controlled":"1","publisher":"Korean Mathematical Society","oa":1,"year":"2015","day":"31","publication":"Bulletin of the Korean Mathematical Society","page":"977 - 986","date_published":"2015-05-31T00:00:00Z","doi":"10.4134/BKMS.2015.52.3.977","date_created":"2018-12-11T11:52:39Z","citation":{"ista":"Mohammadi F, Moradi S. 2015. Resolution of unmixed bipartite graphs. Bulletin of the Korean Mathematical Society. 52(3), 977–986.","chicago":"Mohammadi, Fatemeh, and Somayeh Moradi. “Resolution of Unmixed Bipartite Graphs.” Bulletin of the Korean Mathematical Society. Korean Mathematical Society, 2015. https://doi.org/10.4134/BKMS.2015.52.3.977.","ieee":"F. Mohammadi and S. Moradi, “Resolution of unmixed bipartite graphs,” Bulletin of the Korean Mathematical Society, vol. 52, no. 3. Korean Mathematical Society, pp. 977–986, 2015.","short":"F. Mohammadi, S. Moradi, Bulletin of the Korean Mathematical Society 52 (2015) 977–986.","ama":"Mohammadi F, Moradi S. Resolution of unmixed bipartite graphs. Bulletin of the Korean Mathematical Society. 2015;52(3):977-986. doi:10.4134/BKMS.2015.52.3.977","apa":"Mohammadi, F., & Moradi, S. (2015). Resolution of unmixed bipartite graphs. Bulletin of the Korean Mathematical Society. Korean Mathematical Society. https://doi.org/10.4134/BKMS.2015.52.3.977","mla":"Mohammadi, Fatemeh, and Somayeh Moradi. “Resolution of Unmixed Bipartite Graphs.” Bulletin of the Korean Mathematical Society, vol. 52, no. 3, Korean Mathematical Society, 2015, pp. 977–86, doi:10.4134/BKMS.2015.52.3.977."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"2C29581E-F248-11E8-B48F-1D18A9856A87","first_name":"Fatemeh","full_name":"Mohammadi, Fatemeh","last_name":"Mohammadi"},{"first_name":"Somayeh","last_name":"Moradi","full_name":"Moradi, Somayeh"}],"publist_id":"5624","title":"Resolution of unmixed bipartite graphs"},{"intvolume":" 66","month":"08","scopus_import":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"The elongator complex subunit 2 (ELP2) protein, one subunit of an evolutionarily conserved histone acetyltransferase complex, has been shown to participate in leaf patterning, plant immune and abiotic stress responses in Arabidopsis thaliana. Here, its role in root development was explored. Compared to the wild type, the elp2 mutant exhibited an accelerated differentiation of its root stem cells and cell division was more active in its quiescent centre (QC). The key transcription factors responsible for maintaining root stem cell and QC identity, such as AP2 transcription factors PLT1 (PLETHORA1) and PLT2 (PLETHORA2), GRAS transcription factors such as SCR (SCARECROW) and SHR (SHORT ROOT) and WUSCHEL-RELATED HOMEOBOX5 transcription factor WOX5, were all strongly down-regulated in the mutant. On the other hand, expression of the G2/M transition activator CYCB1 was substantially induced in elp2. The auxin efflux transporters PIN1 and PIN2 showed decreased protein levels and PIN1 also displayed mild polarity alterations in elp2, which resulted in a reduced auxin content in the root tip. Either the acetylation or methylation level of each of these genes differed between the mutant and the wild type, suggesting that the ELP2 regulation of root development involves the epigenetic modification of a range of transcription factors and other developmental regulators."}],"volume":66,"issue":"15","language":[{"iso":"eng"}],"file":[{"creator":"system","date_updated":"2020-07-14T12:45:02Z","file_size":7753043,"date_created":"2018-12-12T10:14:02Z","file_name":"IST-2016-480-v1+1_J._Exp._Bot.-2015-Jia-4631-42.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"257919be0ce3d306185d3891ad7acf39","file_id":"5051"}],"publication_status":"published","pubrep_id":"480","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":"1556","file_date_updated":"2020-07-14T12:45:02Z","department":[{"_id":"JiFr"}],"ddc":["570"],"date_updated":"2021-01-12T06:51:35Z","oa":1,"publisher":"Oxford University Press","quality_controlled":"1","date_created":"2018-12-11T11:52:42Z","date_published":"2015-08-01T00:00:00Z","doi":"10.1093/jxb/erv230","page":"4631 - 4642","publication":"Journal of Experimental Botany","day":"01","year":"2015","has_accepted_license":"1","title":"The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root development","author":[{"full_name":"Jia, Yuebin","last_name":"Jia","first_name":"Yuebin"},{"first_name":"Huiyu","last_name":"Tian","full_name":"Tian, Huiyu"},{"full_name":"Li, Hongjiang","orcid":"0000-0001-5039-9660","last_name":"Li","first_name":"Hongjiang","id":"33CA54A6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Yu, Qianqian","last_name":"Yu","first_name":"Qianqian"},{"last_name":"Wang","full_name":"Wang, Lei","first_name":"Lei"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596"},{"last_name":"Ding","full_name":"Ding, Zhaojun","first_name":"Zhaojun"}],"publist_id":"5615","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Jia Y, Tian H, Li H, et al. The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root development. Journal of Experimental Botany. 2015;66(15):4631-4642. doi:10.1093/jxb/erv230","apa":"Jia, Y., Tian, H., Li, H., Yu, Q., Wang, L., Friml, J., & Ding, Z. (2015). The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root development. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/erv230","short":"Y. Jia, H. Tian, H. Li, Q. Yu, L. Wang, J. Friml, Z. Ding, Journal of Experimental Botany 66 (2015) 4631–4642.","ieee":"Y. Jia et al., “The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root development,” Journal of Experimental Botany, vol. 66, no. 15. Oxford University Press, pp. 4631–4642, 2015.","mla":"Jia, Yuebin, et al. “The Arabidopsis Thaliana Elongator Complex Subunit 2 Epigenetically Affects Root Development.” Journal of Experimental Botany, vol. 66, no. 15, Oxford University Press, 2015, pp. 4631–42, doi:10.1093/jxb/erv230.","ista":"Jia Y, Tian H, Li H, Yu Q, Wang L, Friml J, Ding Z. 2015. The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root development. Journal of Experimental Botany. 66(15), 4631–4642.","chicago":"Jia, Yuebin, Huiyu Tian, Hongjiang Li, Qianqian Yu, Lei Wang, Jiří Friml, and Zhaojun Ding. “The Arabidopsis Thaliana Elongator Complex Subunit 2 Epigenetically Affects Root Development.” Journal of Experimental Botany. Oxford University Press, 2015. https://doi.org/10.1093/jxb/erv230."}},{"main_file_link":[{"open_access":"1","url":"http://discovery.ucl.ac.uk/1473750/1/99393.pdf"}],"scopus_import":1,"intvolume":" 14","month":"01","abstract":[{"lang":"eng","text":"We show that incorporating spatial dispersal of individuals into a simple vaccination epidemic model may give rise to a model that exhibits rich dynamical behavior. Using an SIVS (susceptible-infected-vaccinated-susceptible) model as a basis, we describe the spread of an infectious disease in a population split into two regions. In each subpopulation, both forward and backward bifurcations can occur. This implies that for disconnected regions the two-patch system may admit several steady states. We consider traveling between the regions and investigate the impact of spatial dispersal of individuals on the model dynamics. We establish conditions for the existence of multiple nontrivial steady states in the system, and we study the structure of the equilibria. The mathematical analysis reveals an unusually rich dynamical behavior, not normally found in the simple epidemic models. In addition to the disease-free equilibrium, eight endemic equilibria emerge from backward transcritical and saddle-node bifurcation points, forming an interesting bifurcation diagram. Stability of steady states, their bifurcations, and the global dynamics are investigated with analytical tools, numerical simulations, and rigorous set-oriented numerical computations."}],"oa_version":"Published Version","ec_funded":1,"issue":"2","volume":14,"publication_status":"published","publication_identifier":{"eissn":["1536-0040"]},"language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","status":"public","_id":"1555","department":[{"_id":"HeEd"}],"date_updated":"2021-01-12T06:51:34Z","ddc":["510"],"oa":1,"publisher":"Society for Industrial and Applied Mathematics ","quality_controlled":"1","acknowledgement":"Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria (pawel.pilarczyk@ist.ac.at). This author’s work was partially supported by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement 622033, by Fundo Europeu de Desenvolvimento Regional (FEDER) through COMPETE—Programa Operacional Factores de Competitividade (POFC), by the Portuguese national funds through Funda ̧caoparaaCiˆencia e a Tecnologia (FCT) in the framework of the research project FCOMP-01-0124-FEDER-010645 (ref. FCT PTDC/MAT/098871/2008), and by European Research Council through StG 259559 in the framework of the EPIDELAY project.","page":"980 - 1017","date_created":"2018-12-11T11:52:42Z","doi":"10.1137/140993934","date_published":"2015-01-01T00:00:00Z","year":"2015","publication":"SIAM Journal on Applied Dynamical Systems","day":"01","project":[{"call_identifier":"FP7","_id":"255F06BE-B435-11E9-9278-68D0E5697425","name":"Persistent Homology - Images, Data and Maps","grant_number":"622033"}],"article_processing_charge":"No","publist_id":"5616","author":[{"first_name":"Diána","last_name":"Knipl","full_name":"Knipl, Diána"},{"id":"3768D56A-F248-11E8-B48F-1D18A9856A87","first_name":"Pawel","full_name":"Pilarczyk, Pawel","last_name":"Pilarczyk"},{"first_name":"Gergely","full_name":"Röst, Gergely","last_name":"Röst"}],"title":"Rich bifurcation structure in a two patch vaccination model","citation":{"ista":"Knipl D, Pilarczyk P, Röst G. 2015. Rich bifurcation structure in a two patch vaccination model. SIAM Journal on Applied Dynamical Systems. 14(2), 980–1017.","chicago":"Knipl, Diána, Pawel Pilarczyk, and Gergely Röst. “Rich Bifurcation Structure in a Two Patch Vaccination Model.” SIAM Journal on Applied Dynamical Systems. Society for Industrial and Applied Mathematics , 2015. https://doi.org/10.1137/140993934.","ama":"Knipl D, Pilarczyk P, Röst G. Rich bifurcation structure in a two patch vaccination model. SIAM Journal on Applied Dynamical Systems. 2015;14(2):980-1017. doi:10.1137/140993934","apa":"Knipl, D., Pilarczyk, P., & Röst, G. (2015). Rich bifurcation structure in a two patch vaccination model. SIAM Journal on Applied Dynamical Systems. Society for Industrial and Applied Mathematics . https://doi.org/10.1137/140993934","short":"D. Knipl, P. Pilarczyk, G. Röst, SIAM Journal on Applied Dynamical Systems 14 (2015) 980–1017.","ieee":"D. Knipl, P. Pilarczyk, and G. Röst, “Rich bifurcation structure in a two patch vaccination model,” SIAM Journal on Applied Dynamical Systems, vol. 14, no. 2. Society for Industrial and Applied Mathematics , pp. 980–1017, 2015.","mla":"Knipl, Diána, et al. “Rich Bifurcation Structure in a Two Patch Vaccination Model.” SIAM Journal on Applied Dynamical Systems, vol. 14, no. 2, Society for Industrial and Applied Mathematics , 2015, pp. 980–1017, doi:10.1137/140993934."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"publist_id":"5613","author":[{"last_name":"Ivanchenko","full_name":"Ivanchenko, Maria","first_name":"Maria"},{"full_name":"Zhu, Jinsheng","last_name":"Zhu","first_name":"Jinsheng"},{"full_name":"Wang, Bangjun","last_name":"Wang","first_name":"Bangjun"},{"last_name":"Medvecka","full_name":"Medvecka, Eva","first_name":"Eva","id":"298814E2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Du, Yunlong","last_name":"Du","first_name":"Yunlong"},{"first_name":"Elisa","full_name":"Azzarello, Elisa","last_name":"Azzarello"},{"first_name":"Stefano","full_name":"Mancuso, Stefano","last_name":"Mancuso"},{"last_name":"Megraw","full_name":"Megraw, Molly","first_name":"Molly"},{"first_name":"Sergei","full_name":"Filichkin, Sergei","last_name":"Filichkin"},{"full_name":"Dubrovsky, Joseph","last_name":"Dubrovsky","first_name":"Joseph"},{"last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Geisler","full_name":"Geisler, Markus","first_name":"Markus"}],"department":[{"_id":"JiFr"}],"title":"The cyclophilin a DIAGEOTROPICA gene affects auxin transport in both root and shoot to control lateral root formation","date_updated":"2021-01-12T06:51:35Z","citation":{"ama":"Ivanchenko M, Zhu J, Wang B, et al. The cyclophilin a DIAGEOTROPICA gene affects auxin transport in both root and shoot to control lateral root formation. Development. 2015;142(4):712-721. doi:10.1242/dev.113225","apa":"Ivanchenko, M., Zhu, J., Wang, B., Medvecka, E., Du, Y., Azzarello, E., … Geisler, M. (2015). The cyclophilin a DIAGEOTROPICA gene affects auxin transport in both root and shoot to control lateral root formation. Development. Company of Biologists. https://doi.org/10.1242/dev.113225","short":"M. Ivanchenko, J. Zhu, B. Wang, E. Medvecka, Y. Du, E. Azzarello, S. Mancuso, M. Megraw, S. Filichkin, J. Dubrovsky, J. Friml, M. Geisler, Development 142 (2015) 712–721.","ieee":"M. Ivanchenko et al., “The cyclophilin a DIAGEOTROPICA gene affects auxin transport in both root and shoot to control lateral root formation,” Development, vol. 142, no. 4. Company of Biologists, pp. 712–721, 2015.","mla":"Ivanchenko, Maria, et al. “The Cyclophilin a DIAGEOTROPICA Gene Affects Auxin Transport in Both Root and Shoot to Control Lateral Root Formation.” Development, vol. 142, no. 4, Company of Biologists, 2015, pp. 712–21, doi:10.1242/dev.113225.","ista":"Ivanchenko M, Zhu J, Wang B, Medvecka E, Du Y, Azzarello E, Mancuso S, Megraw M, Filichkin S, Dubrovsky J, Friml J, Geisler M. 2015. The cyclophilin a DIAGEOTROPICA gene affects auxin transport in both root and shoot to control lateral root formation. Development. 142(4), 712–721.","chicago":"Ivanchenko, Maria, Jinsheng Zhu, Bangjun Wang, Eva Medvecka, Yunlong Du, Elisa Azzarello, Stefano Mancuso, et al. “The Cyclophilin a DIAGEOTROPICA Gene Affects Auxin Transport in Both Root and Shoot to Control Lateral Root Formation.” Development. Company of Biologists, 2015. https://doi.org/10.1242/dev.113225."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","status":"public","_id":"1558","page":"712 - 721","date_created":"2018-12-11T11:52:42Z","volume":142,"doi":"10.1242/dev.113225","date_published":"2015-02-15T00:00:00Z","issue":"4","publication_status":"published","year":"2015","publication":"Development","language":[{"iso":"eng"}],"day":"15","scopus_import":1,"quality_controlled":"1","publisher":"Company of Biologists","intvolume":" 142","month":"02","abstract":[{"text":"CyclophilinAis a conserved peptidyl-prolyl cis-trans isomerase (PPIase) best known as the cellular receptor of the immunosuppressant cyclosporine A. Despite significant effort, evidence of developmental functions of cyclophilin A in non-plant systems has remained obscure. Mutations in a tomato (Solanum lycopersicum) cyclophilin A ortholog, DIAGEOTROPICA (DGT), have been shown to abolish the organogenesis of lateral roots; however, a mechanistic explanation of the phenotype is lacking. Here, we show that the dgt mutant lacks auxin maxima relevant to priming and specification of lateral root founder cells. DGT is expressed in shoot and root, and localizes to both the nucleus and cytoplasm during lateral root organogenesis. Mutation of ENTIRE/ IAA9, a member of the auxin-responsive Aux/IAA protein family of transcriptional repressors, partially restores the inability of dgt to initiate lateral root primordia but not the primordia outgrowth. By comparison, grafting of a wild-type scion restores the process of lateral root formation, consistent with participation of a mobile signal. Antibodies do not detect movement of the DGT protein into the dgt rootstock; however, experiments with radiolabeled auxin and an auxin-specific microelectrode demonstrate abnormal auxin fluxes. Functional studies of DGT in heterologous yeast and tobacco-leaf auxin-transport systems demonstrate that DGT negatively regulates PIN-FORMED (PIN) auxin efflux transporters by affecting their plasma membrane localization. Studies in tomato support complex effects of the dgt mutation on PIN expression level, expression domain and plasma membrane localization. Our data demonstrate that DGT regulates auxin transport in lateral root formation.","lang":"eng"}],"oa_version":"None"},{"_id":"1557","status":"public","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Javdani F, Holló K, Hegedűs K, Kis G, Hegyi Z, Dócs K, Kasugai Y, Fukazawa Y, Shigemoto R, Antal M. 2015. Differential expression patterns of K+Cl- cotransporter 2 in neurons within the superficial spinal dorsal horn of rats. Journal of Comparative Neurology. 523(13), 1967–1983.","chicago":"Javdani, Fariba, Krisztina Holló, Krisztina Hegedűs, Gréta Kis, Zoltán Hegyi, Klaudia Dócs, Yu Kasugai, Yugo Fukazawa, Ryuichi Shigemoto, and Miklós Antal. “Differential Expression Patterns of K+Cl- Cotransporter 2 in Neurons within the Superficial Spinal Dorsal Horn of Rats.” Journal of Comparative Neurology. Wiley-Blackwell, 2015. https://doi.org/10.1002/cne.23774.","short":"F. Javdani, K. Holló, K. Hegedűs, G. Kis, Z. Hegyi, K. Dócs, Y. Kasugai, Y. Fukazawa, R. Shigemoto, M. Antal, Journal of Comparative Neurology 523 (2015) 1967–1983.","ieee":"F. Javdani et al., “Differential expression patterns of K+Cl- cotransporter 2 in neurons within the superficial spinal dorsal horn of rats,” Journal of Comparative Neurology, vol. 523, no. 13. Wiley-Blackwell, pp. 1967–1983, 2015.","ama":"Javdani F, Holló K, Hegedűs K, et al. Differential expression patterns of K+Cl- cotransporter 2 in neurons within the superficial spinal dorsal horn of rats. Journal of Comparative Neurology. 2015;523(13):1967-1983. doi:10.1002/cne.23774","apa":"Javdani, F., Holló, K., Hegedűs, K., Kis, G., Hegyi, Z., Dócs, K., … Antal, M. (2015). Differential expression patterns of K+Cl- cotransporter 2 in neurons within the superficial spinal dorsal horn of rats. Journal of Comparative Neurology. Wiley-Blackwell. https://doi.org/10.1002/cne.23774","mla":"Javdani, Fariba, et al. “Differential Expression Patterns of K+Cl- Cotransporter 2 in Neurons within the Superficial Spinal Dorsal Horn of Rats.” Journal of Comparative Neurology, vol. 523, no. 13, Wiley-Blackwell, 2015, pp. 1967–83, doi:10.1002/cne.23774."},"date_updated":"2021-01-12T06:51:35Z","title":"Differential expression patterns of K+Cl- cotransporter 2 in neurons within the superficial spinal dorsal horn of rats","department":[{"_id":"RySh"}],"publist_id":"5614","author":[{"full_name":"Javdani, Fariba","last_name":"Javdani","first_name":"Fariba"},{"full_name":"Holló, Krisztina","last_name":"Holló","first_name":"Krisztina"},{"first_name":"Krisztina","full_name":"Hegedűs, Krisztina","last_name":"Hegedűs"},{"last_name":"Kis","full_name":"Kis, Gréta","first_name":"Gréta"},{"last_name":"Hegyi","full_name":"Hegyi, Zoltán","first_name":"Zoltán"},{"first_name":"Klaudia","full_name":"Dócs, Klaudia","last_name":"Dócs"},{"first_name":"Yu","full_name":"Kasugai, Yu","last_name":"Kasugai"},{"first_name":"Yugo","last_name":"Fukazawa","full_name":"Fukazawa, Yugo"},{"last_name":"Shigemoto","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi"},{"last_name":"Antal","full_name":"Antal, Miklós","first_name":"Miklós"}],"acknowledgement":"Funded by:\r\nHungarian Academy of Sciences. Grant Number: MTA-TKI 242\r\nHungarian Brain Research Program. Grant Number: KTIA_NAP_13-1-2013-0001\r\nSolution Oriented Research for Science and Technology from the Japan Science and Technology Agency Japanese Ministry of Education, Culture, Sports, Science and Technology","oa_version":"None","abstract":[{"lang":"eng","text":"γ-Aminobutyric acid (GABA)- and glycine-mediated hyperpolarizing inhibition is associated with a chloride influx that depends on the inwardly directed chloride electrochemical gradient. In neurons, the extrusion of chloride from the cytosol primarily depends on the expression of an isoform of potassium-chloride cotransporters (KCC2s). KCC2 is crucial in the regulation of the inhibitory tone of neural circuits, including pain processing neural assemblies. Thus we investigated the cellular distribution of KCC2 in neurons underlying pain processing in the superficial spinal dorsal horn of rats by using high-resolution immunocytochemical methods. We demonstrated that perikarya and dendrites widely expressed KCC2, but axon terminals proved to be negative for KCC2. In single ultrathin sections, silver deposits labeling KCC2 molecules showed different densities on the surface of dendritic profiles, some of which were negative for KCC2. In freeze fracture replicas and tissue sections double stained for the β3-subunit of GABAA receptors and KCC2, GABAA receptors were revealed on dendritic segments with high and also with low KCC2 densities. By measuring the distances between spots immunoreactive for gephyrin (a scaffolding protein of GABAA and glycine receptors) and KCC2 on the surface of neurokinin 1 (NK1) receptor-immunoreactive dendrites, we found that gephyrin-immunoreactive spots were located at various distances from KCC2 cotransporters; 5.7 % of them were recovered in the middle of 4-10-μm-long dendritic segments that were free of KCC2 immunostaining. The variable local densities of KCC2 may result in variable postsynaptic potentials evoked by the activation of GABAA and glycine receptors along the dendrites of spinal neurons."}],"intvolume":" 523","month":"09","quality_controlled":"1","publisher":"Wiley-Blackwell","scopus_import":1,"language":[{"iso":"eng"}],"publication":"Journal of Comparative Neurology","day":"01","year":"2015","publication_status":"published","date_created":"2018-12-11T11:52:42Z","date_published":"2015-09-01T00:00:00Z","issue":"13","volume":523,"doi":"10.1002/cne.23774","page":"1967 - 1983"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Ibsen-Jensen R, Chatterjee K, Nowak M. 2015. Computational complexity of ecological and evolutionary spatial dynamics. PNAS. 112(51), 15636–15641.","chicago":"Ibsen-Jensen, Rasmus, Krishnendu Chatterjee, and Martin Nowak. “Computational Complexity of Ecological and Evolutionary Spatial Dynamics.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1511366112.","ama":"Ibsen-Jensen R, Chatterjee K, Nowak M. Computational complexity of ecological and evolutionary spatial dynamics. PNAS. 2015;112(51):15636-15641. doi:10.1073/pnas.1511366112","apa":"Ibsen-Jensen, R., Chatterjee, K., & Nowak, M. (2015). Computational complexity of ecological and evolutionary spatial dynamics. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1511366112","short":"R. Ibsen-Jensen, K. Chatterjee, M. Nowak, PNAS 112 (2015) 15636–15641.","ieee":"R. Ibsen-Jensen, K. Chatterjee, and M. Nowak, “Computational complexity of ecological and evolutionary spatial dynamics,” PNAS, vol. 112, no. 51. National Academy of Sciences, pp. 15636–15641, 2015.","mla":"Ibsen-Jensen, Rasmus, et al. “Computational Complexity of Ecological and Evolutionary Spatial Dynamics.” PNAS, vol. 112, no. 51, National Academy of Sciences, 2015, pp. 15636–41, doi:10.1073/pnas.1511366112."},"title":"Computational complexity of ecological and evolutionary spatial dynamics","external_id":{"pmid":["26644569"]},"publist_id":"5612","author":[{"orcid":"0000-0003-4783-0389","full_name":"Ibsen-Jensen, Rasmus","last_name":"Ibsen-Jensen","id":"3B699956-F248-11E8-B48F-1D18A9856A87","first_name":"Rasmus"},{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"last_name":"Nowak","full_name":"Nowak, Martin","first_name":"Martin"}],"oa":1,"quality_controlled":"1","publisher":"National Academy of Sciences","publication":"PNAS","day":"22","year":"2015","date_created":"2018-12-11T11:52:43Z","date_published":"2015-12-22T00:00:00Z","doi":"10.1073/pnas.1511366112","page":"15636 - 15641","_id":"1559","status":"public","type":"journal_article","date_updated":"2021-01-12T06:51:36Z","department":[{"_id":"KrCh"}],"oa_version":"Submitted Version","pmid":1,"abstract":[{"lang":"eng","text":"There are deep, yet largely unexplored, connections between computer science and biology. Both disciplines examine how information proliferates in time and space. Central results in computer science describe the complexity of algorithms that solve certain classes of problems. An algorithm is deemed efficient if it can solve a problem in polynomial time, which means the running time of the algorithm is a polynomial function of the length of the input. There are classes of harder problems for which the fastest possible algorithm requires exponential time. Another criterion is the space requirement of the algorithm. There is a crucial distinction between algorithms that can find a solution, verify a solution, or list several distinct solutions in given time and space. The complexity hierarchy that is generated in this way is the foundation of theoretical computer science. Precise complexity results can be notoriously difficult. The famous question whether polynomial time equals nondeterministic polynomial time (i.e., P = NP) is one of the hardest open problems in computer science and all of mathematics. Here, we consider simple processes of ecological and evolutionary spatial dynamics. The basic question is: What is the probability that a new invader (or a new mutant)will take over a resident population?We derive precise complexity results for a variety of scenarios. We therefore show that some fundamental questions in this area cannot be answered by simple equations (assuming that P is not equal to NP)."}],"intvolume":" 112","month":"12","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4697423/"}],"scopus_import":1,"language":[{"iso":"eng"}],"publication_status":"published","volume":112,"issue":"51"},{"page":"1614 - 1620","date_created":"2018-12-11T11:52:44Z","volume":45,"doi":"10.1002/eji.201545457","issue":"6","date_published":"2015-06-01T00:00:00Z","year":"2015","publication_status":"published","language":[{"iso":"eng"}],"publication":"European Journal of Immunology","day":"01","publisher":"Wiley","scopus_import":1,"quality_controlled":"1","intvolume":" 45","month":"06","abstract":[{"lang":"eng","text":"Replication-deficient recombinant adenoviruses are potent vectors for the efficient transient expression of exogenous genes in resting immune cells. However, most leukocytes are refractory to efficient adenoviral transduction as they lack expression of the coxsackie/adenovirus receptor (CAR). To circumvent this obstacle, we generated the R26/CAG-CARΔ1StopF (where R26 is ROSA26 and CAG is CMV early enhancer/chicken β actin promoter) knock-in mouse line. This strain allows monitoring of in situ Cre recombinase activity through expression of CARΔ1. Simultaneously, CARΔ1 expression permits selective and highly efficient adenoviral transduction of immune cell populations, such as mast cells or T cells, directly ex vivo in bulk cultures without prior cell purification or activation. Furthermore, we show that CARΔ1 expression dramatically improves adenoviral infection of in vitro differentiated conventional and plasmacytoid dendritic cells (DCs), basophils, mast cells, as well as Hoxb8-immortalized hematopoietic progenitor cells. This novel dual function mouse strain will hence be a valuable tool to rapidly dissect the function of specific genes in leukocyte physiology."}],"oa_version":"None","publist_id":"5610","author":[{"full_name":"Heger, Klaus","last_name":"Heger","first_name":"Klaus"},{"full_name":"Kober, Maike","last_name":"Kober","first_name":"Maike"},{"full_name":"Rieß, David","last_name":"Rieß","first_name":"David"},{"first_name":"Christoph","full_name":"Drees, Christoph","last_name":"Drees"},{"id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","first_name":"Ingrid","full_name":"De Vries, Ingrid","last_name":"De Vries"},{"full_name":"Bertossi, Arianna","last_name":"Bertossi","first_name":"Arianna"},{"full_name":"Roers, Axel","last_name":"Roers","first_name":"Axel"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","last_name":"Sixt"},{"first_name":"Marc","last_name":"Schmidt Supprian","full_name":"Schmidt Supprian, Marc"}],"department":[{"_id":"MiSi"}],"title":"A novel Cre recombinase reporter mouse strain facilitates selective and efficient infection of primary immune cells with adenoviral vectors","date_updated":"2021-01-12T06:51:36Z","citation":{"ista":"Heger K, Kober M, Rieß D, Drees C, de Vries I, Bertossi A, Roers A, Sixt MK, Schmidt Supprian M. 2015. A novel Cre recombinase reporter mouse strain facilitates selective and efficient infection of primary immune cells with adenoviral vectors. European Journal of Immunology. 45(6), 1614–1620.","chicago":"Heger, Klaus, Maike Kober, David Rieß, Christoph Drees, Ingrid de Vries, Arianna Bertossi, Axel Roers, Michael K Sixt, and Marc Schmidt Supprian. “A Novel Cre Recombinase Reporter Mouse Strain Facilitates Selective and Efficient Infection of Primary Immune Cells with Adenoviral Vectors.” European Journal of Immunology. Wiley, 2015. https://doi.org/10.1002/eji.201545457.","short":"K. Heger, M. Kober, D. Rieß, C. Drees, I. de Vries, A. Bertossi, A. Roers, M.K. Sixt, M. Schmidt Supprian, European Journal of Immunology 45 (2015) 1614–1620.","ieee":"K. Heger et al., “A novel Cre recombinase reporter mouse strain facilitates selective and efficient infection of primary immune cells with adenoviral vectors,” European Journal of Immunology, vol. 45, no. 6. Wiley, pp. 1614–1620, 2015.","ama":"Heger K, Kober M, Rieß D, et al. A novel Cre recombinase reporter mouse strain facilitates selective and efficient infection of primary immune cells with adenoviral vectors. European Journal of Immunology. 2015;45(6):1614-1620. doi:10.1002/eji.201545457","apa":"Heger, K., Kober, M., Rieß, D., Drees, C., de Vries, I., Bertossi, A., … Schmidt Supprian, M. (2015). A novel Cre recombinase reporter mouse strain facilitates selective and efficient infection of primary immune cells with adenoviral vectors. European Journal of Immunology. Wiley. https://doi.org/10.1002/eji.201545457","mla":"Heger, Klaus, et al. “A Novel Cre Recombinase Reporter Mouse Strain Facilitates Selective and Efficient Infection of Primary Immune Cells with Adenoviral Vectors.” European Journal of Immunology, vol. 45, no. 6, Wiley, 2015, pp. 1614–20, doi:10.1002/eji.201545457."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","status":"public","_id":"1561"},{"title":"Reporters for sensitive and quantitative measurement of auxin response","publist_id":"5617","author":[{"last_name":"Liao","full_name":"Liao, Cheyang","first_name":"Cheyang"},{"first_name":"Wouter","last_name":"Smet","full_name":"Smet, Wouter"},{"full_name":"Brunoud, Géraldine","last_name":"Brunoud","first_name":"Géraldine"},{"last_name":"Yoshida","full_name":"Yoshida, Saiko","first_name":"Saiko","id":"2E46069C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Vernoux","full_name":"Vernoux, Teva","first_name":"Teva"},{"first_name":"Dolf","last_name":"Weijers","full_name":"Weijers, Dolf"}],"external_id":{"pmid":["25643149"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Liao C, Smet W, Brunoud G, Yoshida S, Vernoux T, Weijers D. 2015. Reporters for sensitive and quantitative measurement of auxin response. Nature Methods. 12(3), 207–210.","chicago":"Liao, Cheyang, Wouter Smet, Géraldine Brunoud, Saiko Yoshida, Teva Vernoux, and Dolf Weijers. “Reporters for Sensitive and Quantitative Measurement of Auxin Response.” Nature Methods. Nature Publishing Group, 2015. https://doi.org/10.1038/nmeth.3279.","ama":"Liao C, Smet W, Brunoud G, Yoshida S, Vernoux T, Weijers D. Reporters for sensitive and quantitative measurement of auxin response. Nature Methods. 2015;12(3):207-210. doi:10.1038/nmeth.3279","apa":"Liao, C., Smet, W., Brunoud, G., Yoshida, S., Vernoux, T., & Weijers, D. (2015). Reporters for sensitive and quantitative measurement of auxin response. Nature Methods. Nature Publishing Group. https://doi.org/10.1038/nmeth.3279","ieee":"C. Liao, W. Smet, G. Brunoud, S. Yoshida, T. Vernoux, and D. Weijers, “Reporters for sensitive and quantitative measurement of auxin response,” Nature Methods, vol. 12, no. 3. Nature Publishing Group, pp. 207–210, 2015.","short":"C. Liao, W. Smet, G. Brunoud, S. Yoshida, T. Vernoux, D. Weijers, Nature Methods 12 (2015) 207–210.","mla":"Liao, Cheyang, et al. “Reporters for Sensitive and Quantitative Measurement of Auxin Response.” Nature Methods, vol. 12, no. 3, Nature Publishing Group, 2015, pp. 207–10, doi:10.1038/nmeth.3279."},"date_published":"2015-02-26T00:00:00Z","doi":"10.1038/nmeth.3279","date_created":"2018-12-11T11:52:41Z","page":"207 - 210","day":"26","publication":"Nature Methods","year":"2015","quality_controlled":"1","publisher":"Nature Publishing Group","oa":1,"department":[{"_id":"JiFr"}],"date_updated":"2021-01-12T06:51:34Z","status":"public","type":"journal_article","_id":"1554","issue":"3","volume":12,"language":[{"iso":"eng"}],"publication_status":"published","month":"02","intvolume":" 12","scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4344836/"}],"pmid":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"The visualization of hormonal signaling input and output is key to understanding how multicellular development is regulated. The plant signaling molecule auxin triggers many growth and developmental responses, but current tools lack the sensitivity or precision to visualize these. We developed a set of fluorescent reporters that allow sensitive and semiquantitative readout of auxin responses at cellular resolution in Arabidopsis thaliana. These generic tools are suitable for any transformable plant species."}]},{"abstract":[{"text":"Stromal cells in the subcapsular sinus of the lymph node 'decide' which cells and molecules are allowed access to the deeper parenchyma. The glycoprotein PLVAP is a crucial component of this selector function.","lang":"eng"}],"oa_version":"None","scopus_import":1,"publisher":"Nature Publishing Group","quality_controlled":"1","intvolume":" 16","month":"03","year":"2015","publication_status":"published","publication":"Nature Immunology","language":[{"iso":"eng"}],"day":"19","page":"338 - 340","date_created":"2018-12-11T11:52:43Z","doi":"10.1038/ni.3126","volume":16,"issue":"4","date_published":"2015-03-19T00:00:00Z","_id":"1560","type":"journal_article","status":"public","citation":{"mla":"Hons, Miroslav, and Michael K. Sixt. “The Lymph Node Filter Revealed.” Nature Immunology, vol. 16, no. 4, Nature Publishing Group, 2015, pp. 338–40, doi:10.1038/ni.3126.","short":"M. Hons, M.K. Sixt, Nature Immunology 16 (2015) 338–340.","ieee":"M. Hons and M. K. Sixt, “The lymph node filter revealed,” Nature Immunology, vol. 16, no. 4. Nature Publishing Group, pp. 338–340, 2015.","ama":"Hons M, Sixt MK. The lymph node filter revealed. Nature Immunology. 2015;16(4):338-340. doi:10.1038/ni.3126","apa":"Hons, M., & Sixt, M. K. (2015). The lymph node filter revealed. Nature Immunology. Nature Publishing Group. https://doi.org/10.1038/ni.3126","chicago":"Hons, Miroslav, and Michael K Sixt. “The Lymph Node Filter Revealed.” Nature Immunology. Nature Publishing Group, 2015. https://doi.org/10.1038/ni.3126.","ista":"Hons M, Sixt MK. 2015. The lymph node filter revealed. Nature Immunology. 16(4), 338–340."},"date_updated":"2021-01-12T06:51:36Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"4167FE56-F248-11E8-B48F-1D18A9856A87","first_name":"Miroslav","full_name":"Hons, Miroslav","orcid":"0000-0002-6625-3348","last_name":"Hons"},{"last_name":"Sixt","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K"}],"publist_id":"5611","title":"The lymph node filter revealed","department":[{"_id":"MiSi"}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Gavello D, Vandael DH, Gosso S, Carbone E, Carabelli V. 2015. Dual action of leptin on rest-firing and stimulated catecholamine release via phosphoinositide 3-kinase-riven BK channel up-regulation in mouse chromaffin cells. Journal of Physiology. 593(22), 4835–4853.","chicago":"Gavello, Daniela, David H Vandael, Sara Gosso, Emilio Carbone, and Valentina Carabelli. “Dual Action of Leptin on Rest-Firing and Stimulated Catecholamine Release via Phosphoinositide 3-Kinase-Riven BK Channel up-Regulation in Mouse Chromaffin Cells.” Journal of Physiology. Wiley-Blackwell, 2015. https://doi.org/10.1113/JP271078.","ieee":"D. Gavello, D. H. Vandael, S. Gosso, E. Carbone, and V. Carabelli, “Dual action of leptin on rest-firing and stimulated catecholamine release via phosphoinositide 3-kinase-riven BK channel up-regulation in mouse chromaffin cells,” Journal of Physiology, vol. 593, no. 22. Wiley-Blackwell, pp. 4835–4853, 2015.","short":"D. Gavello, D.H. Vandael, S. Gosso, E. Carbone, V. Carabelli, Journal of Physiology 593 (2015) 4835–4853.","apa":"Gavello, D., Vandael, D. H., Gosso, S., Carbone, E., & Carabelli, V. (2015). Dual action of leptin on rest-firing and stimulated catecholamine release via phosphoinositide 3-kinase-riven BK channel up-regulation in mouse chromaffin cells. Journal of Physiology. Wiley-Blackwell. https://doi.org/10.1113/JP271078","ama":"Gavello D, Vandael DH, Gosso S, Carbone E, Carabelli V. Dual action of leptin on rest-firing and stimulated catecholamine release via phosphoinositide 3-kinase-riven BK channel up-regulation in mouse chromaffin cells. Journal of Physiology. 2015;593(22):4835-4853. doi:10.1113/JP271078","mla":"Gavello, Daniela, et al. “Dual Action of Leptin on Rest-Firing and Stimulated Catecholamine Release via Phosphoinositide 3-Kinase-Riven BK Channel up-Regulation in Mouse Chromaffin Cells.” Journal of Physiology, vol. 593, no. 22, Wiley-Blackwell, 2015, pp. 4835–53, doi:10.1113/JP271078."},"title":"Dual action of leptin on rest-firing and stimulated catecholamine release via phosphoinositide 3-kinase-riven BK channel up-regulation in mouse chromaffin cells","author":[{"first_name":"Daniela","last_name":"Gavello","full_name":"Gavello, Daniela"},{"full_name":"Vandael, David H","orcid":"0000-0001-7577-1676","last_name":"Vandael","first_name":"David H","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sara","full_name":"Gosso, Sara","last_name":"Gosso"},{"last_name":"Carbone","full_name":"Carbone, Emilio","first_name":"Emilio"},{"full_name":"Carabelli, Valentina","last_name":"Carabelli","first_name":"Valentina"}],"publist_id":"5606","external_id":{"pmid":["26282459"]},"acknowledgement":"This work was supported by the Compagnia di San Paolo Foundation ‘Neuroscience Program’ to VC and ‘Progetto di Ateneo 2011-13’ to EC.\r\nWe thank Dr Claudio Franchino for cell preparation and for providing excellent technical support.","quality_controlled":"1","publisher":"Wiley-Blackwell","oa":1,"day":"15","publication":"Journal of Physiology","year":"2015","date_published":"2015-11-15T00:00:00Z","doi":"10.1113/JP271078","date_created":"2018-12-11T11:52:45Z","page":"4835 - 4853","_id":"1565","status":"public","type":"journal_article","date_updated":"2021-01-12T06:51:38Z","department":[{"_id":"PeJo"}],"pmid":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Leptin is an adipokine produced by the adipose tissue regulating body weight through its appetite-suppressing effect. Besides being expressed in the hypothalamus and hippocampus, leptin receptors (ObRs) are also present in chromaffin cells of the adrenal medulla. In the present study, we report the effect of leptin on mouse chromaffin cell (MCC) functionality, focusing on cell excitability and catecholamine secretion. Acute application of leptin (1 nm) on spontaneously firing MCCs caused a slowly developing membrane hyperpolarization followed by complete blockade of action potential (AP) firing. This inhibitory effect at rest was abolished by the BK channel blocker paxilline (1 μm), suggesting the involvement of BK potassium channels. Single-channel recordings in 'perforated microvesicles' confirmed that leptin increased BK channel open probability without altering its unitary conductance. BK channel up-regulation was associated with the phosphoinositide 3-kinase (PI3K) signalling cascade because the PI3K specific inhibitor wortmannin (100 nm) fully prevented BK current increase. We also tested the effect of leptin on evoked AP firing and Ca2+-driven exocytosis. Although leptin preserves well-adapted AP trains of lower frequency, APs are broader and depolarization-evoked exocytosis is increased as a result of the larger size of the ready-releasable pool and higher frequency of vesicle release. The kinetics and quantal size of single secretory events remained unaltered. Leptin had no effect on firing and secretion in db-/db- mice lacking the ObR gene, confirming its specificity. In conclusion, leptin exhibits a dual action on MCC activity. It dampens AP firing at rest but preserves AP firing and increases catecholamine secretion during sustained stimulation, highlighting the importance of the adipo-adrenal axis in the leptin-mediated increase of sympathetic tone and catecholamine release."}],"month":"11","intvolume":" 593","scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4650409/"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":593,"issue":"22"},{"status":"public","article_type":"original","type":"journal_article","_id":"1562","department":[{"_id":"JiFr"},{"_id":"EM-Fac"}],"date_updated":"2023-02-23T10:04:26Z","intvolume":" 66","month":"08","scopus_import":1,"oa_version":"None","abstract":[{"text":"The plant hormone auxin is a key regulator of plant growth and development. Auxin levels are sensed and interpreted by distinct receptor systems that activate a broad range of cellular responses. The Auxin-Binding Protein1 (ABP1) that has been identified based on its ability to bind auxin with high affinity is a prime candidate for the extracellular receptor responsible for mediating a range of auxin effects, in particular, the fast non-transcriptional ones. Contradictory genetic studies suggested prominent or no importance of ABP1 in many developmental processes. However, how crucial the role of auxin binding to ABP1 is for its functions has not been addressed. Here, we show that the auxin-binding pocket of ABP1 is essential for its gain-of-function cellular and developmental roles. In total, 16 different abp1 mutants were prepared that possessed substitutions in the metal core or in the hydrophobic amino acids of the auxin-binding pocket as well as neutral mutations. Their analysis revealed that an intact auxin-binding pocket is a prerequisite for ABP1 to activate downstream components of the ABP1 signalling pathway, such as Rho of Plants (ROPs) and to mediate the clathrin association with membranes for endocytosis regulation. In planta analyses demonstrated the importance of the auxin binding pocket for all known ABP1-mediated postembryonic developmental processes, including morphology of leaf epidermal cells, root growth and root meristem activity, and vascular tissue differentiation. Taken together, these findings suggest that auxin binding to ABP1 is central to its function, supporting the role of ABP1 as auxin receptor.","lang":"eng"}],"ec_funded":1,"volume":66,"issue":"16","language":[{"iso":"eng"}],"publication_status":"published","project":[{"grant_number":"282300","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"title":"Auxin-binding pocket of ABP1 is crucial for its gain-of-function cellular and developmental roles","author":[{"id":"399876EC-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","full_name":"Grones, Peter","last_name":"Grones"},{"last_name":"Chen","full_name":"Chen, Xu","first_name":"Xu","id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Simon","full_name":"Simon, Sibu","orcid":"0000-0002-1998-6741","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","first_name":"Sibu"},{"id":"3F99E422-F248-11E8-B48F-1D18A9856A87","first_name":"Walter","last_name":"Kaufmann","orcid":"0000-0001-9735-5315","full_name":"Kaufmann, Walter"},{"first_name":"Riet","last_name":"De Rycke","full_name":"De Rycke, Riet"},{"first_name":"Tomasz","full_name":"Nodzyński, Tomasz","last_name":"Nodzyński"},{"first_name":"Eva","last_name":"Zažímalová","full_name":"Zažímalová, Eva"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml"}],"publist_id":"5609","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Grones, Peter, et al. “Auxin-Binding Pocket of ABP1 Is Crucial for Its Gain-of-Function Cellular and Developmental Roles.” Journal of Experimental Botany, vol. 66, no. 16, Oxford University Press, 2015, pp. 5055–65, doi:10.1093/jxb/erv177.","apa":"Grones, P., Chen, X., Simon, S., Kaufmann, W., De Rycke, R., Nodzyński, T., … Friml, J. (2015). Auxin-binding pocket of ABP1 is crucial for its gain-of-function cellular and developmental roles. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/erv177","ama":"Grones P, Chen X, Simon S, et al. Auxin-binding pocket of ABP1 is crucial for its gain-of-function cellular and developmental roles. Journal of Experimental Botany. 2015;66(16):5055-5065. doi:10.1093/jxb/erv177","short":"P. Grones, X. Chen, S. Simon, W. Kaufmann, R. De Rycke, T. Nodzyński, E. Zažímalová, J. Friml, Journal of Experimental Botany 66 (2015) 5055–5065.","ieee":"P. Grones et al., “Auxin-binding pocket of ABP1 is crucial for its gain-of-function cellular and developmental roles,” Journal of Experimental Botany, vol. 66, no. 16. Oxford University Press, pp. 5055–5065, 2015.","chicago":"Grones, Peter, Xu Chen, Sibu Simon, Walter Kaufmann, Riet De Rycke, Tomasz Nodzyński, Eva Zažímalová, and Jiří Friml. “Auxin-Binding Pocket of ABP1 Is Crucial for Its Gain-of-Function Cellular and Developmental Roles.” Journal of Experimental Botany. Oxford University Press, 2015. https://doi.org/10.1093/jxb/erv177.","ista":"Grones P, Chen X, Simon S, Kaufmann W, De Rycke R, Nodzyński T, Zažímalová E, Friml J. 2015. Auxin-binding pocket of ABP1 is crucial for its gain-of-function cellular and developmental roles. Journal of Experimental Botany. 66(16), 5055–5065."},"publisher":"Oxford University Press","quality_controlled":"1","acknowledgement":"This work was supported by ERC Independent Research grant (ERC-2011-StG- 20101109-PSDP to JF); the European Social Fund and the state budget of the Czech Republic [the project ‘Employment of Newly Graduated Doctors of Science for Scientific Excellence’ (CZ.1.07/2.3.00/30.0009) to TN]; the Czech Science Foundation (GACR) [project 13-40637S to JF].","date_created":"2018-12-11T11:52:44Z","doi":"10.1093/jxb/erv177","date_published":"2015-08-01T00:00:00Z","page":"5055 - 5065","publication":"Journal of Experimental Botany","day":"01","year":"2015"},{"publication_status":"published","file":[{"checksum":"cea73b6d3ef1579f32da10b82f4de4fd","file_id":"4927","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:12:09Z","file_name":"IST-2016-479-v1+1_fncom-09-00145.pdf","creator":"system","date_updated":"2020-07-14T12:45:02Z","file_size":187038}],"language":[{"iso":"eng"}],"issue":"11","volume":9,"ec_funded":1,"oa_version":"Published Version","scopus_import":1,"month":"11","intvolume":" 9","date_updated":"2021-01-12T06:51:37Z","ddc":["570"],"file_date_updated":"2020-07-14T12:45:02Z","department":[{"_id":"GaTk"}],"_id":"1564","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":"479","has_accepted_license":"1","year":"2015","day":"30","publication":"Frontiers in Computational Neuroscience","date_published":"2015-11-30T00:00:00Z","doi":"10.3389/fncom.2015.00145","date_created":"2018-12-11T11:52:45Z","quality_controlled":"1","publisher":"Frontiers Research Foundation","oa":1,"citation":{"mla":"Gilson, Matthieu, et al. “Editorial: Emergent Neural Computation from the Interaction of Different Forms of Plasticity.” Frontiers in Computational Neuroscience, vol. 9, no. 11, 145, Frontiers Research Foundation, 2015, doi:10.3389/fncom.2015.00145.","ieee":"M. Gilson, C. Savin, and F. Zenke, “Editorial: Emergent neural computation from the interaction of different forms of plasticity,” Frontiers in Computational Neuroscience, vol. 9, no. 11. Frontiers Research Foundation, 2015.","short":"M. Gilson, C. Savin, F. Zenke, Frontiers in Computational Neuroscience 9 (2015).","apa":"Gilson, M., Savin, C., & Zenke, F. (2015). Editorial: Emergent neural computation from the interaction of different forms of plasticity. Frontiers in Computational Neuroscience. Frontiers Research Foundation. https://doi.org/10.3389/fncom.2015.00145","ama":"Gilson M, Savin C, Zenke F. Editorial: Emergent neural computation from the interaction of different forms of plasticity. Frontiers in Computational Neuroscience. 2015;9(11). doi:10.3389/fncom.2015.00145","chicago":"Gilson, Matthieu, Cristina Savin, and Friedemann Zenke. “Editorial: Emergent Neural Computation from the Interaction of Different Forms of Plasticity.” Frontiers in Computational Neuroscience. Frontiers Research Foundation, 2015. https://doi.org/10.3389/fncom.2015.00145.","ista":"Gilson M, Savin C, Zenke F. 2015. Editorial: Emergent neural computation from the interaction of different forms of plasticity. Frontiers in Computational Neuroscience. 9(11), 145."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"5607","author":[{"full_name":"Gilson, Matthieu","last_name":"Gilson","first_name":"Matthieu"},{"first_name":"Cristina","id":"3933349E-F248-11E8-B48F-1D18A9856A87","last_name":"Savin","full_name":"Savin, Cristina"},{"first_name":"Friedemann","full_name":"Zenke, Friedemann","last_name":"Zenke"}],"title":"Editorial: Emergent neural computation from the interaction of different forms of plasticity","article_number":"145","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}]},{"status":"public","conference":{"start_date":"2014-09-22","end_date":"2014-09-25","location":"Timisoara, Romania","name":"SYNASC: Symbolic and Numeric Algorithms for Scientific Computing"},"type":"conference","_id":"1568","department":[{"_id":"HeEd"}],"title":"The classification of endoscopy images with persistent homology","author":[{"last_name":"Dunaeva","full_name":"Dunaeva, Olga","first_name":"Olga"},{"last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lukyanov, Anton","last_name":"Lukyanov","first_name":"Anton"},{"first_name":"Michael","full_name":"Machin, Michael","last_name":"Machin"},{"last_name":"Malkova","full_name":"Malkova, Daria","first_name":"Daria"}],"publist_id":"5603","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Dunaeva O, Edelsbrunner H, Lukyanov A, Machin M, Malkova D. 2015. The classification of endoscopy images with persistent homology. Proceedings - 16th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing. SYNASC: Symbolic and Numeric Algorithms for Scientific Computing, 7034731.","chicago":"Dunaeva, Olga, Herbert Edelsbrunner, Anton Lukyanov, Michael Machin, and Daria Malkova. “The Classification of Endoscopy Images with Persistent Homology.” In Proceedings - 16th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing, 7034731. IEEE, 2015. https://doi.org/10.1109/SYNASC.2014.81.","ama":"Dunaeva O, Edelsbrunner H, Lukyanov A, Machin M, Malkova D. The classification of endoscopy images with persistent homology. In: Proceedings - 16th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing. IEEE; 2015:7034731. doi:10.1109/SYNASC.2014.81","apa":"Dunaeva, O., Edelsbrunner, H., Lukyanov, A., Machin, M., & Malkova, D. (2015). The classification of endoscopy images with persistent homology. In Proceedings - 16th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing (p. 7034731). Timisoara, Romania: IEEE. https://doi.org/10.1109/SYNASC.2014.81","ieee":"O. Dunaeva, H. Edelsbrunner, A. Lukyanov, M. Machin, and D. Malkova, “The classification of endoscopy images with persistent homology,” in Proceedings - 16th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing, Timisoara, Romania, 2015, p. 7034731.","short":"O. Dunaeva, H. Edelsbrunner, A. Lukyanov, M. Machin, D. Malkova, in:, Proceedings - 16th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing, IEEE, 2015, p. 7034731.","mla":"Dunaeva, Olga, et al. “The Classification of Endoscopy Images with Persistent Homology.” Proceedings - 16th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing, IEEE, 2015, p. 7034731, doi:10.1109/SYNASC.2014.81."},"date_updated":"2023-02-21T16:57:29Z","month":"02","publisher":"IEEE","quality_controlled":"1","scopus_import":1,"acknowledgement":"This research is supported by the project No. 477 of P.G. Demidov Yaroslavl State University within State Assignment for Research.","oa_version":"None","abstract":[{"text":"Aiming at the automatic diagnosis of tumors from narrow band imaging (NBI) magnifying endoscopy (ME) images of the stomach, we combine methods from image processing, computational topology, and machine learning to classify patterns into normal, tubular, vessel. Training the algorithm on a small number of images of each type, we achieve a high rate of correct classifications. The analysis of the learning algorithm reveals that a handful of geometric and topological features are responsible for the overwhelming majority of decisions.","lang":"eng"}],"date_created":"2018-12-11T11:52:46Z","related_material":{"record":[{"relation":"later_version","status":"public","id":"1289"}]},"doi":"10.1109/SYNASC.2014.81","date_published":"2015-02-05T00:00:00Z","page":"7034731","publication":"Proceedings - 16th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing","language":[{"iso":"eng"}],"day":"05","publication_status":"published","year":"2015"},{"_id":"1567","status":"public","type":"conference","conference":{"start_date":"2015-09-24","end_date":"2015-09-26","location":"Los Angeles, CA, United States","name":"GD: Graph Drawing and Network Visualization"},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2022-01-28T08:25:00Z","citation":{"mla":"Edelsbrunner, Herbert. “Shape, Homology, Persistence, and Stability.” 23rd International Symposium, vol. 9411, Springer Nature, 2015.","short":"H. Edelsbrunner, in:, 23rd International Symposium, Springer Nature, 2015.","ieee":"H. Edelsbrunner, “Shape, homology, persistence, and stability,” in 23rd International Symposium, Los Angeles, CA, United States, 2015, vol. 9411.","ama":"Edelsbrunner H. Shape, homology, persistence, and stability. In: 23rd International Symposium. Vol 9411. Springer Nature; 2015.","apa":"Edelsbrunner, H. (2015). Shape, homology, persistence, and stability. In 23rd International Symposium (Vol. 9411). Los Angeles, CA, United States: Springer Nature.","chicago":"Edelsbrunner, Herbert. “Shape, Homology, Persistence, and Stability.” In 23rd International Symposium, Vol. 9411. Springer Nature, 2015.","ista":"Edelsbrunner H. 2015. Shape, homology, persistence, and stability. 23rd International Symposium. GD: Graph Drawing and Network Visualization, LNCS, vol. 9411."},"title":"Shape, homology, persistence, and stability","department":[{"_id":"HeEd"}],"author":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner"}],"publist_id":"5604","article_processing_charge":"No","oa_version":"None","abstract":[{"lang":"eng","text":"My personal journey to the fascinating world of geometric forms started more than 30 years ago with the invention of alpha shapes in the plane. It took about 10 years before we generalized the concept to higher dimensions, we produced working software with a graphics interface for the three-dimensional case. At the same time, we added homology to the computations. Needless to say that this foreshadowed the inception of persistent homology, because it suggested the study of filtrations to capture the scale of a shape or data set. Importantly, this method has fast algorithms. The arguably most useful result on persistent homology is the stability of its diagrams under perturbations."}],"month":"01","intvolume":" 9411","quality_controlled":"1","publisher":"Springer Nature","scopus_import":"1","alternative_title":["LNCS"],"day":"01","publication":"23rd International Symposium","language":[{"iso":"eng"}],"publication_status":"published","year":"2015","volume":9411,"date_published":"2015-01-01T00:00:00Z","date_created":"2018-12-11T11:52:46Z"},{"_id":"1563","status":"public","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:51:37Z","citation":{"chicago":"Graff, Grzegorz, and Pawel Pilarczyk. “An Algorithmic Approach to Estimating the Minimal Number of Periodic Points for Smooth Self-Maps of Simply-Connected Manifolds.” Topological Methods in Nonlinear Analysis. Juliusz Schauder Center for Nonlinear Studies, 2015. https://doi.org/10.12775/TMNA.2015.014.","ista":"Graff G, Pilarczyk P. 2015. An algorithmic approach to estimating the minimal number of periodic points for smooth self-maps of simply-connected manifolds. Topological Methods in Nonlinear Analysis. 45(1), 273–286.","mla":"Graff, Grzegorz, and Pawel Pilarczyk. “An Algorithmic Approach to Estimating the Minimal Number of Periodic Points for Smooth Self-Maps of Simply-Connected Manifolds.” Topological Methods in Nonlinear Analysis, vol. 45, no. 1, Juliusz Schauder Center for Nonlinear Studies, 2015, pp. 273–86, doi:10.12775/TMNA.2015.014.","short":"G. Graff, P. Pilarczyk, Topological Methods in Nonlinear Analysis 45 (2015) 273–286.","ieee":"G. Graff and P. Pilarczyk, “An algorithmic approach to estimating the minimal number of periodic points for smooth self-maps of simply-connected manifolds,” Topological Methods in Nonlinear Analysis, vol. 45, no. 1. Juliusz Schauder Center for Nonlinear Studies, pp. 273–286, 2015.","apa":"Graff, G., & Pilarczyk, P. (2015). An algorithmic approach to estimating the minimal number of periodic points for smooth self-maps of simply-connected manifolds. Topological Methods in Nonlinear Analysis. Juliusz Schauder Center for Nonlinear Studies. https://doi.org/10.12775/TMNA.2015.014","ama":"Graff G, Pilarczyk P. An algorithmic approach to estimating the minimal number of periodic points for smooth self-maps of simply-connected manifolds. Topological Methods in Nonlinear Analysis. 2015;45(1):273-286. doi:10.12775/TMNA.2015.014"},"title":"An algorithmic approach to estimating the minimal number of periodic points for smooth self-maps of simply-connected manifolds","department":[{"_id":"HeEd"}],"publist_id":"5608","author":[{"last_name":"Graff","full_name":"Graff, Grzegorz","first_name":"Grzegorz"},{"last_name":"Pilarczyk","full_name":"Pilarczyk, Pawel","id":"3768D56A-F248-11E8-B48F-1D18A9856A87","first_name":"Pawel"}],"oa_version":"None","abstract":[{"text":"For a given self-map $f$ of $M$, a closed smooth connected and simply-connected manifold of dimension $m\\geq 4$, we provide an algorithm for estimating the values of the topological invariant $D^m_r[f]$, which equals the minimal number of $r$-periodic points in the smooth homotopy class of $f$. Our results are based on the combinatorial scheme for computing $D^m_r[f]$ introduced by G. Graff and J. Jezierski [J. Fixed Point Theory Appl. 13 (2013), 63-84]. An open-source implementation of the algorithm programmed in C++ is publicly available at {\\tt http://www.pawelpilarczyk.com/combtop/}.","lang":"eng"}],"intvolume":" 45","month":"03","quality_controlled":"1","scopus_import":1,"publisher":"Juliusz Schauder Center for Nonlinear Studies","language":[{"iso":"eng"}],"publication":"Topological Methods in Nonlinear Analysis","day":"01","year":"2015","publication_status":"published","date_created":"2018-12-11T11:52:44Z","doi":"10.12775/TMNA.2015.014","issue":"1","volume":45,"date_published":"2015-03-01T00:00:00Z","page":"273 - 286"},{"abstract":[{"text":"Multiple plant developmental processes, such as lateral root development, depend on auxin distribution patterns that are in part generated by the PIN-formed family of auxin-efflux transporters. Here we propose that AUXIN RESPONSE FACTOR7 (ARF7) and the ARF7-regulated FOUR LIPS/MYB124 (FLP) transcription factors jointly form a coherent feed-forward motif that mediates the auxin-responsive PIN3 transcription in planta to steer the early steps of lateral root formation. This regulatory mechanism might endow the PIN3 circuitry with a temporal 'memory' of auxin stimuli, potentially maintaining and enhancing the robustness of the auxin flux directionality during lateral root development. The cooperative action between canonical auxin signalling and other transcription factors might constitute a general mechanism by which transcriptional auxin-sensitivity can be regulated at a tissue-specific level.","lang":"eng"}],"oa_version":"Published Version","scopus_import":1,"intvolume":" 6","month":"11","publication_status":"published","language":[{"iso":"eng"}],"file":[{"creator":"system","file_size":1701815,"date_updated":"2020-07-14T12:45:02Z","file_name":"IST-2016-477-v1+1_ncomms9821.pdf","date_created":"2018-12-12T10:14:32Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"5085","checksum":"8ff5c108899b548806e1cb7a302fe76d"}],"volume":6,"_id":"1574","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":"477","status":"public","date_updated":"2021-01-12T06:51:42Z","ddc":["580"],"department":[{"_id":"EvBe"},{"_id":"JiFr"}],"file_date_updated":"2020-07-14T12:45:02Z","acknowledgement":"of the European Research Council (project ERC-2011-StG-20101109-PSDP) (to J.F.), a FEBS long-term fellowship (to P.M.) ","oa":1,"quality_controlled":"1","publisher":"Nature Publishing Group","year":"2015","has_accepted_license":"1","publication":"Nature Communications","day":"18","date_created":"2018-12-11T11:52:48Z","doi":"10.1038/ncomms9821","date_published":"2015-11-18T00:00:00Z","article_number":"8821","citation":{"ama":"Chen Q, Liu Y, Maere S, et al. A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development. Nature Communications. 2015;6. doi:10.1038/ncomms9821","apa":"Chen, Q., Liu, Y., Maere, S., Lee, E., Van Isterdael, G., Xie, Z., … Vanneste, S. (2015). A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms9821","ieee":"Q. Chen et al., “A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development,” Nature Communications, vol. 6. Nature Publishing Group, 2015.","short":"Q. Chen, Y. Liu, S. Maere, E. Lee, G. Van Isterdael, Z. Xie, W. Xuan, J. Lucas, V. Vassileva, S. Kitakura, P. Marhavý, K.T. Wabnik, N. Geldner, E. Benková, J. Le, H. Fukaki, E. Grotewold, C. Li, J. Friml, F. Sack, T. Beeckman, S. Vanneste, Nature Communications 6 (2015).","mla":"Chen, Qian, et al. “A Coherent Transcriptional Feed-Forward Motif Model for Mediating Auxin-Sensitive PIN3 Expression during Lateral Root Development.” Nature Communications, vol. 6, 8821, Nature Publishing Group, 2015, doi:10.1038/ncomms9821.","ista":"Chen Q, Liu Y, Maere S, Lee E, Van Isterdael G, Xie Z, Xuan W, Lucas J, Vassileva V, Kitakura S, Marhavý P, Wabnik KT, Geldner N, Benková E, Le J, Fukaki H, Grotewold E, Li C, Friml J, Sack F, Beeckman T, Vanneste S. 2015. A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development. Nature Communications. 6, 8821.","chicago":"Chen, Qian, Yang Liu, Steven Maere, Eunkyoung Lee, Gert Van Isterdael, Zidian Xie, Wei Xuan, et al. “A Coherent Transcriptional Feed-Forward Motif Model for Mediating Auxin-Sensitive PIN3 Expression during Lateral Root Development.” Nature Communications. Nature Publishing Group, 2015. https://doi.org/10.1038/ncomms9821."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Qian","last_name":"Chen","full_name":"Chen, Qian"},{"full_name":"Liu, Yang","last_name":"Liu","first_name":"Yang"},{"full_name":"Maere, Steven","last_name":"Maere","first_name":"Steven"},{"first_name":"Eunkyoung","last_name":"Lee","full_name":"Lee, Eunkyoung"},{"full_name":"Van Isterdael, Gert","last_name":"Van Isterdael","first_name":"Gert"},{"full_name":"Xie, Zidian","last_name":"Xie","first_name":"Zidian"},{"first_name":"Wei","last_name":"Xuan","full_name":"Xuan, Wei"},{"first_name":"Jessica","last_name":"Lucas","full_name":"Lucas, Jessica"},{"full_name":"Vassileva, Valya","last_name":"Vassileva","first_name":"Valya"},{"full_name":"Kitakura, Saeko","last_name":"Kitakura","first_name":"Saeko"},{"id":"3F45B078-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","last_name":"Marhavy","full_name":"Marhavy, Peter","orcid":"0000-0001-5227-5741"},{"first_name":"Krzysztof T","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","last_name":"Wabnik","full_name":"Wabnik, Krzysztof T","orcid":"0000-0001-7263-0560"},{"last_name":"Geldner","full_name":"Geldner, Niko","first_name":"Niko"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","last_name":"Benková"},{"first_name":"Jie","last_name":"Le","full_name":"Le, Jie"},{"first_name":"Hidehiro","last_name":"Fukaki","full_name":"Fukaki, Hidehiro"},{"last_name":"Grotewold","full_name":"Grotewold, Erich","first_name":"Erich"},{"full_name":"Li, Chuanyou","last_name":"Li","first_name":"Chuanyou"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml"},{"first_name":"Fred","full_name":"Sack, Fred","last_name":"Sack"},{"last_name":"Beeckman","full_name":"Beeckman, Tom","first_name":"Tom"},{"last_name":"Vanneste","full_name":"Vanneste, Steffen","first_name":"Steffen"}],"publist_id":"5597","title":"A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development"},{"date_created":"2018-12-11T11:52:48Z","date_published":"2015-06-25T00:00:00Z","doi":"10.1038/ncomms8526","publication":"Nature Communications","day":"25","year":"2015","has_accepted_license":"1","oa":1,"publisher":"Nature Publishing Group","quality_controlled":"1","acknowledgement":"M.C. and M.L.H. were supported by fellowships from the Fondation pour la Recherche Médicale and the Association pour la Recherche contre le Cancer, respectively. This work was funded by grants from the City of Paris and the European Research Council to A.-M.L.-D. (Strapacemi 243103), the Association Nationale pour la Recherche (ANR-09-PIRI-0027-PCVI) and the InnaBiosanté foundation (Micemico) to A.-M.L.-D., M.P. and R.V., and the DCBIOL Labex from the French Government (ANR-10-IDEX-0001-02-PSL* and ANR-11-LABX-0043). The super-resolution SIM microscope was funded through an ERC Advanced Investigator Grant (250367) to Edith Heard (CNRS UMR3215/Inserm U934, Institut Curie).","title":"Cell migration and antigen capture are antagonistic processes coupled by myosin II in dendritic cells","publist_id":"5596","author":[{"first_name":"Mélanie","full_name":"Chabaud, Mélanie","last_name":"Chabaud"},{"full_name":"Heuzé, Mélina","last_name":"Heuzé","first_name":"Mélina"},{"first_name":"Marine","full_name":"Bretou, Marine","last_name":"Bretou"},{"last_name":"Vargas","full_name":"Vargas, Pablo","first_name":"Pablo"},{"full_name":"Maiuri, Paolo","last_name":"Maiuri","first_name":"Paolo"},{"last_name":"Solanes","full_name":"Solanes, Paola","first_name":"Paola"},{"full_name":"Maurin, Mathieu","last_name":"Maurin","first_name":"Mathieu"},{"last_name":"Terriac","full_name":"Terriac, Emmanuel","first_name":"Emmanuel"},{"full_name":"Le Berre, Maël","last_name":"Le Berre","first_name":"Maël"},{"last_name":"Lankar","full_name":"Lankar, Danielle","first_name":"Danielle"},{"first_name":"Tristan","last_name":"Piolot","full_name":"Piolot, Tristan"},{"last_name":"Adelstein","full_name":"Adelstein, Robert","first_name":"Robert"},{"first_name":"Yingfan","last_name":"Zhang","full_name":"Zhang, Yingfan"},{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K"},{"last_name":"Jacobelli","full_name":"Jacobelli, Jordan","first_name":"Jordan"},{"first_name":"Olivier","full_name":"Bénichou, Olivier","last_name":"Bénichou"},{"first_name":"Raphaël","last_name":"Voituriez","full_name":"Voituriez, Raphaël"},{"full_name":"Piel, Matthieu","last_name":"Piel","first_name":"Matthieu"},{"full_name":"Lennon Duménil, Ana","last_name":"Lennon Duménil","first_name":"Ana"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Chabaud M, Heuzé M, Bretou M, Vargas P, Maiuri P, Solanes P, Maurin M, Terriac E, Le Berre M, Lankar D, Piolot T, Adelstein R, Zhang Y, Sixt MK, Jacobelli J, Bénichou O, Voituriez R, Piel M, Lennon Duménil A. 2015. Cell migration and antigen capture are antagonistic processes coupled by myosin II in dendritic cells. Nature Communications. 6, 7526.","chicago":"Chabaud, Mélanie, Mélina Heuzé, Marine Bretou, Pablo Vargas, Paolo Maiuri, Paola Solanes, Mathieu Maurin, et al. “Cell Migration and Antigen Capture Are Antagonistic Processes Coupled by Myosin II in Dendritic Cells.” Nature Communications. Nature Publishing Group, 2015. https://doi.org/10.1038/ncomms8526.","apa":"Chabaud, M., Heuzé, M., Bretou, M., Vargas, P., Maiuri, P., Solanes, P., … Lennon Duménil, A. (2015). Cell migration and antigen capture are antagonistic processes coupled by myosin II in dendritic cells. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms8526","ama":"Chabaud M, Heuzé M, Bretou M, et al. Cell migration and antigen capture are antagonistic processes coupled by myosin II in dendritic cells. Nature Communications. 2015;6. doi:10.1038/ncomms8526","ieee":"M. Chabaud et al., “Cell migration and antigen capture are antagonistic processes coupled by myosin II in dendritic cells,” Nature Communications, vol. 6. Nature Publishing Group, 2015.","short":"M. Chabaud, M. Heuzé, M. Bretou, P. Vargas, P. Maiuri, P. Solanes, M. Maurin, E. Terriac, M. Le Berre, D. Lankar, T. Piolot, R. Adelstein, Y. Zhang, M.K. Sixt, J. Jacobelli, O. Bénichou, R. Voituriez, M. Piel, A. Lennon Duménil, Nature Communications 6 (2015).","mla":"Chabaud, Mélanie, et al. “Cell Migration and Antigen Capture Are Antagonistic Processes Coupled by Myosin II in Dendritic Cells.” Nature Communications, vol. 6, 7526, Nature Publishing Group, 2015, doi:10.1038/ncomms8526."},"article_number":"7526","volume":6,"language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-12T10:11:58Z","file_name":"IST-2016-476-v1+1_ncomms8526.pdf","date_updated":"2020-07-14T12:45:02Z","file_size":4530215,"creator":"system","checksum":"bae12e86be2adb28253f890b8bba8315","file_id":"4915","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"publication_status":"published","intvolume":" 6","month":"06","scopus_import":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"The immune response relies on the migration of leukocytes and on their ability to stop in precise anatomical locations to fulfil their task. How leukocyte migration and function are coordinated is unknown. Here we show that in immature dendritic cells, which patrol their environment by engulfing extracellular material, cell migration and antigen capture are antagonistic. This antagonism results from transient enrichment of myosin IIA at the cell front, which disrupts the back-to-front gradient of the motor protein, slowing down locomotion but promoting antigen capture. We further highlight that myosin IIA enrichment at the cell front requires the MHC class II-associated invariant chain (Ii). Thus, by controlling myosin IIA localization, Ii imposes on dendritic cells an intermittent antigen capture behaviour that might facilitate environment patrolling. We propose that the requirement for myosin II in both cell migration and specific cell functions may provide a general mechanism for their coordination in time and space."}],"file_date_updated":"2020-07-14T12:45:02Z","department":[{"_id":"MiSi"}],"ddc":["570"],"date_updated":"2021-01-12T06:51:42Z","pubrep_id":"476","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":"1575"},{"acknowledgement":"This work was supported by Vetenskapsrådet and Vinnova (Verket för Innovationssystemet) (S.M.D., T.V., M.Ł., and S.R.), Knut och Alice Wallenbergs Stiftelse (S.M.D., A.R., and C.V.), Kempestiftelserna (A.H. and Q.M.), Carl Tryggers Stiftelse för Vetenskaplig Forskning (Q.M.), European Research Council Grant ERC-2011-StG-20101109-PSDP (to J.F.), US Department of Energy Grant DE-FG02-02ER15295 (to N.V.R.), and National Science Foundation Grant MCB-0817916 (to N.V.R. and G.R.H.). ","publisher":"National Academy of Sciences","quality_controlled":"1","oa":1,"day":"17","publication":"PNAS","year":"2015","date_published":"2015-02-17T00:00:00Z","doi":"10.1073/pnas.1424856112","date_created":"2018-12-11T11:52:46Z","page":"E806 - E815","project":[{"name":"Polarity and subcellular dynamics in plants","grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Doyle, Siamsa, Ash Haegera, Thomas Vain, Adeline Rigala, Corrado Viotti, Małgorzata Łangowskaa, Qian Maa, et al. “An Early Secretory Pathway Mediated by Gnom-like 1 and Gnom Is Essential for Basal Polarity Establishment in Arabidopsis Thaliana.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1424856112.","ista":"Doyle S, Haegera A, Vain T, Rigala A, Viotti C, Łangowskaa M, Maa Q, Friml J, Raikhel N, Hickse G, Robert S. 2015. An early secretory pathway mediated by gnom-like 1 and gnom is essential for basal polarity establishment in Arabidopsis thaliana. PNAS. 112(7), E806–E815.","mla":"Doyle, Siamsa, et al. “An Early Secretory Pathway Mediated by Gnom-like 1 and Gnom Is Essential for Basal Polarity Establishment in Arabidopsis Thaliana.” PNAS, vol. 112, no. 7, National Academy of Sciences, 2015, pp. E806–15, doi:10.1073/pnas.1424856112.","ama":"Doyle S, Haegera A, Vain T, et al. An early secretory pathway mediated by gnom-like 1 and gnom is essential for basal polarity establishment in Arabidopsis thaliana. PNAS. 2015;112(7):E806-E815. doi:10.1073/pnas.1424856112","apa":"Doyle, S., Haegera, A., Vain, T., Rigala, A., Viotti, C., Łangowskaa, M., … Robert, S. (2015). An early secretory pathway mediated by gnom-like 1 and gnom is essential for basal polarity establishment in Arabidopsis thaliana. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1424856112","ieee":"S. Doyle et al., “An early secretory pathway mediated by gnom-like 1 and gnom is essential for basal polarity establishment in Arabidopsis thaliana,” PNAS, vol. 112, no. 7. National Academy of Sciences, pp. E806–E815, 2015.","short":"S. Doyle, A. Haegera, T. Vain, A. Rigala, C. Viotti, M. Łangowskaa, Q. Maa, J. Friml, N. Raikhel, G. Hickse, S. Robert, PNAS 112 (2015) E806–E815."},"title":"An early secretory pathway mediated by gnom-like 1 and gnom is essential for basal polarity establishment in Arabidopsis thaliana","publist_id":"5602","author":[{"full_name":"Doyle, Siamsa","last_name":"Doyle","first_name":"Siamsa"},{"first_name":"Ash","full_name":"Haegera, Ash","last_name":"Haegera"},{"first_name":"Thomas","last_name":"Vain","full_name":"Vain, Thomas"},{"first_name":"Adeline","last_name":"Rigala","full_name":"Rigala, Adeline"},{"last_name":"Viotti","full_name":"Viotti, Corrado","first_name":"Corrado"},{"first_name":"Małgorzata","full_name":"Łangowskaa, Małgorzata","last_name":"Łangowskaa"},{"first_name":"Qian","last_name":"Maa","full_name":"Maa, Qian"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Natasha","full_name":"Raikhel, Natasha","last_name":"Raikhel"},{"last_name":"Hickse","full_name":"Hickse, Glenn","first_name":"Glenn"},{"full_name":"Robert, Stéphanie","last_name":"Robert","first_name":"Stéphanie"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Spatial regulation of the plant hormone indole-3-acetic acid (IAA, or auxin) is essential for plant development. Auxin gradient establishment is mediated by polarly localized auxin transporters, including PIN-FORMED (PIN) proteins. Their localization and abundance at the plasma membrane are tightly regulated by endomembrane machinery, especially the endocytic and recycling pathways mediated by the ADP ribosylation factor guanine nucleotide exchange factor (ARF-GEF) GNOM. We assessed the role of the early secretory pathway in establishing PIN1 polarity in Arabidopsis thaliana by pharmacological and genetic approaches. We identified the compound endosidin 8 (ES8), which selectively interferes with PIN1 basal polarity without altering the polarity of apical proteins. ES8 alters the auxin distribution pattern in the root and induces a strong developmental phenotype, including reduced root length. The ARF-GEF- defective mutants gnom-like 1 ( gnl1-1) and gnom ( van7) are significantly resistant to ES8. The compound does not affect recycling or vacuolar trafficking of PIN1 but leads to its intracellular accumulation, resulting in loss of PIN1 basal polarity at the plasma membrane. Our data confirm a role for GNOM in endoplasmic reticulum (ER) - Golgi trafficking and reveal that a GNL1/GNOM-mediated early secretory pathway selectively regulates PIN1 basal polarity establishment in a manner essential for normal plant development."}],"month":"02","intvolume":" 112","scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4343110/"}],"language":[{"iso":"eng"}],"publication_status":"published","issue":"7","volume":112,"ec_funded":1,"_id":"1569","status":"public","type":"journal_article","date_updated":"2021-01-12T06:51:39Z","department":[{"_id":"JiFr"}]},{"_id":"1570","status":"public","type":"journal_article","date_updated":"2021-01-12T06:51:40Z","department":[{"_id":"ChLa"},{"_id":"GaTk"}],"oa_version":"Submitted Version","pmid":1,"abstract":[{"text":"Grounding autonomous behavior in the nervous system is a fundamental challenge for neuroscience. In particular, self-organized behavioral development provides more questions than answers. Are there special functional units for curiosity, motivation, and creativity? This paper argues that these features can be grounded in synaptic plasticity itself, without requiring any higher-level constructs. We propose differential extrinsic plasticity (DEP) as a new synaptic rule for self-learning systems and apply it to a number of complex robotic systems as a test case. Without specifying any purpose or goal, seemingly purposeful and adaptive rhythmic behavior is developed, displaying a certain level of sensorimotor intelligence. These surprising results require no systemspecific modifications of the DEP rule. They rather arise from the underlying mechanism of spontaneous symmetry breaking,which is due to the tight brain body environment coupling. The new synaptic rule is biologically plausible and would be an interesting target for neurobiological investigation. We also argue that this neuronal mechanism may have been a catalyst in natural evolution.","lang":"eng"}],"intvolume":" 112","month":"11","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4653169/"}],"scopus_import":1,"language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"issue":"45","volume":112,"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Der R, Martius GS. 2015. Novel plasticity rule can explain the development of sensorimotor intelligence. PNAS. 112(45), E6224–E6232.","chicago":"Der, Ralf, and Georg S Martius. “Novel Plasticity Rule Can Explain the Development of Sensorimotor Intelligence.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1508400112.","short":"R. Der, G.S. Martius, PNAS 112 (2015) E6224–E6232.","ieee":"R. Der and G. S. Martius, “Novel plasticity rule can explain the development of sensorimotor intelligence,” PNAS, vol. 112, no. 45. National Academy of Sciences, pp. E6224–E6232, 2015.","apa":"Der, R., & Martius, G. S. (2015). Novel plasticity rule can explain the development of sensorimotor intelligence. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1508400112","ama":"Der R, Martius GS. Novel plasticity rule can explain the development of sensorimotor intelligence. PNAS. 2015;112(45):E6224-E6232. doi:10.1073/pnas.1508400112","mla":"Der, Ralf, and Georg S. Martius. “Novel Plasticity Rule Can Explain the Development of Sensorimotor Intelligence.” PNAS, vol. 112, no. 45, National Academy of Sciences, 2015, pp. E6224–32, doi:10.1073/pnas.1508400112."},"title":"Novel plasticity rule can explain the development of sensorimotor intelligence","external_id":{"pmid":["26504200"]},"publist_id":"5601","author":[{"last_name":"Der","full_name":"Der, Ralf","first_name":"Ralf"},{"full_name":"Martius, Georg S","last_name":"Martius","first_name":"Georg S","id":"3A276B68-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"publisher":"National Academy of Sciences","quality_controlled":"1","publication":"PNAS","day":"10","year":"2015","date_created":"2018-12-11T11:52:47Z","date_published":"2015-11-10T00:00:00Z","doi":"10.1073/pnas.1508400112","page":"E6224 - E6232"},{"type":"journal_article","status":"public","_id":"1571","publist_id":"5600","author":[{"first_name":"Marjon","id":"3111FFAC-F248-11E8-B48F-1D18A9856A87","last_name":"De Vos","full_name":"De Vos, Marjon"},{"first_name":"Alexandre","full_name":"Dawid, Alexandre","last_name":"Dawid"},{"first_name":"Vanda","last_name":"Šunderlíková","full_name":"Šunderlíková, Vanda"},{"first_name":"Sander","last_name":"Tans","full_name":"Tans, Sander"}],"title":"Breaking evolutionary constraint with a tradeoff ratchet","department":[{"_id":"ToBo"}],"citation":{"ieee":"M. de Vos, A. Dawid, V. Šunderlíková, and S. Tans, “Breaking evolutionary constraint with a tradeoff ratchet,” PNAS, vol. 112, no. 48. National Academy of Sciences, pp. 14906–14911, 2015.","short":"M. de Vos, A. Dawid, V. Šunderlíková, S. Tans, PNAS 112 (2015) 14906–14911.","apa":"de Vos, M., Dawid, A., Šunderlíková, V., & Tans, S. (2015). Breaking evolutionary constraint with a tradeoff ratchet. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1510282112","ama":"de Vos M, Dawid A, Šunderlíková V, Tans S. Breaking evolutionary constraint with a tradeoff ratchet. PNAS. 2015;112(48):14906-14911. doi:10.1073/pnas.1510282112","mla":"de Vos, Marjon, et al. “Breaking Evolutionary Constraint with a Tradeoff Ratchet.” PNAS, vol. 112, no. 48, National Academy of Sciences, 2015, pp. 14906–11, doi:10.1073/pnas.1510282112.","ista":"de Vos M, Dawid A, Šunderlíková V, Tans S. 2015. Breaking evolutionary constraint with a tradeoff ratchet. PNAS. 112(48), 14906–14911.","chicago":"Vos, Marjon de, Alexandre Dawid, Vanda Šunderlíková, and Sander Tans. “Breaking Evolutionary Constraint with a Tradeoff Ratchet.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1510282112."},"date_updated":"2021-01-12T06:51:40Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publisher":"National Academy of Sciences","scopus_import":1,"intvolume":" 112","month":"12","abstract":[{"text":"Epistatic interactions can frustrate and shape evolutionary change. Indeed, phenotypes may fail to evolve when essential mutations are only accessible through positive selection if they are fixed simultaneously. How environmental variability affects such constraints is poorly understood. Here, we studied genetic constraints in fixed and fluctuating environments using the Escherichia coli lac operon as a model system for genotype-environment interactions. We found that, in different fixed environments, all trajectories that were reconstructed by applying point mutations within the transcription factor-operator interface became trapped at suboptima, where no additional improvements were possible. Paradoxically, repeated switching between these same environments allows unconstrained adaptation by continuous improvements. This evolutionary mode is explained by pervasive cross-environmental tradeoffs that reposition the peaks in such a way that trapped genotypes can repeatedly climb ascending slopes and hence, escape adaptive stasis. Using a Markov approach, we developed a mathematical framework to quantify the landscape-crossing rates and show that this ratchet-like adaptive mechanism is robust in a wide spectrum of fluctuating environments. Overall, this study shows that genetic constraints can be overcome by environmental change and that crossenvironmental tradeoffs do not necessarily impede but also, can facilitate adaptive evolution. Because tradeoffs and environmental variability are ubiquitous in nature, we speculate this evolutionary mode to be of general relevance.","lang":"eng"}],"acknowledgement":"This work is part of the research program of the Foundation for Fundamental Research on Matter, which is part of the Netherlands Organization for Scientific Research (NWO). M.G.J.d.V. was (partially) funded by NWO Earth and Life Sciences (ALW), project 863.14.015. We thank D. M. Weinreich, J. A. G. M. de Visser, T. Paixão, J. Polechová, T. Friedlander, and A. E. Mayo for reading and commenting on earlier versions of the manuscript and B. Houchmandzadeh, O. Rivoire, and M. Hemery for discussions and suggestions on the Markov computation. Furthermore, we thank F. J. Poelwijk for sharing plasmid pCascade5 and pRD007 and Y. Yokobayashi for sharing plasmid pINV-110. We also thank the anonymous reviewers for remarks on the initial version of the manuscript.","oa_version":"None","page":"14906 - 14911","date_created":"2018-12-11T11:52:47Z","doi":"10.1073/pnas.1510282112","volume":112,"date_published":"2015-12-01T00:00:00Z","issue":"48","publication_status":"published","year":"2015","publication":"PNAS","language":[{"iso":"eng"}],"day":"01"},{"oa_version":"Preprint","abstract":[{"text":"We consider the quantum ferromagnetic Heisenberg model in three dimensions, for all spins S ≥ 1/2. We rigorously prove the validity of the spin-wave approximation for the excitation spectrum, at the level of the first non-trivial contribution to the free energy at low temperatures. Our proof comes with explicit, constructive upper and lower bounds on the error term. It uses in an essential way the bosonic formulation of the model in terms of the Holstein-Primakoff representation. In this language, the model describes interacting bosons with a hard-core on-site repulsion and a nearest-neighbor attraction. This attractive interaction makes the lower bound on the free energy particularly tricky: the key idea there is to prove a differential inequality for the two-particle density, which is thereby shown to be smaller than the probability density of a suitably weighted two-particle random process on the lattice.\r\n","lang":"eng"}],"month":"06","intvolume":" 339","quality_controlled":"1","scopus_import":1,"publisher":"Springer","oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1312.7873"}],"day":"23","publication":"Communications in Mathematical Physics","language":[{"iso":"eng"}],"year":"2015","publication_status":"published","doi":"10.1007/s00220-015-2402-0","date_published":"2015-06-23T00:00:00Z","issue":"1","volume":339,"date_created":"2018-12-11T11:52:47Z","page":"279 - 307","_id":"1572","status":"public","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:51:41Z","citation":{"ista":"Correggi M, Giuliani A, Seiringer R. 2015. Validity of the spin-wave approximation for the free energy of the Heisenberg ferromagnet. Communications in Mathematical Physics. 339(1), 279–307.","chicago":"Correggi, Michele, Alessandro Giuliani, and Robert Seiringer. “Validity of the Spin-Wave Approximation for the Free Energy of the Heisenberg Ferromagnet.” Communications in Mathematical Physics. Springer, 2015. https://doi.org/10.1007/s00220-015-2402-0.","apa":"Correggi, M., Giuliani, A., & Seiringer, R. (2015). Validity of the spin-wave approximation for the free energy of the Heisenberg ferromagnet. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-015-2402-0","ama":"Correggi M, Giuliani A, Seiringer R. Validity of the spin-wave approximation for the free energy of the Heisenberg ferromagnet. Communications in Mathematical Physics. 2015;339(1):279-307. doi:10.1007/s00220-015-2402-0","ieee":"M. Correggi, A. Giuliani, and R. Seiringer, “Validity of the spin-wave approximation for the free energy of the Heisenberg ferromagnet,” Communications in Mathematical Physics, vol. 339, no. 1. Springer, pp. 279–307, 2015.","short":"M. Correggi, A. Giuliani, R. Seiringer, Communications in Mathematical Physics 339 (2015) 279–307.","mla":"Correggi, Michele, et al. “Validity of the Spin-Wave Approximation for the Free Energy of the Heisenberg Ferromagnet.” Communications in Mathematical Physics, vol. 339, no. 1, Springer, 2015, pp. 279–307, doi:10.1007/s00220-015-2402-0."},"title":"Validity of the spin-wave approximation for the free energy of the Heisenberg ferromagnet","department":[{"_id":"RoSe"}],"publist_id":"5599","author":[{"first_name":"Michele","full_name":"Correggi, Michele","last_name":"Correggi"},{"last_name":"Giuliani","full_name":"Giuliani, Alessandro","first_name":"Alessandro"},{"full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","last_name":"Seiringer","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}]},{"project":[{"_id":"26450934-B435-11E9-9278-68D0E5697425","name":"NSERC Postdoctoral fellowship"}],"citation":{"short":"T. Chen, C. Hainzl, N. Pavlović, R. Seiringer, Communications on Pure and Applied Mathematics 68 (2015) 1845–1884.","ieee":"T. Chen, C. Hainzl, N. Pavlović, and R. Seiringer, “Unconditional uniqueness for the cubic gross pitaevskii hierarchy via quantum de finetti,” Communications on Pure and Applied Mathematics, vol. 68, no. 10. Wiley, pp. 1845–1884, 2015.","apa":"Chen, T., Hainzl, C., Pavlović, N., & Seiringer, R. (2015). Unconditional uniqueness for the cubic gross pitaevskii hierarchy via quantum de finetti. Communications on Pure and Applied Mathematics. Wiley. https://doi.org/10.1002/cpa.21552","ama":"Chen T, Hainzl C, Pavlović N, Seiringer R. Unconditional uniqueness for the cubic gross pitaevskii hierarchy via quantum de finetti. Communications on Pure and Applied Mathematics. 2015;68(10):1845-1884. doi:10.1002/cpa.21552","mla":"Chen, Thomas, et al. “Unconditional Uniqueness for the Cubic Gross Pitaevskii Hierarchy via Quantum de Finetti.” Communications on Pure and Applied Mathematics, vol. 68, no. 10, Wiley, 2015, pp. 1845–84, doi:10.1002/cpa.21552.","ista":"Chen T, Hainzl C, Pavlović N, Seiringer R. 2015. Unconditional uniqueness for the cubic gross pitaevskii hierarchy via quantum de finetti. Communications on Pure and Applied Mathematics. 68(10), 1845–1884.","chicago":"Chen, Thomas, Christian Hainzl, Nataša Pavlović, and Robert Seiringer. “Unconditional Uniqueness for the Cubic Gross Pitaevskii Hierarchy via Quantum de Finetti.” Communications on Pure and Applied Mathematics. Wiley, 2015. https://doi.org/10.1002/cpa.21552."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"5598","author":[{"full_name":"Chen, Thomas","last_name":"Chen","first_name":"Thomas"},{"last_name":"Hainzl","full_name":"Hainzl, Christian","first_name":"Christian"},{"first_name":"Nataša","last_name":"Pavlović","full_name":"Pavlović, Nataša"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","last_name":"Seiringer"}],"title":"Unconditional uniqueness for the cubic gross pitaevskii hierarchy via quantum de finetti","oa":1,"publisher":"Wiley","quality_controlled":"1","year":"2015","publication":"Communications on Pure and Applied Mathematics","day":"01","page":"1845 - 1884","date_created":"2018-12-11T11:52:48Z","date_published":"2015-10-01T00:00:00Z","doi":"10.1002/cpa.21552","_id":"1573","type":"journal_article","status":"public","date_updated":"2021-01-12T06:51:41Z","department":[{"_id":"RoSe"}],"abstract":[{"lang":"eng","text":"We present a new, simpler proof of the unconditional uniqueness of solutions to the cubic Gross-Pitaevskii hierarchy in ℝ3. One of the main tools in our analysis is the quantum de Finetti theorem. Our uniqueness result is equivalent to the one established in the celebrated works of Erdos, Schlein, and Yau."}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1307.3168"}],"scopus_import":1,"intvolume":" 68","month":"10","publication_status":"published","language":[{"iso":"eng"}],"issue":"10","volume":68},{"ddc":["570"],"date_updated":"2021-01-12T06:51:44Z","file_date_updated":"2020-07-14T12:45:02Z","department":[{"_id":"PeJo"}],"_id":"1580","status":"public","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"file":[{"file_size":5563015,"date_updated":"2020-07-14T12:45:02Z","creator":"dernst","file_name":"2015_Neuroscience_Brenes.pdf","date_created":"2020-05-15T06:50:20Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"7849","checksum":"af2c4c994718c7be417eba0dc746aac9"}],"publication_status":"published","volume":311,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Synapsins (Syns) are an evolutionarily conserved family of presynaptic proteins crucial for the fine-tuning of synaptic function. A large amount of experimental evidences has shown that Syns are involved in the development of epileptic phenotypes and several mutations in Syn genes have been associated with epilepsy in humans and animal models. Syn mutations induce alterations in circuitry and neurotransmitter release, differentially affecting excitatory and inhibitory synapses, thus causing an excitation/inhibition imbalance in network excitability toward hyperexcitability that may be a determinant with regard to the development of epilepsy. Another approach to investigate epileptogenic mechanisms is to understand how silencing Syn affects the cellular behavior of single neurons and is associated with the hyperexcitable phenotypes observed in epilepsy. Here, we examined the functional effects of antisense-RNA inhibition of Syn expression on individually identified and isolated serotonergic cells of the Helix land snail. We found that Helix synapsin silencing increases cell excitability characterized by a slightly depolarized resting membrane potential, decreases the rheobase, reduces the threshold for action potential (AP) firing and increases the mean and instantaneous firing rates, with respect to control cells. The observed increase of Ca2+ and BK currents in Syn-silenced cells seems to be related to changes in the shape of the AP waveform. These currents sustain the faster spiking in Syn-deficient cells by increasing the after hyperpolarization and limiting the Na+ and Ca2+ channel inactivation during repetitive firing. This in turn speeds up the depolarization phase by reaching the AP threshold faster. Our results provide evidence that Syn silencing increases intrinsic cell excitability associated with increased Ca2+ and Ca2+-dependent BK currents in the absence of excitatory or inhibitory inputs."}],"intvolume":" 311","month":"12","scopus_import":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Brenes O, Vandael DH, Carbone E, Montarolo P, Ghirardi M. 2015. Knock-down of synapsin alters cell excitability and action potential waveform by potentiating BK and voltage gated Ca2 currents in Helix serotonergic neurons. Neuroscience. 311, 430–443.","chicago":"Brenes, Oscar, David H Vandael, Emilio Carbone, Pier Montarolo, and Mirella Ghirardi. “Knock-down of Synapsin Alters Cell Excitability and Action Potential Waveform by Potentiating BK and Voltage Gated Ca2 Currents in Helix Serotonergic Neurons.” Neuroscience. Elsevier, 2015. https://doi.org/10.1016/j.neuroscience.2015.10.046.","apa":"Brenes, O., Vandael, D. H., Carbone, E., Montarolo, P., & Ghirardi, M. (2015). Knock-down of synapsin alters cell excitability and action potential waveform by potentiating BK and voltage gated Ca2 currents in Helix serotonergic neurons. Neuroscience. Elsevier. https://doi.org/10.1016/j.neuroscience.2015.10.046","ama":"Brenes O, Vandael DH, Carbone E, Montarolo P, Ghirardi M. Knock-down of synapsin alters cell excitability and action potential waveform by potentiating BK and voltage gated Ca2 currents in Helix serotonergic neurons. Neuroscience. 2015;311:430-443. doi:10.1016/j.neuroscience.2015.10.046","ieee":"O. Brenes, D. H. Vandael, E. Carbone, P. Montarolo, and M. Ghirardi, “Knock-down of synapsin alters cell excitability and action potential waveform by potentiating BK and voltage gated Ca2 currents in Helix serotonergic neurons,” Neuroscience, vol. 311. Elsevier, pp. 430–443, 2015.","short":"O. Brenes, D.H. Vandael, E. Carbone, P. Montarolo, M. Ghirardi, Neuroscience 311 (2015) 430–443.","mla":"Brenes, Oscar, et al. “Knock-down of Synapsin Alters Cell Excitability and Action Potential Waveform by Potentiating BK and Voltage Gated Ca2 Currents in Helix Serotonergic Neurons.” Neuroscience, vol. 311, Elsevier, 2015, pp. 430–43, doi:10.1016/j.neuroscience.2015.10.046."},"title":"Knock-down of synapsin alters cell excitability and action potential waveform by potentiating BK and voltage gated Ca2 currents in Helix serotonergic neurons","article_processing_charge":"No","publist_id":"5591","author":[{"full_name":"Brenes, Oscar","last_name":"Brenes","first_name":"Oscar"},{"id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","first_name":"David H","last_name":"Vandael","orcid":"0000-0001-7577-1676","full_name":"Vandael, David H"},{"first_name":"Emilio","last_name":"Carbone","full_name":"Carbone, Emilio"},{"first_name":"Pier","full_name":"Montarolo, Pier","last_name":"Montarolo"},{"first_name":"Mirella","full_name":"Ghirardi, Mirella","last_name":"Ghirardi"}],"publication":"Neuroscience","day":"17","year":"2015","has_accepted_license":"1","date_created":"2018-12-11T11:52:50Z","date_published":"2015-12-17T00:00:00Z","doi":"10.1016/j.neuroscience.2015.10.046","page":"430 - 443","oa":1,"quality_controlled":"1","publisher":"Elsevier"},{"date_updated":"2021-01-12T06:51:43Z","department":[{"_id":"BeVi"}],"_id":"1577","status":"public","article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","issue":"40","volume":112,"pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Contrary to the pattern seen in mammalian sex chromosomes, where most Y-linked genes have X-linked homologs, the Drosophila X and Y chromosomes appear to be unrelated. Most of the Y-linked genes have autosomal paralogs, so autosome-to-Y transposition must be the main source of Drosophila Y-linked genes. Here we show how these genes were acquired. We found a previously unidentified gene (flagrante delicto Y, FDY) that originated from a recent duplication of the autosomal gene vig2 to the Y chromosome of Drosophila melanogaster. Four contiguous genes were duplicated along with vig2, but they became pseudogenes through the accumulation of deletions and transposable element insertions, whereas FDY remained functional, acquired testis-specific expression, and now accounts for ∼20% of the vig2-like mRNA in testis. FDY is absent in the closest relatives of D. melanogaster, and DNA sequence divergence indicates that the duplication to the Y chromosome occurred ∼2 million years ago. Thus, FDY provides a snapshot of the early stages of the establishment of a Y-linked gene and demonstrates how the Drosophila Y has been accumulating autosomal genes."}],"month":"10","intvolume":" 112","scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4603513/"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Carvalho, Antonio, Beatriz Vicoso, Claudia Russo, Bonnielin Swenor, and Andrew Clark. “Birth of a New Gene on the Y Chromosome of Drosophila Melanogaster.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1516543112.","ista":"Carvalho A, Vicoso B, Russo C, Swenor B, Clark A. 2015. Birth of a new gene on the Y chromosome of Drosophila melanogaster. PNAS. 112(40), 12450–12455.","mla":"Carvalho, Antonio, et al. “Birth of a New Gene on the Y Chromosome of Drosophila Melanogaster.” PNAS, vol. 112, no. 40, National Academy of Sciences, 2015, pp. 12450–55, doi:10.1073/pnas.1516543112.","ama":"Carvalho A, Vicoso B, Russo C, Swenor B, Clark A. Birth of a new gene on the Y chromosome of Drosophila melanogaster. PNAS. 2015;112(40):12450-12455. doi:10.1073/pnas.1516543112","apa":"Carvalho, A., Vicoso, B., Russo, C., Swenor, B., & Clark, A. (2015). Birth of a new gene on the Y chromosome of Drosophila melanogaster. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1516543112","ieee":"A. Carvalho, B. Vicoso, C. Russo, B. Swenor, and A. Clark, “Birth of a new gene on the Y chromosome of Drosophila melanogaster,” PNAS, vol. 112, no. 40. National Academy of Sciences, pp. 12450–12455, 2015.","short":"A. Carvalho, B. Vicoso, C. Russo, B. Swenor, A. Clark, PNAS 112 (2015) 12450–12455."},"title":"Birth of a new gene on the Y chromosome of Drosophila melanogaster","author":[{"first_name":"Antonio","last_name":"Carvalho","full_name":"Carvalho, Antonio"},{"first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306"},{"full_name":"Russo, Claudia","last_name":"Russo","first_name":"Claudia"},{"first_name":"Bonnielin","full_name":"Swenor, Bonnielin","last_name":"Swenor"},{"full_name":"Clark, Andrew","last_name":"Clark","first_name":"Andrew"}],"publist_id":"5594","external_id":{"pmid":["26385968"]},"article_processing_charge":"No","day":"06","publication":"PNAS","year":"2015","doi":"10.1073/pnas.1516543112","date_published":"2015-10-06T00:00:00Z","date_created":"2018-12-11T11:52:49Z","page":"12450 - 12455","acknowledgement":"This work was supported by grants from Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), FAPERJ, and CAPES (to A.B.C.), and National Institutes of Health Grant R01 GM64590 (to A.G.C. and A.B.C.).\r\nWe thank M. Vibranovski, C. Bergman, and the Berkeley Drosophila Genome Project for access to unpublished data; M. Vibranovski, R. Hoskins, S. Celniker, C. Kennedy, J. Carlson, S. Galasinski, B. Wakimoto, J. Yasuhara, G. Sutton, M. Kuhner, J. Felsenstein, and C. Santos for help in various steps of the work; and B. Bitner-Mathe, R. Ventura, the members of the A.B.C. and A.G.C. laboratories, and two reviewers for many valuable comments on the manuscript.","quality_controlled":"1","publisher":"National Academy of Sciences","oa":1},{"_id":"1579","type":"journal_article","status":"public","date_updated":"2021-01-12T06:51:43Z","department":[{"_id":"CaUh"}],"abstract":[{"lang":"eng","text":"We show that the Galois group of any Schubert problem involving lines in projective space contains the alternating group. This constitutes the largest family of enumerative problems whose Galois groups have been largely determined. Using a criterion of Vakil and a special position argument due to Schubert, our result follows from a particular inequality among Kostka numbers of two-rowed tableaux. In most cases, a combinatorial injection proves the inequality. For the remaining cases, we use the Weyl integral formulas to obtain an integral formula for these Kostka numbers. This rewrites the inequality as an integral, which we estimate to establish the inequality."}],"oa_version":"Preprint","scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1207.4280"}],"month":"06","intvolume":" 367","publication_status":"published","language":[{"iso":"eng"}],"issue":"6","volume":367,"citation":{"mla":"Brooks, Christopher, et al. “Galois Groups of Schubert Problems of Lines Are at Least Alternating.” Transactions of the American Mathematical Society, vol. 367, no. 6, American Mathematical Society, 2015, pp. 4183–206, doi:10.1090/S0002-9947-2014-06192-8.","ieee":"C. Brooks, A. Martin del Campo Sanchez, and F. Sottile, “Galois groups of Schubert problems of lines are at least alternating,” Transactions of the American Mathematical Society, vol. 367, no. 6. American Mathematical Society, pp. 4183–4206, 2015.","short":"C. Brooks, A. Martin del Campo Sanchez, F. Sottile, Transactions of the American Mathematical Society 367 (2015) 4183–4206.","ama":"Brooks C, Martin del Campo Sanchez A, Sottile F. Galois groups of Schubert problems of lines are at least alternating. Transactions of the American Mathematical Society. 2015;367(6):4183-4206. doi:10.1090/S0002-9947-2014-06192-8","apa":"Brooks, C., Martin del Campo Sanchez, A., & Sottile, F. (2015). Galois groups of Schubert problems of lines are at least alternating. Transactions of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/S0002-9947-2014-06192-8","chicago":"Brooks, Christopher, Abraham Martin del Campo Sanchez, and Frank Sottile. “Galois Groups of Schubert Problems of Lines Are at Least Alternating.” Transactions of the American Mathematical Society. American Mathematical Society, 2015. https://doi.org/10.1090/S0002-9947-2014-06192-8.","ista":"Brooks C, Martin del Campo Sanchez A, Sottile F. 2015. Galois groups of Schubert problems of lines are at least alternating. Transactions of the American Mathematical Society. 367(6), 4183–4206."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Christopher","last_name":"Brooks","full_name":"Brooks, Christopher"},{"id":"4CF47F6A-F248-11E8-B48F-1D18A9856A87","first_name":"Abraham","last_name":"Martin Del Campo Sanchez","full_name":"Martin Del Campo Sanchez, Abraham"},{"first_name":"Frank","last_name":"Sottile","full_name":"Sottile, Frank"}],"publist_id":"5592","article_processing_charge":"No","title":"Galois groups of Schubert problems of lines are at least alternating","acknowledgement":"This research was supported in part by NSF grant DMS-915211 and the Institut Mittag-Leffler.\r\n","publisher":"American Mathematical Society","quality_controlled":"1","oa":1,"year":"2015","day":"01","publication":"Transactions of the American Mathematical Society","page":"4183 - 4206","doi":"10.1090/S0002-9947-2014-06192-8","date_published":"2015-06-01T00:00:00Z","date_created":"2018-12-11T11:52:50Z"},{"_id":"1578","status":"public","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:51:43Z","citation":{"apa":"Cao, T., Edelsbrunner, H., & Tan, T. (2015). Triangulations from topologically correct digital Voronoi diagrams. Computational Geometry. Elsevier. https://doi.org/10.1016/j.comgeo.2015.04.001","ama":"Cao T, Edelsbrunner H, Tan T. Triangulations from topologically correct digital Voronoi diagrams. Computational Geometry. 2015;48(7):507-519. doi:10.1016/j.comgeo.2015.04.001","short":"T. Cao, H. Edelsbrunner, T. Tan, Computational Geometry 48 (2015) 507–519.","ieee":"T. Cao, H. Edelsbrunner, and T. Tan, “Triangulations from topologically correct digital Voronoi diagrams,” Computational Geometry, vol. 48, no. 7. Elsevier, pp. 507–519, 2015.","mla":"Cao, Thanhtung, et al. “Triangulations from Topologically Correct Digital Voronoi Diagrams.” Computational Geometry, vol. 48, no. 7, Elsevier, 2015, pp. 507–19, doi:10.1016/j.comgeo.2015.04.001.","ista":"Cao T, Edelsbrunner H, Tan T. 2015. Triangulations from topologically correct digital Voronoi diagrams. Computational Geometry. 48(7), 507–519.","chicago":"Cao, Thanhtung, Herbert Edelsbrunner, and Tiowseng Tan. “Triangulations from Topologically Correct Digital Voronoi Diagrams.” Computational Geometry. Elsevier, 2015. https://doi.org/10.1016/j.comgeo.2015.04.001."},"title":"Triangulations from topologically correct digital Voronoi diagrams","department":[{"_id":"HeEd"}],"publist_id":"5593","author":[{"first_name":"Thanhtung","full_name":"Cao, Thanhtung","last_name":"Cao"},{"last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert"},{"last_name":"Tan","full_name":"Tan, Tiowseng","first_name":"Tiowseng"}],"acknowledgement":"The research of the second author is partially supported by NSF under grant DBI-0820624 and by DARPA under grants HR011-05-1-0057 and HR0011-09-006\r\n","oa_version":"None","abstract":[{"lang":"eng","text":"We prove that the dual of the digital Voronoi diagram constructed by flooding the plane from the data points gives a geometrically and topologically correct dual triangulation. This provides the proof of correctness for recently developed GPU algorithms that outperform traditional CPU algorithms for constructing two-dimensional Delaunay triangulations."}],"intvolume":" 48","month":"08","publisher":"Elsevier","quality_controlled":"1","scopus_import":1,"language":[{"iso":"eng"}],"publication":"Computational Geometry","day":"01","publication_status":"published","year":"2015","date_created":"2018-12-11T11:52:49Z","date_published":"2015-08-01T00:00:00Z","doi":"10.1016/j.comgeo.2015.04.001","issue":"7","volume":48,"page":"507 - 519"},{"page":"431 - 432","date_created":"2018-12-11T11:52:50Z","doi":"10.1016/j.cell.2015.04.009","volume":161,"issue":"3","date_published":"2015-04-23T00:00:00Z","publication_status":"published","year":"2015","publication":"Cell","language":[{"iso":"eng"}],"day":"23","publisher":"Cell Press","scopus_import":"1","quality_controlled":"1","intvolume":" 161","month":"04","abstract":[{"text":"In animal embryos, morphogen gradients determine tissue patterning and morphogenesis. Shyer et al. provide evidence that, during vertebrate gut formation, tissue folding generates graded activity of signals required for subsequent steps of gut growth and differentiation, thereby revealing an intriguing link between tissue morphogenesis and morphogen gradient formation.","lang":"eng"}],"oa_version":"None","article_processing_charge":"No","author":[{"full_name":"Bollenbach, Mark Tobias","orcid":"0000-0003-4398-476X","last_name":"Bollenbach","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Mark Tobias"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566"}],"publist_id":"5590","title":"Gradients are shaping up","department":[{"_id":"ToBo"},{"_id":"CaHe"}],"date_updated":"2022-08-25T13:56:10Z","citation":{"ista":"Bollenbach MT, Heisenberg C-PJ. 2015. Gradients are shaping up. Cell. 161(3), 431–432.","chicago":"Bollenbach, Mark Tobias, and Carl-Philipp J Heisenberg. “Gradients Are Shaping Up.” Cell. Cell Press, 2015. https://doi.org/10.1016/j.cell.2015.04.009.","ama":"Bollenbach MT, Heisenberg C-PJ. Gradients are shaping up. Cell. 2015;161(3):431-432. doi:10.1016/j.cell.2015.04.009","apa":"Bollenbach, M. T., & Heisenberg, C.-P. J. (2015). Gradients are shaping up. Cell. Cell Press. https://doi.org/10.1016/j.cell.2015.04.009","short":"M.T. Bollenbach, C.-P.J. Heisenberg, Cell 161 (2015) 431–432.","ieee":"M. T. Bollenbach and C.-P. J. Heisenberg, “Gradients are shaping up,” Cell, vol. 161, no. 3. Cell Press, pp. 431–432, 2015.","mla":"Bollenbach, Mark Tobias, and Carl-Philipp J. Heisenberg. “Gradients Are Shaping Up.” Cell, vol. 161, no. 3, Cell Press, 2015, pp. 431–32, doi:10.1016/j.cell.2015.04.009."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","type":"journal_article","status":"public","_id":"1581"},{"abstract":[{"lang":"eng","text":"We investigate the dynamics of ferrofluidic wavy vortex flows in the counter-rotating Taylor-Couette system, with a focus on wavy flows with a mixture of the dominant azimuthal modes. Without external magnetic field flows are stable and pro-grade with respect to the rotation of the inner cylinder. More complex behaviors can arise when an axial or a transverse magnetic field is applied. Depending on the direction and strength of the field, multi-stable wavy states and bifurcations can occur. We uncover the phenomenon of flow pattern reversal as the strength of the magnetic field is increased through a critical value. In between the regimes of pro-grade and retrograde flow rotations, standing waves with zero angular velocities can emerge. A striking finding is that, under a transverse magnetic field, a second reversal in the flow pattern direction can occur, where the flow pattern evolves into pro-grade rotation again from a retrograde state. Flow reversal is relevant to intriguing phenomena in nature such as geomagnetic reversal. Our results suggest that, in ferrofluids, flow pattern reversal can be induced by varying a magnetic field in a controlled manner, which can be realized in laboratory experiments with potential applications in the development of modern fluid devices."}],"oa_version":"Published Version","scopus_import":1,"intvolume":" 5","month":"12","publication_status":"published","language":[{"iso":"eng"}],"file":[{"checksum":"927e151674347661ce36eae2818dafdc","file_id":"5036","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:13:49Z","file_name":"IST-2016-472-v1+1_srep18589.pdf","creator":"system","date_updated":"2020-07-14T12:45:03Z","file_size":2771236}],"volume":5,"_id":"1589","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","article_type":"original","pubrep_id":"472","status":"public","date_updated":"2021-01-12T06:51:48Z","ddc":["530","540"],"department":[{"_id":"BjHo"}],"file_date_updated":"2020-07-14T12:45:03Z","oa":1,"publisher":"Nature Publishing Group","quality_controlled":"1","year":"2015","has_accepted_license":"1","publication":"Scientific Reports","day":"21","date_created":"2018-12-11T11:52:53Z","doi":"10.1038/srep18589","date_published":"2015-12-21T00:00:00Z","article_number":"18589","citation":{"apa":"Altmeyer, S., Do, Y., & Lai, Y. (2015). Magnetic field induced flow pattern reversal in a ferrofluidic Taylor-Couette system. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep18589","ama":"Altmeyer S, Do Y, Lai Y. Magnetic field induced flow pattern reversal in a ferrofluidic Taylor-Couette system. Scientific Reports. 2015;5. doi:10.1038/srep18589","ieee":"S. Altmeyer, Y. Do, and Y. Lai, “Magnetic field induced flow pattern reversal in a ferrofluidic Taylor-Couette system,” Scientific Reports, vol. 5. Nature Publishing Group, 2015.","short":"S. Altmeyer, Y. Do, Y. Lai, Scientific Reports 5 (2015).","mla":"Altmeyer, Sebastian, et al. “Magnetic Field Induced Flow Pattern Reversal in a Ferrofluidic Taylor-Couette System.” Scientific Reports, vol. 5, 18589, Nature Publishing Group, 2015, doi:10.1038/srep18589.","ista":"Altmeyer S, Do Y, Lai Y. 2015. Magnetic field induced flow pattern reversal in a ferrofluidic Taylor-Couette system. Scientific Reports. 5, 18589.","chicago":"Altmeyer, Sebastian, Younghae Do, and Ying Lai. “Magnetic Field Induced Flow Pattern Reversal in a Ferrofluidic Taylor-Couette System.” Scientific Reports. Nature Publishing Group, 2015. https://doi.org/10.1038/srep18589."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"5582","author":[{"id":"2EE67FDC-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian","full_name":"Altmeyer, Sebastian","orcid":"0000-0001-5964-0203","last_name":"Altmeyer"},{"first_name":"Younghae","last_name":"Do","full_name":"Do, Younghae"},{"first_name":"Ying","last_name":"Lai","full_name":"Lai, Ying"}],"title":"Magnetic field induced flow pattern reversal in a ferrofluidic Taylor-Couette system"},{"ddc":["000"],"date_updated":"2023-02-23T10:05:22Z","file_date_updated":"2020-07-14T12:45:03Z","department":[{"_id":"HeEd"}],"_id":"1584","pubrep_id":"475","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","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5292","checksum":"5b33719a86f7f4c8e5dc62c1b6893f49","file_size":508379,"date_updated":"2020-07-14T12:45:03Z","creator":"system","file_name":"IST-2016-475-v1+1_1-s2.0-S092577211500005X-main.pdf","date_created":"2018-12-12T10:17:36Z"}],"publication_status":"published","related_material":{"record":[{"relation":"other","status":"public","id":"1582"}]},"issue":"5","volume":48,"oa_version":"Published Version","abstract":[{"text":"We investigate weighted straight skeletons from a geometric, graph-theoretical, and combinatorial point of view. We start with a thorough definition and shed light on some ambiguity issues in the procedural definition. We investigate the geometry, combinatorics, and topology of faces and the roof model, and we discuss in which cases a weighted straight skeleton is connected. Finally, we show that the weighted straight skeleton of even a simple polygon may be non-planar and may contain cycles, and we discuss under which restrictions on the weights and/or the input polygon the weighted straight skeleton still behaves similar to its unweighted counterpart. In particular, we obtain a non-procedural description and a linear-time construction algorithm for the straight skeleton of strictly convex polygons with arbitrary weights.","lang":"eng"}],"intvolume":" 48","month":"07","scopus_import":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Biedl, Therese, et al. “Reprint of: Weighted Straight Skeletons in the Plane.” Computational Geometry: Theory and Applications, vol. 48, no. 5, Elsevier, 2015, pp. 429–42, doi:10.1016/j.comgeo.2015.01.004.","apa":"Biedl, T., Held, M., Huber, S., Kaaser, D., & Palfrader, P. (2015). Reprint of: Weighted straight skeletons in the plane. Computational Geometry: Theory and Applications. Elsevier. https://doi.org/10.1016/j.comgeo.2015.01.004","ama":"Biedl T, Held M, Huber S, Kaaser D, Palfrader P. Reprint of: Weighted straight skeletons in the plane. Computational Geometry: Theory and Applications. 2015;48(5):429-442. doi:10.1016/j.comgeo.2015.01.004","short":"T. Biedl, M. Held, S. Huber, D. Kaaser, P. Palfrader, Computational Geometry: Theory and Applications 48 (2015) 429–442.","ieee":"T. Biedl, M. Held, S. Huber, D. Kaaser, and P. Palfrader, “Reprint of: Weighted straight skeletons in the plane,” Computational Geometry: Theory and Applications, vol. 48, no. 5. Elsevier, pp. 429–442, 2015.","chicago":"Biedl, Therese, Martin Held, Stefan Huber, Dominik Kaaser, and Peter Palfrader. “Reprint of: Weighted Straight Skeletons in the Plane.” Computational Geometry: Theory and Applications. Elsevier, 2015. https://doi.org/10.1016/j.comgeo.2015.01.004.","ista":"Biedl T, Held M, Huber S, Kaaser D, Palfrader P. 2015. Reprint of: Weighted straight skeletons in the plane. Computational Geometry: Theory and Applications. 48(5), 429–442."},"title":"Reprint of: Weighted straight skeletons in the plane","author":[{"full_name":"Biedl, Therese","last_name":"Biedl","first_name":"Therese"},{"first_name":"Martin","full_name":"Held, Martin","last_name":"Held"},{"last_name":"Huber","full_name":"Huber, Stefan","orcid":"0000-0002-8871-5814","id":"4700A070-F248-11E8-B48F-1D18A9856A87","first_name":"Stefan"},{"last_name":"Kaaser","full_name":"Kaaser, Dominik","first_name":"Dominik"},{"first_name":"Peter","full_name":"Palfrader, Peter","last_name":"Palfrader"}],"publist_id":"5587","publication":"Computational Geometry: Theory and Applications","day":"01","year":"2015","has_accepted_license":"1","date_created":"2018-12-11T11:52:51Z","date_published":"2015-07-01T00:00:00Z","doi":"10.1016/j.comgeo.2015.01.004","page":"429 - 442","oa":1,"quality_controlled":"1","publisher":"Elsevier"},{"date_updated":"2023-02-23T10:05:27Z","ddc":["000"],"department":[{"_id":"HeEd"}],"file_date_updated":"2020-07-14T12:45:02Z","_id":"1582","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":"474","publication_status":"published","file":[{"checksum":"c1ef67f6ec925e12f73a96b8fe285ab4","file_id":"5215","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:16:28Z","file_name":"IST-2016-474-v1+1_1-s2.0-S0925772114000807-main.pdf","creator":"system","date_updated":"2020-07-14T12:45:02Z","file_size":505987}],"language":[{"iso":"eng"}],"volume":48,"issue":"2","related_material":{"record":[{"id":"1584","status":"public","relation":"other"}]},"abstract":[{"text":"We investigate weighted straight skeletons from a geometric, graph-theoretical, and combinatorial point of view. We start with a thorough definition and shed light on some ambiguity issues in the procedural definition. We investigate the geometry, combinatorics, and topology of faces and the roof model, and we discuss in which cases a weighted straight skeleton is connected. Finally, we show that the weighted straight skeleton of even a simple polygon may be non-planar and may contain cycles, and we discuss under which restrictions on the weights and/or the input polygon the weighted straight skeleton still behaves similar to its unweighted counterpart. In particular, we obtain a non-procedural description and a linear-time construction algorithm for the straight skeleton of strictly convex polygons with arbitrary weights.","lang":"eng"}],"oa_version":"Published Version","scopus_import":1,"month":"02","intvolume":" 48","citation":{"mla":"Biedl, Therese, et al. “Weighted Straight Skeletons in the Plane.” Computational Geometry: Theory and Applications, vol. 48, no. 2, Elsevier, 2015, pp. 120–33, doi:10.1016/j.comgeo.2014.08.006.","ama":"Biedl T, Held M, Huber S, Kaaser D, Palfrader P. Weighted straight skeletons in the plane. Computational Geometry: Theory and Applications. 2015;48(2):120-133. doi:10.1016/j.comgeo.2014.08.006","apa":"Biedl, T., Held, M., Huber, S., Kaaser, D., & Palfrader, P. (2015). Weighted straight skeletons in the plane. Computational Geometry: Theory and Applications. Elsevier. https://doi.org/10.1016/j.comgeo.2014.08.006","ieee":"T. Biedl, M. Held, S. Huber, D. Kaaser, and P. Palfrader, “Weighted straight skeletons in the plane,” Computational Geometry: Theory and Applications, vol. 48, no. 2. Elsevier, pp. 120–133, 2015.","short":"T. Biedl, M. Held, S. Huber, D. Kaaser, P. Palfrader, Computational Geometry: Theory and Applications 48 (2015) 120–133.","chicago":"Biedl, Therese, Martin Held, Stefan Huber, Dominik Kaaser, and Peter Palfrader. “Weighted Straight Skeletons in the Plane.” Computational Geometry: Theory and Applications. Elsevier, 2015. https://doi.org/10.1016/j.comgeo.2014.08.006.","ista":"Biedl T, Held M, Huber S, Kaaser D, Palfrader P. 2015. Weighted straight skeletons in the plane. Computational Geometry: Theory and Applications. 48(2), 120–133."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Therese","full_name":"Biedl, Therese","last_name":"Biedl"},{"first_name":"Martin","last_name":"Held","full_name":"Held, Martin"},{"full_name":"Huber, Stefan","orcid":"0000-0002-8871-5814","last_name":"Huber","id":"4700A070-F248-11E8-B48F-1D18A9856A87","first_name":"Stefan"},{"last_name":"Kaaser","full_name":"Kaaser, Dominik","first_name":"Dominik"},{"full_name":"Palfrader, Peter","last_name":"Palfrader","first_name":"Peter"}],"publist_id":"5589","title":"Weighted straight skeletons in the plane","has_accepted_license":"1","year":"2015","day":"01","publication":"Computational Geometry: Theory and Applications","page":"120 - 133","date_published":"2015-02-01T00:00:00Z","doi":"10.1016/j.comgeo.2014.08.006","date_created":"2018-12-11T11:52:51Z","quality_controlled":"1","publisher":"Elsevier","oa":1},{"_id":"1583","pubrep_id":"473","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","ddc":["000"],"date_updated":"2021-01-12T06:51:45Z","file_date_updated":"2020-07-14T12:45:03Z","department":[{"_id":"HeEd"}],"oa_version":"Published Version","abstract":[{"text":"We study the characteristics of straight skeletons of monotone polygonal chains and use them to devise an algorithm for computing positively weighted straight skeletons of monotone polygons. Our algorithm runs in O(nlogn) time and O(n) space, where n denotes the number of vertices of the polygon.","lang":"eng"}],"intvolume":" 115","month":"02","scopus_import":1,"language":[{"iso":"eng"}],"file":[{"file_size":270137,"date_updated":"2020-07-14T12:45:03Z","creator":"system","file_name":"IST-2016-473-v1+1_1-s2.0-S0020019014001987-main.pdf","date_created":"2018-12-12T10:18:45Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"2779a648610c9b5c86d0b51a62816d23","file_id":"5367"}],"publication_status":"published","volume":115,"issue":"2","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"T. Biedl, M. Held, S. Huber, D. Kaaser, and P. Palfrader, “A simple algorithm for computing positively weighted straight skeletons of monotone polygons,” Information Processing Letters, vol. 115, no. 2. Elsevier, pp. 243–247, 2015.","short":"T. Biedl, M. Held, S. Huber, D. Kaaser, P. Palfrader, Information Processing Letters 115 (2015) 243–247.","ama":"Biedl T, Held M, Huber S, Kaaser D, Palfrader P. A simple algorithm for computing positively weighted straight skeletons of monotone polygons. Information Processing Letters. 2015;115(2):243-247. doi:10.1016/j.ipl.2014.09.021","apa":"Biedl, T., Held, M., Huber, S., Kaaser, D., & Palfrader, P. (2015). A simple algorithm for computing positively weighted straight skeletons of monotone polygons. Information Processing Letters. Elsevier. https://doi.org/10.1016/j.ipl.2014.09.021","mla":"Biedl, Therese, et al. “A Simple Algorithm for Computing Positively Weighted Straight Skeletons of Monotone Polygons.” Information Processing Letters, vol. 115, no. 2, Elsevier, 2015, pp. 243–47, doi:10.1016/j.ipl.2014.09.021.","ista":"Biedl T, Held M, Huber S, Kaaser D, Palfrader P. 2015. A simple algorithm for computing positively weighted straight skeletons of monotone polygons. Information Processing Letters. 115(2), 243–247.","chicago":"Biedl, Therese, Martin Held, Stefan Huber, Dominik Kaaser, and Peter Palfrader. “A Simple Algorithm for Computing Positively Weighted Straight Skeletons of Monotone Polygons.” Information Processing Letters. Elsevier, 2015. https://doi.org/10.1016/j.ipl.2014.09.021."},"title":"A simple algorithm for computing positively weighted straight skeletons of monotone polygons","publist_id":"5588","author":[{"first_name":"Therese","last_name":"Biedl","full_name":"Biedl, Therese"},{"first_name":"Martin","last_name":"Held","full_name":"Held, Martin"},{"id":"4700A070-F248-11E8-B48F-1D18A9856A87","first_name":"Stefan","last_name":"Huber","full_name":"Huber, Stefan","orcid":"0000-0002-8871-5814"},{"first_name":"Dominik","full_name":"Kaaser, Dominik","last_name":"Kaaser"},{"full_name":"Palfrader, Peter","last_name":"Palfrader","first_name":"Peter"}],"oa":1,"quality_controlled":"1","publisher":"Elsevier","publication":"Information Processing Letters","day":"01","year":"2015","has_accepted_license":"1","date_created":"2018-12-11T11:52:51Z","doi":"10.1016/j.ipl.2014.09.021","date_published":"2015-02-01T00:00:00Z","page":"243 - 247"},{"article_number":"062506","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"citation":{"mla":"Amaro, Pedro, et al. “Quantum Interference Shifts in Laser Spectroscopy with Elliptical Polarization.” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 92, no. 6, 062506, American Physical Society, 2015, doi:10.1103/PhysRevA.92.062506.","ieee":"P. Amaro et al., “Quantum interference shifts in laser spectroscopy with elliptical polarization,” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 92, no. 6. American Physical Society, 2015.","short":"P. Amaro, F. Fratini, L. Safari, A. Antognini, P. Indelicato, R. Pohl, J. Santos, Physical Review A - Atomic, Molecular, and Optical Physics 92 (2015).","ama":"Amaro P, Fratini F, Safari L, et al. Quantum interference shifts in laser spectroscopy with elliptical polarization. Physical Review A - Atomic, Molecular, and Optical Physics. 2015;92(6). doi:10.1103/PhysRevA.92.062506","apa":"Amaro, P., Fratini, F., Safari, L., Antognini, A., Indelicato, P., Pohl, R., & Santos, J. (2015). Quantum interference shifts in laser spectroscopy with elliptical polarization. Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.92.062506","chicago":"Amaro, Pedro, Filippo Fratini, Laleh Safari, Aldo Antognini, Paul Indelicato, Randolf Pohl, and José Santos. “Quantum Interference Shifts in Laser Spectroscopy with Elliptical Polarization.” Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society, 2015. https://doi.org/10.1103/PhysRevA.92.062506.","ista":"Amaro P, Fratini F, Safari L, Antognini A, Indelicato P, Pohl R, Santos J. 2015. Quantum interference shifts in laser spectroscopy with elliptical polarization. Physical Review A - Atomic, Molecular, and Optical Physics. 92(6), 062506."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Pedro","last_name":"Amaro","full_name":"Amaro, Pedro"},{"first_name":"Filippo","full_name":"Fratini, Filippo","last_name":"Fratini"},{"first_name":"Laleh","id":"3C325E5E-F248-11E8-B48F-1D18A9856A87","last_name":"Safari","full_name":"Safari, Laleh"},{"first_name":"Aldo","last_name":"Antognini","full_name":"Antognini, Aldo"},{"last_name":"Indelicato","full_name":"Indelicato, Paul","first_name":"Paul"},{"first_name":"Randolf","last_name":"Pohl","full_name":"Pohl, Randolf"},{"full_name":"Santos, José","last_name":"Santos","first_name":"José"}],"publist_id":"5584","article_processing_charge":"No","external_id":{"arxiv":["1511.03585"]},"title":"Quantum interference shifts in laser spectroscopy with elliptical polarization","publisher":"American Physical Society","quality_controlled":"1","oa":1,"year":"2015","day":"31","publication":"Physical Review A - Atomic, Molecular, and Optical Physics","doi":"10.1103/PhysRevA.92.062506","date_published":"2015-12-31T00:00:00Z","date_created":"2018-12-11T11:52:53Z","_id":"1587","article_type":"original","type":"journal_article","status":"public","date_updated":"2021-01-12T06:51:47Z","department":[{"_id":"MiLe"}],"abstract":[{"text":"We investigate the quantum interference shifts between energetically close states, where the state structure is observed by laser spectroscopy. We report a compact and analytical expression that models the quantum interference induced shift for any admixture of circular polarization of the incident laser and angle of observation. An experimental scenario free of quantum interference can thus be predicted with this formula. Although this study is exemplified here for muonic deuterium, it can be applied to any other laser spectroscopy measurement of ns-n′p frequencies of a nonrelativistic atomic system, via an ns→n′p→n′′s scheme.","lang":"eng"}],"oa_version":"Preprint","scopus_import":1,"main_file_link":[{"url":"https://arxiv.org/abs/1511.03585","open_access":"1"}],"month":"12","intvolume":" 92","publication_status":"published","language":[{"iso":"eng"}],"volume":92,"issue":"6","ec_funded":1},{"language":[{"iso":"eng"}],"publication":"Physical Review E","day":"24","publication_status":"published","year":"2015","date_created":"2018-12-11T11:52:53Z","volume":92,"issue":"5","date_published":"2015-11-24T00:00:00Z","doi":"10.1103/PhysRevE.92.053018","oa_version":"None","abstract":[{"lang":"eng","text":"We investigate the Taylor-Couette system where the radius ratio is close to unity. Systematically increasing the Reynolds number, we observe a number of previously known transitions, such as one from the classical Taylor vortex flow (TVF) to wavy vortex flow (WVF) and the transition to fully developed turbulence. Prior to the onset of turbulence, we observe intermittent bursting patterns of localized turbulent patches, confirming the experimentally observed pattern of very short wavelength bursts (VSWBs). A striking finding is that, for a Reynolds number larger than that for the onset of VSWBs, a new type of intermittently bursting behavior emerges: patterns of azimuthally closed rings of various orders. We call them ring-bursting patterns, which surround the cylinder completely but remain localized and separated in the axial direction through nonturbulent wavy structures. We employ a number of quantitative measures including the cross-flow energy to characterize the ring-bursting patterns and to distinguish them from the background flow. These patterns are interesting because they do not occur in the wide-gap Taylor-Couette flow systems. The narrow-gap regime is less studied but certainly deserves further attention to gain deeper insights into complex flow dynamics in fluids."}],"intvolume":" 92","month":"11","publisher":"American Physical Society","scopus_import":1,"quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:51:47Z","citation":{"ista":"Altmeyer S, Do Y, Lai Y. 2015. Ring-bursting behavior en route to turbulence in narrow-gap Taylor-Couette flows. Physical Review E. 92(5), 053018.","chicago":"Altmeyer, Sebastian, Younghae Do, and Ying Lai. “Ring-Bursting Behavior En Route to Turbulence in Narrow-Gap Taylor-Couette Flows.” Physical Review E. American Physical Society, 2015. https://doi.org/10.1103/PhysRevE.92.053018.","apa":"Altmeyer, S., Do, Y., & Lai, Y. (2015). Ring-bursting behavior en route to turbulence in narrow-gap Taylor-Couette flows. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.92.053018","ama":"Altmeyer S, Do Y, Lai Y. Ring-bursting behavior en route to turbulence in narrow-gap Taylor-Couette flows. Physical Review E. 2015;92(5). doi:10.1103/PhysRevE.92.053018","ieee":"S. Altmeyer, Y. Do, and Y. Lai, “Ring-bursting behavior en route to turbulence in narrow-gap Taylor-Couette flows,” Physical Review E, vol. 92, no. 5. American Physical Society, 2015.","short":"S. Altmeyer, Y. Do, Y. Lai, Physical Review E 92 (2015).","mla":"Altmeyer, Sebastian, et al. “Ring-Bursting Behavior En Route to Turbulence in Narrow-Gap Taylor-Couette Flows.” Physical Review E, vol. 92, no. 5, 053018, American Physical Society, 2015, doi:10.1103/PhysRevE.92.053018."},"department":[{"_id":"BjHo"}],"title":"Ring-bursting behavior en route to turbulence in narrow-gap Taylor-Couette flows","author":[{"first_name":"Sebastian","id":"2EE67FDC-F248-11E8-B48F-1D18A9856A87","full_name":"Altmeyer, Sebastian","orcid":"0000-0001-5964-0203","last_name":"Altmeyer"},{"last_name":"Do","full_name":"Do, Younghae","first_name":"Younghae"},{"last_name":"Lai","full_name":"Lai, Ying","first_name":"Ying"}],"publist_id":"5583","article_number":"053018","_id":"1588","status":"public","type":"journal_article"},{"page":"352 - 361","date_created":"2018-12-11T11:52:52Z","doi":"10.1016/j.tibtech.2015.03.009","issue":"6","volume":33,"date_published":"2015-06-01T00:00:00Z","publication_status":"published","year":"2015","publication":"Trends in Biotechnology","language":[{"iso":"eng"}],"day":"01","scopus_import":1,"publisher":"Elsevier","quality_controlled":"1","intvolume":" 33","month":"06","abstract":[{"lang":"eng","text":"Through metabolic engineering cyanobacteria can be employed in biotechnology. Combining the capacity for oxygenic photosynthesis and carbon fixation with an engineered metabolic pathway allows carbon-based product formation from CO2, light, and water directly. Such cyanobacterial 'cell factories' are constructed to produce biofuels, bioplastics, and commodity chemicals. Efforts of metabolic engineers and synthetic biologists allow the modification of the intermediary metabolism at various branching points, expanding the product range. The new biosynthesis routes 'tap' the metabolism ever more efficiently, particularly through the engineering of driving forces and utilization of cofactors generated during the light reactions of photosynthesis, resulting in higher product titers. High rates of carbon rechanneling ultimately allow an almost-complete allocation of fixed carbon to product above biomass."}],"oa_version":"None","publist_id":"5585","author":[{"first_name":"Andreas","id":"4677C796-F248-11E8-B48F-1D18A9856A87","full_name":"Angermayr, Andreas","orcid":"0000-0001-8619-2223","last_name":"Angermayr"},{"first_name":"Aleix","full_name":"Gorchs, Aleix","last_name":"Gorchs"},{"first_name":"Klaas","last_name":"Hellingwerf","full_name":"Hellingwerf, Klaas"}],"department":[{"_id":"ToBo"}],"title":"Metabolic engineering of cyanobacteria for the synthesis of commodity products","date_updated":"2021-01-12T06:51:46Z","citation":{"ista":"Angermayr A, Gorchs A, Hellingwerf K. 2015. Metabolic engineering of cyanobacteria for the synthesis of commodity products. Trends in Biotechnology. 33(6), 352–361.","chicago":"Angermayr, Andreas, Aleix Gorchs, and Klaas Hellingwerf. “Metabolic Engineering of Cyanobacteria for the Synthesis of Commodity Products.” Trends in Biotechnology. Elsevier, 2015. https://doi.org/10.1016/j.tibtech.2015.03.009.","ieee":"A. Angermayr, A. Gorchs, and K. Hellingwerf, “Metabolic engineering of cyanobacteria for the synthesis of commodity products,” Trends in Biotechnology, vol. 33, no. 6. Elsevier, pp. 352–361, 2015.","short":"A. Angermayr, A. Gorchs, K. Hellingwerf, Trends in Biotechnology 33 (2015) 352–361.","apa":"Angermayr, A., Gorchs, A., & Hellingwerf, K. (2015). Metabolic engineering of cyanobacteria for the synthesis of commodity products. Trends in Biotechnology. Elsevier. https://doi.org/10.1016/j.tibtech.2015.03.009","ama":"Angermayr A, Gorchs A, Hellingwerf K. Metabolic engineering of cyanobacteria for the synthesis of commodity products. Trends in Biotechnology. 2015;33(6):352-361. doi:10.1016/j.tibtech.2015.03.009","mla":"Angermayr, Andreas, et al. “Metabolic Engineering of Cyanobacteria for the Synthesis of Commodity Products.” Trends in Biotechnology, vol. 33, no. 6, Elsevier, 2015, pp. 352–61, doi:10.1016/j.tibtech.2015.03.009."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","type":"journal_article","status":"public","_id":"1586"},{"day":"01","publication":"IEEE Transactions on Information Theory","language":[{"iso":"eng"}],"year":"2015","publication_status":"published","doi":"10.1109/TIT.2015.2421894","date_published":"2015-06-01T00:00:00Z","issue":"6","volume":61,"date_created":"2018-12-11T11:52:52Z","page":"3413 - 3426","oa_version":"None","acknowledgement":"G. Pan was supported by MOE Tier 2 under Grant 2014-T2-2-060 and in part by Tier 1 under Grant RG25/14 through the Nanyang Technological University, Singapore. W. Zhou was supported by the National University of Singapore, Singapore, under Grant R-155-000-131-112.\r\n","abstract":[{"lang":"eng","text":"In this paper, we consider the fluctuation of mutual information statistics of a multiple input multiple output channel communication systems without assuming that the entries of the channel matrix have zero pseudovariance. To this end, we also establish a central limit theorem of the linear spectral statistics for sample covariance matrices under general moment conditions by removing the restrictions imposed on the second moment and fourth moment on the matrix entries in Bai and Silverstein (2004)."}],"month":"06","intvolume":" 61","scopus_import":1,"publisher":"IEEE","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Bao, Zhigang, Guangming Pan, and Wang Zhou. “Asymptotic Mutual Information Statistics of MIMO Channels and CLT of Sample Covariance Matrices.” IEEE Transactions on Information Theory. IEEE, 2015. https://doi.org/10.1109/TIT.2015.2421894.","ista":"Bao Z, Pan G, Zhou W. 2015. Asymptotic mutual information statistics of MIMO channels and CLT of sample covariance matrices. IEEE Transactions on Information Theory. 61(6), 3413–3426.","mla":"Bao, Zhigang, et al. “Asymptotic Mutual Information Statistics of MIMO Channels and CLT of Sample Covariance Matrices.” IEEE Transactions on Information Theory, vol. 61, no. 6, IEEE, 2015, pp. 3413–26, doi:10.1109/TIT.2015.2421894.","ama":"Bao Z, Pan G, Zhou W. Asymptotic mutual information statistics of MIMO channels and CLT of sample covariance matrices. IEEE Transactions on Information Theory. 2015;61(6):3413-3426. doi:10.1109/TIT.2015.2421894","apa":"Bao, Z., Pan, G., & Zhou, W. (2015). Asymptotic mutual information statistics of MIMO channels and CLT of sample covariance matrices. IEEE Transactions on Information Theory. IEEE. https://doi.org/10.1109/TIT.2015.2421894","ieee":"Z. Bao, G. Pan, and W. Zhou, “Asymptotic mutual information statistics of MIMO channels and CLT of sample covariance matrices,” IEEE Transactions on Information Theory, vol. 61, no. 6. IEEE, pp. 3413–3426, 2015.","short":"Z. Bao, G. Pan, W. Zhou, IEEE Transactions on Information Theory 61 (2015) 3413–3426."},"date_updated":"2021-01-12T06:51:46Z","department":[{"_id":"LaEr"}],"title":"Asymptotic mutual information statistics of MIMO channels and CLT of sample covariance matrices","author":[{"first_name":"Zhigang","id":"442E6A6C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3036-1475","full_name":"Bao, Zhigang","last_name":"Bao"},{"first_name":"Guangming","full_name":"Pan, Guangming","last_name":"Pan"},{"first_name":"Wang","last_name":"Zhou","full_name":"Zhou, Wang"}],"publist_id":"5586","_id":"1585","status":"public","type":"journal_article"},{"oa":1,"publisher":"Frontiers Research Foundation","quality_controlled":"1","date_created":"2018-12-11T11:52:55Z","doi":"10.3389/fpls.2015.00218","date_published":"2015-04-14T00:00:00Z","year":"2015","has_accepted_license":"1","publication":"Frontiers in Plant Science","day":"14","project":[{"name":"Hormonal cross-talk in plant organogenesis","grant_number":"207362","_id":"253FCA6A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"publist_id":"5578","author":[{"first_name":"Petra","full_name":"Žádníková, Petra","last_name":"Žádníková"},{"full_name":"Smet, Dajo","last_name":"Smet","first_name":"Dajo"},{"last_name":"Zhu","full_name":"Zhu, Qiang","first_name":"Qiang","id":"40A4B9E6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Dominique","full_name":"Van Der Straeten, Dominique","last_name":"Van Der Straeten"},{"full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","last_name":"Benková","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}],"title":"Strategies of seedlings to overcome their sessile nature: Auxin in mobility control","citation":{"mla":"Žádníková, Petra, et al. “Strategies of Seedlings to Overcome Their Sessile Nature: Auxin in Mobility Control.” Frontiers in Plant Science, vol. 6, no. 4, Frontiers Research Foundation, 2015, doi:10.3389/fpls.2015.00218.","ama":"Žádníková P, Smet D, Zhu Q, Van Der Straeten D, Benková E. Strategies of seedlings to overcome their sessile nature: Auxin in mobility control. Frontiers in Plant Science. 2015;6(4). doi:10.3389/fpls.2015.00218","apa":"Žádníková, P., Smet, D., Zhu, Q., Van Der Straeten, D., & Benková, E. (2015). Strategies of seedlings to overcome their sessile nature: Auxin in mobility control. Frontiers in Plant Science. Frontiers Research Foundation. https://doi.org/10.3389/fpls.2015.00218","short":"P. Žádníková, D. Smet, Q. Zhu, D. Van Der Straeten, E. Benková, Frontiers in Plant Science 6 (2015).","ieee":"P. Žádníková, D. Smet, Q. Zhu, D. Van Der Straeten, and E. Benková, “Strategies of seedlings to overcome their sessile nature: Auxin in mobility control,” Frontiers in Plant Science, vol. 6, no. 4. Frontiers Research Foundation, 2015.","chicago":"Žádníková, Petra, Dajo Smet, Qiang Zhu, Dominique Van Der Straeten, and Eva Benková. “Strategies of Seedlings to Overcome Their Sessile Nature: Auxin in Mobility Control.” Frontiers in Plant Science. Frontiers Research Foundation, 2015. https://doi.org/10.3389/fpls.2015.00218.","ista":"Žádníková P, Smet D, Zhu Q, Van Der Straeten D, Benková E. 2015. Strategies of seedlings to overcome their sessile nature: Auxin in mobility control. Frontiers in Plant Science. 6(4)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"intvolume":" 6","month":"04","abstract":[{"lang":"eng","text":"Plants are sessile organisms that are permanently restricted to their site of germination. To compensate for their lack of mobility, plants evolved unique mechanisms enabling them to rapidly react to ever changing environmental conditions and flexibly adapt their postembryonic developmental program. A prominent demonstration of this developmental plasticity is their ability to bend organs in order to reach the position most optimal for growth and utilization of light, nutrients, and other resources. Shortly after germination, dicotyledonous seedlings form a bended structure, the so-called apical hook, to protect the delicate shoot meristem and cotyledons from damage when penetrating through the soil. Upon perception of a light stimulus, the apical hook rapidly opens and the photomorphogenic developmental program is activated. After germination, plant organs are able to align their growth with the light source and adopt the most favorable orientation through bending, in a process named phototropism. On the other hand, when roots and shoots are diverted from their upright orientation, they immediately detect a change in the gravity vector and bend to maintain a vertical growth direction. Noteworthy, despite the diversity of external stimuli perceived by different plant organs, all plant tropic movements share a common mechanistic basis: differential cell growth. In our review, we will discuss the molecular principles underlying various tropic responses with the focus on mechanisms mediating the perception of external signals, transduction cascades and downstream responses that regulate differential cell growth and consequently, organ bending. In particular, we highlight common and specific features of regulatory pathways in control of the bending of organs and a role for the plant hormone auxin as a key regulatory component."}],"oa_version":"Published Version","ec_funded":1,"issue":"4","volume":6,"publication_status":"published","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5142","checksum":"c454d642e18dfa86820b97a86cd6d3cc","file_size":965690,"date_updated":"2020-07-14T12:45:03Z","creator":"system","file_name":"IST-2016-471-v1+1_fpls-06-00218.pdf","date_created":"2018-12-12T10:15:23Z"}],"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":"471","status":"public","_id":"1593","department":[{"_id":"EvBe"}],"file_date_updated":"2020-07-14T12:45:03Z","date_updated":"2021-01-12T06:51:50Z","ddc":["570"]},{"project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"publist_id":"5576","author":[{"orcid":"0000-0001-8485-1774","full_name":"Fulek, Radoslav","last_name":"Fulek","first_name":"Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pelsmajer","full_name":"Pelsmajer, Michael","first_name":"Michael"},{"first_name":"Marcus","last_name":"Schaefer","full_name":"Schaefer, Marcus"}],"title":"Hanani-Tutte for radial planarity","citation":{"short":"R. Fulek, M. Pelsmajer, M. Schaefer, in:, Springer, 2015, pp. 99–110.","ieee":"R. Fulek, M. Pelsmajer, and M. Schaefer, “Hanani-Tutte for radial planarity,” presented at the GD: Graph Drawing and Network Visualization, Los Angeles, CA, USA, 2015, vol. 9411, pp. 99–110.","ama":"Fulek R, Pelsmajer M, Schaefer M. Hanani-Tutte for radial planarity. In: Vol 9411. Springer; 2015:99-110. doi:10.1007/978-3-319-27261-0_9","apa":"Fulek, R., Pelsmajer, M., & Schaefer, M. (2015). Hanani-Tutte for radial planarity (Vol. 9411, pp. 99–110). Presented at the GD: Graph Drawing and Network Visualization, Los Angeles, CA, USA: Springer. https://doi.org/10.1007/978-3-319-27261-0_9","mla":"Fulek, Radoslav, et al. Hanani-Tutte for Radial Planarity. Vol. 9411, Springer, 2015, pp. 99–110, doi:10.1007/978-3-319-27261-0_9.","ista":"Fulek R, Pelsmajer M, Schaefer M. 2015. Hanani-Tutte for radial planarity. GD: Graph Drawing and Network Visualization, LNCS, vol. 9411, 99–110.","chicago":"Fulek, Radoslav, Michael Pelsmajer, and Marcus Schaefer. “Hanani-Tutte for Radial Planarity,” 9411:99–110. Springer, 2015. https://doi.org/10.1007/978-3-319-27261-0_9."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa":1,"publisher":"Springer","quality_controlled":"1","acknowledgement":"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].","page":"99 - 110","date_created":"2018-12-11T11:52:55Z","doi":"10.1007/978-3-319-27261-0_9","date_published":"2015-11-27T00:00:00Z","year":"2015","has_accepted_license":"1","day":"27","conference":{"name":"GD: Graph Drawing and Network Visualization","start_date":"2015-09-24","location":"Los Angeles, CA, USA","end_date":"2015-09-26"},"type":"conference","pubrep_id":"594","status":"public","_id":"1595","department":[{"_id":"UlWa"}],"file_date_updated":"2020-07-14T12:45:03Z","date_updated":"2023-02-21T16:23:36Z","ddc":["510"],"alternative_title":["LNCS"],"scopus_import":1,"intvolume":" 9411","month":"11","abstract":[{"text":"A drawing of a graph G is radial if the vertices of G are placed on concentric circles C1, . . . , Ck with common center c, and edges are drawn radially: every edge intersects every circle centered at c at most once. G is radial planar if it has a radial embedding, that is, a crossing- free radial drawing. If the vertices of G are ordered or partitioned into ordered levels (as they are for leveled graphs), we require that the assignment of vertices to circles corresponds to the given ordering or leveling. We show that a graph G is radial planar if G has a radial drawing in which every two edges cross an even number of times; the radial embedding has the same leveling as the radial drawing. In other words, we establish the weak variant of the Hanani-Tutte theorem for radial planarity. This generalizes a result by Pach and Tóth.","lang":"eng"}],"oa_version":"Submitted Version","ec_funded":1,"related_material":{"record":[{"status":"public","id":"1113","relation":"later_version"},{"id":"1164","status":"public","relation":"later_version"}]},"volume":9411,"publication_status":"published","language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"685f91bd077a951ba067d42cce75409e","file_id":"4697","creator":"system","file_size":330135,"date_updated":"2020-07-14T12:45:03Z","file_name":"IST-2016-594-v1+1_HTCylinder_GD_Revision.pdf","date_created":"2018-12-12T10:08:36Z"}]}]