[{"day":"01","publication":"Journal of Insect Physiology","isi":1,"year":"2018","date_published":"2018-05-01T00:00:00Z","doi":"10.1016/j.jinsphys.2017.12.003","date_created":"2018-12-11T11:46:25Z","page":"284-290","acknowledgement":"Research with C. obscurior from Brazil was permitted by Instituto Brasileiro do Meio Ambiente e dos Recursos Naturais Renováveis, IBAMA (permit no. 20324-1). We thank the German Science Foundation ( DFG ) for funding ( Schr1135/2-1 ), T. Suckert for help with sperm length measurements and A.K. Huylmans for advice concerning graphs. One referee made helpful comments on the manuscript.\r\n","quality_controlled":"1","publisher":"Elsevier","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Metzler S, Schrempf A, Heinze J. 2018. Individual- and ejaculate-specific sperm traits in ant males. Journal of Insect Physiology. 107, 284–290.","chicago":"Metzler, Sina, Alexandra Schrempf, and Jürgen Heinze. “Individual- and Ejaculate-Specific Sperm Traits in Ant Males.” Journal of Insect Physiology. Elsevier, 2018. https://doi.org/10.1016/j.jinsphys.2017.12.003.","short":"S. Metzler, A. Schrempf, J. Heinze, Journal of Insect Physiology 107 (2018) 284–290.","ieee":"S. Metzler, A. Schrempf, and J. Heinze, “Individual- and ejaculate-specific sperm traits in ant males,” Journal of Insect Physiology, vol. 107. Elsevier, pp. 284–290, 2018.","apa":"Metzler, S., Schrempf, A., & Heinze, J. (2018). Individual- and ejaculate-specific sperm traits in ant males. Journal of Insect Physiology. Elsevier. https://doi.org/10.1016/j.jinsphys.2017.12.003","ama":"Metzler S, Schrempf A, Heinze J. Individual- and ejaculate-specific sperm traits in ant males. Journal of Insect Physiology. 2018;107:284-290. doi:10.1016/j.jinsphys.2017.12.003","mla":"Metzler, Sina, et al. “Individual- and Ejaculate-Specific Sperm Traits in Ant Males.” Journal of Insect Physiology, vol. 107, Elsevier, 2018, pp. 284–90, doi:10.1016/j.jinsphys.2017.12.003."},"title":"Individual- and ejaculate-specific sperm traits in ant males","author":[{"id":"48204546-F248-11E8-B48F-1D18A9856A87","first_name":"Sina","full_name":"Metzler, Sina","orcid":"0000-0002-9547-2494","last_name":"Metzler"},{"first_name":"Alexandra","full_name":"Schrempf, Alexandra","last_name":"Schrempf"},{"first_name":"Jürgen","last_name":"Heinze","full_name":"Heinze, Jürgen"}],"publist_id":"7397","article_processing_charge":"No","external_id":{"isi":["000434751100034"]},"language":[{"iso":"eng"}],"publication_status":"published","volume":107,"oa_version":"None","abstract":[{"text":"Sperm cells are the most morphologically diverse cells across animal taxa. Within species, sperm and ejaculate traits have been suggested to vary with the male's competitive environment, e.g., level of sperm competition, female mating status and quality, and also with male age, body mass, physiological condition, and resource availability. Most previous studies have based their conclusions on the analysis of only one or a few ejaculates per male without investigating differences among the ejaculates of the same individual. This masks potential ejaculate-specific traits. Here, we provide data on the length, quantity, and viability of sperm ejaculated by wingless males of the ant Cardiocondyla obscurior. Males of this ant species are relatively long-lived and can mate with large numbers of female sexuals throughout their lives. We analyzed all ejaculates across the individuals' lifespan and manipulated the availability of mating partners. Our study shows that both the number and size of sperm cells transferred during copulations differ among individuals and also among ejaculates of the same male. Sperm quality does not decrease with male age, but the variation in sperm number between ejaculates indicates that males need considerable time to replenish their sperm supplies. Producing many ejaculates in a short time appears to be traded-off against male longevity rather than sperm quality.","lang":"eng"}],"month":"05","intvolume":" 107","scopus_import":"1","date_updated":"2023-09-12T07:43:26Z","department":[{"_id":"SyCr"}],"_id":"426","status":"public","type":"journal_article"},{"date_updated":"2023-09-12T07:44:01Z","department":[{"_id":"ToHe"}],"_id":"5788","conference":{"name":"14th International Conference on Web and Internet Economics, WINE","start_date":"2018-12-15","location":"Oxford, UK","end_date":"2018-12-17"},"type":"conference","status":"public","publication_identifier":{"isbn":["9783030046118"],"issn":["03029743"]},"language":[{"iso":"eng"}],"volume":11316,"abstract":[{"text":"In two-player games on graphs, the players move a token through a graph to produce an infinite path, which determines the winner or payoff of the game. Such games are central in formal verification since they model the interaction between a non-terminating system and its environment. We study bidding games in which the players bid for the right to move the token. Two bidding rules have been defined. In Richman bidding, in each round, the players simultaneously submit bids, and the higher bidder moves the token and pays the other player. Poorman bidding is similar except that the winner of the bidding pays the “bank” rather than the other player. While poorman reachability games have been studied before, we present, for the first time, results on infinite-duration poorman games. A central quantity in these games is the ratio between the two players’ initial budgets. The questions we study concern a necessary and sufficient ratio with which a player can achieve a goal. For reachability objectives, such threshold ratios are known to exist for both bidding rules. We show that the properties of poorman reachability games extend to complex qualitative objectives such as parity, similarly to the Richman case. Our most interesting results concern quantitative poorman games, namely poorman mean-payoff games, where we construct optimal strategies depending on the initial ratio, by showing a connection with random-turn based games. The connection in itself is interesting, because it does not hold for reachability poorman games. We also solve the complexity problems that arise in poorman bidding games.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1804.04372","open_access":"1"}],"scopus_import":"1","alternative_title":["LNCS"],"intvolume":" 11316","month":"11","citation":{"mla":"Avni, Guy, et al. Infinite-Duration Poorman-Bidding Games. Vol. 11316, Springer, 2018, pp. 21–36, doi:10.1007/978-3-030-04612-5_2.","apa":"Avni, G., Henzinger, T. A., & Ibsen-Jensen, R. (2018). Infinite-duration poorman-bidding games (Vol. 11316, pp. 21–36). Presented at the 14th International Conference on Web and Internet Economics, WINE, Oxford, UK: Springer. https://doi.org/10.1007/978-3-030-04612-5_2","ama":"Avni G, Henzinger TA, Ibsen-Jensen R. Infinite-duration poorman-bidding games. In: Vol 11316. Springer; 2018:21-36. doi:10.1007/978-3-030-04612-5_2","ieee":"G. Avni, T. A. Henzinger, and R. Ibsen-Jensen, “Infinite-duration poorman-bidding games,” presented at the 14th International Conference on Web and Internet Economics, WINE, Oxford, UK, 2018, vol. 11316, pp. 21–36.","short":"G. Avni, T.A. Henzinger, R. Ibsen-Jensen, in:, Springer, 2018, pp. 21–36.","chicago":"Avni, Guy, Thomas A Henzinger, and Rasmus Ibsen-Jensen. “Infinite-Duration Poorman-Bidding Games,” 11316:21–36. Springer, 2018. https://doi.org/10.1007/978-3-030-04612-5_2.","ista":"Avni G, Henzinger TA, Ibsen-Jensen R. 2018. Infinite-duration poorman-bidding games. 14th International Conference on Web and Internet Economics, WINE, LNCS, vol. 11316, 21–36."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"arxiv":["1804.04372"],"isi":["000865933000002"]},"author":[{"full_name":"Avni, Guy","orcid":"0000-0001-5588-8287","last_name":"Avni","first_name":"Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"orcid":"0000-0003-4783-0389","full_name":"Ibsen-Jensen, Rasmus","last_name":"Ibsen-Jensen","first_name":"Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87"}],"title":"Infinite-duration poorman-bidding games","project":[{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"_id":"264B3912-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Formal Methods meets Algorithmic Game Theory","grant_number":"M02369"}],"year":"2018","isi":1,"day":"21","page":"21-36","date_created":"2018-12-30T22:59:14Z","date_published":"2018-11-21T00:00:00Z","doi":"10.1007/978-3-030-04612-5_2","oa":1,"quality_controlled":"1","publisher":"Springer"},{"oa_version":"Submitted Version","pmid":1,"abstract":[{"text":"A short, 14-amino-acid segment called SP1, located in the Gag structural protein1, has a critical role during the formation of the HIV-1 virus particle. During virus assembly, the SP1 peptide and seven preceding residues fold into a six-helix bundle, which holds together the Gag hexamer and facilitates the formation of a curved immature hexagonal lattice underneath the viral membrane2,3. Upon completion of assembly and budding, proteolytic cleavage of Gag leads to virus maturation, in which the immature lattice is broken down; the liberated CA domain of Gag then re-assembles into the mature conical capsid that encloses the viral genome and associated enzymes. Folding and proteolysis of the six-helix bundle are crucial rate-limiting steps of both Gag assembly and disassembly, and the six-helix bundle is an established target of HIV-1 inhibitors4,5. Here, using a combination of structural and functional analyses, we show that inositol hexakisphosphate (InsP6, also known as IP6) facilitates the formation of the six-helix bundle and assembly of the immature HIV-1 Gag lattice. IP6 makes ionic contacts with two rings of lysine residues at the centre of the Gag hexamer. Proteolytic cleavage then unmasks an alternative binding site, where IP6 interaction promotes the assembly of the mature capsid lattice. These studies identify IP6 as a naturally occurring small molecule that promotes both assembly and maturation of HIV-1.","lang":"eng"}],"intvolume":" 560","month":"08","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6242333/","open_access":"1"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1476-4687"]},"volume":560,"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41586-018-0505-4"}]},"issue":"7719","_id":"150","status":"public","article_type":"original","type":"journal_article","date_updated":"2023-09-12T07:44:37Z","department":[{"_id":"FlSc"}],"oa":1,"quality_controlled":"1","publisher":"Nature Publishing Group","publication":"Nature","day":"29","year":"2018","isi":1,"date_created":"2018-12-11T11:44:53Z","date_published":"2018-08-29T00:00:00Z","doi":"10.1038/s41586-018-0396-4","page":"509–512","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Dick, Robert, et al. “Inositol Phosphates Are Assembly Co-Factors for HIV-1.” Nature, vol. 560, no. 7719, Nature Publishing Group, 2018, pp. 509–512, doi:10.1038/s41586-018-0396-4.","ieee":"R. Dick et al., “Inositol phosphates are assembly co-factors for HIV-1,” Nature, vol. 560, no. 7719. Nature Publishing Group, pp. 509–512, 2018.","short":"R. Dick, K.K. Zadrozny, C. Xu, F.K. Schur, T.D. Lyddon, C.L. Ricana, J.M. Wagner, J.R. Perilla, P.B.K. Ganser, M.C. Johnson, O. Pornillos, V. Vogt, Nature 560 (2018) 509–512.","apa":"Dick, R., Zadrozny, K. K., Xu, C., Schur, F. K., Lyddon, T. D., Ricana, C. L., … Vogt, V. (2018). Inositol phosphates are assembly co-factors for HIV-1. Nature. Nature Publishing Group. https://doi.org/10.1038/s41586-018-0396-4","ama":"Dick R, Zadrozny KK, Xu C, et al. Inositol phosphates are assembly co-factors for HIV-1. Nature. 2018;560(7719):509–512. doi:10.1038/s41586-018-0396-4","chicago":"Dick, Robert, Kaneil K Zadrozny, Chaoyi Xu, Florian KM Schur, Terri D Lyddon, Clifton L Ricana, Jonathan M Wagner, et al. “Inositol Phosphates Are Assembly Co-Factors for HIV-1.” Nature. Nature Publishing Group, 2018. https://doi.org/10.1038/s41586-018-0396-4.","ista":"Dick R, Zadrozny KK, Xu C, Schur FK, Lyddon TD, Ricana CL, Wagner JM, Perilla JR, Ganser PBK, Johnson MC, Pornillos O, Vogt V. 2018. Inositol phosphates are assembly co-factors for HIV-1. Nature. 560(7719), 509–512."},"title":"Inositol phosphates are assembly co-factors for HIV-1","external_id":{"isi":["000442483400046"],"pmid":["30158708"]},"article_processing_charge":"No","author":[{"full_name":"Dick, Robert","last_name":"Dick","first_name":"Robert"},{"first_name":"Kaneil K","full_name":"Zadrozny, Kaneil K","last_name":"Zadrozny"},{"full_name":"Xu, Chaoyi","last_name":"Xu","first_name":"Chaoyi"},{"orcid":"0000-0003-4790-8078","full_name":"Schur, Florian","last_name":"Schur","first_name":"Florian","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Terri D","full_name":"Lyddon, Terri D","last_name":"Lyddon"},{"first_name":"Clifton L","last_name":"Ricana","full_name":"Ricana, Clifton L"},{"first_name":"Jonathan M","full_name":"Wagner, Jonathan M","last_name":"Wagner"},{"full_name":"Perilla, Juan R","last_name":"Perilla","first_name":"Juan R"},{"first_name":"Pornillos Barbie K","full_name":"Ganser, Pornillos Barbie K","last_name":"Ganser"},{"first_name":"Marc C","full_name":"Johnson, Marc C","last_name":"Johnson"},{"last_name":"Pornillos","full_name":"Pornillos, Owen","first_name":"Owen"},{"first_name":"Volker","last_name":"Vogt","full_name":"Vogt, Volker"}]},{"citation":{"chicago":"Kalinin, Nikita, and Mikhail Shkolnikov. “Introduction to Tropical Series and Wave Dynamic on Them.” Discrete and Continuous Dynamical Systems- Series A. AIMS, 2018. https://doi.org/10.3934/dcds.2018120.","ista":"Kalinin N, Shkolnikov M. 2018. Introduction to tropical series and wave dynamic on them. Discrete and Continuous Dynamical Systems- Series A. 38(6), 2827–2849.","mla":"Kalinin, Nikita, and Mikhail Shkolnikov. “Introduction to Tropical Series and Wave Dynamic on Them.” Discrete and Continuous Dynamical Systems- Series A, vol. 38, no. 6, AIMS, 2018, pp. 2827–49, doi:10.3934/dcds.2018120.","ama":"Kalinin N, Shkolnikov M. Introduction to tropical series and wave dynamic on them. Discrete and Continuous Dynamical Systems- Series A. 2018;38(6):2827-2849. doi:10.3934/dcds.2018120","apa":"Kalinin, N., & Shkolnikov, M. (2018). Introduction to tropical series and wave dynamic on them. Discrete and Continuous Dynamical Systems- Series A. AIMS. https://doi.org/10.3934/dcds.2018120","ieee":"N. Kalinin and M. Shkolnikov, “Introduction to tropical series and wave dynamic on them,” Discrete and Continuous Dynamical Systems- Series A, vol. 38, no. 6. AIMS, pp. 2827–2849, 2018.","short":"N. Kalinin, M. Shkolnikov, Discrete and Continuous Dynamical Systems- Series A 38 (2018) 2827–2849."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"arxiv":["1706.03062"],"isi":["000438818400007"]},"article_processing_charge":"No","author":[{"full_name":"Kalinin, Nikita","last_name":"Kalinin","first_name":"Nikita"},{"id":"35084A62-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","full_name":"Shkolnikov, Mikhail","orcid":"0000-0002-4310-178X","last_name":"Shkolnikov"}],"publist_id":"7576","title":"Introduction to tropical series and wave dynamic on them","year":"2018","isi":1,"publication":"Discrete and Continuous Dynamical Systems- Series A","day":"01","page":"2827 - 2849","date_created":"2018-12-11T11:45:43Z","doi":"10.3934/dcds.2018120","date_published":"2018-06-01T00:00:00Z","acknowledgement":"The first author, Nikita Kalinin, is funded by SNCF PostDoc.Mobility grant 168647. Support from the Basic Research Program of the National Research University Higher School of Economics is gratefully acknowledged. The second author, Mikhail Shkolnikov, is supported in part by the grant 159240 of the Swiss National Science Foundation as well as by the National Center of Competence in Research SwissMAP of the Swiss National Science Foundation.","oa":1,"quality_controlled":"1","publisher":"AIMS","date_updated":"2023-09-12T07:45:37Z","department":[{"_id":"TaHa"}],"_id":"303","type":"journal_article","status":"public","publication_status":"published","language":[{"iso":"eng"}],"volume":38,"issue":"6","abstract":[{"lang":"eng","text":"The theory of tropical series, that we develop here, firstly appeared in the study of the growth of pluriharmonic functions. Motivated by waves in sandpile models we introduce a dynamic on the set of tropical series, and it is experimentally observed that this dynamic obeys a power law. So, this paper serves as a compilation of results we need for other articles and also introduces several objects interesting by themselves."}],"oa_version":"Submitted Version","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1706.03062"}],"scopus_import":"1","intvolume":" 38","month":"06"},{"citation":{"ista":"Sachdeva H, Barton NH. 2018. Introgression of a block of genome under infinitesimal selection. Genetics. 209(4), 1279–1303.","chicago":"Sachdeva, Himani, and Nicholas H Barton. “Introgression of a Block of Genome under Infinitesimal Selection.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.118.301018.","apa":"Sachdeva, H., & Barton, N. H. (2018). Introgression of a block of genome under infinitesimal selection. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.118.301018","ama":"Sachdeva H, Barton NH. Introgression of a block of genome under infinitesimal selection. Genetics. 2018;209(4):1279-1303. doi:10.1534/genetics.118.301018","short":"H. Sachdeva, N.H. Barton, Genetics 209 (2018) 1279–1303.","ieee":"H. Sachdeva and N. H. Barton, “Introgression of a block of genome under infinitesimal selection,” Genetics, vol. 209, no. 4. Genetics Society of America, pp. 1279–1303, 2018.","mla":"Sachdeva, Himani, and Nicholas H. Barton. “Introgression of a Block of Genome under Infinitesimal Selection.” Genetics, vol. 209, no. 4, Genetics Society of America, 2018, pp. 1279–303, doi:10.1534/genetics.118.301018."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000440014100020"]},"article_processing_charge":"No","publist_id":"7617","author":[{"full_name":"Sachdeva, Himani","last_name":"Sachdeva","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","first_name":"Himani"},{"last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"title":"Introgression of a block of genome under infinitesimal selection","oa":1,"publisher":"Genetics Society of America","quality_controlled":"1","year":"2018","isi":1,"publication":"Genetics","day":"01","page":"1279 - 1303","date_created":"2018-12-11T11:45:36Z","date_published":"2018-08-01T00:00:00Z","doi":"10.1534/genetics.118.301018","_id":"282","type":"journal_article","status":"public","date_updated":"2023-09-13T08:22:32Z","department":[{"_id":"NiBa"}],"abstract":[{"lang":"eng","text":"Adaptive introgression is common in nature and can be driven by selection acting on multiple, linked genes. We explore the effects of polygenic selection on introgression under the infinitesimal model with linkage. This model assumes that the introgressing block has an effectively infinite number of genes, each with an infinitesimal effect on the trait under selection. The block is assumed to introgress under directional selection within a native population that is genetically homogeneous. We use individual-based simulations and a branching process approximation to compute various statistics of the introgressing block, and explore how these depend on parameters such as the map length and initial trait value associated with the introgressing block, the genetic variability along the block, and the strength of selection. Our results show that the introgression dynamics of a block under infinitesimal selection is qualitatively different from the dynamics of neutral introgression. We also find that in the long run, surviving descendant blocks are likely to have intermediate lengths, and clarify how the length is shaped by the interplay between linkage and infinitesimal selection. Our results suggest that it may be difficult to distinguish introgression of single loci from that of genomic blocks with multiple, tightly linked and weakly selected loci."}],"oa_version":"Submitted Version","main_file_link":[{"url":"https://www.biorxiv.org/content/early/2017/11/30/227082","open_access":"1"}],"scopus_import":"1","intvolume":" 209","month":"08","publication_status":"published","language":[{"iso":"eng"}],"issue":"4","volume":209},{"title":"Inverted leftover hash lemma","external_id":{"isi":["000448139300368"]},"article_processing_charge":"No","author":[{"last_name":"Obremski","full_name":"Obremski, Marciej","first_name":"Marciej"},{"id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","first_name":"Maciej","last_name":"Skorski","full_name":"Skorski, Maciej"}],"publist_id":"7946","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"apa":"Obremski, M., & Skórski, M. (2018). Inverted leftover hash lemma (Vol. 2018). Presented at the ISIT: International Symposium on Information Theory, Vail, CO, USA: IEEE. https://doi.org/10.1109/ISIT.2018.8437654","ama":"Obremski M, Skórski M. Inverted leftover hash lemma. In: Vol 2018. IEEE; 2018. doi:10.1109/ISIT.2018.8437654","ieee":"M. Obremski and M. Skórski, “Inverted leftover hash lemma,” presented at the ISIT: International Symposium on Information Theory, Vail, CO, USA, 2018, vol. 2018.","short":"M. Obremski, M. Skórski, in:, IEEE, 2018.","mla":"Obremski, Marciej, and Maciej Skórski. Inverted Leftover Hash Lemma. Vol. 2018, IEEE, 2018, doi:10.1109/ISIT.2018.8437654.","ista":"Obremski M, Skórski M. 2018. Inverted leftover hash lemma. ISIT: International Symposium on Information Theory, ISIT Proceedings, vol. 2018.","chicago":"Obremski, Marciej, and Maciej Skórski. “Inverted Leftover Hash Lemma,” Vol. 2018. IEEE, 2018. https://doi.org/10.1109/ISIT.2018.8437654."},"date_created":"2018-12-11T11:44:40Z","date_published":"2018-08-16T00:00:00Z","doi":"10.1109/ISIT.2018.8437654","day":"16","year":"2018","isi":1,"oa":1,"publisher":"IEEE","quality_controlled":"1","department":[{"_id":"KrPi"}],"date_updated":"2023-09-13T08:23:18Z","status":"public","conference":{"name":"ISIT: International Symposium on Information Theory","location":"Vail, CO, USA","end_date":"2018-06-22","start_date":"2018-06-17 "},"type":"conference","_id":"108","volume":2018,"language":[{"iso":"eng"}],"publication_status":"published","intvolume":" 2018","month":"08","main_file_link":[{"url":"https://eprint.iacr.org/2017/507","open_access":"1"}],"scopus_import":"1","alternative_title":["ISIT Proceedings"],"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Universal hashing found a lot of applications in computer science. In cryptography the most important fact about universal families is the so called Leftover Hash Lemma, proved by Impagliazzo, Levin and Luby. In the language of modern cryptography it states that almost universal families are good extractors. In this work we provide a somewhat surprising characterization in the opposite direction. Namely, every extractor with sufficiently good parameters yields a universal family on a noticeable fraction of its inputs. Our proof technique is based on tools from extremal graph theory applied to the \\'collision graph\\' induced by the extractor, and may be of independent interest. We discuss possible applications to the theory of randomness extractors and non-malleable codes."}]},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Kragl B, Qadeer S. 2018. Layered Concurrent Programs. CAV: Computer Aided Verification, LNCS, vol. 10981, 79–102.","chicago":"Kragl, Bernhard, and Shaz Qadeer. “Layered Concurrent Programs,” 10981:79–102. Springer, 2018. https://doi.org/10.1007/978-3-319-96145-3_5.","ieee":"B. Kragl and S. Qadeer, “Layered Concurrent Programs,” presented at the CAV: Computer Aided Verification, Oxford, UK, 2018, vol. 10981, pp. 79–102.","short":"B. Kragl, S. Qadeer, in:, Springer, 2018, pp. 79–102.","ama":"Kragl B, Qadeer S. Layered Concurrent Programs. In: Vol 10981. Springer; 2018:79-102. doi:10.1007/978-3-319-96145-3_5","apa":"Kragl, B., & Qadeer, S. (2018). Layered Concurrent Programs (Vol. 10981, pp. 79–102). Presented at the CAV: Computer Aided Verification, Oxford, UK: Springer. https://doi.org/10.1007/978-3-319-96145-3_5","mla":"Kragl, Bernhard, and Shaz Qadeer. Layered Concurrent Programs. Vol. 10981, Springer, 2018, pp. 79–102, doi:10.1007/978-3-319-96145-3_5."},"title":"Layered Concurrent Programs","author":[{"id":"320FC952-F248-11E8-B48F-1D18A9856A87","first_name":"Bernhard","last_name":"Kragl","orcid":"0000-0001-7745-9117","full_name":"Kragl, Bernhard"},{"full_name":"Qadeer, Shaz","last_name":"Qadeer","first_name":"Shaz"}],"publist_id":"7761","external_id":{"isi":["000491481600005"]},"article_processing_charge":"No","project":[{"name":"The Wittgenstein Prize","grant_number":"Z211","_id":"25F42A32-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"}],"day":"18","has_accepted_license":"1","isi":1,"year":"2018","doi":"10.1007/978-3-319-96145-3_5","date_published":"2018-07-18T00:00:00Z","date_created":"2018-12-11T11:44:57Z","page":"79 - 102","quality_controlled":"1","publisher":"Springer","oa":1,"ddc":["000"],"date_updated":"2023-09-13T08:45:09Z","department":[{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:45:04Z","_id":"160","status":"public","type":"conference","conference":{"start_date":"2018-07-14","location":"Oxford, UK","end_date":"2018-07-17","name":"CAV: Computer Aided Verification"},"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)"},"file":[{"file_name":"2018_LNCS_Kragl.pdf","date_created":"2018-12-17T12:52:12Z","file_size":1603844,"date_updated":"2020-07-14T12:45:04Z","creator":"dernst","checksum":"c64fff560fe5a7532ec10626ad1c215e","file_id":"5705","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":10981,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8332"}]},"oa_version":"Published Version","abstract":[{"text":"We present layered concurrent programs, a compact and expressive notation for specifying refinement proofs of concurrent programs. A layered concurrent program specifies a sequence of connected concurrent programs, from most concrete to most abstract, such that common parts of different programs are written exactly once. These programs are expressed in the ordinary syntax of imperative concurrent programs using gated atomic actions, sequencing, choice, and (recursive) procedure calls. Each concurrent program is automatically extracted from the layered program. We reduce refinement to the safety of a sequence of concurrent checker programs, one each to justify the connection between every two consecutive concurrent programs. These checker programs are also automatically extracted from the layered program. Layered concurrent programs have been implemented in the CIVL verifier which has been successfully used for the verification of several complex concurrent programs.","lang":"eng"}],"month":"07","intvolume":" 10981","alternative_title":["LNCS"],"scopus_import":"1"},{"date_published":"2018-05-28T00:00:00Z","doi":"10.1038/s41477-018-0160-7","date_created":"2018-12-11T11:45:35Z","page":"365 - 375","day":"28","publication":"Nature Plants","isi":1,"year":"2018","publisher":"Nature Publishing Group","quality_controlled":"1","acknowledgement":"We gratefully acknowledge funding from the Chinese Scholarship Council (CSC; project number 201206910025 to Z.G.), the Fonds Wetenschappelijk Onderzoek (FWO; project number G005112N to A.D.; fellowship number 12I7417N to Z.L.), the Belgian Federal Science Policy Office (BELSPO; to Y.S.), the Agency for Innovation by Science and Technology of Belgium (IWT; fellowship number 121110 to M.V.D.), the Hercules foundation (grant AUGE-09-029 to K.D.), and the ERC StG PROCELLDEATH (project number 639234 to M.K.N.).","title":"KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis","author":[{"first_name":"Zhen","full_name":"Gao, Zhen","last_name":"Gao"},{"first_name":"Anna","full_name":"Daneva, Anna","last_name":"Daneva"},{"full_name":"Salanenka, Yuliya","last_name":"Salanenka","first_name":"Yuliya","id":"46DAAE7E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Van Durme, Matthias","last_name":"Van Durme","first_name":"Matthias"},{"first_name":"Marlies","last_name":"Huysmans","full_name":"Huysmans, Marlies"},{"full_name":"Lin, Zongcheng","last_name":"Lin","first_name":"Zongcheng"},{"first_name":"Freya","last_name":"De Winter","full_name":"De Winter, Freya"},{"last_name":"Vanneste","full_name":"Vanneste, Steffen","first_name":"Steffen"},{"full_name":"Karimi, Mansour","last_name":"Karimi","first_name":"Mansour"},{"last_name":"Van De Velde","full_name":"Van De Velde, Jan","first_name":"Jan"},{"first_name":"Klaas","full_name":"Vandepoele, Klaas","last_name":"Vandepoele"},{"last_name":"Van De Walle","full_name":"Van De Walle, Davy","first_name":"Davy"},{"last_name":"Dewettinck","full_name":"Dewettinck, Koen","first_name":"Koen"},{"first_name":"Bart","last_name":"Lambrecht","full_name":"Lambrecht, Bart"},{"full_name":"Nowack, Moritz","last_name":"Nowack","first_name":"Moritz"}],"publist_id":"7619","external_id":{"isi":["000435571000017"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Gao Z, Daneva A, Salanenka Y, Van Durme M, Huysmans M, Lin Z, De Winter F, Vanneste S, Karimi M, Van De Velde J, Vandepoele K, Van De Walle D, Dewettinck K, Lambrecht B, Nowack M. 2018. KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis. Nature Plants. 4(6), 365–375.","chicago":"Gao, Zhen, Anna Daneva, Yuliya Salanenka, Matthias Van Durme, Marlies Huysmans, Zongcheng Lin, Freya De Winter, et al. “KIRA1 and ORESARA1 Terminate Flower Receptivity by Promoting Cell Death in the Stigma of Arabidopsis.” Nature Plants. Nature Publishing Group, 2018. https://doi.org/10.1038/s41477-018-0160-7.","ama":"Gao Z, Daneva A, Salanenka Y, et al. KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis. Nature Plants. 2018;4(6):365-375. doi:10.1038/s41477-018-0160-7","apa":"Gao, Z., Daneva, A., Salanenka, Y., Van Durme, M., Huysmans, M., Lin, Z., … Nowack, M. (2018). KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis. Nature Plants. Nature Publishing Group. https://doi.org/10.1038/s41477-018-0160-7","short":"Z. Gao, A. Daneva, Y. Salanenka, M. Van Durme, M. Huysmans, Z. Lin, F. De Winter, S. Vanneste, M. Karimi, J. Van De Velde, K. Vandepoele, D. Van De Walle, K. Dewettinck, B. Lambrecht, M. Nowack, Nature Plants 4 (2018) 365–375.","ieee":"Z. Gao et al., “KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis,” Nature Plants, vol. 4, no. 6. Nature Publishing Group, pp. 365–375, 2018.","mla":"Gao, Zhen, et al. “KIRA1 and ORESARA1 Terminate Flower Receptivity by Promoting Cell Death in the Stigma of Arabidopsis.” Nature Plants, vol. 4, no. 6, Nature Publishing Group, 2018, pp. 365–75, doi:10.1038/s41477-018-0160-7."},"issue":"6","volume":4,"language":[{"iso":"eng"}],"publication_status":"published","month":"05","intvolume":" 4","scopus_import":"1","oa_version":"None","abstract":[{"lang":"eng","text":"Flowers have a species-specific functional life span that determines the time window in which pollination, fertilization and seed set can occur. The stigma tissue plays a key role in flower receptivity by intercepting pollen and initiating pollen tube growth toward the ovary. In this article, we show that a developmentally controlled cell death programme terminates the functional life span of stigma cells in Arabidopsis. We identified the leaf senescence regulator ORESARA1 (also known as ANAC092) and the previously uncharacterized KIRA1 (also known as ANAC074) as partially redundant transcription factors that modulate stigma longevity by controlling the expression of programmed cell death-associated genes. KIRA1 expression is sufficient to induce cell death and terminate floral receptivity, whereas lack of both KIRA1 and ORESARA1 substantially increases stigma life span. Surprisingly, the extension of stigma longevity is accompanied by only a moderate extension of flower receptivity, suggesting that additional processes participate in the control of the flower's receptive life span."}],"department":[{"_id":"JiFr"}],"date_updated":"2023-09-13T08:24:17Z","status":"public","type":"journal_article","_id":"280"},{"department":[{"_id":"CaGu"}],"date_updated":"2023-09-13T08:24:51Z","status":"public","type":"journal_article","_id":"503","volume":268,"language":[{"iso":"eng"}],"publication_status":"published","intvolume":" 268","month":"02","scopus_import":"1","oa_version":"None","abstract":[{"lang":"eng","text":"Buffers are essential for diluting bacterial cultures for flow cytometry analysis in order to study bacterial physiology and gene expression parameters based on fluorescence signals. Using a variety of constitutively expressed fluorescent proteins in Escherichia coli K-12 strain MG1655, we found strong artifactual changes in fluorescence levels after dilution into the commonly used flow cytometry buffer phosphate-buffered saline (PBS) and two other buffer solutions, Tris-HCl and M9 salts. These changes appeared very rapidly after dilution, and were linked to increased membrane permeability and loss in cell viability. We observed buffer-related effects in several different E. coli strains, K-12, C and W, but not E. coli B, which can be partially explained by differences in lipopolysaccharide (LPS) and outer membrane composition. Supplementing the buffers with divalent cations responsible for outer membrane stability, Mg2+ and Ca2+, preserved fluorescence signals, membrane integrity and viability of E. coli. Thus, stabilizing the bacterial outer membrane is essential for precise and unbiased measurements of fluorescence parameters using flow cytometry."}],"acknowledged_ssus":[{"_id":"Bio"}],"title":"Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains","external_id":{"isi":["000425715100006"]},"article_processing_charge":"No","publist_id":"7317","author":[{"id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","first_name":"Kathrin","orcid":"0000-0003-3768-877X","full_name":"Tomasek, Kathrin","last_name":"Tomasek"},{"orcid":"0000-0001-5396-4346","full_name":"Bergmiller, Tobias","last_name":"Bergmiller","first_name":"Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Guet","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ieee":"K. Tomasek, T. Bergmiller, and C. C. Guet, “Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains,” Journal of Biotechnology, vol. 268. Elsevier, pp. 40–52, 2018.","short":"K. Tomasek, T. Bergmiller, C.C. Guet, Journal of Biotechnology 268 (2018) 40–52.","apa":"Tomasek, K., Bergmiller, T., & Guet, C. C. (2018). Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains. Journal of Biotechnology. Elsevier. https://doi.org/10.1016/j.jbiotec.2018.01.008","ama":"Tomasek K, Bergmiller T, Guet CC. Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains. Journal of Biotechnology. 2018;268:40-52. doi:10.1016/j.jbiotec.2018.01.008","mla":"Tomasek, Kathrin, et al. “Lack of Cations in Flow Cytometry Buffers Affect Fluorescence Signals by Reducing Membrane Stability and Viability of Escherichia Coli Strains.” Journal of Biotechnology, vol. 268, Elsevier, 2018, pp. 40–52, doi:10.1016/j.jbiotec.2018.01.008.","ista":"Tomasek K, Bergmiller T, Guet CC. 2018. Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains. Journal of Biotechnology. 268, 40–52.","chicago":"Tomasek, Kathrin, Tobias Bergmiller, and Calin C Guet. “Lack of Cations in Flow Cytometry Buffers Affect Fluorescence Signals by Reducing Membrane Stability and Viability of Escherichia Coli Strains.” Journal of Biotechnology. Elsevier, 2018. https://doi.org/10.1016/j.jbiotec.2018.01.008."},"date_created":"2018-12-11T11:46:50Z","doi":"10.1016/j.jbiotec.2018.01.008","date_published":"2018-02-20T00:00:00Z","page":"40 - 52","publication":"Journal of Biotechnology","day":"20","year":"2018","isi":1,"publisher":"Elsevier","quality_controlled":"1","acknowledgement":"We thank R Chait and M Lagator for sharing Bacillus subtilis CR_Y1 and pZS*_2R-cIPtet-Venus-Prm, respectively. We are grateful to T Pilizota and all members of the Guet lab for critically reading the manuscript. We also thank the Bioimaging facility at IST Austria for assistance using the FACSAria III system.\r\n\r\n"},{"ddc":["570"],"date_updated":"2023-09-13T08:45:41Z","department":[{"_id":"CaGu"}],"file_date_updated":"2020-07-14T12:48:10Z","_id":"82","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)"},"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"527076f78265cd4ea192cd1569851587","file_id":"5706","file_size":4007095,"date_updated":"2020-07-14T12:48:10Z","creator":"dernst","file_name":"2018_Plos_Chaudhry.pdf","date_created":"2018-12-17T12:55:31Z"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":16,"related_material":{"record":[{"id":"9810","status":"public","relation":"research_data"}]},"issue":"8","oa_version":"Published Version","abstract":[{"text":"In experimental cultures, when bacteria are mixed with lytic (virulent) bacteriophage, bacterial cells resistant to the phage commonly emerge and become the dominant population of bacteria. Following the ascent of resistant mutants, the densities of bacteria in these simple communities become limited by resources rather than the phage. Despite the evolution of resistant hosts, upon which the phage cannot replicate, the lytic phage population is most commonly maintained in an apparently stable state with the resistant bacteria. Several mechanisms have been put forward to account for this result. Here we report the results of population dynamic/evolution experiments with a virulent mutant of phage Lambda, λVIR, and Escherichia coli in serial transfer cultures. We show that, following the ascent of λVIR-resistant bacteria, λVIRis maintained in the majority of cases in maltose-limited minimal media and in all cases in nutrient-rich broth. Using mathematical models and experiments, we show that the dominant mechanism responsible for maintenance of λVIRin these resource-limited populations dominated by resistant E. coli is a high rate of either phenotypic or genetic transition from resistance to susceptibility—a hitherto undemonstrated mechanism we term "leaky resistance." We discuss the implications of leaky resistance to our understanding of the conditions for the maintenance of phage in populations of bacteria—their “existence conditions.”.","lang":"eng"}],"month":"08","intvolume":" 16","scopus_import":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Chaudhry, Waqas, Maros Pleska, Nilang Shah, Howard Weiss, Ingrid Mccall, Justin Meyer, Animesh Gupta, Calin C Guet, and Bruce Levin. “Leaky Resistance and the Conditions for the Existence of Lytic Bacteriophage.” PLoS Biology. Public Library of Science, 2018. https://doi.org/10.1371/journal.pbio.2005971.","ista":"Chaudhry W, Pleska M, Shah N, Weiss H, Mccall I, Meyer J, Gupta A, Guet CC, Levin B. 2018. Leaky resistance and the conditions for the existence of lytic bacteriophage. PLoS Biology. 16(8), 2005971.","mla":"Chaudhry, Waqas, et al. “Leaky Resistance and the Conditions for the Existence of Lytic Bacteriophage.” PLoS Biology, vol. 16, no. 8, 2005971, Public Library of Science, 2018, doi:10.1371/journal.pbio.2005971.","ieee":"W. Chaudhry et al., “Leaky resistance and the conditions for the existence of lytic bacteriophage,” PLoS Biology, vol. 16, no. 8. Public Library of Science, 2018.","short":"W. Chaudhry, M. Pleska, N. Shah, H. Weiss, I. Mccall, J. Meyer, A. Gupta, C.C. Guet, B. Levin, PLoS Biology 16 (2018).","ama":"Chaudhry W, Pleska M, Shah N, et al. Leaky resistance and the conditions for the existence of lytic bacteriophage. PLoS Biology. 2018;16(8). doi:10.1371/journal.pbio.2005971","apa":"Chaudhry, W., Pleska, M., Shah, N., Weiss, H., Mccall, I., Meyer, J., … Levin, B. (2018). Leaky resistance and the conditions for the existence of lytic bacteriophage. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2005971"},"title":"Leaky resistance and the conditions for the existence of lytic bacteriophage","author":[{"full_name":"Chaudhry, Waqas","last_name":"Chaudhry","first_name":"Waqas"},{"id":"4569785E-F248-11E8-B48F-1D18A9856A87","first_name":"Maros","last_name":"Pleska","full_name":"Pleska, Maros","orcid":"0000-0001-7460-7479"},{"first_name":"Nilang","last_name":"Shah","full_name":"Shah, Nilang"},{"first_name":"Howard","full_name":"Weiss, Howard","last_name":"Weiss"},{"full_name":"Mccall, Ingrid","last_name":"Mccall","first_name":"Ingrid"},{"full_name":"Meyer, Justin","last_name":"Meyer","first_name":"Justin"},{"first_name":"Animesh","full_name":"Gupta, Animesh","last_name":"Gupta"},{"first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","last_name":"Guet"},{"first_name":"Bruce","last_name":"Levin","full_name":"Levin, Bruce"}],"publist_id":"7972","external_id":{"isi":["000443383300024"]},"article_processing_charge":"Yes","article_number":"2005971","day":"16","publication":"PLoS Biology","has_accepted_license":"1","isi":1,"year":"2018","date_published":"2018-08-16T00:00:00Z","doi":"10.1371/journal.pbio.2005971","date_created":"2018-12-11T11:44:32Z","publisher":"Public Library of Science","quality_controlled":"1","oa":1},{"publication":"ACM Trans. Graph.","day":"04","year":"2018","has_accepted_license":"1","isi":1,"date_created":"2018-12-11T11:44:06Z","date_published":"2018-08-04T00:00:00Z","doi":"10.1145/3197517.3201325","oa":1,"publisher":"ACM","quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Umetani, Nobuyuki, and Bernd Bickel. “Learning Three-Dimensional Flow for Interactive Aerodynamic Design.” ACM Trans. Graph. ACM, 2018. https://doi.org/10.1145/3197517.3201325.","ista":"Umetani N, Bickel B. 2018. Learning three-dimensional flow for interactive aerodynamic design. ACM Trans. Graph. 37(4), 89.","mla":"Umetani, Nobuyuki, and Bernd Bickel. “Learning Three-Dimensional Flow for Interactive Aerodynamic Design.” ACM Trans. Graph., vol. 37, no. 4, 89, ACM, 2018, doi:10.1145/3197517.3201325.","ieee":"N. Umetani and B. Bickel, “Learning three-dimensional flow for interactive aerodynamic design,” ACM Trans. Graph., vol. 37, no. 4. ACM, 2018.","short":"N. Umetani, B. Bickel, ACM Trans. Graph. 37 (2018).","ama":"Umetani N, Bickel B. Learning three-dimensional flow for interactive aerodynamic design. ACM Trans Graph. 2018;37(4). doi:10.1145/3197517.3201325","apa":"Umetani, N., & Bickel, B. (2018). Learning three-dimensional flow for interactive aerodynamic design. ACM Trans. Graph. ACM. https://doi.org/10.1145/3197517.3201325"},"title":"Learning three-dimensional flow for interactive aerodynamic design","article_processing_charge":"No","external_id":{"isi":["000448185000050"]},"author":[{"full_name":"Umetani, Nobuyuki","last_name":"Umetani","first_name":"Nobuyuki"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","last_name":"Bickel"}],"publist_id":"8053","article_number":"89","project":[{"call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling"}],"language":[{"iso":"eng"}],"file":[{"creator":"system","file_size":22803163,"date_updated":"2020-07-14T12:46:22Z","file_name":"IST-2018-1049-v1+1_2018_sigg_Learning3DAerodynamics.pdf","date_created":"2018-12-12T10:16:28Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"7a2243668f215821bc6aecad0320079a","file_id":"5216"}],"publication_status":"published","ec_funded":1,"volume":37,"related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/new-interactive-machine-learning-tool-makes-car-designs-more-aerodynamic/","description":"News on IST Homepage"}]},"issue":"4","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"We present a data-driven technique to instantly predict how fluid flows around various three-dimensional objects. Such simulation is useful for computational fabrication and engineering, but is usually computationally expensive since it requires solving the Navier-Stokes equation for many time steps. To accelerate the process, we propose a machine learning framework which predicts aerodynamic forces and velocity and pressure fields given a threedimensional shape input. Handling detailed free-form three-dimensional shapes in a data-driven framework is challenging because machine learning approaches usually require a consistent parametrization of input and output. We present a novel PolyCube maps-based parametrization that can be computed for three-dimensional shapes at interactive rates. This allows us to efficiently learn the nonlinear response of the flow using a Gaussian process regression. We demonstrate the effectiveness of our approach for the interactive design and optimization of a car body."}],"intvolume":" 37","month":"08","scopus_import":"1","ddc":["003","004"],"date_updated":"2023-09-13T08:46:15Z","file_date_updated":"2020-07-14T12:46:22Z","department":[{"_id":"BeBi"}],"_id":"4","pubrep_id":"1049","status":"public","type":"journal_article"},{"status":"public","conference":{"start_date":"2018-04-11","end_date":"2018-04-13","location":"Porto, Portugal","name":"HSCC: Hybrid Systems: Computation and Control"},"type":"conference","_id":"183","department":[{"_id":"ToHe"}],"date_updated":"2023-09-13T08:48:46Z","month":"04","alternative_title":["HSCC Proceedings"],"scopus_import":"1","oa_version":"None","abstract":[{"lang":"eng","text":"Fault-localization is considered to be a very tedious and time-consuming activity in the design of complex Cyber-Physical Systems (CPS). This laborious task essentially requires expert knowledge of the system in order to discover the cause of the fault. In this context, we propose a new procedure that AIDS designers in debugging Simulink/Stateflow hybrid system models, guided by Signal Temporal Logic (STL) specifications. The proposed method relies on three main ingredients: (1) a monitoring and a trace diagnostics procedure that checks whether a tested behavior satisfies or violates an STL specification, localizes time segments and interfaces variables contributing to the property violations; (2) a slicing procedure that maps these observable behavior segments to the internal states and transitions of the Simulink model; and (3) a spectrum-based fault-localization method that combines the previous analysis from multiple tests to identify the internal states and/or transitions that are the most likely to explain the fault. We demonstrate the applicability of our approach on two Simulink models from the automotive and the avionics domain."}],"language":[{"iso":"eng"}],"publication_status":"published","project":[{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"title":"Localizing faults in simulink/stateflow models with STL","article_processing_charge":"No","external_id":{"isi":["000474781600022"]},"author":[{"last_name":"Bartocci","full_name":"Bartocci, Ezio","first_name":"Ezio"},{"last_name":"Ferrere","orcid":"0000-0001-5199-3143","full_name":"Ferrere, Thomas","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas"},{"last_name":"Manjunath","full_name":"Manjunath, Niveditha","first_name":"Niveditha"},{"last_name":"Nickovic","full_name":"Nickovic, Dejan","first_name":"Dejan"}],"publist_id":"7738","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Bartocci, Ezio, Thomas Ferrere, Niveditha Manjunath, and Dejan Nickovic. “Localizing Faults in Simulink/Stateflow Models with STL,” 197–206. Association for Computing Machinery, Inc, 2018. https://doi.org/10.1145/3178126.3178131.","ista":"Bartocci E, Ferrere T, Manjunath N, Nickovic D. 2018. Localizing faults in simulink/stateflow models with STL. HSCC: Hybrid Systems: Computation and Control, HSCC Proceedings, , 197–206.","mla":"Bartocci, Ezio, et al. Localizing Faults in Simulink/Stateflow Models with STL. Association for Computing Machinery, Inc, 2018, pp. 197–206, doi:10.1145/3178126.3178131.","apa":"Bartocci, E., Ferrere, T., Manjunath, N., & Nickovic, D. (2018). Localizing faults in simulink/stateflow models with STL (pp. 197–206). Presented at the HSCC: Hybrid Systems: Computation and Control, Porto, Portugal: Association for Computing Machinery, Inc. https://doi.org/10.1145/3178126.3178131","ama":"Bartocci E, Ferrere T, Manjunath N, Nickovic D. Localizing faults in simulink/stateflow models with STL. In: Association for Computing Machinery, Inc; 2018:197-206. doi:10.1145/3178126.3178131","short":"E. Bartocci, T. Ferrere, N. Manjunath, D. Nickovic, in:, Association for Computing Machinery, Inc, 2018, pp. 197–206.","ieee":"E. Bartocci, T. Ferrere, N. Manjunath, and D. Nickovic, “Localizing faults in simulink/stateflow models with STL,” presented at the HSCC: Hybrid Systems: Computation and Control, Porto, Portugal, 2018, pp. 197–206."},"publisher":"Association for Computing Machinery, Inc","quality_controlled":"1","acknowledgement":"This work was partially supported by the Austrian Science Fund (FWF) under grants S11402-N23 and S11405-N23 (RiSE/SHiNE), the CPS/IoT project (HRSM), the EU ICT COST Action IC1402 on Run-time Verification beyond Monitoring (ARVI), the AMASS project (ECSEL 692474), and the ENABLE-S3 project (ECSEL 692455). The CPS/IoT project receives support from the Austrian government through the Federal Ministry of Science, Research and Economy (BMWFW) in the funding program Hochschulraum-Strukturmittel (HRSM) 2016. The ECSEL Joint Undertaking receives support from the European Union’s Horizon 2020 research and innovation programme and Austria, Denmark, Germany, Finland, Czech Republic, Italy, Spain, Portugal, Poland, Ireland, Belgium, France, Netherlands, United Kingdom, Slovakia, Norway.","date_created":"2018-12-11T11:45:04Z","date_published":"2018-04-11T00:00:00Z","doi":"10.1145/3178126.3178131","page":"197 - 206","day":"11","year":"2018","isi":1},{"project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"338804","name":"Random matrices, universality and disordered quantum systems"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Alt J, Erdös L, Krüger TH. 2018. Local inhomogeneous circular law. Annals Applied Probability . 28(1), 148–203.","chicago":"Alt, Johannes, László Erdös, and Torben H Krüger. “Local Inhomogeneous Circular Law.” Annals Applied Probability . Institute of Mathematical Statistics, 2018. https://doi.org/10.1214/17-AAP1302.","short":"J. Alt, L. Erdös, T.H. Krüger, Annals Applied Probability 28 (2018) 148–203.","ieee":"J. Alt, L. Erdös, and T. H. Krüger, “Local inhomogeneous circular law,” Annals Applied Probability , vol. 28, no. 1. Institute of Mathematical Statistics, pp. 148–203, 2018.","apa":"Alt, J., Erdös, L., & Krüger, T. H. (2018). Local inhomogeneous circular law. Annals Applied Probability . Institute of Mathematical Statistics. https://doi.org/10.1214/17-AAP1302","ama":"Alt J, Erdös L, Krüger TH. Local inhomogeneous circular law. Annals Applied Probability . 2018;28(1):148-203. doi:10.1214/17-AAP1302","mla":"Alt, Johannes, et al. “Local Inhomogeneous Circular Law.” Annals Applied Probability , vol. 28, no. 1, Institute of Mathematical Statistics, 2018, pp. 148–203, doi:10.1214/17-AAP1302."},"title":"Local inhomogeneous circular law","external_id":{"arxiv":["1612.07776 "],"isi":["000431721800005"]},"article_processing_charge":"No","author":[{"id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes","last_name":"Alt","full_name":"Alt, Johannes"},{"last_name":"Erdös","orcid":"0000-0001-5366-9603","full_name":"Erdös, László","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Krüger, Torben H","orcid":"0000-0002-4821-3297","last_name":"Krüger","first_name":"Torben H","id":"3020C786-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"quality_controlled":"1","publisher":"Institute of Mathematical Statistics","publication":"Annals Applied Probability ","day":"03","year":"2018","isi":1,"date_created":"2018-12-11T11:47:13Z","date_published":"2018-03-03T00:00:00Z","doi":"10.1214/17-AAP1302","page":"148-203","_id":"566","status":"public","article_type":"original","type":"journal_article","date_updated":"2023-09-13T08:47:52Z","department":[{"_id":"LaEr"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We consider large random matrices X with centered, independent entries which have comparable but not necessarily identical variances. Girko's circular law asserts that the spectrum is supported in a disk and in case of identical variances, the limiting density is uniform. In this special case, the local circular law by Bourgade et. al. [11,12] shows that the empirical density converges even locally on scales slightly above the typical eigenvalue spacing. In the general case, the limiting density is typically inhomogeneous and it is obtained via solving a system of deterministic equations. Our main result is the local inhomogeneous circular law in the bulk spectrum on the optimal scale for a general variance profile of the entries of X. \r\n\r\n"}],"intvolume":" 28","month":"03","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1612.07776 "}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"related_material":{"record":[{"id":"149","status":"public","relation":"dissertation_contains"}]},"volume":28,"issue":"1"},{"status":"public","type":"journal_article","_id":"106","department":[{"_id":"HeEd"}],"date_updated":"2023-09-13T08:49:16Z","intvolume":" 40","month":"09","main_file_link":[{"url":"https://arxiv.org/abs/1702.05172","open_access":"1"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"text":"The goal of this article is to introduce the reader to the theory of intrinsic geometry of convex surfaces. We illustrate the power of the tools by proving a theorem on convex surfaces containing an arbitrarily long closed simple geodesic. Let us remind ourselves that a curve in a surface is called geodesic if every sufficiently short arc of the curve is length minimizing; if, in addition, it has no self-intersections, we call it simple geodesic. A tetrahedron with equal opposite edges is called isosceles. The axiomatic method of Alexandrov geometry allows us to work with the metrics of convex surfaces directly, without approximating it first by a smooth or polyhedral metric. Such approximations destroy the closed geodesics on the surface; therefore it is difficult (if at all possible) to apply approximations in the proof of our theorem. On the other hand, a proof in the smooth or polyhedral case usually admits a translation into Alexandrov’s language; such translation makes the result more general. In fact, our proof resembles a translation of the proof given by Protasov. Note that the main theorem implies in particular that a smooth convex surface does not have arbitrarily long simple closed geodesics. However we do not know a proof of this corollary that is essentially simpler than the one presented below.","lang":"eng"}],"volume":40,"issue":"3","language":[{"iso":"eng"}],"publication_status":"published","title":"Long geodesics on convex surfaces","external_id":{"arxiv":["1702.05172"],"isi":["000444141200005"]},"article_processing_charge":"No","author":[{"last_name":"Akopyan","orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","first_name":"Arseniy"},{"last_name":"Petrunin","full_name":"Petrunin, Anton","first_name":"Anton"}],"publist_id":"7948","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Akopyan A, Petrunin A. 2018. Long geodesics on convex surfaces. Mathematical Intelligencer. 40(3), 26–31.","chicago":"Akopyan, Arseniy, and Anton Petrunin. “Long Geodesics on Convex Surfaces.” Mathematical Intelligencer. Springer, 2018. https://doi.org/10.1007/s00283-018-9795-5.","ama":"Akopyan A, Petrunin A. Long geodesics on convex surfaces. Mathematical Intelligencer. 2018;40(3):26-31. doi:10.1007/s00283-018-9795-5","apa":"Akopyan, A., & Petrunin, A. (2018). Long geodesics on convex surfaces. Mathematical Intelligencer. Springer. https://doi.org/10.1007/s00283-018-9795-5","ieee":"A. Akopyan and A. Petrunin, “Long geodesics on convex surfaces,” Mathematical Intelligencer, vol. 40, no. 3. Springer, pp. 26–31, 2018.","short":"A. Akopyan, A. Petrunin, Mathematical Intelligencer 40 (2018) 26–31.","mla":"Akopyan, Arseniy, and Anton Petrunin. “Long Geodesics on Convex Surfaces.” Mathematical Intelligencer, vol. 40, no. 3, Springer, 2018, pp. 26–31, doi:10.1007/s00283-018-9795-5."},"oa":1,"quality_controlled":"1","publisher":"Springer","date_created":"2018-12-11T11:44:40Z","doi":"10.1007/s00283-018-9795-5","date_published":"2018-09-01T00:00:00Z","page":"26 - 31","publication":"Mathematical Intelligencer","day":"01","year":"2018","isi":1},{"status":"public","type":"research_data_reference","_id":"9810","department":[{"_id":"CaGu"}],"title":"Numerical data used in figures","author":[{"last_name":"Chaudhry","full_name":"Chaudhry, Waqas","first_name":"Waqas"},{"id":"4569785E-F248-11E8-B48F-1D18A9856A87","first_name":"Maros","last_name":"Pleska","orcid":"0000-0001-7460-7479","full_name":"Pleska, Maros"},{"last_name":"Shah","full_name":"Shah, Nilang","first_name":"Nilang"},{"last_name":"Weiss","full_name":"Weiss, Howard","first_name":"Howard"},{"first_name":"Ingrid","full_name":"Mccall, Ingrid","last_name":"Mccall"},{"last_name":"Meyer","full_name":"Meyer, Justin","first_name":"Justin"},{"full_name":"Gupta, Animesh","last_name":"Gupta","first_name":"Animesh"},{"first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052"},{"first_name":"Bruce","last_name":"Levin","full_name":"Levin, Bruce"}],"article_processing_charge":"No","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"mla":"Chaudhry, Waqas, et al. Numerical Data Used in Figures. Public Library of Science, 2018, doi:10.1371/journal.pbio.2005971.s008.","apa":"Chaudhry, W., Pleska, M., Shah, N., Weiss, H., Mccall, I., Meyer, J., … Levin, B. (2018). Numerical data used in figures. Public Library of Science. https://doi.org/10.1371/journal.pbio.2005971.s008","ama":"Chaudhry W, Pleska M, Shah N, et al. Numerical data used in figures. 2018. doi:10.1371/journal.pbio.2005971.s008","short":"W. Chaudhry, M. Pleska, N. Shah, H. Weiss, I. Mccall, J. Meyer, A. Gupta, C.C. Guet, B. Levin, (2018).","ieee":"W. Chaudhry et al., “Numerical data used in figures.” Public Library of Science, 2018.","chicago":"Chaudhry, Waqas, Maros Pleska, Nilang Shah, Howard Weiss, Ingrid Mccall, Justin Meyer, Animesh Gupta, Calin C Guet, and Bruce Levin. “Numerical Data Used in Figures.” Public Library of Science, 2018. https://doi.org/10.1371/journal.pbio.2005971.s008.","ista":"Chaudhry W, Pleska M, Shah N, Weiss H, Mccall I, Meyer J, Gupta A, Guet CC, Levin B. 2018. Numerical data used in figures, Public Library of Science, 10.1371/journal.pbio.2005971.s008."},"date_updated":"2023-09-13T08:45:41Z","month":"08","publisher":"Public Library of Science","oa_version":"Published Version","related_material":{"record":[{"status":"public","id":"82","relation":"used_in_publication"}]},"doi":"10.1371/journal.pbio.2005971.s008","date_published":"2018-08-16T00:00:00Z","date_created":"2021-08-06T12:43:44Z","day":"16","year":"2018"},{"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":"275","file_date_updated":"2020-07-14T12:45:45Z","department":[{"_id":"MiSi"},{"_id":"Bio"}],"ddc":["570"],"date_updated":"2023-09-13T08:51:29Z","intvolume":" 217","month":"04","scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"text":"Lymphatic endothelial cells (LECs) release extracellular chemokines to guide the migration of dendritic cells. In this study, we report that LECs also release basolateral exosome-rich endothelial vesicles (EEVs) that are secreted in greater numbers in the presence of inflammatory cytokines and accumulate in the perivascular stroma of small lymphatic vessels in human chronic inflammatory diseases. Proteomic analyses of EEV fractions identified > 1,700 cargo proteins and revealed a dominant motility-promoting protein signature. In vitro and ex vivo EEV fractions augmented cellular protrusion formation in a CX3CL1/fractalkine-dependent fashion and enhanced the directional migratory response of human dendritic cells along guidance cues. We conclude that perilymphatic LEC exosomes enhance exploratory behavior and thus promote directional migration of CX3CR1-expressing cells in complex tissue environments.","lang":"eng"}],"ec_funded":1,"volume":217,"issue":"6","language":[{"iso":"eng"}],"file":[{"file_name":"2018_JournalCellBiology_Brown.pdf","date_created":"2018-12-17T12:50:07Z","file_size":2252043,"date_updated":"2020-07-14T12:45:45Z","creator":"dernst","checksum":"9c7eba51a35c62da8c13f98120b64df4","file_id":"5704","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"publication_status":"published","project":[{"_id":"25A8E5EA-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Y 564-B12","name":"Cytoskeletal force generation and transduction of leukocytes (FWF)"},{"_id":"25A603A2-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"281556","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)"}],"title":"Lymphatic exosomes promote dendritic cell migration along guidance cues","external_id":{"isi":["000438077800026"],"pmid":["29650776"]},"article_processing_charge":"No","author":[{"last_name":"Brown","full_name":"Brown, Markus","id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87","first_name":"Markus"},{"last_name":"Johnson","full_name":"Johnson, Louise","first_name":"Louise"},{"last_name":"Leone","full_name":"Leone, Dario","first_name":"Dario"},{"first_name":"Peter","last_name":"Májek","full_name":"Májek, Peter"},{"first_name":"Kari","id":"368EE576-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7829-3518","full_name":"Vaahtomeri, Kari","last_name":"Vaahtomeri"},{"last_name":"Senfter","full_name":"Senfter, Daniel","first_name":"Daniel"},{"first_name":"Nora","last_name":"Bukosza","full_name":"Bukosza, Nora"},{"last_name":"Schachner","full_name":"Schachner, Helga","first_name":"Helga"},{"first_name":"Gabriele","full_name":"Asfour, Gabriele","last_name":"Asfour"},{"first_name":"Brigitte","last_name":"Langer","full_name":"Langer, Brigitte"},{"first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert"},{"full_name":"Parapatics, Katja","last_name":"Parapatics","first_name":"Katja"},{"last_name":"Hong","full_name":"Hong, Young","first_name":"Young"},{"last_name":"Bennett","full_name":"Bennett, Keiryn","first_name":"Keiryn"},{"last_name":"Kain","full_name":"Kain, Renate","first_name":"Renate"},{"full_name":"Detmar, Michael","last_name":"Detmar","first_name":"Michael"},{"last_name":"Sixt","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K"},{"full_name":"Jackson, David","last_name":"Jackson","first_name":"David"},{"full_name":"Kerjaschki, Dontscho","last_name":"Kerjaschki","first_name":"Dontscho"}],"publist_id":"7627","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Brown M, Johnson L, Leone D, Májek P, Vaahtomeri K, Senfter D, Bukosza N, Schachner H, Asfour G, Langer B, Hauschild R, Parapatics K, Hong Y, Bennett K, Kain R, Detmar M, Sixt MK, Jackson D, Kerjaschki D. 2018. Lymphatic exosomes promote dendritic cell migration along guidance cues. Journal of Cell Biology. 217(6), 2205–2221.","chicago":"Brown, Markus, Louise Johnson, Dario Leone, Peter Májek, Kari Vaahtomeri, Daniel Senfter, Nora Bukosza, et al. “Lymphatic Exosomes Promote Dendritic Cell Migration along Guidance Cues.” Journal of Cell Biology. Rockefeller University Press, 2018. https://doi.org/10.1083/jcb.201612051.","ama":"Brown M, Johnson L, Leone D, et al. Lymphatic exosomes promote dendritic cell migration along guidance cues. Journal of Cell Biology. 2018;217(6):2205-2221. doi:10.1083/jcb.201612051","apa":"Brown, M., Johnson, L., Leone, D., Májek, P., Vaahtomeri, K., Senfter, D., … Kerjaschki, D. (2018). Lymphatic exosomes promote dendritic cell migration along guidance cues. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.201612051","ieee":"M. Brown et al., “Lymphatic exosomes promote dendritic cell migration along guidance cues,” Journal of Cell Biology, vol. 217, no. 6. Rockefeller University Press, pp. 2205–2221, 2018.","short":"M. Brown, L. Johnson, D. Leone, P. Májek, K. Vaahtomeri, D. Senfter, N. Bukosza, H. Schachner, G. Asfour, B. Langer, R. Hauschild, K. Parapatics, Y. Hong, K. Bennett, R. Kain, M. Detmar, M.K. Sixt, D. Jackson, D. Kerjaschki, Journal of Cell Biology 217 (2018) 2205–2221.","mla":"Brown, Markus, et al. “Lymphatic Exosomes Promote Dendritic Cell Migration along Guidance Cues.” Journal of Cell Biology, vol. 217, no. 6, Rockefeller University Press, 2018, pp. 2205–21, doi:10.1083/jcb.201612051."},"oa":1,"quality_controlled":"1","publisher":"Rockefeller University Press","acknowledgement":"M. Brown was supported by the Cell Communication in Health and Disease Graduate Study Program of the Austrian Science Fund and Medizinische Universität Wien, M. Sixt by the European Research Council (ERC GA 281556) and an Austrian Science Fund START award, K.L. Bennett by the Austrian Academy of Sciences, D.G. Jackson and L.A. Johnson by Unit Funding (MC_UU_12010/2) and project grants from the Medical Research Council (G1100134 and MR/L008610/1), and M. Detmar by the Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung and Advanced European Research Council grant LYVICAM. K. Vaahtomeri was supported by an Academy of Finland postdoctoral research grant (287853). This project has received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement No. 668036 (RELENT).","date_created":"2018-12-11T11:45:33Z","date_published":"2018-04-12T00:00:00Z","doi":"10.1083/jcb.201612051","page":"2205 - 2221","publication":"Journal of Cell Biology","day":"12","year":"2018","has_accepted_license":"1","isi":1},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Robert H, Park C, Gutièrrez C, Wójcikowska B, Pěnčík A, Novák O, Chen J, Grunewald W, Dresselhaus T, Friml J, Laux T. 2018. Maternal auxin supply contributes to early embryo patterning in Arabidopsis. Nature Plants. 4(8), 548–553.","chicago":"Robert, Hélène, Chulmin Park, Carla Gutièrrez, Barbara Wójcikowska, Aleš Pěnčík, Ondřej Novák, Junyi Chen, et al. “Maternal Auxin Supply Contributes to Early Embryo Patterning in Arabidopsis.” Nature Plants. Nature Publishing Group, 2018. https://doi.org/10.1038/s41477-018-0204-z.","ieee":"H. Robert et al., “Maternal auxin supply contributes to early embryo patterning in Arabidopsis,” Nature Plants, vol. 4, no. 8. Nature Publishing Group, pp. 548–553, 2018.","short":"H. Robert, C. Park, C. Gutièrrez, B. Wójcikowska, A. Pěnčík, O. Novák, J. Chen, W. Grunewald, T. Dresselhaus, J. Friml, T. Laux, Nature Plants 4 (2018) 548–553.","apa":"Robert, H., Park, C., Gutièrrez, C., Wójcikowska, B., Pěnčík, A., Novák, O., … Laux, T. (2018). Maternal auxin supply contributes to early embryo patterning in Arabidopsis. Nature Plants. Nature Publishing Group. https://doi.org/10.1038/s41477-018-0204-z","ama":"Robert H, Park C, Gutièrrez C, et al. Maternal auxin supply contributes to early embryo patterning in Arabidopsis. Nature Plants. 2018;4(8):548-553. doi:10.1038/s41477-018-0204-z","mla":"Robert, Hélène, et al. “Maternal Auxin Supply Contributes to Early Embryo Patterning in Arabidopsis.” Nature Plants, vol. 4, no. 8, Nature Publishing Group, 2018, pp. 548–53, doi:10.1038/s41477-018-0204-z."},"title":"Maternal auxin supply contributes to early embryo patterning in Arabidopsis","article_processing_charge":"No","external_id":{"pmid":["30013211"],"isi":["000443861300011"]},"publist_id":"7763","author":[{"first_name":"Hélène","full_name":"Robert, Hélène","last_name":"Robert"},{"first_name":"Chulmin","last_name":"Park","full_name":"Park, Chulmin"},{"full_name":"Gutièrrez, Carla","last_name":"Gutièrrez","first_name":"Carla"},{"full_name":"Wójcikowska, Barbara","last_name":"Wójcikowska","first_name":"Barbara"},{"last_name":"Pěnčík","full_name":"Pěnčík, Aleš","first_name":"Aleš"},{"full_name":"Novák, Ondřej","last_name":"Novák","first_name":"Ondřej"},{"first_name":"Junyi","last_name":"Chen","full_name":"Chen, Junyi"},{"first_name":"Wim","last_name":"Grunewald","full_name":"Grunewald, Wim"},{"last_name":"Dresselhaus","full_name":"Dresselhaus, Thomas","first_name":"Thomas"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml"},{"first_name":"Thomas","last_name":"Laux","full_name":"Laux, Thomas"}],"project":[{"call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","name":"Polarity and subcellular dynamics in plants"}],"publication":"Nature Plants","day":"16","year":"2018","isi":1,"date_created":"2018-12-11T11:44:56Z","doi":"10.1038/s41477-018-0204-z","date_published":"2018-07-16T00:00:00Z","page":"548 - 553","acknowledgement":"This work was further supported by the Czech Science Foundation GACR (GA13-40637S) to J.F.;","oa":1,"publisher":"Nature Publishing Group","quality_controlled":"1","date_updated":"2023-09-13T08:53:28Z","department":[{"_id":"JiFr"}],"_id":"158","status":"public","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/plant-mothers-talk-to-their-embryos-via-the-hormone-auxin/","description":"News on IST Homepage"}]},"issue":"8","volume":4,"oa_version":"Submitted Version","pmid":1,"abstract":[{"text":"The angiosperm seed is composed of three genetically distinct tissues: the diploid embryo that originates from the fertilized egg cell, the triploid endosperm that is produced from the fertilized central cell, and the maternal sporophytic integuments that develop into the seed coat1. At the onset of embryo development in Arabidopsis thaliana, the zygote divides asymmetrically, producing a small apical embryonic cell and a larger basal cell that connects the embryo to the maternal tissue2. The coordinated and synchronous development of the embryo and the surrounding integuments, and the alignment of their growth axes, suggest communication between maternal tissues and the embryo. In contrast to animals, however, where a network of maternal factors that direct embryo patterning have been identified3,4, only a few maternal mutations have been described to affect embryo development in plants5–7. Early embryo patterning in Arabidopsis requires accumulation of the phytohormone auxin in the apical cell by directed transport from the suspensor8–10. However, the origin of this auxin has remained obscure. Here we investigate the source of auxin for early embryogenesis and provide evidence that the mother plant coordinates seed development by supplying auxin to the early embryo from the integuments of the ovule. We show that auxin response increases in ovules after fertilization, due to upregulated auxin biosynthesis in the integuments, and this maternally produced auxin is required for correct embryo development.","lang":"eng"}],"intvolume":" 4","month":"07","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30013211","open_access":"1"}],"scopus_import":"1"},{"quality_controlled":"1","publisher":"Elsevier","oa":1,"doi":"10.1016/j.tcb.2018.06.006","date_published":"2018-07-26T00:00:00Z","date_created":"2018-12-11T11:44:54Z","page":"835 - 867","day":"26","publication":"Trends in Cell Biology","isi":1,"has_accepted_license":"1","year":"2018","title":"Mammalian mitochondrial complex I structure and disease causing mutations","author":[{"full_name":"Fiedorczuk, Karol","last_name":"Fiedorczuk","first_name":"Karol","id":"5BFF67CE-02D1-11E9-B11A-A5A4D7DFFFD0"},{"last_name":"Sazanov","orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7769","external_id":{"isi":["000445118200007"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Fiedorczuk, Karol, and Leonid A Sazanov. “Mammalian Mitochondrial Complex I Structure and Disease Causing Mutations.” Trends in Cell Biology. Elsevier, 2018. https://doi.org/10.1016/j.tcb.2018.06.006.","ista":"Fiedorczuk K, Sazanov LA. 2018. Mammalian mitochondrial complex I structure and disease causing mutations. Trends in Cell Biology. 28(10), 835–867.","mla":"Fiedorczuk, Karol, and Leonid A. Sazanov. “Mammalian Mitochondrial Complex I Structure and Disease Causing Mutations.” Trends in Cell Biology, vol. 28, no. 10, Elsevier, 2018, pp. 835–67, doi:10.1016/j.tcb.2018.06.006.","ama":"Fiedorczuk K, Sazanov LA. Mammalian mitochondrial complex I structure and disease causing mutations. Trends in Cell Biology. 2018;28(10):835-867. doi:10.1016/j.tcb.2018.06.006","apa":"Fiedorczuk, K., & Sazanov, L. A. (2018). Mammalian mitochondrial complex I structure and disease causing mutations. Trends in Cell Biology. Elsevier. https://doi.org/10.1016/j.tcb.2018.06.006","short":"K. Fiedorczuk, L.A. Sazanov, Trends in Cell Biology 28 (2018) 835–867.","ieee":"K. Fiedorczuk and L. A. Sazanov, “Mammalian mitochondrial complex I structure and disease causing mutations,” Trends in Cell Biology, vol. 28, no. 10. Elsevier, pp. 835–867, 2018."},"month":"07","intvolume":" 28","scopus_import":"1","oa_version":"Submitted Version","abstract":[{"text":"Complex I has an essential role in ATP production by coupling electron transfer from NADH to quinone with translocation of protons across the inner mitochondrial membrane. Isolated complex I deficiency is a frequent cause of mitochondrial inherited diseases. Complex I has also been implicated in cancer, ageing, and neurodegenerative conditions. Until recently, the understanding of complex I deficiency on the molecular level was limited due to the lack of high-resolution structures of the enzyme. However, due to developments in single particle cryo-electron microscopy (cryo-EM), recent studies have reported nearly atomic resolution maps and models of mitochondrial complex I. These structures significantly add to our understanding of complex I mechanism and assembly. The disease-causing mutations are discussed here in their structural context.","lang":"eng"}],"volume":28,"issue":"10","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"6994","checksum":"ef6d2b4e1fd63948539639242610bfa6","creator":"lsazanov","file_size":2185385,"date_updated":"2020-07-14T12:45:00Z","file_name":"SasanovFinalMS+EdComments_LS_allacc_withFigs.pdf","date_created":"2019-11-07T12:55:20Z"}],"language":[{"iso":"eng"}],"publication_status":"published","status":"public","type":"journal_article","article_type":"original","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"},"_id":"152","file_date_updated":"2020-07-14T12:45:00Z","department":[{"_id":"LeSa"}],"ddc":["572"],"date_updated":"2023-09-13T08:51:56Z"},{"_id":"310","conference":{"name":"SODA: Symposium on Discrete Algorithms","start_date":"2018-01-07","location":"New Orleans, Louisiana, United States","end_date":"2018-01-10"},"type":"conference","status":"public","date_updated":"2023-09-13T08:50:16Z","department":[{"_id":"KrCh"}],"abstract":[{"lang":"eng","text":"A model of computation that is widely used in the formal analysis of reactive systems is symbolic algorithms. In this model the access to the input graph is restricted to consist of symbolic operations, which are expensive in comparison to the standard RAM operations. We give lower bounds on the number of symbolic operations for basic graph problems such as the computation of the strongly connected components and of the approximate diameter as well as for fundamental problems in model checking such as safety, liveness, and coliveness. Our lower bounds are linear in the number of vertices of the graph, even for constant-diameter graphs. For none of these problems lower bounds on the number of symbolic operations were known before. The lower bounds show an interesting separation of these problems from the reachability problem, which can be solved with O(D) symbolic operations, where D is the diameter of the graph. Additionally we present an approximation algorithm for the graph diameter which requires Õ(n/D) symbolic steps to achieve a (1 +ϵ)-approximation for any constant > 0. This compares to O(n/D) symbolic steps for the (naive) exact algorithm and O(D) symbolic steps for a 2-approximation. Finally we also give a refined analysis of the strongly connected components algorithms of [15], showing that it uses an optimal number of symbolic steps that is proportional to the sum of the diameters of the strongly connected components."}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1711.09148"}],"scopus_import":"1","month":"01","publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"project":[{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"}],"citation":{"ama":"Chatterjee K, Dvorák W, Henzinger MH, Loitzenbauer V. Lower bounds for symbolic computation on graphs: Strongly connected components, liveness, safety, and diameter. In: ACM; 2018:2341-2356. doi:10.1137/1.9781611975031.151","apa":"Chatterjee, K., Dvorák, W., Henzinger, M. H., & Loitzenbauer, V. (2018). Lower bounds for symbolic computation on graphs: Strongly connected components, liveness, safety, and diameter (pp. 2341–2356). Presented at the SODA: Symposium on Discrete Algorithms, New Orleans, Louisiana, United States: ACM. https://doi.org/10.1137/1.9781611975031.151","ieee":"K. Chatterjee, W. Dvorák, M. H. Henzinger, and V. Loitzenbauer, “Lower bounds for symbolic computation on graphs: Strongly connected components, liveness, safety, and diameter,” presented at the SODA: Symposium on Discrete Algorithms, New Orleans, Louisiana, United States, 2018, pp. 2341–2356.","short":"K. Chatterjee, W. Dvorák, M.H. Henzinger, V. Loitzenbauer, in:, ACM, 2018, pp. 2341–2356.","mla":"Chatterjee, Krishnendu, et al. Lower Bounds for Symbolic Computation on Graphs: Strongly Connected Components, Liveness, Safety, and Diameter. ACM, 2018, pp. 2341–56, doi:10.1137/1.9781611975031.151.","ista":"Chatterjee K, Dvorák W, Henzinger MH, Loitzenbauer V. 2018. Lower bounds for symbolic computation on graphs: Strongly connected components, liveness, safety, and diameter. SODA: Symposium on Discrete Algorithms, 2341–2356.","chicago":"Chatterjee, Krishnendu, Wolfgang Dvorák, Monika H Henzinger, and Veronika Loitzenbauer. “Lower Bounds for Symbolic Computation on Graphs: Strongly Connected Components, Liveness, Safety, and Diameter,” 2341–56. ACM, 2018. https://doi.org/10.1137/1.9781611975031.151."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"arxiv":["1711.09148"],"isi":["000483921200152"]},"article_processing_charge":"No","publist_id":"7555","author":[{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Wolfgang","full_name":"Dvorák, Wolfgang","last_name":"Dvorák"},{"first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","last_name":"Henzinger"},{"first_name":"Veronika","last_name":"Loitzenbauer","full_name":"Loitzenbauer, Veronika"}],"title":"Lower bounds for symbolic computation on graphs: Strongly connected components, liveness, safety, and diameter","oa":1,"quality_controlled":"1","publisher":"ACM","year":"2018","isi":1,"day":"01","page":"2341 - 2356","date_created":"2018-12-11T11:45:45Z","date_published":"2018-01-01T00:00:00Z","doi":"10.1137/1.9781611975031.151"},{"date_created":"2018-12-11T11:46:28Z","doi":"10.1103/PhysRevLett.120.060601","date_published":"2018-02-07T00:00:00Z","publication":"Physical Review Letters","day":"07","year":"2018","isi":1,"oa":1,"publisher":"American Physical Society","quality_controlled":"1","title":"Manipulating the flow of thermal noise in quantum devices","external_id":{"isi":["000424382100004"],"arxiv":["1706.09051"]},"article_processing_charge":"No","publist_id":"7387","author":[{"last_name":"Barzanjeh","orcid":"0000-0003-0415-1423","full_name":"Barzanjeh, Shabir","first_name":"Shabir","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Matteo","full_name":"Aquilina, Matteo","last_name":"Aquilina"},{"full_name":"Xuereb, André","last_name":"Xuereb","first_name":"André"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Barzanjeh, Shabir, Matteo Aquilina, and André Xuereb. “Manipulating the Flow of Thermal Noise in Quantum Devices.” Physical Review Letters. American Physical Society, 2018. https://doi.org/10.1103/PhysRevLett.120.060601.","ista":"Barzanjeh S, Aquilina M, Xuereb A. 2018. Manipulating the flow of thermal noise in quantum devices. Physical Review Letters. 120(6), 060601.","mla":"Barzanjeh, Shabir, et al. “Manipulating the Flow of Thermal Noise in Quantum Devices.” Physical Review Letters, vol. 120, no. 6, 060601, American Physical Society, 2018, doi:10.1103/PhysRevLett.120.060601.","short":"S. Barzanjeh, M. Aquilina, A. Xuereb, Physical Review Letters 120 (2018).","ieee":"S. Barzanjeh, M. Aquilina, and A. Xuereb, “Manipulating the flow of thermal noise in quantum devices,” Physical Review Letters, vol. 120, no. 6. American Physical Society, 2018.","apa":"Barzanjeh, S., Aquilina, M., & Xuereb, A. (2018). Manipulating the flow of thermal noise in quantum devices. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.120.060601","ama":"Barzanjeh S, Aquilina M, Xuereb A. Manipulating the flow of thermal noise in quantum devices. Physical Review Letters. 2018;120(6). doi:10.1103/PhysRevLett.120.060601"},"project":[{"call_identifier":"H2020","_id":"257EB838-B435-11E9-9278-68D0E5697425","grant_number":"732894","name":"Hybrid Optomechanical Technologies"},{"_id":"258047B6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics SUPEREOM","grant_number":"707438"}],"article_number":"060601 ","ec_funded":1,"volume":120,"related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/interference-as-a-new-method-for-cooling-quantum-devices/","relation":"press_release"}]},"issue":"6","language":[{"iso":"eng"}],"publication_status":"published","intvolume":" 120","month":"02","main_file_link":[{"url":"https://arxiv.org/abs/1706.09051","open_access":"1"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"lang":"eng","text":"There has been significant interest recently in using complex quantum systems to create effective nonreciprocal dynamics. Proposals have been put forward for the realization of artificial magnetic fields for photons and phonons; experimental progress is fast making these proposals a reality. Much work has concentrated on the use of such systems for controlling the flow of signals, e.g., to create isolators or directional amplifiers for optical signals. In this Letter, we build on this work but move in a different direction. We develop the theory of and discuss a potential realization for the controllable flow of thermal noise in quantum systems. We demonstrate theoretically that the unidirectional flow of thermal noise is possible within quantum cascaded systems. Viewing an optomechanical platform as a cascaded system we show here that one can ultimately control the direction of the flow of thermal noise. By appropriately engineering the mechanical resonator, which acts as an artificial reservoir, the flow of thermal noise can be constrained to a desired direction, yielding a thermal rectifier. The proposed quantum thermal noise rectifier could potentially be used to develop devices such as a thermal modulator, a thermal router, and a thermal amplifier for nanoelectronic devices and superconducting circuits."}],"department":[{"_id":"JoFi"}],"date_updated":"2023-09-13T08:52:27Z","status":"public","type":"journal_article","_id":"436"}]