[{"intvolume":" 215","title":"IgM's exit route","ddc":["570"],"status":"public","_id":"5672","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:47:09Z","date_created":"2019-02-06T08:49:52Z","checksum":"687beea1d64c213f4cb9e3c29ec11a14","relation":"main_file","file_id":"5931","file_size":1216437,"content_type":"application/pdf","creator":"dernst","file_name":"2018_JournalExperMed_Reversat.pdf","access_level":"open_access"}],"type":"journal_article","issue":"12","abstract":[{"text":"The release of IgM is the first line of an antibody response and precedes the generation of high affinity IgG in germinal centers. Once secreted by freshly activated plasmablasts, IgM is released into the efferent lymph of reactive lymph nodes as early as 3 d after immunization. As pentameric IgM has an enormous size of 1,000 kD, its diffusibility is low, and one might wonder how it can pass through the densely lymphocyte-packed environment of a lymph node parenchyma in order to reach its exit. In this issue of JEM, Thierry et al. show that, in order to reach the blood stream, IgM molecules take a specific micro-anatomical route via lymph node conduits.","lang":"eng"}],"page":"2959-2961","citation":{"ista":"Reversat A, Sixt MK. 2018. IgM’s exit route. Journal of Experimental Medicine. 215(12), 2959–2961.","ieee":"A. Reversat and M. K. Sixt, “IgM’s exit route,” Journal of Experimental Medicine, vol. 215, no. 12. Rockefeller University Press, pp. 2959–2961, 2018.","apa":"Reversat, A., & Sixt, M. K. (2018). IgM’s exit route. Journal of Experimental Medicine. Rockefeller University Press. https://doi.org/10.1084/jem.20181934","ama":"Reversat A, Sixt MK. IgM’s exit route. Journal of Experimental Medicine. 2018;215(12):2959-2961. doi:10.1084/jem.20181934","chicago":"Reversat, Anne, and Michael K Sixt. “IgM’s Exit Route.” Journal of Experimental Medicine. Rockefeller University Press, 2018. https://doi.org/10.1084/jem.20181934.","mla":"Reversat, Anne, and Michael K. Sixt. “IgM’s Exit Route.” Journal of Experimental Medicine, vol. 215, no. 12, Rockefeller University Press, 2018, pp. 2959–61, doi:10.1084/jem.20181934.","short":"A. Reversat, M.K. Sixt, Journal of Experimental Medicine 215 (2018) 2959–2961."},"publication":"Journal of Experimental Medicine","date_published":"2018-11-20T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"20","department":[{"_id":"MiSi"}],"publisher":"Rockefeller University Press","publication_status":"published","year":"2018","volume":215,"date_updated":"2023-09-11T14:12:06Z","date_created":"2018-12-16T22:59:18Z","author":[{"full_name":"Reversat, Anne","first_name":"Anne","last_name":"Reversat","id":"35B76592-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0666-8928"},{"last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K"}],"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","file_date_updated":"2020-07-14T12:47:09Z","quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"oa":1,"external_id":{"isi":["000451920600002"]},"language":[{"iso":"eng"}],"doi":"10.1084/jem.20181934","publication_identifier":{"issn":["00221007"]},"month":"11"},{"citation":{"apa":"Akopyan, A., & Bobenko, A. (2018). Incircular nets and confocal conics. Transactions of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/tran/7292","ieee":"A. Akopyan and A. Bobenko, “Incircular nets and confocal conics,” Transactions of the American Mathematical Society, vol. 370, no. 4. American Mathematical Society, pp. 2825–2854, 2018.","ista":"Akopyan A, Bobenko A. 2018. Incircular nets and confocal conics. Transactions of the American Mathematical Society. 370(4), 2825–2854.","ama":"Akopyan A, Bobenko A. Incircular nets and confocal conics. Transactions of the American Mathematical Society. 2018;370(4):2825-2854. doi:10.1090/tran/7292","chicago":"Akopyan, Arseniy, and Alexander Bobenko. “Incircular Nets and Confocal Conics.” Transactions of the American Mathematical Society. American Mathematical Society, 2018. https://doi.org/10.1090/tran/7292.","short":"A. Akopyan, A. Bobenko, Transactions of the American Mathematical Society 370 (2018) 2825–2854.","mla":"Akopyan, Arseniy, and Alexander Bobenko. “Incircular Nets and Confocal Conics.” Transactions of the American Mathematical Society, vol. 370, no. 4, American Mathematical Society, 2018, pp. 2825–54, doi:10.1090/tran/7292."},"publication":"Transactions of the American Mathematical Society","page":"2825 - 2854","date_published":"2018-04-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"458","intvolume":" 370","title":"Incircular nets and confocal conics","status":"public","oa_version":"Preprint","type":"journal_article","issue":"4","abstract":[{"text":"We consider congruences of straight lines in a plane with the combinatorics of the square grid, with all elementary quadrilaterals possessing an incircle. It is shown that all the vertices of such nets (we call them incircular or IC-nets) lie on confocal conics. Our main new results are on checkerboard IC-nets in the plane. These are congruences of straight lines in the plane with the combinatorics of the square grid, combinatorially colored as a checkerboard, such that all black coordinate quadrilaterals possess inscribed circles. We show how this larger class of IC-nets appears quite naturally in Laguerre geometry of oriented planes and spheres and leads to new remarkable incidence theorems. Most of our results are valid in hyperbolic and spherical geometries as well. We present also generalizations in spaces of higher dimension, called checkerboard IS-nets. The construction of these nets is based on a new 9 inspheres incidence theorem.","lang":"eng"}],"external_id":{"isi":["000423197800019"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1602.04637"}],"oa":1,"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"quality_controlled":"1","isi":1,"doi":"10.1090/tran/7292","language":[{"iso":"eng"}],"month":"04","year":"2018","acknowledgement":"DFG Collaborative Research Center TRR 109 “Discretization in Geometry and Dynamics”; People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) REA grant agreement n◦[291734]","department":[{"_id":"HeEd"}],"publisher":"American Mathematical Society","publication_status":"published","author":[{"first_name":"Arseniy","last_name":"Akopyan","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy"},{"first_name":"Alexander","last_name":"Bobenko","full_name":"Bobenko, Alexander"}],"volume":370,"date_updated":"2023-09-11T14:19:12Z","date_created":"2018-12-11T11:46:35Z","publist_id":"7363","ec_funded":1},{"author":[{"full_name":"Avni, Guy","orcid":"0000-0001-5588-8287","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","last_name":"Avni","first_name":"Guy"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger"},{"last_name":"Ibsen-Jensen","first_name":"Rasmus","orcid":"0000-0003-4783-0389","id":"3B699956-F248-11E8-B48F-1D18A9856A87","full_name":"Ibsen-Jensen, Rasmus"}],"date_created":"2018-12-30T22:59:14Z","date_updated":"2023-09-12T07:44:01Z","volume":11316,"year":"2018","publisher":"Springer","department":[{"_id":"ToHe"}],"month":"11","publication_identifier":{"isbn":["9783030046118"],"issn":["03029743"]},"conference":{"end_date":"2018-12-17","start_date":"2018-12-15","location":"Oxford, UK","name":"14th International Conference on Web and Internet Economics, WINE"},"doi":"10.1007/978-3-030-04612-5_2","language":[{"iso":"eng"}],"external_id":{"isi":["000865933000002"],"arxiv":["1804.04372"]},"main_file_link":[{"url":"https://arxiv.org/abs/1804.04372","open_access":"1"}],"oa":1,"quality_controlled":"1","isi":1,"project":[{"name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"call_identifier":"FWF","name":"Formal Methods meets Algorithmic Game Theory","_id":"264B3912-B435-11E9-9278-68D0E5697425","grant_number":"M02369"}],"abstract":[{"lang":"eng","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."}],"type":"conference","alternative_title":["LNCS"],"oa_version":"Preprint","_id":"5788","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"Infinite-duration poorman-bidding games","intvolume":" 11316","day":"21","article_processing_charge":"No","scopus_import":"1","date_published":"2018-11-21T00:00:00Z","citation":{"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.","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","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.","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","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.","short":"G. Avni, T.A. Henzinger, R. Ibsen-Jensen, in:, Springer, 2018, pp. 21–36.","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."},"page":"21-36"},{"scopus_import":"1","day":"29","article_processing_charge":"No","article_type":"original","page":"509–512","publication":"Nature","citation":{"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","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.","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","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.","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.","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.","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."},"date_published":"2018-08-29T00:00:00Z","type":"journal_article","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"}],"issue":"7719","status":"public","title":"Inositol phosphates are assembly co-factors for HIV-1","intvolume":" 560","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"150","oa_version":"Submitted Version","month":"08","publication_identifier":{"eissn":["1476-4687"]},"quality_controlled":"1","isi":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6242333/","open_access":"1"}],"oa":1,"external_id":{"pmid":["30158708"],"isi":["000442483400046"]},"language":[{"iso":"eng"}],"doi":"10.1038/s41586-018-0396-4","publication_status":"published","department":[{"_id":"FlSc"}],"publisher":"Nature Publishing Group","year":"2018","pmid":1,"date_created":"2018-12-11T11:44:53Z","date_updated":"2023-09-12T07:44:37Z","volume":560,"author":[{"last_name":"Dick","first_name":"Robert","full_name":"Dick, Robert"},{"first_name":"Kaneil K","last_name":"Zadrozny","full_name":"Zadrozny, Kaneil K"},{"full_name":"Xu, Chaoyi","first_name":"Chaoyi","last_name":"Xu"},{"last_name":"Schur","first_name":"Florian","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian"},{"first_name":"Terri D","last_name":"Lyddon","full_name":"Lyddon, Terri D"},{"first_name":"Clifton L","last_name":"Ricana","full_name":"Ricana, Clifton L"},{"first_name":"Jonathan M","last_name":"Wagner","full_name":"Wagner, Jonathan M"},{"full_name":"Perilla, Juan R","last_name":"Perilla","first_name":"Juan R"},{"full_name":"Ganser, Pornillos Barbie K","last_name":"Ganser","first_name":"Pornillos Barbie K"},{"full_name":"Johnson, Marc C","last_name":"Johnson","first_name":"Marc C"},{"full_name":"Pornillos, Owen","first_name":"Owen","last_name":"Pornillos"},{"first_name":"Volker","last_name":"Vogt","full_name":"Vogt, Volker"}],"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41586-018-0505-4"}]}},{"doi":"10.3934/dcds.2018120","language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["000438818400007"],"arxiv":["1706.03062"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1706.03062"}],"quality_controlled":"1","isi":1,"month":"06","author":[{"full_name":"Kalinin, Nikita","first_name":"Nikita","last_name":"Kalinin"},{"full_name":"Shkolnikov, Mikhail","first_name":"Mikhail","last_name":"Shkolnikov","id":"35084A62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4310-178X"}],"volume":38,"date_updated":"2023-09-12T07:45:37Z","date_created":"2018-12-11T11:45:43Z","year":"2018","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.","department":[{"_id":"TaHa"}],"publisher":"AIMS","publication_status":"published","publist_id":"7576","date_published":"2018-06-01T00:00:00Z","citation":{"short":"N. Kalinin, M. Shkolnikov, Discrete and Continuous Dynamical Systems- Series A 38 (2018) 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.","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.","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","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.","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","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."},"publication":"Discrete and Continuous Dynamical Systems- Series A","page":"2827 - 2849","article_processing_charge":"No","day":"01","scopus_import":"1","oa_version":"Submitted Version","_id":"303","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 38","status":"public","title":"Introduction to tropical series and wave dynamic on them","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."}],"type":"journal_article"},{"article_processing_charge":"No","day":"06","scopus_import":"1","date_published":"2018-06-06T00:00:00Z","citation":{"ieee":"F. Locatello, G. Dresdner, R. Khanna, I. Valera, and G. Rätsch, “Boosting black box variational inference,” in Advances in Neural Information Processing Systems, Montreal, Canada, 2018, vol. 31.","apa":"Locatello, F., Dresdner, G., Khanna, R., Valera, I., & Rätsch, G. (2018). Boosting black box variational inference. In Advances in Neural Information Processing Systems (Vol. 31). Montreal, Canada: Neural Information Processing Systems Foundation.","ista":"Locatello F, Dresdner G, Khanna R, Valera I, Rätsch G. 2018. Boosting black box variational inference. Advances in Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 31.","ama":"Locatello F, Dresdner G, Khanna R, Valera I, Rätsch G. Boosting black box variational inference. In: Advances in Neural Information Processing Systems. Vol 31. Neural Information Processing Systems Foundation; 2018.","chicago":"Locatello, Francesco, Gideon Dresdner, Rajiv Khanna, Isabel Valera, and Gunnar Rätsch. “Boosting Black Box Variational Inference.” In Advances in Neural Information Processing Systems, Vol. 31. Neural Information Processing Systems Foundation, 2018.","short":"F. Locatello, G. Dresdner, R. Khanna, I. Valera, G. Rätsch, in:, Advances in Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2018.","mla":"Locatello, Francesco, et al. “Boosting Black Box Variational Inference.” Advances in Neural Information Processing Systems, vol. 31, Neural Information Processing Systems Foundation, 2018."},"publication":"Advances in Neural Information Processing Systems","abstract":[{"text":"Approximating a probability density in a tractable manner is a central task\r\nin Bayesian statistics. Variational Inference (VI) is a popular technique that\r\nachieves tractability by choosing a relatively simple variational family.\r\nBorrowing ideas from the classic boosting framework, recent approaches attempt\r\nto \\emph{boost} VI by replacing the selection of a single density with a\r\ngreedily constructed mixture of densities. In order to guarantee convergence,\r\nprevious works impose stringent assumptions that require significant effort for\r\npractitioners. Specifically, they require a custom implementation of the greedy\r\nstep (called the LMO) for every probabilistic model with respect to an\r\nunnatural variational family of truncated distributions. Our work fixes these\r\nissues with novel theoretical and algorithmic insights. On the theoretical\r\nside, we show that boosting VI satisfies a relaxed smoothness assumption which\r\nis sufficient for the convergence of the functional Frank-Wolfe (FW) algorithm.\r\nFurthermore, we rephrase the LMO problem and propose to maximize the Residual\r\nELBO (RELBO) which replaces the standard ELBO optimization in VI. These\r\ntheoretical enhancements allow for black box implementation of the boosting\r\nsubroutine. Finally, we present a stopping criterion drawn from the duality gap\r\nin the classic FW analyses and exhaustive experiments to illustrate the\r\nusefulness of our theoretical and algorithmic contributions.","lang":"eng"}],"type":"conference","oa_version":"Preprint","intvolume":" 31","title":"Boosting black box variational inference","status":"public","_id":"14202","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"isbn":["9781510884472"],"eissn":["1049-5258"]},"month":"06","language":[{"iso":"eng"}],"conference":{"start_date":"2018-12-03","location":"Montreal, Canada","end_date":"2018-12-08","name":"NeurIPS: Neural Information Processing Systems"},"quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1806.02185","open_access":"1"}],"external_id":{"arxiv":["1806.02185"]},"oa":1,"extern":"1","volume":31,"date_updated":"2023-09-13T07:38:24Z","date_created":"2023-08-22T14:15:40Z","author":[{"full_name":"Locatello, Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683","first_name":"Francesco","last_name":"Locatello"},{"last_name":"Dresdner","first_name":"Gideon","full_name":"Dresdner, Gideon"},{"full_name":"Khanna, Rajiv","first_name":"Rajiv","last_name":"Khanna"},{"full_name":"Valera, Isabel","first_name":"Isabel","last_name":"Valera"},{"full_name":"Rätsch, Gunnar","first_name":"Gunnar","last_name":"Rätsch"}],"department":[{"_id":"FrLo"}],"publisher":"Neural Information Processing Systems Foundation","publication_status":"published","year":"2018"},{"page":"464-472","publication":"Proceedings of the 21st International Conference on Artificial Intelligence and Statistics","citation":{"chicago":"Locatello, Francesco, Rajiv Khanna, Joydeep Ghosh, and Gunnar Rätsch. “Boosting Variational Inference: An Optimization Perspective.” In Proceedings of the 21st International Conference on Artificial Intelligence and Statistics, 84:464–72. ML Research Press, 2018.","short":"F. Locatello, R. Khanna, J. Ghosh, G. Rätsch, in:, Proceedings of the 21st International Conference on Artificial Intelligence and Statistics, ML Research Press, 2018, pp. 464–472.","mla":"Locatello, Francesco, et al. “Boosting Variational Inference: An Optimization Perspective.” Proceedings of the 21st International Conference on Artificial Intelligence and Statistics, vol. 84, ML Research Press, 2018, pp. 464–72.","apa":"Locatello, F., Khanna, R., Ghosh, J., & Rätsch, G. (2018). Boosting variational inference: An optimization perspective. In Proceedings of the 21st International Conference on Artificial Intelligence and Statistics (Vol. 84, pp. 464–472). Playa Blanca, Lanzarote: ML Research Press.","ieee":"F. Locatello, R. Khanna, J. Ghosh, and G. Rätsch, “Boosting variational inference: An optimization perspective,” in Proceedings of the 21st International Conference on Artificial Intelligence and Statistics, Playa Blanca, Lanzarote, 2018, vol. 84, pp. 464–472.","ista":"Locatello F, Khanna R, Ghosh J, Rätsch G. 2018. Boosting variational inference: An optimization perspective. Proceedings of the 21st International Conference on Artificial Intelligence and Statistics. AISTATS: Conference on Artificial Intelligence and Statistics, PMLR, vol. 84, 464–472.","ama":"Locatello F, Khanna R, Ghosh J, Rätsch G. Boosting variational inference: An optimization perspective. In: Proceedings of the 21st International Conference on Artificial Intelligence and Statistics. Vol 84. ML Research Press; 2018:464-472."},"date_published":"2018-04-15T00:00:00Z","scopus_import":"1","day":"15","article_processing_charge":"No","status":"public","title":"Boosting variational inference: An optimization perspective","intvolume":" 84","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14201","oa_version":"Preprint","alternative_title":["PMLR"],"type":"conference","abstract":[{"lang":"eng","text":"Variational inference is a popular technique to approximate a possibly\r\nintractable Bayesian posterior with a more tractable one. Recently, boosting\r\nvariational inference has been proposed as a new paradigm to approximate the\r\nposterior by a mixture of densities by greedily adding components to the\r\nmixture. However, as is the case with many other variational inference\r\nalgorithms, its theoretical properties have not been studied. In the present\r\nwork, we study the convergence properties of this approach from a modern\r\noptimization viewpoint by establishing connections to the classic Frank-Wolfe\r\nalgorithm. Our analyses yields novel theoretical insights regarding the\r\nsufficient conditions for convergence, explicit rates, and algorithmic\r\nsimplifications. Since a lot of focus in previous works for variational\r\ninference has been on tractability, our work is especially important as a much\r\nneeded attempt to bridge the gap between probabilistic models and their\r\ncorresponding theoretical properties."}],"quality_controlled":"1","oa":1,"external_id":{"arxiv":["1708.01733"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1708.01733"}],"language":[{"iso":"eng"}],"conference":{"name":"AISTATS: Conference on Artificial Intelligence and Statistics","location":"Playa Blanca, Lanzarote","start_date":"2018-04-09","end_date":"2018-04-11"},"month":"04","publication_status":"published","publisher":"ML Research Press","department":[{"_id":"FrLo"}],"year":"2018","date_created":"2023-08-22T14:15:20Z","date_updated":"2023-09-13T07:52:40Z","volume":84,"author":[{"full_name":"Locatello, Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683","first_name":"Francesco","last_name":"Locatello"},{"full_name":"Khanna, Rajiv","first_name":"Rajiv","last_name":"Khanna"},{"full_name":"Ghosh, Joydeep","last_name":"Ghosh","first_name":"Joydeep"},{"full_name":"Rätsch, Gunnar","last_name":"Rätsch","first_name":"Gunnar"}],"extern":"1"},{"article_processing_charge":"No","month":"06","day":"06","date_published":"2018-06-06T00:00:00Z","conference":{"name":"ICLR: International Conference on Learning Representations","start_date":"2019-05-06","location":"New Orleans, LA, United States","end_date":"2019-05-09"},"language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1806.02199"}],"citation":{"ieee":"V. Fortuin, M. Hüser, F. Locatello, H. Strathmann, and G. Rätsch, “SOM-VAE: Interpretable discrete representation learning on time series,” in International Conference on Learning Representations, New Orleans, LA, United States, 2018.","apa":"Fortuin, V., Hüser, M., Locatello, F., Strathmann, H., & Rätsch, G. (2018). SOM-VAE: Interpretable discrete representation learning on time series. In International Conference on Learning Representations. New Orleans, LA, United States.","ista":"Fortuin V, Hüser M, Locatello F, Strathmann H, Rätsch G. 2018. SOM-VAE: Interpretable discrete representation learning on time series. International Conference on Learning Representations. ICLR: International Conference on Learning Representations.","ama":"Fortuin V, Hüser M, Locatello F, Strathmann H, Rätsch G. SOM-VAE: Interpretable discrete representation learning on time series. In: International Conference on Learning Representations. ; 2018.","chicago":"Fortuin, Vincent, Matthias Hüser, Francesco Locatello, Heiko Strathmann, and Gunnar Rätsch. “SOM-VAE: Interpretable Discrete Representation Learning on Time Series.” In International Conference on Learning Representations, 2018.","short":"V. Fortuin, M. Hüser, F. Locatello, H. Strathmann, G. Rätsch, in:, International Conference on Learning Representations, 2018.","mla":"Fortuin, Vincent, et al. “SOM-VAE: Interpretable Discrete Representation Learning on Time Series.” International Conference on Learning Representations, 2018."},"external_id":{"arxiv":["1806.02199"]},"publication":"International Conference on Learning Representations","quality_controlled":"1","abstract":[{"text":"High-dimensional time series are common in many domains. Since human\r\ncognition is not optimized to work well in high-dimensional spaces, these areas\r\ncould benefit from interpretable low-dimensional representations. However, most\r\nrepresentation learning algorithms for time series data are difficult to\r\ninterpret. This is due to non-intuitive mappings from data features to salient\r\nproperties of the representation and non-smoothness over time. To address this\r\nproblem, we propose a new representation learning framework building on ideas\r\nfrom interpretable discrete dimensionality reduction and deep generative\r\nmodeling. This framework allows us to learn discrete representations of time\r\nseries, which give rise to smooth and interpretable embeddings with superior\r\nclustering performance. We introduce a new way to overcome the\r\nnon-differentiability in discrete representation learning and present a\r\ngradient-based version of the traditional self-organizing map algorithm that is\r\nmore performant than the original. Furthermore, to allow for a probabilistic\r\ninterpretation of our method, we integrate a Markov model in the representation\r\nspace. This model uncovers the temporal transition structure, improves\r\nclustering performance even further and provides additional explanatory\r\ninsights as well as a natural representation of uncertainty. We evaluate our\r\nmodel in terms of clustering performance and interpretability on static\r\n(Fashion-)MNIST data, a time series of linearly interpolated (Fashion-)MNIST\r\nimages, a chaotic Lorenz attractor system with two macro states, as well as on\r\na challenging real world medical time series application on the eICU data set.\r\nOur learned representations compare favorably with competitor methods and\r\nfacilitate downstream tasks on the real world data.","lang":"eng"}],"extern":"1","type":"conference","author":[{"full_name":"Fortuin, Vincent","last_name":"Fortuin","first_name":"Vincent"},{"first_name":"Matthias","last_name":"Hüser","full_name":"Hüser, Matthias"},{"full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello","first_name":"Francesco"},{"first_name":"Heiko","last_name":"Strathmann","full_name":"Strathmann, Heiko"},{"full_name":"Rätsch, Gunnar","last_name":"Rätsch","first_name":"Gunnar"}],"oa_version":"Preprint","date_created":"2023-08-22T14:12:48Z","date_updated":"2023-09-13T06:35:12Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14198","year":"2018","department":[{"_id":"FrLo"}],"title":"SOM-VAE: Interpretable discrete representation learning on time series","status":"public","publication_status":"published"},{"quality_controlled":"1","external_id":{"arxiv":["1804.08544"]},"main_file_link":[{"url":"https://arxiv.org/abs/1804.08544","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"conference":{"location":"Stockholm, Sweden","start_date":"2018-07-10","end_date":"2018-07-15","name":"ICML: International Conference on Machine Learning"},"month":"07","department":[{"_id":"FrLo"}],"publisher":"ML Research Press","publication_status":"published","year":"2018","volume":80,"date_updated":"2023-09-13T08:13:39Z","date_created":"2023-08-22T14:16:01Z","author":[{"last_name":"Yurtsever","first_name":"Alp","full_name":"Yurtsever, Alp"},{"full_name":"Fercoq, Olivier","first_name":"Olivier","last_name":"Fercoq"},{"full_name":"Locatello, Francesco","last_name":"Locatello","first_name":"Francesco","orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4"},{"full_name":"Cevher, Volkan","first_name":"Volkan","last_name":"Cevher"}],"extern":"1","page":"5727-5736","citation":{"ista":"Yurtsever A, Fercoq O, Locatello F, Cevher V. 2018. A conditional gradient framework for composite convex minimization with applications to semidefinite programming. Proceedings of the 35th International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 80, 5727–5736.","apa":"Yurtsever, A., Fercoq, O., Locatello, F., & Cevher, V. (2018). A conditional gradient framework for composite convex minimization with applications to semidefinite programming. In Proceedings of the 35th International Conference on Machine Learning (Vol. 80, pp. 5727–5736). Stockholm, Sweden: ML Research Press.","ieee":"A. Yurtsever, O. Fercoq, F. Locatello, and V. Cevher, “A conditional gradient framework for composite convex minimization with applications to semidefinite programming,” in Proceedings of the 35th International Conference on Machine Learning, Stockholm, Sweden, 2018, vol. 80, pp. 5727–5736.","ama":"Yurtsever A, Fercoq O, Locatello F, Cevher V. A conditional gradient framework for composite convex minimization with applications to semidefinite programming. In: Proceedings of the 35th International Conference on Machine Learning. Vol 80. ML Research Press; 2018:5727-5736.","chicago":"Yurtsever, Alp, Olivier Fercoq, Francesco Locatello, and Volkan Cevher. “A Conditional Gradient Framework for Composite Convex Minimization with Applications to Semidefinite Programming.” In Proceedings of the 35th International Conference on Machine Learning, 80:5727–36. ML Research Press, 2018.","mla":"Yurtsever, Alp, et al. “A Conditional Gradient Framework for Composite Convex Minimization with Applications to Semidefinite Programming.” Proceedings of the 35th International Conference on Machine Learning, vol. 80, ML Research Press, 2018, pp. 5727–36.","short":"A. Yurtsever, O. Fercoq, F. Locatello, V. Cevher, in:, Proceedings of the 35th International Conference on Machine Learning, ML Research Press, 2018, pp. 5727–5736."},"publication":"Proceedings of the 35th International Conference on Machine Learning","date_published":"2018-07-15T00:00:00Z","article_processing_charge":"No","day":"15","intvolume":" 80","title":"A conditional gradient framework for composite convex minimization with applications to semidefinite programming","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14203","oa_version":"Preprint","alternative_title":["PMLR"],"type":"conference","abstract":[{"lang":"eng","text":"We propose a conditional gradient framework for a composite convex minimization template with broad applications. Our approach combines smoothing and homotopy techniques under the CGM framework, and provably achieves the optimal O(1/k−−√) convergence rate. We demonstrate that the same rate holds if the linear subproblems are solved approximately with additive or multiplicative error. In contrast with the relevant work, we are able to characterize the convergence when the non-smooth term is an indicator function. Specific applications of our framework include the non-smooth minimization, semidefinite programming, and minimization with linear inclusion constraints over a compact domain. Numerical evidence demonstrates the benefits of our framework."}]},{"oa_version":"Submitted Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"282","status":"public","title":"Introgression of a block of genome under infinitesimal selection","intvolume":" 209","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."}],"issue":"4","type":"journal_article","date_published":"2018-08-01T00:00:00Z","publication":"Genetics","citation":{"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.","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.","short":"H. Sachdeva, N.H. Barton, Genetics 209 (2018) 1279–1303.","ista":"Sachdeva H, Barton NH. 2018. Introgression of a block of genome under infinitesimal selection. Genetics. 209(4), 1279–1303.","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","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.","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"},"page":"1279 - 1303","day":"01","article_processing_charge":"No","scopus_import":"1","author":[{"id":"42377A0A-F248-11E8-B48F-1D18A9856A87","last_name":"Sachdeva","first_name":"Himani","full_name":"Sachdeva, Himani"},{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"}],"date_created":"2018-12-11T11:45:36Z","date_updated":"2023-09-13T08:22:32Z","volume":209,"year":"2018","publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Genetics Society of America","publist_id":"7617","doi":"10.1534/genetics.118.301018","language":[{"iso":"eng"}],"external_id":{"isi":["000440014100020"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/early/2017/11/30/227082"}],"quality_controlled":"1","isi":1,"month":"08"},{"title":"Inverted leftover hash lemma","status":"public","intvolume":" 2018","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"108","oa_version":"Submitted Version","alternative_title":["ISIT Proceedings"],"type":"conference","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."}],"citation":{"ama":"Obremski M, Skórski M. Inverted leftover hash lemma. In: 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.","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.","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","mla":"Obremski, Marciej, and Maciej Skórski. Inverted Leftover Hash Lemma. Vol. 2018, IEEE, 2018, doi:10.1109/ISIT.2018.8437654.","short":"M. Obremski, M. Skórski, in:, IEEE, 2018.","chicago":"Obremski, Marciej, and Maciej Skórski. “Inverted Leftover Hash Lemma,” Vol. 2018. IEEE, 2018. https://doi.org/10.1109/ISIT.2018.8437654."},"date_published":"2018-08-16T00:00:00Z","scopus_import":"1","day":"16","article_processing_charge":"No","publication_status":"published","publisher":"IEEE","department":[{"_id":"KrPi"}],"year":"2018","date_created":"2018-12-11T11:44:40Z","date_updated":"2023-09-13T08:23:18Z","volume":2018,"author":[{"last_name":"Obremski","first_name":"Marciej","full_name":"Obremski, Marciej"},{"first_name":"Maciej","last_name":"Skorski","id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","full_name":"Skorski, Maciej"}],"publist_id":"7946","isi":1,"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2017/507"}],"external_id":{"isi":["000448139300368"]},"language":[{"iso":"eng"}],"conference":{"location":"Vail, CO, USA","start_date":"2018-06-17 ","end_date":"2018-06-22","name":"ISIT: International Symposium on Information Theory"},"doi":"10.1109/ISIT.2018.8437654","month":"08"},{"alternative_title":["PMLR"],"type":"conference","abstract":[{"text":"Two popular examples of first-order optimization methods over linear spaces are coordinate descent and matching pursuit algorithms, with their randomized variants. While the former targets the optimization by moving along coordinates, the latter considers a generalized notion of directions. Exploiting the connection between the two algorithms, we present a unified analysis of both, providing affine invariant sublinear O(1/t) rates on smooth objectives and linear convergence on strongly convex objectives. As a byproduct of our affine invariant analysis of matching pursuit, our rates for steepest coordinate descent are the tightest known. Furthermore, we show the first accelerated convergence rate O(1/t2) for matching pursuit and steepest coordinate descent on convex objectives.","lang":"eng"}],"intvolume":" 80","status":"public","title":"On matching pursuit and coordinate descent","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14204","oa_version":"Preprint","scopus_import":"1","article_processing_charge":"No","day":"01","page":"3198-3207","citation":{"ama":"Locatello F, Raj A, Karimireddy SP, et al. On matching pursuit and coordinate descent. In: Proceedings of the 35th International Conference on Machine Learning. Vol 80. ML Research Press; 2018:3198-3207.","ista":"Locatello F, Raj A, Karimireddy SP, Rätsch G, Schölkopf B, Stich SU, Jaggi M. 2018. On matching pursuit and coordinate descent. Proceedings of the 35th International Conference on Machine Learning. , PMLR, vol. 80, 3198–3207.","ieee":"F. Locatello et al., “On matching pursuit and coordinate descent,” in Proceedings of the 35th International Conference on Machine Learning, 2018, vol. 80, pp. 3198–3207.","apa":"Locatello, F., Raj, A., Karimireddy, S. P., Rätsch, G., Schölkopf, B., Stich, S. U., & Jaggi, M. (2018). On matching pursuit and coordinate descent. In Proceedings of the 35th International Conference on Machine Learning (Vol. 80, pp. 3198–3207). ML Research Press.","mla":"Locatello, Francesco, et al. “On Matching Pursuit and Coordinate Descent.” Proceedings of the 35th International Conference on Machine Learning, vol. 80, ML Research Press, 2018, pp. 3198–207.","short":"F. Locatello, A. Raj, S.P. Karimireddy, G. Rätsch, B. Schölkopf, S.U. Stich, M. Jaggi, in:, Proceedings of the 35th International Conference on Machine Learning, ML Research Press, 2018, pp. 3198–3207.","chicago":"Locatello, Francesco, Anant Raj, Sai Praneeth Karimireddy, Gunnar Rätsch, Bernhard Schölkopf, Sebastian U. Stich, and Martin Jaggi. “On Matching Pursuit and Coordinate Descent.” In Proceedings of the 35th International Conference on Machine Learning, 80:3198–3207. ML Research Press, 2018."},"publication":"Proceedings of the 35th International Conference on Machine Learning","date_published":"2018-07-01T00:00:00Z","extern":"1","department":[{"_id":"FrLo"}],"publisher":"ML Research Press","publication_status":"published","year":"2018","volume":80,"date_created":"2023-08-22T14:16:25Z","date_updated":"2023-09-13T08:19:05Z","author":[{"first_name":"Francesco","last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco"},{"full_name":"Raj, Anant","last_name":"Raj","first_name":"Anant"},{"full_name":"Karimireddy, Sai Praneeth","first_name":"Sai Praneeth","last_name":"Karimireddy"},{"last_name":"Rätsch","first_name":"Gunnar","full_name":"Rätsch, Gunnar"},{"full_name":"Schölkopf, Bernhard","first_name":"Bernhard","last_name":"Schölkopf"},{"full_name":"Stich, Sebastian U.","first_name":"Sebastian U.","last_name":"Stich"},{"last_name":"Jaggi","first_name":"Martin","full_name":"Jaggi, Martin"}],"month":"07","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1803.09539"}],"external_id":{"arxiv":["1803.09539"]},"oa":1,"language":[{"iso":"eng"}]},{"type":"conference","alternative_title":["LNCS"],"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"}],"_id":"160","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["000"],"title":"Layered Concurrent Programs","status":"public","intvolume":" 10981","oa_version":"Published Version","file":[{"file_id":"5705","relation":"main_file","date_created":"2018-12-17T12:52:12Z","date_updated":"2020-07-14T12:45:04Z","checksum":"c64fff560fe5a7532ec10626ad1c215e","file_name":"2018_LNCS_Kragl.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":1603844}],"scopus_import":"1","day":"18","has_accepted_license":"1","article_processing_charge":"No","citation":{"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","ieee":"B. Kragl and S. Qadeer, “Layered Concurrent Programs,” presented at the CAV: Computer Aided Verification, Oxford, UK, 2018, vol. 10981, pp. 79–102.","ista":"Kragl B, Qadeer S. 2018. Layered Concurrent Programs. CAV: Computer Aided Verification, LNCS, vol. 10981, 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","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.","short":"B. Kragl, S. Qadeer, in:, Springer, 2018, pp. 79–102.","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."},"page":"79 - 102","date_published":"2018-07-18T00:00:00Z","file_date_updated":"2020-07-14T12:45:04Z","publist_id":"7761","year":"2018","publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"Springer","author":[{"full_name":"Kragl, Bernhard","last_name":"Kragl","first_name":"Bernhard","orcid":"0000-0001-7745-9117","id":"320FC952-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Qadeer","first_name":"Shaz","full_name":"Qadeer, Shaz"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8332"}]},"date_created":"2018-12-11T11:44:57Z","date_updated":"2023-09-13T08:45:09Z","volume":10981,"month":"07","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000491481600005"]},"oa":1,"quality_controlled":"1","isi":1,"project":[{"call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"}],"conference":{"name":"CAV: Computer Aided Verification","start_date":"2018-07-14","location":"Oxford, UK","end_date":"2018-07-17"},"doi":"10.1007/978-3-319-96145-3_5","language":[{"iso":"eng"}]},{"article_number":"2005971","publist_id":"7972","file_date_updated":"2020-07-14T12:48:10Z","year":"2018","department":[{"_id":"CaGu"}],"publisher":"Public Library of Science","publication_status":"published","related_material":{"record":[{"id":"9810","relation":"research_data","status":"public"}]},"author":[{"full_name":"Chaudhry, Waqas","first_name":"Waqas","last_name":"Chaudhry"},{"first_name":"Maros","last_name":"Pleska","id":"4569785E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7460-7479","full_name":"Pleska, Maros"},{"first_name":"Nilang","last_name":"Shah","full_name":"Shah, Nilang"},{"first_name":"Howard","last_name":"Weiss","full_name":"Weiss, Howard"},{"last_name":"Mccall","first_name":"Ingrid","full_name":"Mccall, Ingrid"},{"full_name":"Meyer, Justin","first_name":"Justin","last_name":"Meyer"},{"first_name":"Animesh","last_name":"Gupta","full_name":"Gupta, Animesh"},{"first_name":"Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C"},{"full_name":"Levin, Bruce","first_name":"Bruce","last_name":"Levin"}],"volume":16,"date_updated":"2023-09-13T08:45:41Z","date_created":"2018-12-11T11:44:32Z","month":"08","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000443383300024"]},"quality_controlled":"1","isi":1,"doi":"10.1371/journal.pbio.2005971","language":[{"iso":"eng"}],"type":"journal_article","issue":"8","abstract":[{"lang":"eng","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.”."}],"_id":"82","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 16","title":"Leaky resistance and the conditions for the existence of lytic bacteriophage","status":"public","ddc":["570"],"oa_version":"Published Version","file":[{"creator":"dernst","content_type":"application/pdf","file_size":4007095,"access_level":"open_access","file_name":"2018_Plos_Chaudhry.pdf","checksum":"527076f78265cd4ea192cd1569851587","date_updated":"2020-07-14T12:48:10Z","date_created":"2018-12-17T12:55:31Z","file_id":"5706","relation":"main_file"}],"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes","day":"16","citation":{"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.","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","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.","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","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.","short":"W. Chaudhry, M. Pleska, N. Shah, H. Weiss, I. Mccall, J. Meyer, A. Gupta, C.C. Guet, B. Levin, PLoS Biology 16 (2018).","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."},"publication":"PLoS Biology","date_published":"2018-08-16T00:00:00Z"},{"issue":"4","abstract":[{"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.","lang":"eng"}],"type":"journal_article","pubrep_id":"1049","file":[{"access_level":"open_access","file_name":"IST-2018-1049-v1+1_2018_sigg_Learning3DAerodynamics.pdf","file_size":22803163,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"5216","checksum":"7a2243668f215821bc6aecad0320079a","date_updated":"2020-07-14T12:46:22Z","date_created":"2018-12-12T10:16:28Z"}],"oa_version":"Submitted Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"4","intvolume":" 37","title":"Learning three-dimensional flow for interactive aerodynamic design","status":"public","ddc":["003","004"],"has_accepted_license":"1","article_processing_charge":"No","day":"04","scopus_import":"1","date_published":"2018-08-04T00:00:00Z","citation":{"ama":"Umetani N, Bickel B. Learning three-dimensional flow for interactive aerodynamic design. ACM Trans Graph. 2018;37(4). doi:10.1145/3197517.3201325","ista":"Umetani N, Bickel B. 2018. Learning three-dimensional flow for interactive aerodynamic design. ACM Trans. Graph. 37(4), 89.","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","ieee":"N. Umetani and B. Bickel, “Learning three-dimensional flow for interactive aerodynamic design,” ACM Trans. Graph., vol. 37, no. 4. ACM, 2018.","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.","short":"N. Umetani, B. Bickel, ACM Trans. Graph. 37 (2018).","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."},"publication":"ACM Trans. Graph.","publist_id":"8053","ec_funded":1,"file_date_updated":"2020-07-14T12:46:22Z","article_number":"89","related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/new-interactive-machine-learning-tool-makes-car-designs-more-aerodynamic/"}]},"author":[{"first_name":"Nobuyuki","last_name":"Umetani","full_name":"Umetani, Nobuyuki"},{"full_name":"Bickel, Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","first_name":"Bernd","last_name":"Bickel"}],"volume":37,"date_created":"2018-12-11T11:44:06Z","date_updated":"2023-09-13T08:46:15Z","year":"2018","department":[{"_id":"BeBi"}],"publisher":"ACM","publication_status":"published","month":"08","doi":"10.1145/3197517.3201325","language":[{"iso":"eng"}],"external_id":{"isi":["000448185000050"]},"oa":1,"project":[{"call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767"}],"quality_controlled":"1","isi":1},{"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"149"}]},"author":[{"full_name":"Alt, Johannes","id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes","last_name":"Alt"},{"full_name":"Erdös, László","first_name":"László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603"},{"orcid":"0000-0002-4821-3297","id":"3020C786-F248-11E8-B48F-1D18A9856A87","last_name":"Krüger","first_name":"Torben H","full_name":"Krüger, Torben H"}],"volume":28,"date_created":"2018-12-11T11:47:13Z","date_updated":"2023-09-13T08:47:52Z","year":"2018","department":[{"_id":"LaEr"}],"publisher":"Institute of Mathematical Statistics","publication_status":"published","ec_funded":1,"doi":"10.1214/17-AAP1302","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1612.07776 ","open_access":"1"}],"external_id":{"isi":["000431721800005"],"arxiv":["1612.07776 "]},"oa":1,"project":[{"call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","month":"03","oa_version":"Preprint","_id":"566","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 28","title":"Local inhomogeneous circular law","status":"public","issue":"1","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"}],"type":"journal_article","date_published":"2018-03-03T00:00:00Z","citation":{"short":"J. Alt, L. Erdös, T.H. Krüger, Annals Applied Probability 28 (2018) 148–203.","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.","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.","ama":"Alt J, Erdös L, Krüger TH. Local inhomogeneous circular law. Annals Applied Probability . 2018;28(1):148-203. doi:10.1214/17-AAP1302","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","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.","ista":"Alt J, Erdös L, Krüger TH. 2018. Local inhomogeneous circular law. Annals Applied Probability . 28(1), 148–203."},"publication":"Annals Applied Probability ","page":"148-203","article_type":"original","article_processing_charge":"No","day":"03","scopus_import":"1"},{"type":"journal_article","issue":"3","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"}],"_id":"106","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 40","status":"public","title":"Long geodesics on convex surfaces","oa_version":"Preprint","scopus_import":"1","article_processing_charge":"No","day":"01","citation":{"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.","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.","ista":"Akopyan A, Petrunin A. 2018. Long geodesics on convex surfaces. Mathematical Intelligencer. 40(3), 26–31."},"publication":"Mathematical Intelligencer","page":"26 - 31","date_published":"2018-09-01T00:00:00Z","publist_id":"7948","year":"2018","department":[{"_id":"HeEd"}],"publisher":"Springer","publication_status":"published","author":[{"full_name":"Akopyan, Arseniy","first_name":"Arseniy","last_name":"Akopyan","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2548-617X"},{"first_name":"Anton","last_name":"Petrunin","full_name":"Petrunin, Anton"}],"volume":40,"date_created":"2018-12-11T11:44:40Z","date_updated":"2023-09-13T08:49:16Z","month":"09","external_id":{"isi":["000444141200005"],"arxiv":["1702.05172"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1702.05172"}],"quality_controlled":"1","isi":1,"doi":"10.1007/s00283-018-9795-5","language":[{"iso":"eng"}]},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["29650776"],"isi":["000438077800026"]},"isi":1,"quality_controlled":"1","project":[{"_id":"25A8E5EA-B435-11E9-9278-68D0E5697425","grant_number":"Y 564-B12","name":"Cytoskeletal force generation and transduction of leukocytes (FWF)","call_identifier":"FWF"},{"grant_number":"281556","_id":"25A603A2-B435-11E9-9278-68D0E5697425","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)","call_identifier":"FP7"}],"doi":"10.1083/jcb.201612051","language":[{"iso":"eng"}],"month":"04","year":"2018","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).","pmid":1,"publication_status":"published","department":[{"_id":"MiSi"},{"_id":"Bio"}],"publisher":"Rockefeller University Press","author":[{"full_name":"Brown, Markus","id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87","first_name":"Markus","last_name":"Brown"},{"full_name":"Johnson, Louise","first_name":"Louise","last_name":"Johnson"},{"first_name":"Dario","last_name":"Leone","full_name":"Leone, Dario"},{"first_name":"Peter","last_name":"Májek","full_name":"Májek, Peter"},{"full_name":"Vaahtomeri, Kari","first_name":"Kari","last_name":"Vaahtomeri","id":"368EE576-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7829-3518"},{"full_name":"Senfter, Daniel","last_name":"Senfter","first_name":"Daniel"},{"last_name":"Bukosza","first_name":"Nora","full_name":"Bukosza, Nora"},{"full_name":"Schachner, Helga","last_name":"Schachner","first_name":"Helga"},{"first_name":"Gabriele","last_name":"Asfour","full_name":"Asfour, Gabriele"},{"full_name":"Langer, Brigitte","first_name":"Brigitte","last_name":"Langer"},{"full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","first_name":"Robert"},{"last_name":"Parapatics","first_name":"Katja","full_name":"Parapatics, Katja"},{"last_name":"Hong","first_name":"Young","full_name":"Hong, Young"},{"first_name":"Keiryn","last_name":"Bennett","full_name":"Bennett, Keiryn"},{"full_name":"Kain, Renate","last_name":"Kain","first_name":"Renate"},{"full_name":"Detmar, Michael","first_name":"Michael","last_name":"Detmar"},{"first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"},{"last_name":"Jackson","first_name":"David","full_name":"Jackson, David"},{"full_name":"Kerjaschki, Dontscho","last_name":"Kerjaschki","first_name":"Dontscho"}],"date_updated":"2023-09-13T08:51:29Z","date_created":"2018-12-11T11:45:33Z","volume":217,"file_date_updated":"2020-07-14T12:45:45Z","ec_funded":1,"publist_id":"7627","publication":"Journal of Cell Biology","citation":{"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.","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.","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.","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."},"page":"2205 - 2221","date_published":"2018-04-12T00:00:00Z","scopus_import":"1","day":"12","article_processing_charge":"No","has_accepted_license":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"275","title":"Lymphatic exosomes promote dendritic cell migration along guidance cues","status":"public","ddc":["570"],"intvolume":" 217","oa_version":"Published Version","file":[{"creator":"dernst","file_size":2252043,"content_type":"application/pdf","access_level":"open_access","file_name":"2018_JournalCellBiology_Brown.pdf","checksum":"9c7eba51a35c62da8c13f98120b64df4","date_created":"2018-12-17T12:50:07Z","date_updated":"2020-07-14T12:45:45Z","file_id":"5704","relation":"main_file"}],"type":"journal_article","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"}],"issue":"6"},{"doi":"10.1038/s41477-018-0204-z","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30013211","open_access":"1"}],"oa":1,"external_id":{"pmid":["30013211"],"isi":["000443861300011"]},"project":[{"call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300"}],"quality_controlled":"1","isi":1,"month":"07","related_material":{"link":[{"url":"https://ist.ac.at/en/news/plant-mothers-talk-to-their-embryos-via-the-hormone-auxin/","relation":"press_release","description":"News on IST Homepage"}]},"author":[{"full_name":"Robert, Hélène","first_name":"Hélène","last_name":"Robert"},{"last_name":"Park","first_name":"Chulmin","full_name":"Park, Chulmin"},{"full_name":"Gutièrrez, Carla","last_name":"Gutièrrez","first_name":"Carla"},{"full_name":"Wójcikowska, Barbara","first_name":"Barbara","last_name":"Wójcikowska"},{"full_name":"Pěnčík, Aleš","first_name":"Aleš","last_name":"Pěnčík"},{"first_name":"Ondřej","last_name":"Novák","full_name":"Novák, Ondřej"},{"full_name":"Chen, Junyi","first_name":"Junyi","last_name":"Chen"},{"first_name":"Wim","last_name":"Grunewald","full_name":"Grunewald, Wim"},{"full_name":"Dresselhaus, Thomas","first_name":"Thomas","last_name":"Dresselhaus"},{"full_name":"Friml, Jirí","last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Laux","first_name":"Thomas","full_name":"Laux, Thomas"}],"volume":4,"date_created":"2018-12-11T11:44:56Z","date_updated":"2023-09-13T08:53:28Z","pmid":1,"acknowledgement":"This work was further supported by the Czech Science Foundation GACR (GA13-40637S) to J.F.;","year":"2018","publisher":"Nature Publishing Group","department":[{"_id":"JiFr"}],"publication_status":"published","ec_funded":1,"publist_id":"7763","date_published":"2018-07-16T00:00:00Z","citation":{"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","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","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.","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.","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.","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.","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."},"publication":"Nature Plants","page":"548 - 553","article_processing_charge":"No","day":"16","scopus_import":"1","oa_version":"Submitted Version","_id":"158","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 4","status":"public","title":"Maternal auxin supply contributes to early embryo patterning in Arabidopsis","issue":"8","abstract":[{"lang":"eng","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."}],"type":"journal_article"},{"day":"26","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2018-07-26T00:00:00Z","article_type":"original","page":"835 - 867","publication":"Trends in Cell Biology","citation":{"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","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.","ista":"Fiedorczuk K, Sazanov LA. 2018. Mammalian mitochondrial complex I structure and disease causing mutations. Trends in Cell Biology. 28(10), 835–867.","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","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.","short":"K. Fiedorczuk, L.A. Sazanov, Trends in Cell Biology 28 (2018) 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."},"abstract":[{"lang":"eng","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."}],"issue":"10","type":"journal_article","oa_version":"Submitted Version","file":[{"date_created":"2019-11-07T12:55:20Z","date_updated":"2020-07-14T12:45:00Z","checksum":"ef6d2b4e1fd63948539639242610bfa6","relation":"main_file","file_id":"6994","file_size":2185385,"content_type":"application/pdf","creator":"lsazanov","file_name":"SasanovFinalMS+EdComments_LS_allacc_withFigs.pdf","access_level":"open_access"}],"title":"Mammalian mitochondrial complex I structure and disease causing mutations","status":"public","ddc":["572"],"intvolume":" 28","_id":"152","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","month":"07","language":[{"iso":"eng"}],"doi":"10.1016/j.tcb.2018.06.006","isi":1,"quality_controlled":"1","external_id":{"isi":["000445118200007"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"file_date_updated":"2020-07-14T12:45:00Z","publist_id":"7769","date_created":"2018-12-11T11:44:54Z","date_updated":"2023-09-13T08:51:56Z","volume":28,"author":[{"id":"5BFF67CE-02D1-11E9-B11A-A5A4D7DFFFD0","first_name":"Karol","last_name":"Fiedorczuk","full_name":"Fiedorczuk, Karol"},{"full_name":"Sazanov, Leonid A","first_name":"Leonid A","last_name":"Sazanov","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989"}],"publication_status":"published","department":[{"_id":"LeSa"}],"publisher":"Elsevier","year":"2018"}]