[{"publication":"Opera Medica et Physiologica","day":"30","year":"2018","date_created":"2021-03-07T23:01:25Z","doi":"10.20388/omp2018.00s1.001","date_published":"2018-06-30T00:00:00Z","page":"11","oa":1,"publisher":"Lobachevsky State University of Nizhny Novgorod","quality_controlled":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"mla":"Danzl, Johann G. “Diffraction-Unlimited Optical Imaging for Synaptic Physiology.” Opera Medica et Physiologica, vol. 4, no. S1, Lobachevsky State University of Nizhny Novgorod, 2018, p. 11, doi:10.20388/omp2018.00s1.001.","ieee":"J. G. Danzl, “Diffraction-unlimited optical imaging for synaptic physiology,” Opera Medica et Physiologica, vol. 4, no. S1. Lobachevsky State University of Nizhny Novgorod, p. 11, 2018.","short":"J.G. Danzl, Opera Medica et Physiologica 4 (2018) 11.","apa":"Danzl, J. G. (2018). Diffraction-unlimited optical imaging for synaptic physiology. Opera Medica et Physiologica. Lobachevsky State University of Nizhny Novgorod. https://doi.org/10.20388/omp2018.00s1.001","ama":"Danzl JG. Diffraction-unlimited optical imaging for synaptic physiology. Opera Medica et Physiologica. 2018;4(S1):11. doi:10.20388/omp2018.00s1.001","chicago":"Danzl, Johann G. “Diffraction-Unlimited Optical Imaging for Synaptic Physiology.” Opera Medica et Physiologica. Lobachevsky State University of Nizhny Novgorod, 2018. https://doi.org/10.20388/omp2018.00s1.001.","ista":"Danzl JG. 2018. Diffraction-unlimited optical imaging for synaptic physiology. Opera Medica et Physiologica. 4(S1), 11."},"title":"Diffraction-unlimited optical imaging for synaptic physiology","article_processing_charge":"No","author":[{"first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G"}],"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["2500-2295"],"issn":["2500-2287"]},"volume":4,"issue":"S1","oa_version":"Published Version","intvolume":" 4","month":"06","main_file_link":[{"open_access":"1","url":"http://operamedphys.org/content/molecular-and-cellular-neuroscience"}],"scopus_import":"1","alternative_title":["Molecular and cellular neuroscience"],"date_updated":"2021-12-03T07:31:05Z","department":[{"_id":"JoDa"}],"_id":"9229","status":"public","type":"journal_article","article_type":"letter_note"},{"date_created":"2019-02-14T14:12:09Z","date_published":"2018-08-01T00:00:00Z","doi":"10.4230/LIPICS.MFCS.2018.23","year":"2018","has_accepted_license":"1","day":"01","oa":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","article_processing_charge":"No","author":[{"last_name":"Avni","orcid":"0000-0001-5588-8287","full_name":"Avni, Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","first_name":"Guy"},{"first_name":"Shibashis","last_name":"Guha","full_name":"Guha, Shibashis"},{"full_name":"Kupferman, Orna","last_name":"Kupferman","first_name":"Orna"}],"title":"Timed network games with clocks","citation":{"chicago":"Avni, Guy, Shibashis Guha, and Orna Kupferman. “Timed Network Games with Clocks,” Vol. 117. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPICS.MFCS.2018.23.","ista":"Avni G, Guha S, Kupferman O. 2018. Timed network games with clocks. MFCS: Mathematical Foundations of Computer Science, LIPIcs, vol. 117, 23.","mla":"Avni, Guy, et al. Timed Network Games with Clocks. Vol. 117, 23, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:10.4230/LIPICS.MFCS.2018.23.","short":"G. Avni, S. Guha, O. Kupferman, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","ieee":"G. Avni, S. Guha, and O. Kupferman, “Timed network games with clocks,” presented at the MFCS: Mathematical Foundations of Computer Science, Liverpool, United Kingdom, 2018, vol. 117.","apa":"Avni, G., Guha, S., & Kupferman, O. (2018). Timed network games with clocks (Vol. 117). Presented at the MFCS: Mathematical Foundations of Computer Science, Liverpool, United Kingdom: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.MFCS.2018.23","ama":"Avni G, Guha S, Kupferman O. Timed network games with clocks. In: Vol 117. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPICS.MFCS.2018.23"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"name":"The Wittgenstein Prize","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"264B3912-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Formal Methods meets Algorithmic Game Theory","grant_number":"M02369"}],"article_number":"23","volume":117,"related_material":{"record":[{"relation":"earlier_version","id":"963","status":"public"}]},"publication_status":"published","publication_identifier":{"issn":["1868-8969"]},"language":[{"iso":"eng"}],"file":[{"date_updated":"2020-07-14T12:47:15Z","file_size":542889,"creator":"dernst","date_created":"2019-02-14T14:22:04Z","file_name":"2018_LIPIcs_Avni.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"6007","checksum":"41ab2ae9b63f5eb49fa995250c0ba128"}],"scopus_import":"1","alternative_title":["LIPIcs"],"intvolume":" 117","month":"08","abstract":[{"lang":"eng","text":"Network games are widely used as a model for selfish resource-allocation problems. In the classicalmodel, each player selects a path connecting her source and target vertices. The cost of traversingan edge depends on theload; namely, number of players that traverse it. Thus, it abstracts the factthat different users may use a resource at different times and for different durations, which playsan important role in determining the costs of the users in reality. For example, when transmittingpackets in a communication network, routing traffic in a road network, or processing a task in aproduction system, actual sharing and congestion of resources crucially depends on time.In [13], we introducedtimed network games, which add a time component to network games.Each vertexvin the network is associated with a cost function, mapping the load onvto theprice that a player pays for staying invfor one time unit with this load. Each edge in thenetwork is guarded by the time intervals in which it can be traversed, which forces the players tospend time in the vertices. In this work we significantly extend the way time can be referred toin timed network games. In the model we study, the network is equipped withclocks, and, as intimed automata, edges are guarded by constraints on the values of the clocks, and their traversalmay involve a reset of some clocks. We argue that the stronger model captures many realisticnetworks. The addition of clocks breaks the techniques we developed in [13] and we developnew techniques in order to show that positive results on classic network games carry over to thestronger timed setting."}],"oa_version":"Published Version","department":[{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:47:15Z","date_updated":"2023-02-23T14:02:58Z","ddc":["000"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"start_date":"2018-08-27","location":"Liverpool, United Kingdom","end_date":"2018-08-31","name":"MFCS: Mathematical Foundations of Computer Science"},"type":"conference","status":"public","_id":"6005"},{"article_number":"e2005372","title":"Is the sky the limit? On the expansion threshold of a species’ range","author":[{"full_name":"Polechova, Jitka","orcid":"0000-0003-0951-3112","last_name":"Polechova","first_name":"Jitka","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7550","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Polechova J. Is the sky the limit? On the expansion threshold of a species’ range. PLoS Biology. 2018;16(6). doi:10.1371/journal.pbio.2005372","apa":"Polechova, J. (2018). Is the sky the limit? On the expansion threshold of a species’ range. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2005372","short":"J. Polechova, PLoS Biology 16 (2018).","ieee":"J. Polechova, “Is the sky the limit? On the expansion threshold of a species’ range,” PLoS Biology, vol. 16, no. 6. Public Library of Science, 2018.","mla":"Polechova, Jitka. “Is the Sky the Limit? On the Expansion Threshold of a Species’ Range.” PLoS Biology, vol. 16, no. 6, e2005372, Public Library of Science, 2018, doi:10.1371/journal.pbio.2005372.","ista":"Polechova J. 2018. Is the sky the limit? On the expansion threshold of a species’ range. PLoS Biology. 16(6), e2005372.","chicago":"Polechova, Jitka. “Is the Sky the Limit? On the Expansion Threshold of a Species’ Range.” PLoS Biology. Public Library of Science, 2018. https://doi.org/10.1371/journal.pbio.2005372."},"oa":1,"quality_controlled":"1","publisher":"Public Library of Science","date_created":"2018-12-11T11:45:46Z","date_published":"2018-06-15T00:00:00Z","doi":"10.1371/journal.pbio.2005372","publication":"PLoS Biology","day":"15","year":"2018","has_accepted_license":"1","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":"315","department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:46:01Z","ddc":["576"],"date_updated":"2023-02-23T14:10:16Z","intvolume":" 16","month":"06","scopus_import":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"More than 100 years after Grigg’s influential analysis of species’ borders, the causes of limits to species’ ranges still represent a puzzle that has never been understood with clarity. The topic has become especially important recently as many scientists have become interested in the potential for species’ ranges to shift in response to climate change—and yet nearly all of those studies fail to recognise or incorporate evolutionary genetics in a way that relates to theoretical developments. I show that range margins can be understood based on just two measurable parameters: (i) the fitness cost of dispersal—a measure of environmental heterogeneity—and (ii) the strength of genetic drift, which reduces genetic diversity. Together, these two parameters define an ‘expansion threshold’: adaptation fails when genetic drift reduces genetic diversity below that required for adaptation to a heterogeneous environment. When the key parameters drop below this expansion threshold locally, a sharp range margin forms. When they drop below this threshold throughout the species’ range, adaptation collapses everywhere, resulting in either extinction or formation of a fragmented metapopulation. Because the effects of dispersal differ fundamentally with dimension, the second parameter—the strength of genetic drift—is qualitatively different compared to a linear habitat. In two-dimensional habitats, genetic drift becomes effectively independent of selection. It decreases with ‘neighbourhood size’—the number of individuals accessible by dispersal within one generation. Moreover, in contrast to earlier predictions, which neglected evolution of genetic variance and/or stochasticity in two dimensions, dispersal into small marginal populations aids adaptation. This is because the reduction of both genetic and demographic stochasticity has a stronger effect than the cost of dispersal through increased maladaptation. The expansion threshold thus provides a novel, theoretically justified, and testable prediction for formation of the range margin and collapse of the species’ range."}],"volume":16,"issue":"6","related_material":{"record":[{"id":"9839","status":"public","relation":"research_data"}]},"language":[{"iso":"eng"}],"file":[{"creator":"dernst","date_updated":"2020-07-14T12:46:01Z","file_size":6968201,"date_created":"2019-01-22T08:30:03Z","file_name":"2017_PLOS_Polechova.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"5870","checksum":"908c52751bba30c55ed36789e5e4c84d"}],"publication_status":"published","publication_identifier":{"issn":["15449173"]}},{"author":[{"full_name":"Frost, Jennifer M.","last_name":"Frost","first_name":"Jennifer M."},{"first_name":"M. Yvonne","full_name":"Kim, M. Yvonne","last_name":"Kim"},{"first_name":"Guen Tae","last_name":"Park","full_name":"Park, Guen Tae"},{"last_name":"Hsieh","full_name":"Hsieh, Ping-Hung","first_name":"Ping-Hung"},{"last_name":"Nakamura","full_name":"Nakamura, Miyuki","first_name":"Miyuki"},{"first_name":"Samuel J. H.","full_name":"Lin, Samuel J. H.","last_name":"Lin"},{"first_name":"Hyunjin","full_name":"Yoo, Hyunjin","last_name":"Yoo"},{"first_name":"Jaemyung","full_name":"Choi, Jaemyung","last_name":"Choi"},{"last_name":"Ikeda","full_name":"Ikeda, Yoko","first_name":"Yoko"},{"full_name":"Kinoshita, Tetsu","last_name":"Kinoshita","first_name":"Tetsu"},{"last_name":"Choi","full_name":"Choi, Yeonhee","first_name":"Yeonhee"},{"first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649"},{"full_name":"Fischer, Robert L.","last_name":"Fischer","first_name":"Robert L."}],"article_processing_charge":"No","external_id":{"pmid":["29712855"]},"title":"FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis","citation":{"short":"J.M. Frost, M.Y. Kim, G.T. Park, P.-H. Hsieh, M. Nakamura, S.J.H. Lin, H. Yoo, J. Choi, Y. Ikeda, T. Kinoshita, Y. Choi, D. Zilberman, R.L. Fischer, Proceedings of the National Academy of Sciences 115 (2018) E4720–E4729.","ieee":"J. M. Frost et al., “FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis,” Proceedings of the National Academy of Sciences, vol. 115, no. 20. National Academy of Sciences, pp. E4720–E4729, 2018.","ama":"Frost JM, Kim MY, Park GT, et al. FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis. Proceedings of the National Academy of Sciences. 2018;115(20):E4720-E4729. doi:10.1073/pnas.1713333115","apa":"Frost, J. M., Kim, M. Y., Park, G. T., Hsieh, P.-H., Nakamura, M., Lin, S. J. H., … Fischer, R. L. (2018). FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1713333115","mla":"Frost, Jennifer M., et al. “FACT Complex Is Required for DNA Demethylation at Heterochromatin during Reproduction in Arabidopsis.” Proceedings of the National Academy of Sciences, vol. 115, no. 20, National Academy of Sciences, 2018, pp. E4720–29, doi:10.1073/pnas.1713333115.","ista":"Frost JM, Kim MY, Park GT, Hsieh P-H, Nakamura M, Lin SJH, Yoo H, Choi J, Ikeda Y, Kinoshita T, Choi Y, Zilberman D, Fischer RL. 2018. FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis. Proceedings of the National Academy of Sciences. 115(20), E4720–E4729.","chicago":"Frost, Jennifer M., M. Yvonne Kim, Guen Tae Park, Ping-Hung Hsieh, Miyuki Nakamura, Samuel J. H. Lin, Hyunjin Yoo, et al. “FACT Complex Is Required for DNA Demethylation at Heterochromatin during Reproduction in Arabidopsis.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1713333115."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publisher":"National Academy of Sciences","quality_controlled":"1","oa":1,"page":"E4720-E4729","date_published":"2018-05-15T00:00:00Z","doi":"10.1073/pnas.1713333115","date_created":"2021-06-07T06:11:28Z","has_accepted_license":"1","year":"2018","day":"15","publication":"Proceedings of the National Academy of Sciences","article_type":"original","type":"journal_article","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"},"status":"public","keyword":["Multidisciplinary"],"_id":"9471","file_date_updated":"2021-06-07T06:16:38Z","department":[{"_id":"DaZi"}],"date_updated":"2021-12-14T07:53:40Z","extern":"1","ddc":["580"],"scopus_import":"1","month":"05","intvolume":" 115","abstract":[{"text":"The DEMETER (DME) DNA glycosylase catalyzes genome-wide DNA demethylation and is required for endosperm genomic imprinting and embryo viability. Targets of DME-mediated DNA demethylation reside in small, euchromatic, AT-rich transposons and at the boundaries of large transposons, but how DME interacts with these diverse chromatin states is unknown. The STRUCTURE SPECIFIC RECOGNITION PROTEIN 1 (SSRP1) subunit of the chromatin remodeler FACT (facilitates chromatin transactions), was previously shown to be involved in the DME-dependent regulation of genomic imprinting in Arabidopsis endosperm. Therefore, to investigate the interaction between DME and chromatin, we focused on the activity of the two FACT subunits, SSRP1 and SUPPRESSOR of TY16 (SPT16), during reproduction in Arabidopsis. We found that FACT colocalizes with nuclear DME in vivo, and that DME has two classes of target sites, the first being euchromatic and accessible to DME, but the second, representing over half of DME targets, requiring the action of FACT for DME-mediated DNA demethylation genome-wide. Our results show that the FACT-dependent DME targets are GC-rich heterochromatin domains with high nucleosome occupancy enriched with H3K9me2 and H3K27me1. Further, we demonstrate that heterochromatin-associated linker histone H1 specifically mediates the requirement for FACT at a subset of DME-target loci. Overall, our results demonstrate that FACT is required for DME targeting by facilitating its access to heterochromatin.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"volume":115,"related_material":{"link":[{"relation":"earlier_version","url":"https://doi.org/10.1101/187674 "}]},"issue":"20","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"publication_status":"published","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"810260dc0e3cc3033e15c19ad0dc123e","file_id":"9472","file_size":3045260,"date_updated":"2021-06-07T06:16:38Z","creator":"asandaue","file_name":"2018_PNAS_Frost.pdf","date_created":"2021-06-07T06:16:38Z"}],"language":[{"iso":"eng"}]},{"project":[{"call_identifier":"FWF","_id":"261FA626-B435-11E9-9278-68D0E5697425","grant_number":"M02281","name":"Eliminating intersections in drawings of graphs"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Fulek R, Kynčl J. 2018. The ℤ2-Genus of Kuratowski minors. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 99, 40.1-40.14.","chicago":"Fulek, Radoslav, and Jan Kynčl. “The ℤ2-Genus of Kuratowski Minors,” 99:40.1-40.14. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPIcs.SoCG.2018.40.","ama":"Fulek R, Kynčl J. The ℤ2-Genus of Kuratowski minors. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018:40.1-40.14. doi:10.4230/LIPIcs.SoCG.2018.40","apa":"Fulek, R., & Kynčl, J. (2018). The ℤ2-Genus of Kuratowski minors (Vol. 99, p. 40.1-40.14). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2018.40","short":"R. Fulek, J. Kynčl, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 40.1-40.14.","ieee":"R. Fulek and J. Kynčl, “The ℤ2-Genus of Kuratowski minors,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99, p. 40.1-40.14.","mla":"Fulek, Radoslav, and Jan Kynčl. The ℤ2-Genus of Kuratowski Minors. Vol. 99, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 40.1-40.14, doi:10.4230/LIPIcs.SoCG.2018.40."},"title":"The ℤ2-Genus of Kuratowski minors","article_processing_charge":"No","external_id":{"arxiv":["1803.05085"]},"publist_id":"7734","author":[{"last_name":"Fulek","orcid":"0000-0001-8485-1774","full_name":"Fulek, Radoslav","first_name":"Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jan","last_name":"Kynčl","full_name":"Kynčl, Jan"}],"oa":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","day":"11","year":"2018","date_created":"2018-12-11T11:45:05Z","date_published":"2018-06-11T00:00:00Z","doi":"10.4230/LIPIcs.SoCG.2018.40","page":"40.1 - 40.14","_id":"186","status":"public","conference":{"name":"SoCG: Symposium on Computational Geometry","location":"Budapest, Hungary","end_date":"2018-06-14","start_date":"2018-06-11"},"type":"conference","date_updated":"2023-08-14T12:43:51Z","department":[{"_id":"UlWa"}],"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"A drawing of a graph on a surface is independently even if every pair of nonadjacent edges in the drawing crosses an even number of times. The ℤ2-genus of a graph G is the minimum g such that G has an independently even drawing on the orientable surface of genus g. An unpublished result by Robertson and Seymour implies that for every t, every graph of sufficiently large genus contains as a minor a projective t × t grid or one of the following so-called t-Kuratowski graphs: K3, t, or t copies of K5 or K3,3 sharing at most 2 common vertices. We show that the ℤ2-genus of graphs in these families is unbounded in t; in fact, equal to their genus. Together, this implies that the genus of a graph is bounded from above by a function of its ℤ2-genus, solving a problem posed by Schaefer and Štefankovič, and giving an approximate version of the Hanani-Tutte theorem on orientable surfaces."}],"intvolume":" 99","month":"06","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1803.05085"}],"alternative_title":["LIPIcs"],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","volume":99,"related_material":{"record":[{"status":"public","id":"11593","relation":"later_version"}]}},{"date_updated":"2023-08-24T14:39:32Z","department":[{"_id":"UlWa"}],"_id":"433","type":"conference","conference":{"name":"GD 2017: Graph Drawing and Network Visualization","start_date":"201-09-25","end_date":"2017-09-27","location":"Boston, MA, United States"},"status":"public","publication_status":"published","language":[{"iso":"eng"}],"volume":10692,"related_material":{"record":[{"relation":"later_version","id":"5857","status":"public"}]},"abstract":[{"lang":"eng","text":"A thrackle is a graph drawn in the plane so that every pair of its edges meet exactly once: either at a common end vertex or in a proper crossing. We prove that any thrackle of n vertices has at most 1.3984n edges. Quasi-thrackles are defined similarly, except that every pair of edges that do not share a vertex are allowed to cross an odd number of times. It is also shown that the maximum number of edges of a quasi-thrackle on n vertices is 3/2(n-1), and that this bound is best possible for infinitely many values of n."}],"oa_version":"Submitted Version","scopus_import":1,"alternative_title":["LNCS"],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1708.08037"}],"month":"01","intvolume":" 10692","citation":{"chicago":"Fulek, Radoslav, and János Pach. “Thrackles: An Improved Upper Bound,” 10692:160–66. Springer, 2018. https://doi.org/10.1007/978-3-319-73915-1_14.","ista":"Fulek R, Pach J. 2018. Thrackles: An improved upper bound. GD 2017: Graph Drawing and Network Visualization, LNCS, vol. 10692, 160–166.","mla":"Fulek, Radoslav, and János Pach. Thrackles: An Improved Upper Bound. Vol. 10692, Springer, 2018, pp. 160–66, doi:10.1007/978-3-319-73915-1_14.","ieee":"R. Fulek and J. Pach, “Thrackles: An improved upper bound,” presented at the GD 2017: Graph Drawing and Network Visualization, Boston, MA, United States, 2018, vol. 10692, pp. 160–166.","short":"R. Fulek, J. Pach, in:, Springer, 2018, pp. 160–166.","apa":"Fulek, R., & Pach, J. (2018). Thrackles: An improved upper bound (Vol. 10692, pp. 160–166). Presented at the GD 2017: Graph Drawing and Network Visualization, Boston, MA, United States: Springer. https://doi.org/10.1007/978-3-319-73915-1_14","ama":"Fulek R, Pach J. Thrackles: An improved upper bound. In: Vol 10692. Springer; 2018:160-166. doi:10.1007/978-3-319-73915-1_14"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","last_name":"Fulek","full_name":"Fulek, Radoslav","orcid":"0000-0001-8485-1774"},{"first_name":"János","last_name":"Pach","full_name":"Pach, János"}],"publist_id":"7390","external_id":{"arxiv":["1708.08037"]},"title":"Thrackles: An improved upper bound","year":"2018","day":"21","page":"160 - 166","date_published":"2018-01-21T00:00:00Z","doi":"10.1007/978-3-319-73915-1_14","date_created":"2018-12-11T11:46:27Z","quality_controlled":"1","publisher":"Springer","oa":1},{"date_created":"2021-08-09T12:46:39Z","date_published":"2018-10-09T00:00:00Z","doi":"10.5061/dryad.72cg113","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"6095"}]},"day":"09","year":"2018","month":"10","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.72cg113"}],"oa":1,"publisher":"Dryad","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Both classical and recent studies suggest that chromosomal inversion polymorphisms are important in adaptation and speciation. However, biases in discovery and reporting of inversions make it difficult to assess their prevalence and biological importance. Here, we use an approach based on linkage disequilibrium among markers genotyped for samples collected across a transect between contrasting habitats to detect chromosomal rearrangements de novo. We report 17 polymorphic rearrangements in a single locality for the coastal marine snail, Littorina saxatilis. Patterns of diversity in the field and of recombination in controlled crosses provide strong evidence that at least the majority of these rearrangements are inversions. Most show clinal changes in frequency between habitats, suggestive of divergent selection, but only one appears to be fixed for different arrangements in the two habitats. Consistent with widespread evidence for balancing selection on inversion polymorphisms, we argue that a combination of heterosis and divergent selection can explain the observed patterns and should be considered in other systems spanning environmental gradients."}],"department":[{"_id":"NiBa"}],"title":"Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes","article_processing_charge":"No","author":[{"first_name":"Rui","full_name":"Faria, Rui","last_name":"Faria"},{"first_name":"Pragya","last_name":"Chaube","full_name":"Chaube, Pragya"},{"first_name":"Hernán E.","full_name":"Morales, Hernán E.","last_name":"Morales"},{"full_name":"Larsson, Tomas","last_name":"Larsson","first_name":"Tomas"},{"first_name":"Alan R.","last_name":"Lemmon","full_name":"Lemmon, Alan R."},{"first_name":"Emily M.","last_name":"Lemmon","full_name":"Lemmon, Emily M."},{"last_name":"Rafajlović","full_name":"Rafajlović, Marina","first_name":"Marina"},{"first_name":"Marina","last_name":"Panova","full_name":"Panova, Marina"},{"first_name":"Mark","full_name":"Ravinet, Mark","last_name":"Ravinet"},{"last_name":"Johannesson","full_name":"Johannesson, Kerstin","first_name":"Kerstin"},{"last_name":"Westram","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M"},{"last_name":"Butlin","full_name":"Butlin, Roger K.","first_name":"Roger K."}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-08-24T14:50:26Z","citation":{"ista":"Faria R, Chaube P, Morales HE, Larsson T, Lemmon AR, Lemmon EM, Rafajlović M, Panova M, Ravinet M, Johannesson K, Westram AM, Butlin RK. 2018. Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes, Dryad, 10.5061/dryad.72cg113.","chicago":"Faria, Rui, Pragya Chaube, Hernán E. Morales, Tomas Larsson, Alan R. Lemmon, Emily M. Lemmon, Marina Rafajlović, et al. “Data from: Multiple Chromosomal Rearrangements in a Hybrid Zone between Littorina Saxatilis Ecotypes.” Dryad, 2018. https://doi.org/10.5061/dryad.72cg113.","short":"R. Faria, P. Chaube, H.E. Morales, T. Larsson, A.R. Lemmon, E.M. Lemmon, M. Rafajlović, M. Panova, M. Ravinet, K. Johannesson, A.M. Westram, R.K. Butlin, (2018).","ieee":"R. Faria et al., “Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes.” Dryad, 2018.","apa":"Faria, R., Chaube, P., Morales, H. E., Larsson, T., Lemmon, A. R., Lemmon, E. M., … Butlin, R. K. (2018). Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. Dryad. https://doi.org/10.5061/dryad.72cg113","ama":"Faria R, Chaube P, Morales HE, et al. Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. 2018. doi:10.5061/dryad.72cg113","mla":"Faria, Rui, et al. Data from: Multiple Chromosomal Rearrangements in a Hybrid Zone between Littorina Saxatilis Ecotypes. Dryad, 2018, doi:10.5061/dryad.72cg113."},"status":"public","type":"research_data_reference","_id":"9837"},{"status":"public","type":"book_chapter","series_title":"OCTR","_id":"10864","department":[{"_id":"VlKo"}],"date_updated":"2023-09-05T15:37:18Z","intvolume":" 16","month":"03","place":"Cham","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1502.01072"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"text":"We prove that every congruence distributive variety has directed Jónsson terms, and every congruence modular variety has directed Gumm terms. The directed terms we construct witness every case of absorption witnessed by the original Jónsson or Gumm terms. This result is equivalent to a pair of claims about absorption for admissible preorders in congruence distributive and congruence modular varieties, respectively. For finite algebras, these absorption theorems have already seen significant applications, but until now, it was not clear if the theorems hold for general algebras as well. Our method also yields a novel proof of a result by P. Lipparini about the existence of a chain of terms (which we call Pixley terms) in varieties that are at the same time congruence distributive and k-permutable for some k.","lang":"eng"}],"volume":16,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["2211-2766"],"isbn":["9783319747712"],"issn":["2211-2758"],"eisbn":["9783319747729"]},"editor":[{"first_name":"J","full_name":"Czelakowski, J","last_name":"Czelakowski"}],"title":"Absorption and directed Jónsson terms","article_processing_charge":"No","external_id":{"arxiv":["1502.01072"]},"author":[{"full_name":"Kazda, Alexandr","last_name":"Kazda","first_name":"Alexandr","id":"3B32BAA8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kozik, Marcin","last_name":"Kozik","first_name":"Marcin"},{"first_name":"Ralph","full_name":"McKenzie, Ralph","last_name":"McKenzie"},{"first_name":"Matthew","full_name":"Moore, Matthew","last_name":"Moore"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Kazda A, Kozik M, McKenzie R, Moore M. 2018.Absorption and directed Jónsson terms. In: Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science. vol. 16, 203–220.","chicago":"Kazda, Alexandr, Marcin Kozik, Ralph McKenzie, and Matthew Moore. “Absorption and Directed Jónsson Terms.” In Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science, edited by J Czelakowski, 16:203–20. OCTR. Cham: Springer Nature, 2018. https://doi.org/10.1007/978-3-319-74772-9_7.","ieee":"A. Kazda, M. Kozik, R. McKenzie, and M. Moore, “Absorption and directed Jónsson terms,” in Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science, vol. 16, J. Czelakowski, Ed. Cham: Springer Nature, 2018, pp. 203–220.","short":"A. Kazda, M. Kozik, R. McKenzie, M. Moore, in:, J. Czelakowski (Ed.), Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science, Springer Nature, Cham, 2018, pp. 203–220.","apa":"Kazda, A., Kozik, M., McKenzie, R., & Moore, M. (2018). Absorption and directed Jónsson terms. In J. Czelakowski (Ed.), Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science (Vol. 16, pp. 203–220). Cham: Springer Nature. https://doi.org/10.1007/978-3-319-74772-9_7","ama":"Kazda A, Kozik M, McKenzie R, Moore M. Absorption and directed Jónsson terms. In: Czelakowski J, ed. Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science. Vol 16. OCTR. Cham: Springer Nature; 2018:203-220. doi:10.1007/978-3-319-74772-9_7","mla":"Kazda, Alexandr, et al. “Absorption and Directed Jónsson Terms.” Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science, edited by J Czelakowski, vol. 16, Springer Nature, 2018, pp. 203–20, doi:10.1007/978-3-319-74772-9_7."},"oa":1,"publisher":"Springer Nature","quality_controlled":"1","acknowledgement":"The second author was supported by National Science Center grant DEC-2011-/01/B/ST6/01006.","date_created":"2022-03-18T10:30:32Z","doi":"10.1007/978-3-319-74772-9_7","date_published":"2018-03-21T00:00:00Z","page":"203-220","publication":"Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science","day":"21","year":"2018"},{"_id":"184","status":"public","conference":{"location":"Budapest, Hungary","end_date":"2018-06-14","start_date":"2018-06-11","name":"SoCG: Symposium on Computational Geometry"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"conference","ddc":["516","000"],"date_updated":"2023-09-06T11:10:57Z","department":[{"_id":"UlWa"}],"file_date_updated":"2020-07-14T12:45:18Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"We prove that for every d ≥ 2, deciding if a pure, d-dimensional, simplicial complex is shellable is NP-hard, hence NP-complete. This resolves a question raised, e.g., by Danaraj and Klee in 1978. Our reduction also yields that for every d ≥ 2 and k ≥ 0, deciding if a pure, d-dimensional, simplicial complex is k-decomposable is NP-hard. For d ≥ 3, both problems remain NP-hard when restricted to contractible pure d-dimensional complexes."}],"intvolume":" 99","month":"06","scopus_import":1,"alternative_title":["Leibniz International Proceedings in Information, LIPIcs"],"language":[{"iso":"eng"}],"file":[{"date_updated":"2020-07-14T12:45:18Z","file_size":718414,"creator":"dernst","date_created":"2018-12-17T16:35:02Z","file_name":"2018_LIPIcs_Goaoc.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"d12bdd60f04a57307867704b5f930afd","file_id":"5725"}],"publication_status":"published","related_material":{"record":[{"relation":"later_version","status":"public","id":"7108"}]},"volume":99,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Goaoc, Xavier, et al. Shellability Is NP-Complete. Vol. 99, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 41:1-41:16, doi:10.4230/LIPIcs.SoCG.2018.41.","ama":"Goaoc X, Paták P, Patakova Z, Tancer M, Wagner U. Shellability is NP-complete. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018:41:1-41:16. doi:10.4230/LIPIcs.SoCG.2018.41","apa":"Goaoc, X., Paták, P., Patakova, Z., Tancer, M., & Wagner, U. (2018). Shellability is NP-complete (Vol. 99, p. 41:1-41:16). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2018.41","short":"X. Goaoc, P. Paták, Z. Patakova, M. Tancer, U. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 41:1-41:16.","ieee":"X. Goaoc, P. Paták, Z. Patakova, M. Tancer, and U. Wagner, “Shellability is NP-complete,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99, p. 41:1-41:16.","chicago":"Goaoc, Xavier, Pavel Paták, Zuzana Patakova, Martin Tancer, and Uli Wagner. “Shellability Is NP-Complete,” 99:41:1-41:16. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPIcs.SoCG.2018.41.","ista":"Goaoc X, Paták P, Patakova Z, Tancer M, Wagner U. 2018. Shellability is NP-complete. SoCG: Symposium on Computational Geometry, Leibniz International Proceedings in Information, LIPIcs, vol. 99, 41:1-41:16."},"title":"Shellability is NP-complete","publist_id":"7736","author":[{"last_name":"Goaoc","full_name":"Goaoc, Xavier","first_name":"Xavier"},{"first_name":"Pavel","last_name":"Paták","full_name":"Paták, Pavel"},{"last_name":"Patakova","full_name":"Patakova, Zuzana","orcid":"0000-0002-3975-1683","id":"48B57058-F248-11E8-B48F-1D18A9856A87","first_name":"Zuzana"},{"full_name":"Tancer, Martin","orcid":"0000-0002-1191-6714","last_name":"Tancer","id":"38AC689C-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"},{"id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli","last_name":"Wagner","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli"}],"acknowledgement":"Partially supported by the project EMBEDS II (CZ: 7AMB17FR029, FR: 38087RM) of Czech-French collaboration.","oa":1,"quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","day":"11","year":"2018","has_accepted_license":"1","date_created":"2018-12-11T11:45:04Z","date_published":"2018-06-11T00:00:00Z","doi":"10.4230/LIPIcs.SoCG.2018.41","page":"41:1 - 41:16"},{"article_number":"46","article_processing_charge":"No","external_id":{"arxiv":["1712.00434"]},"publist_id":"7614","author":[{"first_name":"Kristóf","id":"33C26278-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5445-5057","full_name":"Huszár, Kristóf","last_name":"Huszár"},{"first_name":"Jonathan","full_name":"Spreer, Jonathan","last_name":"Spreer"},{"last_name":"Wagner","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli"}],"title":"On the treewidth of triangulated 3-manifolds","citation":{"mla":"Huszár, Kristóf, et al. On the Treewidth of Triangulated 3-Manifolds. Vol. 99, 46, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:10.4230/LIPIcs.SoCG.2018.46.","apa":"Huszár, K., Spreer, J., & Wagner, U. (2018). On the treewidth of triangulated 3-manifolds (Vol. 99). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2018.46","ama":"Huszár K, Spreer J, Wagner U. On the treewidth of triangulated 3-manifolds. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPIcs.SoCG.2018.46","short":"K. Huszár, J. Spreer, U. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","ieee":"K. Huszár, J. Spreer, and U. Wagner, “On the treewidth of triangulated 3-manifolds,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99.","chicago":"Huszár, Kristóf, Jonathan Spreer, and Uli Wagner. “On the Treewidth of Triangulated 3-Manifolds,” Vol. 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPIcs.SoCG.2018.46.","ista":"Huszár K, Spreer J, Wagner U. 2018. On the treewidth of triangulated 3-manifolds. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 99, 46."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","acknowledgement":"Research of the second author was supported by the Einstein Foundation (project “Einstein Visiting Fellow Santos”) and by the Simons Foundation (“Simons Visiting Professors” program).","date_created":"2018-12-11T11:45:37Z","doi":"10.4230/LIPIcs.SoCG.2018.46","date_published":"2018-06-01T00:00:00Z","year":"2018","has_accepted_license":"1","day":"01","conference":{"name":"SoCG: Symposium on Computational Geometry","location":"Budapest, Hungary","end_date":"2018-06-14","start_date":"2018-06-11"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"conference","status":"public","_id":"285","file_date_updated":"2020-07-14T12:45:51Z","department":[{"_id":"UlWa"}],"date_updated":"2023-09-06T11:13:41Z","ddc":["516","000"],"scopus_import":1,"alternative_title":["LIPIcs"],"intvolume":" 99","month":"06","abstract":[{"lang":"eng","text":"In graph theory, as well as in 3-manifold topology, there exist several width-type parameters to describe how "simple" or "thin" a given graph or 3-manifold is. These parameters, such as pathwidth or treewidth for graphs, or the concept of thin position for 3-manifolds, play an important role when studying algorithmic problems; in particular, there is a variety of problems in computational 3-manifold topology - some of them known to be computationally hard in general - that become solvable in polynomial time as soon as the dual graph of the input triangulation has bounded treewidth. In view of these algorithmic results, it is natural to ask whether every 3-manifold admits a triangulation of bounded treewidth. We show that this is not the case, i.e., that there exists an infinite family of closed 3-manifolds not admitting triangulations of bounded pathwidth or treewidth (the latter implies the former, but we present two separate proofs). We derive these results from work of Agol and of Scharlemann and Thompson, by exhibiting explicit connections between the topology of a 3-manifold M on the one hand and width-type parameters of the dual graphs of triangulations of M on the other hand, answering a question that had been raised repeatedly by researchers in computational 3-manifold topology. In particular, we show that if a closed, orientable, irreducible, non-Haken 3-manifold M has a triangulation of treewidth (resp. pathwidth) k then the Heegaard genus of M is at most 48(k+1) (resp. 4(3k+1))."}],"oa_version":"Submitted Version","related_material":{"record":[{"relation":"later_version","status":"public","id":"7093"}]},"volume":99,"publication_status":"published","publication_identifier":{"issn":["18688969"]},"language":[{"iso":"eng"}],"file":[{"file_id":"5713","checksum":"530d084116778135d5bffaa317479cac","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-17T15:32:38Z","file_name":"2018_LIPIcs_Huszar.pdf","date_updated":"2020-07-14T12:45:51Z","file_size":642522,"creator":"dernst"}]},{"_id":"13059","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":"research_data_reference","status":"public","date_updated":"2023-09-06T14:32:51Z","citation":{"mla":"Garriga, Edgar, et al. Fast and Accurate Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method. Zenodo, 2018, doi:10.5281/ZENODO.2025846.","apa":"Garriga, E., di Tommaso, P., Magis, C., Erb, I., Mansouri, L., Baltzis, A., … Notredame, C. (2018). Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method. Zenodo. https://doi.org/10.5281/ZENODO.2025846","ama":"Garriga E, di Tommaso P, Magis C, et al. Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method. 2018. doi:10.5281/ZENODO.2025846","ieee":"E. Garriga et al., “Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method.” Zenodo, 2018.","short":"E. Garriga, P. di Tommaso, C. Magis, I. Erb, L. Mansouri, A. Baltzis, H. Laayouni, F. Kondrashov, E. Floden, C. Notredame, (2018).","chicago":"Garriga, Edgar, Paolo di Tommaso, Cedrik Magis, Ionas Erb, Leila Mansouri, Athanasios Baltzis, Hafid Laayouni, Fyodor Kondrashov, Evan Floden, and Cedric Notredame. “Fast and Accurate Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method.” Zenodo, 2018. https://doi.org/10.5281/ZENODO.2025846.","ista":"Garriga E, di Tommaso P, Magis C, Erb I, Mansouri L, Baltzis A, Laayouni H, Kondrashov F, Floden E, Notredame C. 2018. Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method, Zenodo, 10.5281/ZENODO.2025846."},"ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"first_name":"Edgar","last_name":"Garriga","full_name":"Garriga, Edgar"},{"full_name":"di Tommaso, Paolo","last_name":"di Tommaso","first_name":"Paolo"},{"first_name":"Cedrik","full_name":"Magis, Cedrik","last_name":"Magis"},{"first_name":"Ionas","full_name":"Erb, Ionas","last_name":"Erb"},{"last_name":"Mansouri","full_name":"Mansouri, Leila","first_name":"Leila"},{"first_name":"Athanasios","full_name":"Baltzis, Athanasios","last_name":"Baltzis"},{"first_name":"Hafid","last_name":"Laayouni","full_name":"Laayouni, Hafid"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","last_name":"Kondrashov"},{"last_name":"Floden","full_name":"Floden, Evan","first_name":"Evan"},{"first_name":"Cedric","full_name":"Notredame, Cedric","last_name":"Notredame"}],"department":[{"_id":"FyKo"}],"title":"Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method","abstract":[{"text":"This dataset contains a GitHub repository containing all the data, analysis, Nextflow workflows and Jupyter notebooks to replicate the manuscript titled \"Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method\".\r\nIt also contains the Multiple Sequence Alignments (MSAs) generated and well as the main figures and tables from the manuscript.\r\nThe repository is also available at GitHub (https://github.com/cbcrg/dpa-analysis) release `v1.2`.\r\nFor details on how to use the regressive alignment algorithm, see the T-Coffee software suite (https://github.com/cbcrg/tcoffee).","lang":"eng"}],"oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.3271452"}],"oa":1,"publisher":"Zenodo","month":"12","year":"2018","day":"07","date_created":"2023-05-23T16:08:20Z","related_material":{"record":[{"id":"7181","status":"public","relation":"used_in_publication"}]},"date_published":"2018-12-07T00:00:00Z","doi":"10.5281/ZENODO.2025846"},{"file":[{"checksum":"b653b5216251f938ddbeafd1de88667c","file_id":"6249","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2018_Thesis_Watzinger.pdf","date_created":"2019-04-09T07:13:28Z","file_size":85539748,"date_updated":"2020-07-14T12:46:35Z","creator":"dernst"},{"content_type":"application/zip","relation":"source_file","access_level":"closed","file_id":"6250","checksum":"39bcf8de7ac5b1bb516b11ce2f966785","file_size":21830697,"date_updated":"2020-07-14T12:46:35Z","creator":"dernst","file_name":"2018_Thesis_Watzinger_source.zip","date_created":"2019-04-09T07:13:27Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","oa_version":"Published Version","abstract":[{"text":"Nowadays, quantum computation is receiving more and more attention as an alternative to the classical way of computing. For realizing a quantum computer, different devices are investigated as potential quantum bits. In this thesis, the focus is on Ge hut wires, which turned out to be promising candidates for implementing hole spin quantum bits. The advantages of Ge as a material system are the low hyperfine interaction for holes and the strong spin orbit coupling, as well as the compatibility with the highly developed CMOS processes in industry. In addition, Ge can also be isotopically purified which is expected to boost the spin coherence times. The strong spin orbit interaction for holes in Ge on the one hand enables the full electrical control of the quantum bit and on the other hand should allow short spin manipulation times. Starting with a bare Si wafer, this work covers the entire process reaching from growth over the fabrication and characterization of hut wire devices up to the demonstration of hole spin resonance. From experiments with single quantum dots, a large g-factor anisotropy between the in-plane and the out-of-plane direction was found. A comparison to a theoretical model unveiled the heavy-hole character of the lowest energy states. The second part of the thesis addresses double quantum dot devices, which were realized by adding two gate electrodes to a hut wire. In such devices, Pauli spin blockade was observed, which can serve as a read-out mechanism for spin quantum bits. Applying oscillating electric fields in spin blockade allowed the demonstration of continuous spin rotations and the extraction of a lower bound for the spin dephasing time. Despite the strong spin orbit coupling in Ge, the obtained value for the dephasing time is comparable to what has been recently reported for holes in Si. All in all, the presented results point out the high potential of Ge hut wires as a platform for long-lived, fast and fully electrically tunable hole spin quantum bits.","lang":"eng"}],"month":"07","alternative_title":["ISTA Thesis"],"ddc":["530"],"supervisor":[{"first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios","last_name":"Katsaros"}],"date_updated":"2023-09-07T12:27:43Z","department":[{"_id":"GeKa"}],"file_date_updated":"2020-07-14T12:46:35Z","_id":"49","status":"public","pubrep_id":"1033","type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"day":"30","has_accepted_license":"1","year":"2018","date_published":"2018-07-30T00:00:00Z","doi":"10.15479/AT:ISTA:th_1033","date_created":"2018-12-11T11:44:21Z","page":"77","publisher":"Institute of Science and Technology Austria","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Watzinger, Hannes. “Ge Hut Wires - from Growth to Hole Spin Resonance.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_1033.","ista":"Watzinger H. 2018. Ge hut wires - from growth to hole spin resonance. Institute of Science and Technology Austria.","mla":"Watzinger, Hannes. Ge Hut Wires - from Growth to Hole Spin Resonance. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_1033.","short":"H. Watzinger, Ge Hut Wires - from Growth to Hole Spin Resonance, Institute of Science and Technology Austria, 2018.","ieee":"H. Watzinger, “Ge hut wires - from growth to hole spin resonance,” Institute of Science and Technology Austria, 2018.","apa":"Watzinger, H. (2018). Ge hut wires - from growth to hole spin resonance. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_1033","ama":"Watzinger H. Ge hut wires - from growth to hole spin resonance. 2018. doi:10.15479/AT:ISTA:th_1033"},"title":"Ge hut wires - from growth to hole spin resonance","publist_id":"8005","author":[{"id":"35DF8E50-F248-11E8-B48F-1D18A9856A87","first_name":"Hannes","full_name":"Watzinger, Hannes","last_name":"Watzinger"}],"article_processing_charge":"No"},{"oa":1,"publisher":"Institute of Science and Technology Austria","date_created":"2018-12-11T11:45:10Z","doi":"10.15479/AT:ISTA:th_1026","date_published":"2018-06-11T00:00:00Z","page":"171","day":"11","year":"2018","has_accepted_license":"1","title":"Multiple covers with balls","article_processing_charge":"No","author":[{"full_name":"Iglesias Ham, Mabel","last_name":"Iglesias Ham","first_name":"Mabel","id":"41B58C0C-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7712","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Iglesias Ham, Mabel. Multiple Covers with Balls. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_1026.","short":"M. Iglesias Ham, Multiple Covers with Balls, Institute of Science and Technology Austria, 2018.","ieee":"M. Iglesias Ham, “Multiple covers with balls,” Institute of Science and Technology Austria, 2018.","apa":"Iglesias Ham, M. (2018). Multiple covers with balls. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_1026","ama":"Iglesias Ham M. Multiple covers with balls. 2018. doi:10.15479/AT:ISTA:th_1026","chicago":"Iglesias Ham, Mabel. “Multiple Covers with Balls.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_1026.","ista":"Iglesias Ham M. 2018. Multiple covers with balls. Institute of Science and Technology Austria."},"month":"06","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"We describe arrangements of three-dimensional spheres from a geometrical and topological point of view. Real data (fitting this setup) often consist of soft spheres which show certain degree of deformation while strongly packing against each other. In this context, we answer the following questions: If we model a soft packing of spheres by hard spheres that are allowed to overlap, can we measure the volume in the overlapped areas? Can we be more specific about the overlap volume, i.e. quantify how much volume is there covered exactly twice, three times, or k times? What would be a good optimization criteria that rule the arrangement of soft spheres while making a good use of the available space? Fixing a particular criterion, what would be the optimal sphere configuration? The first result of this thesis are short formulas for the computation of volumes covered by at least k of the balls. The formulas exploit information contained in the order-k Voronoi diagrams and its closely related Level-k complex. The used complexes lead to a natural generalization into poset diagrams, a theoretical formalism that contains the order-k and degree-k diagrams as special cases. In parallel, we define different criteria to determine what could be considered an optimal arrangement from a geometrical point of view. Fixing a criterion, we find optimal soft packing configurations in 2D and 3D where the ball centers lie on a lattice. As a last step, we use tools from computational topology on real physical data, to show the potentials of higher-order diagrams in the description of melting crystals. The results of the experiments leaves us with an open window to apply the theories developed in this thesis in real applications."}],"language":[{"iso":"eng"}],"file":[{"access_level":"closed","relation":"source_file","content_type":"application/zip","file_id":"5918","checksum":"dd699303623e96d1478a6ae07210dd05","creator":"kschuh","date_updated":"2020-07-14T12:45:24Z","file_size":11827713,"date_created":"2019-02-05T07:43:31Z","file_name":"IST-2018-1025-v2+5_ist-thesis-iglesias-11June2018(1).zip"},{"file_id":"5919","checksum":"ba163849a190d2b41d66fef0e4983294","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2018-1025-v2+4_ThesisIglesiasFinal11June2018.pdf","date_created":"2019-02-05T07:43:45Z","creator":"kschuh","file_size":4783846,"date_updated":"2020-07-14T12:45:24Z"}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"pubrep_id":"1026","status":"public","type":"dissertation","_id":"201","file_date_updated":"2020-07-14T12:45:24Z","department":[{"_id":"HeEd"}],"ddc":["514","516"],"date_updated":"2023-09-07T12:25:32Z","supervisor":[{"full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert"}]},{"oa":1,"publisher":"Institute of Science and Technology Austria","page":"92","date_created":"2018-12-11T11:44:27Z","date_published":"2018-09-01T00:00:00Z","doi":"10.15479/AT:ISTA:TH1048","year":"2018","has_accepted_license":"1","day":"01","project":[{"_id":"2532554C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"308036","name":"Lifelong Learning of Visual Scene Understanding"}],"article_processing_charge":"No","author":[{"full_name":"Zimin, Alexander","last_name":"Zimin","first_name":"Alexander","id":"37099E9C-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7986","title":"Learning from dependent data","citation":{"chicago":"Zimin, Alexander. “Learning from Dependent Data.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:TH1048.","ista":"Zimin A. 2018. Learning from dependent data. Institute of Science and Technology Austria.","mla":"Zimin, Alexander. Learning from Dependent Data. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:TH1048.","ama":"Zimin A. Learning from dependent data. 2018. doi:10.15479/AT:ISTA:TH1048","apa":"Zimin, A. (2018). Learning from dependent data. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH1048","short":"A. Zimin, Learning from Dependent Data, Institute of Science and Technology Austria, 2018.","ieee":"A. Zimin, “Learning from dependent data,” Institute of Science and Technology Austria, 2018."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","alternative_title":["ISTA Thesis"],"month":"09","abstract":[{"text":"The most common assumption made in statistical learning theory is the assumption of the independent and identically distributed (i.i.d.) data. While being very convenient mathematically, it is often very clearly violated in practice. This disparity between the machine learning theory and applications underlies a growing demand in the development of algorithms that learn from dependent data and theory that can provide generalization guarantees similar to the independent situations. This thesis is dedicated to two variants of dependencies that can arise in practice. One is a dependence on the level of samples in a single learning task. Another dependency type arises in the multi-task setting when the tasks are dependent on each other even though the data for them can be i.i.d. In both cases we model the data (samples or tasks) as stochastic processes and introduce new algorithms for both settings that take into account and exploit the resulting dependencies. We prove the theoretical guarantees on the performance of the introduced algorithms under different evaluation criteria and, in addition, we compliment the theoretical study by the empirical one, where we evaluate some of the algorithms on two real world datasets to highlight their practical applicability.","lang":"eng"}],"oa_version":"Published Version","ec_funded":1,"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2019-04-09T07:32:47Z","file_name":"2018_Thesis_Zimin.pdf","date_updated":"2020-07-14T12:47:40Z","file_size":1036137,"creator":"dernst","file_id":"6253","checksum":"e849dd40a915e4d6c5572b51b517f098","content_type":"application/pdf","access_level":"open_access","relation":"main_file"},{"creator":"dernst","file_size":637490,"date_updated":"2020-07-14T12:47:40Z","file_name":"2018_Thesis_Zimin_Source.zip","date_created":"2019-04-09T07:32:47Z","relation":"source_file","access_level":"closed","content_type":"application/zip","file_id":"6254","checksum":"da092153cec55c97461bd53c45c5d139"}],"type":"dissertation","pubrep_id":"1048","status":"public","_id":"68","file_date_updated":"2020-07-14T12:47:40Z","department":[{"_id":"ChLa"}],"date_updated":"2023-09-07T12:29:07Z","supervisor":[{"last_name":"Lampert","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"ddc":["004","519"]},{"doi":"10.15479/AT:ISTA:TH_1046","date_published":"2018-09-05T00:00:00Z","date_created":"2018-12-11T11:44:32Z","page":"59","day":"05","has_accepted_license":"1","year":"2018","publisher":"Institute of Science and Technology Austria","oa":1,"title":"Proof systems for sustainable decentralized cryptocurrencies","author":[{"full_name":"Abusalah, Hamza M","last_name":"Abusalah","first_name":"Hamza M","id":"40297222-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7971","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Abusalah, Hamza M. Proof Systems for Sustainable Decentralized Cryptocurrencies. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:TH_1046.","short":"H.M. Abusalah, Proof Systems for Sustainable Decentralized Cryptocurrencies, Institute of Science and Technology Austria, 2018.","ieee":"H. M. Abusalah, “Proof systems for sustainable decentralized cryptocurrencies,” Institute of Science and Technology Austria, 2018.","apa":"Abusalah, H. M. (2018). Proof systems for sustainable decentralized cryptocurrencies. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH_1046","ama":"Abusalah HM. Proof systems for sustainable decentralized cryptocurrencies. 2018. doi:10.15479/AT:ISTA:TH_1046","chicago":"Abusalah, Hamza M. “Proof Systems for Sustainable Decentralized Cryptocurrencies.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:TH_1046.","ista":"Abusalah HM. 2018. Proof systems for sustainable decentralized cryptocurrencies. Institute of Science and Technology Austria."},"project":[{"call_identifier":"FP7","_id":"258C570E-B435-11E9-9278-68D0E5697425","name":"Provable Security for Physical Cryptography","grant_number":"259668"},{"name":"Teaching Old Crypto New Tricks","grant_number":"682815","call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"}],"related_material":{"record":[{"status":"public","id":"1229","relation":"part_of_dissertation"},{"id":"1235","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"1236"},{"relation":"part_of_dissertation","id":"559","status":"public"}]},"ec_funded":1,"file":[{"date_updated":"2020-07-14T12:48:11Z","file_size":876241,"creator":"dernst","date_created":"2019-04-09T06:43:41Z","file_name":"2018_Thesis_Abusalah.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"c4b5f7d111755d1396787f41886fc674","file_id":"6245"},{"checksum":"0f382ac56b471c48fd907d63eb87dafe","file_id":"6246","relation":"source_file","access_level":"closed","content_type":"application/x-gzip","file_name":"2018_Thesis_Abusalah_source.tar.gz","date_created":"2019-04-09T06:43:41Z","creator":"dernst","file_size":2029190,"date_updated":"2020-07-14T12:48:11Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","month":"09","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"A proof system is a protocol between a prover and a verifier over a common input in which an honest prover convinces the verifier of the validity of true statements. Motivated by the success of decentralized cryptocurrencies, exemplified by Bitcoin, the focus of this thesis will be on proof systems which found applications in some sustainable alternatives to Bitcoin, such as the Spacemint and Chia cryptocurrencies. In particular, we focus on proofs of space and proofs of sequential work.\r\nProofs of space (PoSpace) were suggested as more ecological, economical, and egalitarian alternative to the energy-wasteful proof-of-work mining of Bitcoin. However, the state-of-the-art constructions of PoSpace are based on sophisticated graph pebbling lower bounds, and are therefore complex. Moreover, when these PoSpace are used in cryptocurrencies like Spacemint, miners can only start mining after ensuring that a commitment to their space is already added in a special transaction to the blockchain. Proofs of sequential work (PoSW) are proof systems in which a prover, upon receiving a statement x and a time parameter T, computes a proof which convinces the verifier that T time units had passed since x was received. Whereas Spacemint assumes synchrony to retain some interesting Bitcoin dynamics, Chia requires PoSW with unique proofs, i.e., PoSW in which it is hard to come up with more than one accepting proof for any true statement. In this thesis we construct simple and practically-efficient PoSpace and PoSW. When using our PoSpace in cryptocurrencies, miners can start mining on the fly, like in Bitcoin, and unlike current constructions of PoSW, which either achieve efficient verification of sequential work, or faster-than-recomputing verification of correctness of proofs, but not both at the same time, ours achieve the best of these two worlds."}],"department":[{"_id":"KrPi"}],"file_date_updated":"2020-07-14T12:48:11Z","ddc":["004"],"supervisor":[{"last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z"}],"date_updated":"2023-09-07T12:30:23Z","status":"public","pubrep_id":"1046","type":"dissertation","_id":"83"},{"type":"dissertation","pubrep_id":"1021","status":"public","_id":"197","department":[{"_id":"ChLa"}],"file_date_updated":"2020-07-14T12:45:22Z","date_updated":"2023-09-07T12:51:46Z","supervisor":[{"last_name":"Lampert","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"ddc":["004"],"alternative_title":["ISTA Thesis"],"month":"05","abstract":[{"lang":"eng","text":"Modern computer vision systems heavily rely on statistical machine learning models, which typically require large amounts of labeled data to be learned reliably. Moreover, very recently computer vision research widely adopted techniques for representation learning, which further increase the demand for labeled data. However, for many important practical problems there is relatively small amount of labeled data available, so it is problematic to leverage full potential of the representation learning methods. One way to overcome this obstacle is to invest substantial resources into producing large labelled datasets. Unfortunately, this can be prohibitively expensive in practice. In this thesis we focus on the alternative way of tackling the aforementioned issue. We concentrate on methods, which make use of weakly-labeled or even unlabeled data. Specifically, the first half of the thesis is dedicated to the semantic image segmentation task. We develop a technique, which achieves competitive segmentation performance and only requires annotations in a form of global image-level labels instead of dense segmentation masks. Subsequently, we present a new methodology, which further improves segmentation performance by leveraging tiny additional feedback from a human annotator. By using our methods practitioners can greatly reduce the amount of data annotation effort, which is required to learn modern image segmentation models. In the second half of the thesis we focus on methods for learning from unlabeled visual data. We study a family of autoregressive models for modeling structure of natural images and discuss potential applications of these models. Moreover, we conduct in-depth study of one of these applications, where we develop the state-of-the-art model for the probabilistic image colorization task."}],"oa_version":"Published Version","ec_funded":1,"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"file_size":12918758,"date_updated":"2020-07-14T12:45:22Z","creator":"system","file_name":"IST-2018-1021-v1+1_thesis-unsigned-pdfa.pdf","date_created":"2018-12-12T10:14:57Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5113","checksum":"bc678e02468d8ebc39dc7267dfb0a1c4"},{"date_created":"2019-04-05T09:34:49Z","file_name":"2018_Thesis_Kolesnikov_source.zip","creator":"dernst","date_updated":"2020-07-14T12:45:22Z","file_size":55973760,"file_id":"6225","checksum":"bc66973b086da5a043f1162dcfb1fde4","access_level":"closed","relation":"source_file","content_type":"application/zip"}],"project":[{"grant_number":"308036","name":"Lifelong Learning of Visual Scene Understanding","call_identifier":"FP7","_id":"2532554C-B435-11E9-9278-68D0E5697425"}],"article_processing_charge":"No","author":[{"first_name":"Alexander","id":"2D157DB6-F248-11E8-B48F-1D18A9856A87","full_name":"Kolesnikov, Alexander","last_name":"Kolesnikov"}],"publist_id":"7718","title":"Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images","citation":{"chicago":"Kolesnikov, Alexander. “Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_1021.","ista":"Kolesnikov A. 2018. Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images. Institute of Science and Technology Austria.","mla":"Kolesnikov, Alexander. Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_1021.","short":"A. Kolesnikov, Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images, Institute of Science and Technology Austria, 2018.","ieee":"A. Kolesnikov, “Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images,” Institute of Science and Technology Austria, 2018.","ama":"Kolesnikov A. Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images. 2018. doi:10.15479/AT:ISTA:th_1021","apa":"Kolesnikov, A. (2018). Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_1021"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"publisher":"Institute of Science and Technology Austria","acknowledgement":"I also gratefully acknowledge the support of NVIDIA Corporation with the donation of the GPUs used for this research.","page":"113","date_created":"2018-12-11T11:45:09Z","date_published":"2018-05-25T00:00:00Z","doi":"10.15479/AT:ISTA:th_1021","year":"2018","has_accepted_license":"1","day":"25"},{"project":[{"grant_number":"M01980","name":"Robust invariants of Nonlinear Systems","_id":"25F8B9BC-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"FWF Open Access Fund","call_identifier":"FWF","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1"}],"author":[{"first_name":"Marek","id":"3E8AF77E-F248-11E8-B48F-1D18A9856A87","last_name":"Filakovský","full_name":"Filakovský, Marek"},{"first_name":"Peter","id":"473294AE-F248-11E8-B48F-1D18A9856A87","last_name":"Franek","orcid":"0000-0001-8878-8397","full_name":"Franek, Peter"},{"orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli","last_name":"Wagner","first_name":"Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Zhechev","full_name":"Zhechev, Stephan Y","id":"3AA52972-F248-11E8-B48F-1D18A9856A87","first_name":"Stephan Y"}],"title":"Computing simplicial representatives of homotopy group elements","citation":{"ista":"Filakovský M, Franek P, Wagner U, Zhechev SY. 2018. Computing simplicial representatives of homotopy group elements. Journal of Applied and Computational Topology. 2(3–4), 177–231.","chicago":"Filakovský, Marek, Peter Franek, Uli Wagner, and Stephan Y Zhechev. “Computing Simplicial Representatives of Homotopy Group Elements.” Journal of Applied and Computational Topology. Springer, 2018. https://doi.org/10.1007/s41468-018-0021-5.","short":"M. Filakovský, P. Franek, U. Wagner, S.Y. Zhechev, Journal of Applied and Computational Topology 2 (2018) 177–231.","ieee":"M. Filakovský, P. Franek, U. Wagner, and S. Y. Zhechev, “Computing simplicial representatives of homotopy group elements,” Journal of Applied and Computational Topology, vol. 2, no. 3–4. Springer, pp. 177–231, 2018.","apa":"Filakovský, M., Franek, P., Wagner, U., & Zhechev, S. Y. (2018). Computing simplicial representatives of homotopy group elements. Journal of Applied and Computational Topology. Springer. https://doi.org/10.1007/s41468-018-0021-5","ama":"Filakovský M, Franek P, Wagner U, Zhechev SY. Computing simplicial representatives of homotopy group elements. Journal of Applied and Computational Topology. 2018;2(3-4):177-231. doi:10.1007/s41468-018-0021-5","mla":"Filakovský, Marek, et al. “Computing Simplicial Representatives of Homotopy Group Elements.” Journal of Applied and Computational Topology, vol. 2, no. 3–4, Springer, 2018, pp. 177–231, doi:10.1007/s41468-018-0021-5."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer","quality_controlled":"1","oa":1,"page":"177-231","date_published":"2018-12-01T00:00:00Z","doi":"10.1007/s41468-018-0021-5","date_created":"2019-08-08T06:47:40Z","has_accepted_license":"1","year":"2018","day":"01","publication":"Journal of Applied and Computational Topology","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"6774","department":[{"_id":"UlWa"}],"file_date_updated":"2020-07-14T12:47:40Z","date_updated":"2023-09-07T13:10:36Z","ddc":["514"],"month":"12","intvolume":" 2","abstract":[{"text":"A central problem of algebraic topology is to understand the homotopy groups 𝜋𝑑(𝑋) of a topological space X. For the computational version of the problem, it is well known that there is no algorithm to decide whether the fundamental group 𝜋1(𝑋) of a given finite simplicial complex X is trivial. On the other hand, there are several algorithms that, given a finite simplicial complex X that is simply connected (i.e., with 𝜋1(𝑋) trivial), compute the higher homotopy group 𝜋𝑑(𝑋) for any given 𝑑≥2 . However, these algorithms come with a caveat: They compute the isomorphism type of 𝜋𝑑(𝑋) , 𝑑≥2 as an abstract finitely generated abelian group given by generators and relations, but they work with very implicit representations of the elements of 𝜋𝑑(𝑋) . Converting elements of this abstract group into explicit geometric maps from the d-dimensional sphere 𝑆𝑑 to X has been one of the main unsolved problems in the emerging field of computational homotopy theory. Here we present an algorithm that, given a simply connected space X, computes 𝜋𝑑(𝑋) and represents its elements as simplicial maps from a suitable triangulation of the d-sphere 𝑆𝑑 to X. For fixed d, the algorithm runs in time exponential in size(𝑋) , the number of simplices of X. Moreover, we prove that this is optimal: For every fixed 𝑑≥2 , we construct a family of simply connected spaces X such that for any simplicial map representing a generator of 𝜋𝑑(𝑋) , the size of the triangulation of 𝑆𝑑 on which the map is defined, is exponential in size(𝑋) .","lang":"eng"}],"oa_version":"Published Version","issue":"3-4","volume":2,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"6681"}]},"publication_identifier":{"eissn":["2367-1734"],"issn":["2367-1726"]},"publication_status":"published","file":[{"file_size":1056278,"date_updated":"2020-07-14T12:47:40Z","creator":"dernst","file_name":"2018_JourAppliedComputTopology_Filakovsky.pdf","date_created":"2019-08-08T06:55:21Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"6775","checksum":"cf9e7fcd2a113dd4828774fc75cdb7e8"}],"language":[{"iso":"eng"}]},{"department":[{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:44:44Z","ddc":["000"],"date_updated":"2023-09-07T13:18:00Z","pubrep_id":"1039","status":"public","conference":{"name":"CONCUR: International Conference on Concurrency Theory","start_date":"2018-09-04","location":"Beijing, China","end_date":"2018-09-07"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"conference","_id":"133","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"6426"},{"id":"8332","status":"public","relation":"dissertation_contains"}]},"volume":118,"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"c90895f4c5fafc18ddc54d1c8848077e","file_id":"5368","file_size":745438,"date_updated":"2020-07-14T12:44:44Z","creator":"system","file_name":"IST-2018-853-v2+2_concur2018.pdf","date_created":"2018-12-12T10:18:46Z"}],"publication_status":"published","publication_identifier":{"issn":["18688969"]},"intvolume":" 118","month":"08","alternative_title":["LIPIcs"],"scopus_import":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Synchronous programs are easy to specify because the side effects of an operation are finished by the time the invocation of the operation returns to the caller. Asynchronous programs, on the other hand, are difficult to specify because there are side effects due to pending computation scheduled as a result of the invocation of an operation. They are also difficult to verify because of the large number of possible interleavings of concurrent computation threads. We present synchronization, a new proof rule that simplifies the verification of asynchronous programs by introducing the fiction, for proof purposes, that asynchronous operations complete synchronously. Synchronization summarizes an asynchronous computation as immediate atomic effect. Modular verification is enabled via pending asynchronous calls in atomic summaries, and a complementary proof rule that eliminates pending asynchronous calls when components and their specifications are composed. We evaluate synchronization in the context of a multi-layer refinement verification methodology on a collection of benchmark programs."}],"title":"Synchronizing the asynchronous","publist_id":"7790","author":[{"first_name":"Bernhard","id":"320FC952-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7745-9117","full_name":"Kragl, Bernhard","last_name":"Kragl"},{"first_name":"Shaz","full_name":"Qadeer, Shaz","last_name":"Qadeer"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"B. Kragl, S. Qadeer, and T. A. Henzinger, “Synchronizing the asynchronous,” presented at the CONCUR: International Conference on Concurrency Theory, Beijing, China, 2018, vol. 118.","short":"B. Kragl, S. Qadeer, T.A. Henzinger, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","apa":"Kragl, B., Qadeer, S., & Henzinger, T. A. (2018). Synchronizing the asynchronous (Vol. 118). Presented at the CONCUR: International Conference on Concurrency Theory, Beijing, China: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2018.21","ama":"Kragl B, Qadeer S, Henzinger TA. Synchronizing the asynchronous. In: Vol 118. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPIcs.CONCUR.2018.21","mla":"Kragl, Bernhard, et al. Synchronizing the Asynchronous. Vol. 118, 21, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:10.4230/LIPIcs.CONCUR.2018.21.","ista":"Kragl B, Qadeer S, Henzinger TA. 2018. Synchronizing the asynchronous. CONCUR: International Conference on Concurrency Theory, LIPIcs, vol. 118, 21.","chicago":"Kragl, Bernhard, Shaz Qadeer, and Thomas A Henzinger. “Synchronizing the Asynchronous,” Vol. 118. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPIcs.CONCUR.2018.21."},"project":[{"grant_number":"S11402-N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425"},{"name":"Moderne Concurrency Paradigms","grant_number":"S11402-N23","call_identifier":"FWF","_id":"25F5A88A-B435-11E9-9278-68D0E5697425"}],"article_number":"21","date_created":"2018-12-11T11:44:48Z","date_published":"2018-08-13T00:00:00Z","doi":"10.4230/LIPIcs.CONCUR.2018.21","day":"13","year":"2018","has_accepted_license":"1","oa":1,"quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik"},{"doi":"10.4230/LIPIcs.SoCG.2018.34","date_published":"2018-06-11T00:00:00Z","date_created":"2018-12-11T11:45:05Z","day":"11","has_accepted_license":"1","year":"2018","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","oa":1,"acknowledgement":"This work is partially supported by the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, through grant no. I02979-N35 of the Austrian Science Fund (FWF).","title":"The multi-cover persistence of Euclidean balls","publist_id":"7732","author":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert"},{"last_name":"Osang","orcid":"0000-0002-8882-5116","full_name":"Osang, Georg F","first_name":"Georg F","id":"464B40D6-F248-11E8-B48F-1D18A9856A87"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Edelsbrunner, Herbert, and Georg F. Osang. The Multi-Cover Persistence of Euclidean Balls. Vol. 99, 34, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:10.4230/LIPIcs.SoCG.2018.34.","short":"H. Edelsbrunner, G.F. Osang, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","ieee":"H. Edelsbrunner and G. F. Osang, “The multi-cover persistence of Euclidean balls,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99.","ama":"Edelsbrunner H, Osang GF. The multi-cover persistence of Euclidean balls. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPIcs.SoCG.2018.34","apa":"Edelsbrunner, H., & Osang, G. F. (2018). The multi-cover persistence of Euclidean balls (Vol. 99). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2018.34","chicago":"Edelsbrunner, Herbert, and Georg F Osang. “The Multi-Cover Persistence of Euclidean Balls,” Vol. 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPIcs.SoCG.2018.34.","ista":"Edelsbrunner H, Osang GF. 2018. The multi-cover persistence of Euclidean balls. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 99, 34."},"project":[{"call_identifier":"FWF","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35"}],"article_number":"34","volume":99,"related_material":{"record":[{"status":"public","id":"9317","relation":"later_version"},{"relation":"dissertation_contains","id":"9056","status":"public"}]},"file":[{"date_updated":"2020-07-14T12:45:19Z","file_size":528018,"creator":"dernst","date_created":"2018-12-18T09:27:22Z","file_name":"2018_LIPIcs_Edelsbrunner_Osang.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"d8c0533ad0018eb4ed1077475eb8fc18","file_id":"5738"}],"language":[{"iso":"eng"}],"publication_status":"published","month":"06","intvolume":" 99","scopus_import":1,"alternative_title":["LIPIcs"],"oa_version":"Published Version","abstract":[{"text":"Given a locally finite X ⊆ ℝd and a radius r ≥ 0, the k-fold cover of X and r consists of all points in ℝd that have k or more points of X within distance r. We consider two filtrations - one in scale obtained by fixing k and increasing r, and the other in depth obtained by fixing r and decreasing k - and we compute the persistence diagrams of both. While standard methods suffice for the filtration in scale, we need novel geometric and topological concepts for the filtration in depth. In particular, we introduce a rhomboid tiling in ℝd+1 whose horizontal integer slices are the order-k Delaunay mosaics of X, and construct a zigzag module from Delaunay mosaics that is isomorphic to the persistence module of the multi-covers. ","lang":"eng"}],"file_date_updated":"2020-07-14T12:45:19Z","department":[{"_id":"HeEd"}],"ddc":["516"],"date_updated":"2023-09-07T13:29:00Z","status":"public","type":"conference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"location":"Budapest, Hungary","end_date":"2018-06-14","start_date":"2018-06-11","name":"SoCG: Symposium on Computational Geometry"},"_id":"187"},{"citation":{"ista":"Akopyan A. 2018. 3-Webs generated by confocal conics and circles. Geometriae Dedicata. 194(1), 55–64.","chicago":"Akopyan, Arseniy. “3-Webs Generated by Confocal Conics and Circles.” Geometriae Dedicata. Springer, 2018. https://doi.org/10.1007/s10711-017-0265-6.","ieee":"A. Akopyan, “3-Webs generated by confocal conics and circles,” Geometriae Dedicata, vol. 194, no. 1. Springer, pp. 55–64, 2018.","short":"A. Akopyan, Geometriae Dedicata 194 (2018) 55–64.","ama":"Akopyan A. 3-Webs generated by confocal conics and circles. Geometriae Dedicata. 2018;194(1):55-64. doi:10.1007/s10711-017-0265-6","apa":"Akopyan, A. (2018). 3-Webs generated by confocal conics and circles. Geometriae Dedicata. Springer. https://doi.org/10.1007/s10711-017-0265-6","mla":"Akopyan, Arseniy. “3-Webs Generated by Confocal Conics and Circles.” Geometriae Dedicata, vol. 194, no. 1, Springer, 2018, pp. 55–64, doi:10.1007/s10711-017-0265-6."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"7014","author":[{"last_name":"Akopyan","full_name":"Akopyan, Arseniy","orcid":"0000-0002-2548-617X","first_name":"Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000431418800004"]},"title":"3-Webs generated by confocal conics and circles","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"isi":1,"has_accepted_license":"1","year":"2018","day":"01","publication":"Geometriae Dedicata","page":"55 - 64","date_published":"2018-06-01T00:00:00Z","doi":"10.1007/s10711-017-0265-6","date_created":"2018-12-11T11:47:57Z","quality_controlled":"1","publisher":"Springer","oa":1,"date_updated":"2023-09-08T11:40:29Z","ddc":["510"],"department":[{"_id":"HeEd"}],"file_date_updated":"2020-07-14T12:47:44Z","_id":"692","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","publication_status":"published","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"1febcfc1266486053a069e3425ea3713","file_id":"7222","file_size":1140860,"date_updated":"2020-07-14T12:47:44Z","creator":"kschuh","file_name":"2018_Springer_Akopyan.pdf","date_created":"2020-01-03T11:35:08Z"}],"language":[{"iso":"eng"}],"volume":194,"issue":"1","ec_funded":1,"abstract":[{"lang":"eng","text":"We consider families of confocal conics and two pencils of Apollonian circles having the same foci. We will show that these families of curves generate trivial 3-webs and find the exact formulas describing them."}],"oa_version":"Published Version","scopus_import":"1","month":"06","intvolume":" 194"},{"file_date_updated":"2020-07-14T12:48:02Z","department":[{"_id":"GeKa"}],"ddc":["530"],"date_updated":"2023-09-08T11:44:02Z","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","article_type":"original","_id":"77","ec_funded":1,"volume":9,"issue":"3902 ","related_material":{"record":[{"relation":"popular_science","id":"7977"},{"relation":"dissertation_contains","id":"7996","status":"public"}]},"language":[{"iso":"eng"}],"file":[{"file_id":"5687","checksum":"e7148c10a64497e279c4de570b6cc544","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-17T10:28:30Z","file_name":"2018_NatureComm_Watzinger.pdf","creator":"dernst","date_updated":"2020-07-14T12:48:02Z","file_size":1063469}],"publication_status":"published","intvolume":" 9","month":"09","scopus_import":"1","oa_version":"Published Version","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"abstract":[{"lang":"eng","text":"Holes confined in quantum dots have gained considerable interest in the past few years due to their potential as spin qubits. Here we demonstrate two-axis control of a spin 3/2 qubit in natural Ge. The qubit is formed in a hut wire double quantum dot device. The Pauli spin blockade principle allowed us to demonstrate electric dipole spin resonance by applying a radio frequency electric field to one of the electrodes defining the double quantum dot. Coherent hole spin oscillations with Rabi frequencies reaching 140 MHz are demonstrated and dephasing times of 130 ns are measured. The reported results emphasize the potential of Ge as a platform for fast and electrically tunable hole spin qubit devices."}],"title":"A germanium hole spin qubit","external_id":{"isi":["000445560800010"]},"article_processing_charge":"Yes","author":[{"first_name":"Hannes","id":"35DF8E50-F248-11E8-B48F-1D18A9856A87","last_name":"Watzinger","full_name":"Watzinger, Hannes"},{"first_name":"Josip","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","full_name":"Kukucka, Josip","last_name":"Kukucka"},{"orcid":"0000-0003-2424-8636","full_name":"Vukusic, Lada","last_name":"Vukusic","first_name":"Lada","id":"31E9F056-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Fei","full_name":"Gao, Fei","last_name":"Gao"},{"full_name":"Wang, Ting","last_name":"Wang","first_name":"Ting"},{"first_name":"Friedrich","last_name":"Schäffler","full_name":"Schäffler, Friedrich"},{"first_name":"Jian","full_name":"Zhang, Jian","last_name":"Zhang"},{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X","last_name":"Katsaros"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Watzinger, Hannes, et al. “A Germanium Hole Spin Qubit.” Nature Communications, vol. 9, no. 3902, Nature Publishing Group, 2018, doi:10.1038/s41467-018-06418-4.","short":"H. Watzinger, J. Kukucka, L. Vukušić, F. Gao, T. Wang, F. Schäffler, J. Zhang, G. Katsaros, Nature Communications 9 (2018).","ieee":"H. Watzinger et al., “A germanium hole spin qubit,” Nature Communications, vol. 9, no. 3902. Nature Publishing Group, 2018.","apa":"Watzinger, H., Kukucka, J., Vukušić, L., Gao, F., Wang, T., Schäffler, F., … Katsaros, G. (2018). A germanium hole spin qubit. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-018-06418-4","ama":"Watzinger H, Kukucka J, Vukušić L, et al. A germanium hole spin qubit. Nature Communications. 2018;9(3902). doi:10.1038/s41467-018-06418-4","chicago":"Watzinger, Hannes, Josip Kukucka, Lada Vukušić, Fei Gao, Ting Wang, Friedrich Schäffler, Jian Zhang, and Georgios Katsaros. “A Germanium Hole Spin Qubit.” Nature Communications. Nature Publishing Group, 2018. https://doi.org/10.1038/s41467-018-06418-4.","ista":"Watzinger H, Kukucka J, Vukušić L, Gao F, Wang T, Schäffler F, Zhang J, Katsaros G. 2018. A germanium hole spin qubit. Nature Communications. 9(3902)."},"project":[{"_id":"25517E86-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"335497","name":"Towards Spin qubits and Majorana fermions in Germanium selfassembled hut-wires"},{"call_identifier":"FWF","_id":"2552F888-B435-11E9-9278-68D0E5697425","name":"Loch Spin-Qubits und Majorana-Fermionen in Germanium","grant_number":"Y00715"}],"date_created":"2018-12-11T11:44:30Z","date_published":"2018-09-25T00:00:00Z","doi":"10.1038/s41467-018-06418-4","publication":"Nature Communications","day":"25","year":"2018","isi":1,"has_accepted_license":"1","oa":1,"quality_controlled":"1","publisher":"Nature Publishing Group"},{"article_number":"1210","title":"A biochemical network controlling basal myosin oscillation","author":[{"full_name":"Qin, Xiang","last_name":"Qin","first_name":"Xiang"},{"first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B"},{"full_name":"Mangeat, Thomas","last_name":"Mangeat","first_name":"Thomas"},{"first_name":"Chang","last_name":"Liu","full_name":"Liu, Chang"},{"full_name":"Majumder, Pralay","last_name":"Majumder","first_name":"Pralay"},{"first_name":"Jjiaying","full_name":"Liu, Jjiaying","last_name":"Liu"},{"last_name":"Choesmel Cadamuro","full_name":"Choesmel Cadamuro, Valerie","first_name":"Valerie"},{"first_name":"Jocelyn","last_name":"Mcdonald","full_name":"Mcdonald, Jocelyn"},{"last_name":"Liu","full_name":"Liu, Yinyao","first_name":"Yinyao"},{"first_name":"Bin","full_name":"Yi, Bin","last_name":"Yi"},{"last_name":"Wang","full_name":"Wang, Xiaobo","first_name":"Xiaobo"}],"publist_id":"7427","external_id":{"isi":["000428165400009"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Qin, Xiang, Edouard B Hannezo, Thomas Mangeat, Chang Liu, Pralay Majumder, Jjiaying Liu, Valerie Choesmel Cadamuro, et al. “A Biochemical Network Controlling Basal Myosin Oscillation.” Nature Communications. Nature Publishing Group, 2018. https://doi.org/10.1038/s41467-018-03574-5.","ista":"Qin X, Hannezo EB, Mangeat T, Liu C, Majumder P, Liu J, Choesmel Cadamuro V, Mcdonald J, Liu Y, Yi B, Wang X. 2018. A biochemical network controlling basal myosin oscillation. Nature Communications. 9(1), 1210.","mla":"Qin, Xiang, et al. “A Biochemical Network Controlling Basal Myosin Oscillation.” Nature Communications, vol. 9, no. 1, 1210, Nature Publishing Group, 2018, doi:10.1038/s41467-018-03574-5.","ama":"Qin X, Hannezo EB, Mangeat T, et al. A biochemical network controlling basal myosin oscillation. Nature Communications. 2018;9(1). doi:10.1038/s41467-018-03574-5","apa":"Qin, X., Hannezo, E. B., Mangeat, T., Liu, C., Majumder, P., Liu, J., … Wang, X. (2018). A biochemical network controlling basal myosin oscillation. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-018-03574-5","ieee":"X. Qin et al., “A biochemical network controlling basal myosin oscillation,” Nature Communications, vol. 9, no. 1. Nature Publishing Group, 2018.","short":"X. Qin, E.B. Hannezo, T. Mangeat, C. Liu, P. Majumder, J. Liu, V. Choesmel Cadamuro, J. Mcdonald, Y. Liu, B. Yi, X. Wang, Nature Communications 9 (2018)."},"quality_controlled":"1","publisher":"Nature Publishing Group","oa":1,"doi":"10.1038/s41467-018-03574-5","date_published":"2018-03-23T00:00:00Z","date_created":"2018-12-11T11:46:16Z","day":"23","publication":"Nature Communications","isi":1,"has_accepted_license":"1","year":"2018","status":"public","pubrep_id":"996","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"401","file_date_updated":"2020-07-14T12:46:22Z","department":[{"_id":"EdHa"}],"ddc":["539","570"],"date_updated":"2023-09-08T11:41:45Z","month":"03","intvolume":" 9","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"The actomyosin cytoskeleton, a key stress-producing unit in epithelial cells, oscillates spontaneously in a wide variety of systems. Although much of the signal cascade regulating myosin activity has been characterized, the origin of such oscillatory behavior is still unclear. Here, we show that basal myosin II oscillation in Drosophila ovarian epithelium is not controlled by actomyosin cortical tension, but instead relies on a biochemical oscillator involving ROCK and myosin phosphatase. Key to this oscillation is a diffusive ROCK flow, linking junctional Rho1 to medial actomyosin cortex, and dynamically maintained by a self-activation loop reliant on ROCK kinase activity. In response to the resulting myosin II recruitment, myosin phosphatase is locally enriched and shuts off ROCK and myosin II signals. Coupling Drosophila genetics, live imaging, modeling, and optogenetics, we uncover an intrinsic biochemical oscillator at the core of myosin II regulatory network, shedding light on the spatio-temporal dynamics of force generation."}],"issue":"1","volume":9,"file":[{"file_name":"IST-2018-996-v1+1_2018_Hannezo_A-biochemical.pdf","date_created":"2018-12-12T10:11:45Z","file_size":3780491,"date_updated":"2020-07-14T12:46:22Z","creator":"system","file_id":"4902","checksum":"87a427bc2e8724be3dd22a4efdd21a33","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"publication_status":"published"},{"date_updated":"2023-09-08T11:42:28Z","department":[{"_id":"MiSi"}],"_id":"318","type":"journal_article","status":"public","publication_status":"published","language":[{"iso":"eng"}],"volume":44,"issue":"4","abstract":[{"text":"The insect’s fat body combines metabolic and immunological functions. In this issue of Developmental Cell, Franz et al. (2018) show that in Drosophila, cells of the fat body are not static, but can actively “swim” toward sites of epithelial injury, where they physically clog the wound and locally secrete antimicrobial peptides.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/29486189"}],"month":"02","intvolume":" 44","citation":{"mla":"Casano, Alessandra M., and Michael K. Sixt. “A Fat Lot of Good for Wound Healing.” Developmental Cell, vol. 44, no. 4, Cell Press, 2018, pp. 405–06, doi:10.1016/j.devcel.2018.02.009.","ieee":"A. M. Casano and M. K. Sixt, “A fat lot of good for wound healing,” Developmental Cell, vol. 44, no. 4. Cell Press, pp. 405–406, 2018.","short":"A.M. Casano, M.K. Sixt, Developmental Cell 44 (2018) 405–406.","apa":"Casano, A. M., & Sixt, M. K. (2018). A fat lot of good for wound healing. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2018.02.009","ama":"Casano AM, Sixt MK. A fat lot of good for wound healing. Developmental Cell. 2018;44(4):405-406. doi:10.1016/j.devcel.2018.02.009","chicago":"Casano, Alessandra M, and Michael K Sixt. “A Fat Lot of Good for Wound Healing.” Developmental Cell. Cell Press, 2018. https://doi.org/10.1016/j.devcel.2018.02.009.","ista":"Casano AM, Sixt MK. 2018. A fat lot of good for wound healing. Developmental Cell. 44(4), 405–406."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"7547","author":[{"id":"3DBA3F4E-F248-11E8-B48F-1D18A9856A87","first_name":"Alessandra M","full_name":"Casano, Alessandra M","orcid":"0000-0002-6009-6804","last_name":"Casano"},{"last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K"}],"external_id":{"pmid":["29486189"],"isi":["000426150700002"]},"article_processing_charge":"No","title":"A fat lot of good for wound healing","isi":1,"year":"2018","day":"26","publication":"Developmental Cell","page":"405 - 406","date_published":"2018-02-26T00:00:00Z","doi":"10.1016/j.devcel.2018.02.009","date_created":"2018-12-11T11:45:47Z","acknowledgement":"Short Survey","publisher":"Cell Press","quality_controlled":"1","oa":1},{"article_number":"5184","citation":{"ista":"Masís J, Mankus D, Wolff S, Guitchounts G, Jösch MA, Cox D. 2018. A micro-CT-based method for quantitative brain lesion characterization and electrode localization. Scientific Reports. 8(1), 5184.","chicago":"Masís, Javier, David Mankus, Steffen Wolff, Grigori Guitchounts, Maximilian A Jösch, and David Cox. “A Micro-CT-Based Method for Quantitative Brain Lesion Characterization and Electrode Localization.” Scientific Reports. Nature Publishing Group, 2018. https://doi.org/10.1038/s41598-018-23247-z.","apa":"Masís, J., Mankus, D., Wolff, S., Guitchounts, G., Jösch, M. A., & Cox, D. (2018). A micro-CT-based method for quantitative brain lesion characterization and electrode localization. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/s41598-018-23247-z","ama":"Masís J, Mankus D, Wolff S, Guitchounts G, Jösch MA, Cox D. A micro-CT-based method for quantitative brain lesion characterization and electrode localization. Scientific Reports. 2018;8(1). doi:10.1038/s41598-018-23247-z","ieee":"J. Masís, D. Mankus, S. Wolff, G. Guitchounts, M. A. Jösch, and D. Cox, “A micro-CT-based method for quantitative brain lesion characterization and electrode localization,” Scientific Reports, vol. 8, no. 1. Nature Publishing Group, 2018.","short":"J. Masís, D. Mankus, S. Wolff, G. Guitchounts, M.A. Jösch, D. Cox, Scientific Reports 8 (2018).","mla":"Masís, Javier, et al. “A Micro-CT-Based Method for Quantitative Brain Lesion Characterization and Electrode Localization.” Scientific Reports, vol. 8, no. 1, 5184, Nature Publishing Group, 2018, doi:10.1038/s41598-018-23247-z."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000428234100005"]},"article_processing_charge":"No","publist_id":"7419","author":[{"full_name":"Masís, Javier","last_name":"Masís","first_name":"Javier"},{"last_name":"Mankus","full_name":"Mankus, David","first_name":"David"},{"first_name":"Steffen","last_name":"Wolff","full_name":"Wolff, Steffen"},{"first_name":"Grigori","full_name":"Guitchounts, Grigori","last_name":"Guitchounts"},{"first_name":"Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","last_name":"Jösch","full_name":"Jösch, Maximilian A","orcid":"0000-0002-3937-1330"},{"full_name":"Cox, David","last_name":"Cox","first_name":"David"}],"title":"A micro-CT-based method for quantitative brain lesion characterization and electrode localization","oa":1,"quality_controlled":"1","publisher":"Nature Publishing Group","year":"2018","isi":1,"has_accepted_license":"1","publication":"Scientific Reports","day":"26","date_created":"2018-12-11T11:46:19Z","doi":"10.1038/s41598-018-23247-z","date_published":"2018-03-26T00:00:00Z","_id":"410","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"994","status":"public","date_updated":"2023-09-08T11:48:39Z","ddc":["571","572"],"department":[{"_id":"MaJö"}],"file_date_updated":"2020-07-14T12:46:23Z","abstract":[{"text":"Lesion verification and quantification is traditionally done via histological examination of sectioned brains, a time-consuming process that relies heavily on manual estimation. Such methods are particularly problematic in posterior cortical regions (e.g. visual cortex), where sectioning leads to significant damage and distortion of tissue. Even more challenging is the post hoc localization of micro-electrodes, which relies on the same techniques, suffers from similar drawbacks and requires even higher precision. Here, we propose a new, simple method for quantitative lesion characterization and electrode localization that is less labor-intensive and yields more detailed results than conventional methods. We leverage staining techniques standard in electron microscopy with the use of commodity micro-CT imaging. We stain whole rat and zebra finch brains in osmium tetroxide, embed these in resin and scan entire brains in a micro-CT machine. The scans result in 3D reconstructions of the brains with section thickness dependent on sample size (12–15 and 5–6 microns for rat and zebra finch respectively) that can be segmented manually or automatically. Because the method captures the entire intact brain volume, comparisons within and across studies are more tractable, and the extent of lesions and electrodes may be studied with higher accuracy than with current methods.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 8","month":"03","publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_size":2359430,"date_updated":"2020-07-14T12:46:23Z","creator":"system","file_name":"IST-2018-994-v1+1_2018_Joesch_A-micro-CT-based.pdf","date_created":"2018-12-12T10:10:42Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"653fcb852f899c75b00ceee2a670d738","file_id":"4831"}],"issue":"1","volume":8},{"volume":97,"issue":"5","publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_name":"2018_PlantMolecBio_Dokladal.pdf","date_created":"2020-05-14T12:23:08Z","creator":"dernst","file_size":1150679,"date_updated":"2020-07-14T12:45:45Z","file_id":"7834","checksum":"451ae47616e6af2533099f596b2a47fb","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"scopus_import":"1","intvolume":" 97","month":"06","abstract":[{"lang":"eng","text":"Arabidopsis and human ARM protein interact with telomerase. Deregulated mRNA levels of DNA repair and ribosomal protein genes in an Arabidopsis arm mutant suggest non-telomeric ARM function. The human homolog ARMC6 interacts with hTRF2. Abstract: Telomerase maintains telomeres and has proposed non-telomeric functions. We previously identified interaction of the C-terminal domain of Arabidopsis telomerase reverse transcriptase (AtTERT) with an armadillo/β-catenin-like repeat (ARM) containing protein. Here we explore protein–protein interactions of the ARM protein, AtTERT domains, POT1a, TRF-like family and SMH family proteins, and the chromatin remodeling protein CHR19 using bimolecular fluorescence complementation (BiFC), yeast two-hybrid (Y2H) analysis, and co-immunoprecipitation. The ARM protein interacts with both the N- and C-terminal domains of AtTERT in different cellular compartments. ARM interacts with CHR19 and TRF-like I family proteins that also bind AtTERT directly or through interaction with POT1a. The putative human ARM homolog co-precipitates telomerase activity and interacts with hTRF2 protein in vitro. Analysis of Arabidopsis arm mutants shows no obvious changes in telomere length or telomerase activity, suggesting that ARM is not essential for telomere maintenance. The observed interactions with telomerase and Myb-like domain proteins (TRF-like family I) may therefore reflect possible non-telomeric functions. Transcript levels of several DNA repair and ribosomal genes are affected in arm mutants, and ARM, likely in association with other proteins, suppressed expression of XRCC3 and RPSAA promoter constructs in luciferase reporter assays. In conclusion, ARM can participate in non-telomeric functions of telomerase, and can also perform its own telomerase-independent functions."}],"oa_version":"Submitted Version","file_date_updated":"2020-07-14T12:45:45Z","department":[{"_id":"EvBe"}],"date_updated":"2023-09-08T13:21:05Z","ddc":["580"],"type":"journal_article","article_type":"original","status":"public","_id":"277","page":"407 - 420","date_created":"2018-12-11T11:45:34Z","date_published":"2018-06-12T00:00:00Z","doi":"10.1007/s11103-018-0747-4","year":"2018","isi":1,"has_accepted_license":"1","publication":"Plant Molecular Biology","day":"12","oa":1,"publisher":"Springer","quality_controlled":"1","external_id":{"isi":["000438981700009"]},"article_processing_charge":"No","author":[{"first_name":"Ladislav","full_name":"Dokládal, Ladislav","last_name":"Dokládal"},{"last_name":"Benková","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva"},{"last_name":"Honys","full_name":"Honys, David","first_name":"David"},{"first_name":"Nikoleta","last_name":"Dupláková","full_name":"Dupláková, Nikoleta"},{"last_name":"Lee","full_name":"Lee, Lan","first_name":"Lan"},{"first_name":"Stanton","last_name":"Gelvin","full_name":"Gelvin, Stanton"},{"first_name":"Eva","last_name":"Sýkorová","full_name":"Sýkorová, Eva"}],"publist_id":"7625","title":"An armadillo-domain protein participates in a telomerase interaction network","citation":{"ista":"Dokládal L, Benková E, Honys D, Dupláková N, Lee L, Gelvin S, Sýkorová E. 2018. An armadillo-domain protein participates in a telomerase interaction network. Plant Molecular Biology. 97(5), 407–420.","chicago":"Dokládal, Ladislav, Eva Benková, David Honys, Nikoleta Dupláková, Lan Lee, Stanton Gelvin, and Eva Sýkorová. “An Armadillo-Domain Protein Participates in a Telomerase Interaction Network.” Plant Molecular Biology. Springer, 2018. https://doi.org/10.1007/s11103-018-0747-4.","apa":"Dokládal, L., Benková, E., Honys, D., Dupláková, N., Lee, L., Gelvin, S., & Sýkorová, E. (2018). An armadillo-domain protein participates in a telomerase interaction network. Plant Molecular Biology. Springer. https://doi.org/10.1007/s11103-018-0747-4","ama":"Dokládal L, Benková E, Honys D, et al. An armadillo-domain protein participates in a telomerase interaction network. Plant Molecular Biology. 2018;97(5):407-420. doi:10.1007/s11103-018-0747-4","short":"L. Dokládal, E. Benková, D. Honys, N. Dupláková, L. Lee, S. Gelvin, E. Sýkorová, Plant Molecular Biology 97 (2018) 407–420.","ieee":"L. Dokládal et al., “An armadillo-domain protein participates in a telomerase interaction network,” Plant Molecular Biology, vol. 97, no. 5. Springer, pp. 407–420, 2018.","mla":"Dokládal, Ladislav, et al. “An Armadillo-Domain Protein Participates in a Telomerase Interaction Network.” Plant Molecular Biology, vol. 97, no. 5, Springer, 2018, pp. 407–20, doi:10.1007/s11103-018-0747-4."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"author":[{"last_name":"Nickovic","full_name":"Nickovic, Dejan","first_name":"Dejan","id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lebeltel, Olivier","last_name":"Lebeltel","first_name":"Olivier"},{"first_name":"Oded","last_name":"Maler","full_name":"Maler, Oded"},{"orcid":"0000-0001-5199-3143","full_name":"Ferrere, Thomas","last_name":"Ferrere","first_name":"Thomas","id":"40960E6E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Dogan","last_name":"Ulus","full_name":"Ulus, Dogan"}],"publist_id":"7582","external_id":{"isi":["00445822600018"]},"article_processing_charge":"No","title":"AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic","editor":[{"first_name":"Dirk","full_name":"Beyer, Dirk","last_name":"Beyer"},{"first_name":"Marieke","last_name":"Huisman","full_name":"Huisman, Marieke"}],"citation":{"ieee":"D. Nickovic, O. Lebeltel, O. Maler, T. Ferrere, and D. Ulus, “AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic,” presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, Thessaloniki, Greece, 2018, vol. 10806, pp. 303–319.","short":"D. Nickovic, O. Lebeltel, O. Maler, T. Ferrere, D. Ulus, in:, D. Beyer, M. Huisman (Eds.), Springer, 2018, pp. 303–319.","ama":"Nickovic D, Lebeltel O, Maler O, Ferrere T, Ulus D. AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic. In: Beyer D, Huisman M, eds. Vol 10806. Springer; 2018:303-319. doi:10.1007/978-3-319-89963-3_18","apa":"Nickovic, D., Lebeltel, O., Maler, O., Ferrere, T., & Ulus, D. (2018). AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic. In D. Beyer & M. Huisman (Eds.) (Vol. 10806, pp. 303–319). Presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, Thessaloniki, Greece: Springer. https://doi.org/10.1007/978-3-319-89963-3_18","mla":"Nickovic, Dejan, et al. AMT 2.0: Qualitative and Quantitative Trace Analysis with Extended Signal Temporal Logic. Edited by Dirk Beyer and Marieke Huisman, vol. 10806, Springer, 2018, pp. 303–19, doi:10.1007/978-3-319-89963-3_18.","ista":"Nickovic D, Lebeltel O, Maler O, Ferrere T, Ulus D. 2018. AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 10806, 303–319.","chicago":"Nickovic, Dejan, Olivier Lebeltel, Oded Maler, Thomas Ferrere, and Dogan Ulus. “AMT 2.0: Qualitative and Quantitative Trace Analysis with Extended Signal Temporal Logic.” edited by Dirk Beyer and Marieke Huisman, 10806:303–19. Springer, 2018. https://doi.org/10.1007/978-3-319-89963-3_18."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"303 - 319","date_published":"2018-04-14T00:00:00Z","doi":"10.1007/978-3-319-89963-3_18","date_created":"2018-12-11T11:45:41Z","isi":1,"has_accepted_license":"1","year":"2018","day":"14","quality_controlled":"1","publisher":"Springer","oa":1,"department":[{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:45:58Z","date_updated":"2023-09-08T11:52:02Z","ddc":["000"],"type":"conference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"end_date":"2018-04-20","location":"Thessaloniki, Greece","start_date":"2018-04-14","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems"},"status":"public","_id":"299","volume":10806,"related_material":{"record":[{"relation":"later_version","id":"10861","status":"public"}]},"publication_status":"published","file":[{"checksum":"e11db3b9c8e27a1c7d1c738cc5e4d25a","file_id":"5928","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2018_LNCS_Nickovic.pdf","date_created":"2019-02-06T07:33:05Z","file_size":3267209,"date_updated":"2020-07-14T12:45:58Z","creator":"dernst"}],"language":[{"iso":"eng"}],"alternative_title":["LNCS"],"scopus_import":"1","month":"04","intvolume":" 10806","abstract":[{"lang":"eng","text":"We introduce in this paper AMT 2.0 , a tool for qualitative and quantitative analysis of hybrid continuous and Boolean signals that combine numerical values and discrete events. The evaluation of the signals is based on rich temporal specifications expressed in extended Signal Temporal Logic (xSTL), which integrates Timed Regular Expressions (TRE) within Signal Temporal Logic (STL). The tool features qualitative monitoring (property satisfaction checking), trace diagnostics for explaining and justifying property violations and specification-driven measurement of quantitative features of the signal."}],"oa_version":"Published Version"},{"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/29463746"}],"month":"03","intvolume":" 115","abstract":[{"text":"Being cared for when sick is a benefit of sociality that can reduce disease and improve survival of group members. However, individuals providing care risk contracting infectious diseases themselves. If they contract a low pathogen dose, they may develop low-level infections that do not cause disease but still affect host immunity by either decreasing or increasing the host’s vulnerability to subsequent infections. Caring for contagious individuals can thus significantly alter the future disease susceptibility of caregivers. Using ants and their fungal pathogens as a model system, we tested if the altered disease susceptibility of experienced caregivers, in turn, affects their expression of sanitary care behavior. We found that low-level infections contracted during sanitary care had protective or neutral effects on secondary exposure to the same (homologous) pathogen but consistently caused high mortality on superinfection with a different (heterologous) pathogen. In response to this risk, the ants selectively adjusted the expression of their sanitary care. Specifically, the ants performed less grooming and more antimicrobial disinfection when caring for nestmates contaminated with heterologous pathogens compared with homologous ones. By modulating the components of sanitary care in this way the ants acquired less infectious particles of the heterologous pathogens, resulting in reduced superinfection. The performance of risk-adjusted sanitary care reveals the remarkable capacity of ants to react to changes in their disease susceptibility, according to their own infection history and to flexibly adjust collective care to individual risk.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"issue":"11","related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/helping-in-spite-of-risk-ants-perform-risk-averse-sanitary-care-of-infectious-nest-mates/"}]},"volume":115,"ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","status":"public","_id":"413","department":[{"_id":"SyCr"}],"date_updated":"2023-09-08T13:22:21Z","quality_controlled":"1","publisher":"National Academy of Sciences","oa":1,"page":"2782 - 2787","date_published":"2018-03-13T00:00:00Z","doi":"10.1073/pnas.1713501115","date_created":"2018-12-11T11:46:20Z","isi":1,"year":"2018","day":"13","publication":"PNAS","project":[{"call_identifier":"FP7","_id":"25DC711C-B435-11E9-9278-68D0E5697425","name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects","grant_number":"243071"}],"publist_id":"7416","author":[{"first_name":"Matthias","id":"46528076-F248-11E8-B48F-1D18A9856A87","last_name":"Konrad","full_name":"Konrad, Matthias"},{"last_name":"Pull","orcid":"0000-0003-1122-3982","full_name":"Pull, Christopher","first_name":"Christopher","id":"3C7F4840-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Metzler","full_name":"Metzler, Sina","orcid":"0000-0002-9547-2494","first_name":"Sina","id":"48204546-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Seif, Katharina","last_name":"Seif","first_name":"Katharina","id":"90F7894A-02CF-11E9-976E-E38CFE5CBC1D"},{"full_name":"Naderlinger, Elisabeth","last_name":"Naderlinger","id":"31757262-F248-11E8-B48F-1D18A9856A87","first_name":"Elisabeth"},{"full_name":"Grasse, Anna V","last_name":"Grasse","id":"406F989C-F248-11E8-B48F-1D18A9856A87","first_name":"Anna V"},{"last_name":"Cremer","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"pmid":["29463746"],"isi":["000427245400069"]},"article_processing_charge":"No","title":"Ants avoid superinfections by performing risk-adjusted sanitary care","citation":{"mla":"Konrad, Matthias, et al. “Ants Avoid Superinfections by Performing Risk-Adjusted Sanitary Care.” PNAS, vol. 115, no. 11, National Academy of Sciences, 2018, pp. 2782–87, doi:10.1073/pnas.1713501115.","ama":"Konrad M, Pull C, Metzler S, et al. Ants avoid superinfections by performing risk-adjusted sanitary care. PNAS. 2018;115(11):2782-2787. doi:10.1073/pnas.1713501115","apa":"Konrad, M., Pull, C., Metzler, S., Seif, K., Naderlinger, E., Grasse, A. V., & Cremer, S. (2018). Ants avoid superinfections by performing risk-adjusted sanitary care. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1713501115","ieee":"M. Konrad et al., “Ants avoid superinfections by performing risk-adjusted sanitary care,” PNAS, vol. 115, no. 11. National Academy of Sciences, pp. 2782–2787, 2018.","short":"M. Konrad, C. Pull, S. Metzler, K. Seif, E. Naderlinger, A.V. Grasse, S. Cremer, PNAS 115 (2018) 2782–2787.","chicago":"Konrad, Matthias, Christopher Pull, Sina Metzler, Katharina Seif, Elisabeth Naderlinger, Anna V Grasse, and Sylvia Cremer. “Ants Avoid Superinfections by Performing Risk-Adjusted Sanitary Care.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1713501115.","ista":"Konrad M, Pull C, Metzler S, Seif K, Naderlinger E, Grasse AV, Cremer S. 2018. Ants avoid superinfections by performing risk-adjusted sanitary care. PNAS. 115(11), 2782–2787."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"citation":{"mla":"Yakaboylu, Enderalp, and Mikhail Lemeshko. “Anyonic Statistics of Quantum Impurities in Two Dimensions.” Physical Review B - Condensed Matter and Materials Physics, vol. 98, no. 4, 045402, American Physical Society, 2018, doi:10.1103/PhysRevB.98.045402.","ieee":"E. Yakaboylu and M. Lemeshko, “Anyonic statistics of quantum impurities in two dimensions,” Physical Review B - Condensed Matter and Materials Physics, vol. 98, no. 4. American Physical Society, 2018.","short":"E. Yakaboylu, M. Lemeshko, Physical Review B - Condensed Matter and Materials Physics 98 (2018).","apa":"Yakaboylu, E., & Lemeshko, M. (2018). Anyonic statistics of quantum impurities in two dimensions. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.98.045402","ama":"Yakaboylu E, Lemeshko M. Anyonic statistics of quantum impurities in two dimensions. Physical Review B - Condensed Matter and Materials Physics. 2018;98(4). doi:10.1103/PhysRevB.98.045402","chicago":"Yakaboylu, Enderalp, and Mikhail Lemeshko. “Anyonic Statistics of Quantum Impurities in Two Dimensions.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2018. https://doi.org/10.1103/PhysRevB.98.045402.","ista":"Yakaboylu E, Lemeshko M. 2018. Anyonic statistics of quantum impurities in two dimensions. Physical Review B - Condensed Matter and Materials Physics. 98(4), 045402."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"last_name":"Yakaboylu","orcid":"0000-0001-5973-0874","full_name":"Yakaboylu, Enderalp","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87","first_name":"Enderalp"},{"orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail"}],"article_processing_charge":"No","external_id":{"arxiv":["1712.00308"],"isi":["000436939100007"]},"title":"Anyonic statistics of quantum impurities in two dimensions","article_number":"045402","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"},{"_id":"26031614-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Quantum rotations in the presence of a many-body environment","grant_number":"P29902"}],"isi":1,"year":"2018","day":"15","publication":"Physical Review B - Condensed Matter and Materials Physics","doi":"10.1103/PhysRevB.98.045402","date_published":"2018-07-15T00:00:00Z","date_created":"2018-12-11T11:45:08Z","quality_controlled":"1","publisher":"American Physical Society","oa":1,"date_updated":"2023-09-08T13:22:57Z","department":[{"_id":"MiLe"}],"_id":"195","type":"journal_article","status":"public","publication_status":"published","language":[{"iso":"eng"}],"issue":"4","volume":98,"ec_funded":1,"abstract":[{"text":"We demonstrate that identical impurities immersed in a two-dimensional many-particle bath can be viewed as flux-tube-charged-particle composites described by fractional statistics. In particular, we find that the bath manifests itself as an external magnetic flux tube with respect to the impurities, and hence the time-reversal symmetry is broken for the effective Hamiltonian describing the impurities. The emerging flux tube acts as a statistical gauge field after a certain critical coupling. This critical coupling corresponds to the intersection point between the quasiparticle state and the phonon wing, where the angular momentum is transferred from the impurity to the bath. This amounts to a novel configuration with emerging anyons. The proposed setup paves the way to realizing anyons using electrons interacting with superfluid helium or lattice phonons, as well as using atomic impurities in ultracold gases.","lang":"eng"}],"oa_version":"Submitted Version","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1712.00308","open_access":"1"}],"month":"07","intvolume":" 98"},{"isi":1,"year":"2018","publication_status":"published","day":"09","language":[{"iso":"eng"}],"page":"394 - 403","date_published":"2018-07-09T00:00:00Z","volume":"Part F138033","doi":"10.1145/3209108.3209194","date_created":"2018-12-11T11:44:52Z","abstract":[{"lang":"eng","text":"The task of a monitor is to watch, at run-time, the execution of a reactive system, and signal the occurrence of a safety violation in the observed sequence of events. While finite-state monitors have been studied extensively, in practice, monitoring software also makes use of unbounded memory. We define a model of automata equipped with integer-valued registers which can execute only a bounded number of instructions between consecutive events, and thus can form the theoretical basis for the study of infinite-state monitors. We classify these register monitors according to the number k of available registers, and the type of register instructions. In stark contrast to the theory of computability for register machines, we prove that for every k 1, monitors with k + 1 counters (with instruction set 〈+1, =〉) are strictly more expressive than monitors with k counters. We also show that adder monitors (with instruction set 〈1, +, =〉) are strictly more expressive than counter monitors, but are complete for monitoring all computable safety -languages for k = 6. Real-time monitors are further required to signal the occurrence of a safety violation as soon as it occurs. The expressiveness hierarchy for counter monitors carries over to real-time monitors. We then show that 2 adders cannot simulate 3 counters in real-time. Finally, we show that real-time adder monitors with inequalities are as expressive as real-time Turing machines."}],"oa_version":"None","scopus_import":"1","alternative_title":["ACM/IEEE Symposium on Logic in Computer Science"],"quality_controlled":"1","publisher":"IEEE","month":"07","citation":{"ieee":"T. Ferrere, T. A. Henzinger, and E. Saraç, “A theory of register monitors,” presented at the LICS: Logic in Computer Science, Oxford, UK, 2018, vol. Part F138033, pp. 394–403.","short":"T. Ferrere, T.A. Henzinger, E. Saraç, in:, IEEE, 2018, pp. 394–403.","ama":"Ferrere T, Henzinger TA, Saraç E. A theory of register monitors. In: Vol Part F138033. IEEE; 2018:394-403. doi:10.1145/3209108.3209194","apa":"Ferrere, T., Henzinger, T. A., & Saraç, E. (2018). A theory of register monitors (Vol. Part F138033, pp. 394–403). Presented at the LICS: Logic in Computer Science, Oxford, UK: IEEE. https://doi.org/10.1145/3209108.3209194","mla":"Ferrere, Thomas, et al. A Theory of Register Monitors. Vol. Part F138033, IEEE, 2018, pp. 394–403, doi:10.1145/3209108.3209194.","ista":"Ferrere T, Henzinger TA, Saraç E. 2018. A theory of register monitors. LICS: Logic in Computer Science, ACM/IEEE Symposium on Logic in Computer Science, vol. Part F138033, 394–403.","chicago":"Ferrere, Thomas, Thomas A Henzinger, and Ege Saraç. “A Theory of Register Monitors,” Part F138033:394–403. IEEE, 2018. https://doi.org/10.1145/3209108.3209194."},"date_updated":"2023-09-08T11:49:13Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"7779","author":[{"id":"40960E6E-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","orcid":"0000-0001-5199-3143","full_name":"Ferrere, Thomas","last_name":"Ferrere"},{"last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"first_name":"Ege","last_name":"Saraç","full_name":"Saraç, Ege"}],"article_processing_charge":"No","external_id":{"isi":["000545262800041"]},"department":[{"_id":"ToHe"}],"title":"A theory of register monitors","_id":"144","type":"conference","conference":{"location":"Oxford, UK","end_date":"2018-07-12","start_date":"2018-07-09","name":"LICS: Logic in Computer Science"},"status":"public"},{"project":[{"grant_number":"282300","name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Abbas, Mohamad, et al. “Auxin Methylation Is Required for Differential Growth in Arabidopsis.” PNAS, vol. 115, no. 26, National Academy of Sciences, 2018, pp. 6864–69, doi:10.1073/pnas.1806565115.","ieee":"M. Abbas et al., “Auxin methylation is required for differential growth in Arabidopsis,” PNAS, vol. 115, no. 26. National Academy of Sciences, pp. 6864–6869, 2018.","short":"M. Abbas, G.J. Hernández, S. Pollmann, S.L. Samodelov, M. Kolb, J. Friml, U.Z. Hammes, M.D. Zurbriggen, M. Blázquez, D. Alabadí, PNAS 115 (2018) 6864–6869.","apa":"Abbas, M., Hernández, G. J., Pollmann, S., Samodelov, S. L., Kolb, M., Friml, J., … Alabadí, D. (2018). Auxin methylation is required for differential growth in Arabidopsis. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1806565115","ama":"Abbas M, Hernández GJ, Pollmann S, et al. Auxin methylation is required for differential growth in Arabidopsis. PNAS. 2018;115(26):6864-6869. doi:10.1073/pnas.1806565115","chicago":"Abbas, Mohamad, García J Hernández, Stephan Pollmann, Sophia L Samodelov, Martina Kolb, Jiří Friml, Ulrich Z Hammes, Matias D Zurbriggen, Miguel Blázquez, and David Alabadí. “Auxin Methylation Is Required for Differential Growth in Arabidopsis.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1806565115.","ista":"Abbas M, Hernández GJ, Pollmann S, Samodelov SL, Kolb M, Friml J, Hammes UZ, Zurbriggen MD, Blázquez M, Alabadí D. 2018. Auxin methylation is required for differential growth in Arabidopsis. PNAS. 115(26), 6864–6869."},"title":"Auxin methylation is required for differential growth in Arabidopsis","article_processing_charge":"No","external_id":{"isi":["000436245000096"]},"publist_id":"7710","author":[{"id":"47E8FC1C-F248-11E8-B48F-1D18A9856A87","first_name":"Mohamad","full_name":"Abbas, Mohamad","last_name":"Abbas"},{"first_name":"García J","last_name":"Hernández","full_name":"Hernández, García J"},{"first_name":"Stephan","full_name":"Pollmann, Stephan","last_name":"Pollmann"},{"last_name":"Samodelov","full_name":"Samodelov, Sophia L","first_name":"Sophia L"},{"first_name":"Martina","last_name":"Kolb","full_name":"Kolb, Martina"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"},{"first_name":"Ulrich Z","last_name":"Hammes","full_name":"Hammes, Ulrich Z"},{"full_name":"Zurbriggen, Matias D","last_name":"Zurbriggen","first_name":"Matias D"},{"last_name":"Blázquez","full_name":"Blázquez, Miguel","first_name":"Miguel"},{"full_name":"Alabadí, David","last_name":"Alabadí","first_name":"David"}],"oa":1,"publisher":"National Academy of Sciences","quality_controlled":"1","publication":"PNAS","day":"26","year":"2018","isi":1,"date_created":"2018-12-11T11:45:11Z","doi":"10.1073/pnas.1806565115","date_published":"2018-06-26T00:00:00Z","page":"6864-6869","_id":"203","status":"public","type":"journal_article","date_updated":"2023-09-08T13:24:40Z","department":[{"_id":"JiFr"}],"oa_version":"None","abstract":[{"lang":"eng","text":"Asymmetric auxin distribution is instrumental for the differential growth that causes organ bending on tropic stimuli and curvatures during plant development. Local differences in auxin concentrations are achieved mainly by polarized cellular distribution of PIN auxin transporters, but whether other mechanisms involving auxin homeostasis are also relevant for the formation of auxin gradients is not clear. Here we show that auxin methylation is required for asymmetric auxin distribution across the hypocotyl, particularly during its response to gravity. We found that loss-of-function mutants in Arabidopsis IAA CARBOXYL METHYLTRANSFERASE1 (IAMT1) prematurely unfold the apical hook, and that their hypocotyls are impaired in gravitropic reorientation. This defect is linked to an auxin-dependent increase in PIN gene expression, leading to an increased polar auxin transport and lack of asymmetric distribution of PIN3 in the iamt1 mutant. Gravitropic reorientation in the iamt1 mutant could be restored with either endodermis-specific expression of IAMT1 or partial inhibition of polar auxin transport, which also results in normal PIN gene expression levels. We propose that IAA methylation is necessary in gravity-sensing cells to restrict polar auxin transport within the range of auxin levels that allow for differential responses."}],"intvolume":" 115","month":"06","main_file_link":[{"open_access":"1","url":"http://eprints.nottingham.ac.uk/52388/"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"issue":"26","volume":115},{"acknowledgement":"We thank Robert Seiringer and Daniel Ueltschi for bringing the issue of the change in critical temperature to our attention. We also thank the Erwin Schrödinger Institute (all authors) and the Department of Mathematics, University of Copenhagen (MN) for the hospitality during the period this work was carried out. We gratefully acknowledge the financial support by the European Unions Seventh Framework Programme under the ERC Grant Agreement Nos. 321029 (JPS and RR) and 337603 (RR) as well as support by the VIL-LUM FONDEN via the QMATH Centre of Excellence (Grant No. 10059) (JPS and RR), by the National Science Center (NCN) under grant No. 2016/21/D/ST1/02430 and the Austrian Science Fund (FWF) through project No. P 27533-N27 (MN).","quality_controlled":"1","publisher":"IOP Publishing Ltd.","oa":1,"isi":1,"year":"2018","day":"01","publication":"EPL","doi":"10.1209/0295-5075/121/10007","date_published":"2018-01-01T00:00:00Z","date_created":"2018-12-11T11:46:15Z","article_number":"10007","project":[{"name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","grant_number":"P27533_N27","call_identifier":"FWF","_id":"25C878CE-B435-11E9-9278-68D0E5697425"}],"citation":{"ista":"Napiórkowski MM, Reuvers R, Solovej J. 2018. Calculation of the critical temperature of a dilute Bose gas in the Bogoliubov approximation. EPL. 121(1), 10007.","chicago":"Napiórkowski, Marcin M, Robin Reuvers, and Jan Solovej. “Calculation of the Critical Temperature of a Dilute Bose Gas in the Bogoliubov Approximation.” EPL. IOP Publishing Ltd., 2018. https://doi.org/10.1209/0295-5075/121/10007.","ieee":"M. M. Napiórkowski, R. Reuvers, and J. Solovej, “Calculation of the critical temperature of a dilute Bose gas in the Bogoliubov approximation,” EPL, vol. 121, no. 1. IOP Publishing Ltd., 2018.","short":"M.M. Napiórkowski, R. Reuvers, J. Solovej, EPL 121 (2018).","ama":"Napiórkowski MM, Reuvers R, Solovej J. Calculation of the critical temperature of a dilute Bose gas in the Bogoliubov approximation. EPL. 2018;121(1). doi:10.1209/0295-5075/121/10007","apa":"Napiórkowski, M. M., Reuvers, R., & Solovej, J. (2018). Calculation of the critical temperature of a dilute Bose gas in the Bogoliubov approximation. EPL. IOP Publishing Ltd. https://doi.org/10.1209/0295-5075/121/10007","mla":"Napiórkowski, Marcin M., et al. “Calculation of the Critical Temperature of a Dilute Bose Gas in the Bogoliubov Approximation.” EPL, vol. 121, no. 1, 10007, IOP Publishing Ltd., 2018, doi:10.1209/0295-5075/121/10007."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"7432","author":[{"full_name":"Napiórkowski, Marcin M","last_name":"Napiórkowski","id":"4197AD04-F248-11E8-B48F-1D18A9856A87","first_name":"Marcin M"},{"last_name":"Reuvers","full_name":"Reuvers, Robin","first_name":"Robin"},{"last_name":"Solovej","full_name":"Solovej, Jan","first_name":"Jan"}],"external_id":{"isi":["000460003000003"],"arxiv":["1706.01822"]},"article_processing_charge":"No","title":"Calculation of the critical temperature of a dilute Bose gas in the Bogoliubov approximation","abstract":[{"text":"Following an earlier calculation in 3D, we calculate the 2D critical temperature of a dilute, translation-invariant Bose gas using a variational formulation of the Bogoliubov approximation introduced by Critchley and Solomon in 1976. This provides the first analytical calculation of the Kosterlitz-Thouless transition temperature that includes the constant in the logarithm.","lang":"eng"}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1706.01822"}],"month":"01","intvolume":" 121","publication_status":"published","language":[{"iso":"eng"}],"volume":121,"issue":"1","_id":"399","article_type":"original","type":"journal_article","status":"public","date_updated":"2023-09-08T13:30:51Z","department":[{"_id":"RoSe"}]},{"type":"journal_article","status":"public","_id":"5830","author":[{"last_name":"Zhang","full_name":"Zhang, Luosha","first_name":"Luosha"},{"first_name":"Xiong","full_name":"Shi, Xiong","last_name":"Shi"},{"full_name":"Zhang, Yutao","last_name":"Zhang","first_name":"Yutao"},{"first_name":"Jiajing","last_name":"Wang","full_name":"Wang, Jiajing"},{"first_name":"Jingwei","last_name":"Yang","full_name":"Yang, Jingwei"},{"last_name":"Ishida","full_name":"Ishida, Takashi","first_name":"Takashi"},{"first_name":"Wenqian","full_name":"Jiang, Wenqian","last_name":"Jiang"},{"full_name":"Han, Xiangyu","last_name":"Han","first_name":"Xiangyu"},{"last_name":"Kang","full_name":"Kang, Jingke","first_name":"Jingke"},{"first_name":"Xuening","full_name":"Wang, Xuening","last_name":"Wang"},{"full_name":"Pan, Lixia","last_name":"Pan","first_name":"Lixia"},{"full_name":"Lv, Shuo","last_name":"Lv","first_name":"Shuo"},{"first_name":"Bing","last_name":"Cao","full_name":"Cao, Bing"},{"last_name":"Zhang","full_name":"Zhang, Yonghong","first_name":"Yonghong"},{"first_name":"Jinbin","last_name":"Wu","full_name":"Wu, Jinbin"},{"last_name":"Han","full_name":"Han, Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87","first_name":"Huibin"},{"full_name":"Hu, Zhubing","last_name":"Hu","first_name":"Zhubing"},{"first_name":"Langjun","full_name":"Cui, Langjun","last_name":"Cui"},{"full_name":"Sawa, Shinichiro","last_name":"Sawa","first_name":"Shinichiro"},{"full_name":"He, Junmin","last_name":"He","first_name":"Junmin"},{"first_name":"Guodong","last_name":"Wang","full_name":"Wang, Guodong"}],"article_processing_charge":"No","external_id":{"isi":["000459014800021"],"pmid":["30378140"]},"title":"CLE9 peptide-induced stomatal closure is mediated by abscisic acid, hydrogen peroxide, and nitric oxide in arabidopsis thaliana","department":[{"_id":"JiFr"}],"date_updated":"2023-09-11T12:43:31Z","citation":{"chicago":"Zhang, Luosha, Xiong Shi, Yutao Zhang, Jiajing Wang, Jingwei Yang, Takashi Ishida, Wenqian Jiang, et al. “CLE9 Peptide-Induced Stomatal Closure Is Mediated by Abscisic Acid, Hydrogen Peroxide, and Nitric Oxide in Arabidopsis Thaliana.” Plant Cell and Environment. Wiley, 2018. https://doi.org/10.1111/pce.13475.","ista":"Zhang L, Shi X, Zhang Y, Wang J, Yang J, Ishida T, Jiang W, Han X, Kang J, Wang X, Pan L, Lv S, Cao B, Zhang Y, Wu J, Han H, Hu Z, Cui L, Sawa S, He J, Wang G. 2018. CLE9 peptide-induced stomatal closure is mediated by abscisic acid, hydrogen peroxide, and nitric oxide in arabidopsis thaliana. Plant Cell and Environment.","mla":"Zhang, Luosha, et al. “CLE9 Peptide-Induced Stomatal Closure Is Mediated by Abscisic Acid, Hydrogen Peroxide, and Nitric Oxide in Arabidopsis Thaliana.” Plant Cell and Environment, Wiley, 2018, doi:10.1111/pce.13475.","ama":"Zhang L, Shi X, Zhang Y, et al. CLE9 peptide-induced stomatal closure is mediated by abscisic acid, hydrogen peroxide, and nitric oxide in arabidopsis thaliana. Plant Cell and Environment. 2018. doi:10.1111/pce.13475","apa":"Zhang, L., Shi, X., Zhang, Y., Wang, J., Yang, J., Ishida, T., … Wang, G. (2018). CLE9 peptide-induced stomatal closure is mediated by abscisic acid, hydrogen peroxide, and nitric oxide in arabidopsis thaliana. Plant Cell and Environment. Wiley. https://doi.org/10.1111/pce.13475","ieee":"L. Zhang et al., “CLE9 peptide-induced stomatal closure is mediated by abscisic acid, hydrogen peroxide, and nitric oxide in arabidopsis thaliana,” Plant Cell and Environment. Wiley, 2018.","short":"L. Zhang, X. Shi, Y. Zhang, J. Wang, J. Yang, T. Ishida, W. Jiang, X. Han, J. Kang, X. Wang, L. Pan, S. Lv, B. Cao, Y. Zhang, J. Wu, H. Han, Z. Hu, L. Cui, S. Sawa, J. He, G. Wang, Plant Cell and Environment (2018)."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","quality_controlled":"1","publisher":"Wiley","scopus_import":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30378140"}],"month":"10","abstract":[{"text":"CLE peptides have been implicated in various developmental processes of plants and mediate their responses to environmental stimuli. However, the biological relevance of most CLE genes remains to be functionally characterized. Here, we report that CLE9, which is expressed in stomata, acts as an essential regulator in the induction of stomatal closure. Exogenous application of CLE9 peptides or overexpression of CLE9 effectively led to stomatal closure and enhanced drought tolerance, whereas CLE9 loss-of-function mutants were sensitivity to drought stress. CLE9-induced stomatal closure was impaired in abscisic acid (ABA)-deficient mutants, indicating that ABA is required for CLE9-medaited guard cell signalling. We further deciphered that two guard cell ABA-signalling components, OST1 and SLAC1, were responsible for CLE9-induced stomatal closure. MPK3 and MPK6 were activated by the CLE9 peptide, and CLE9 peptides failed to close stomata in mpk3 and mpk6 mutants. In addition, CLE9 peptides stimulated the induction of hydrogen peroxide (H2O2) and nitric oxide (NO) synthesis associated with stomatal closure, which was abolished in the NADPH oxidase-deficient mutants or nitric reductase mutants, respectively. Collectively, our results reveal a novel ABA-dependent function of CLE9 in the regulation of stomatal apertures, thereby suggesting a potential role of CLE9 in the stress acclimatization of plants.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","doi":"10.1111/pce.13475","date_published":"2018-10-31T00:00:00Z","date_created":"2019-01-13T22:59:11Z","isi":1,"publication_identifier":{"issn":["01407791"]},"publication_status":"epub_ahead","year":"2018","day":"31","language":[{"iso":"eng"}],"publication":"Plant Cell and Environment"},{"date_published":"2018-05-21T00:00:00Z","doi":"10.1038/s41556-018-0108-1","date_created":"2018-12-11T11:45:38Z","page":"677 - 687","day":"21","publication":"Nature Cell Biology","isi":1,"year":"2018","publisher":"Nature Publishing Group","quality_controlled":"1","oa":1,"title":"Clonal analysis of Notch1-expressing cells reveals the existence of unipotent stem cells that retain long-term plasticity in the embryonic mammary gland","author":[{"first_name":"Anna","full_name":"Lilja, Anna","last_name":"Lilja"},{"last_name":"Rodilla","full_name":"Rodilla, Veronica","first_name":"Veronica"},{"full_name":"Huyghe, Mathilde","last_name":"Huyghe","first_name":"Mathilde"},{"full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Landragin, Camille","last_name":"Landragin","first_name":"Camille"},{"first_name":"Olivier","last_name":"Renaud","full_name":"Renaud, Olivier"},{"last_name":"Leroy","full_name":"Leroy, Olivier","first_name":"Olivier"},{"first_name":"Steffen","last_name":"Rulands","full_name":"Rulands, Steffen"},{"last_name":"Simons","full_name":"Simons, Benjamin","first_name":"Benjamin"},{"first_name":"Silvia","full_name":"Fré, Silvia","last_name":"Fré"}],"publist_id":"7594","article_processing_charge":"No","external_id":{"isi":["000433237300003"],"pmid":["29784917"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"short":"A. Lilja, V. Rodilla, M. Huyghe, E.B. Hannezo, C. Landragin, O. Renaud, O. Leroy, S. Rulands, B. Simons, S. Fré, Nature Cell Biology 20 (2018) 677–687.","ieee":"A. Lilja et al., “Clonal analysis of Notch1-expressing cells reveals the existence of unipotent stem cells that retain long-term plasticity in the embryonic mammary gland,” Nature Cell Biology, vol. 20, no. 6. Nature Publishing Group, pp. 677–687, 2018.","apa":"Lilja, A., Rodilla, V., Huyghe, M., Hannezo, E. B., Landragin, C., Renaud, O., … Fré, S. (2018). Clonal analysis of Notch1-expressing cells reveals the existence of unipotent stem cells that retain long-term plasticity in the embryonic mammary gland. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/s41556-018-0108-1","ama":"Lilja A, Rodilla V, Huyghe M, et al. Clonal analysis of Notch1-expressing cells reveals the existence of unipotent stem cells that retain long-term plasticity in the embryonic mammary gland. Nature Cell Biology. 2018;20(6):677-687. doi:10.1038/s41556-018-0108-1","mla":"Lilja, Anna, et al. “Clonal Analysis of Notch1-Expressing Cells Reveals the Existence of Unipotent Stem Cells That Retain Long-Term Plasticity in the Embryonic Mammary Gland.” Nature Cell Biology, vol. 20, no. 6, Nature Publishing Group, 2018, pp. 677–87, doi:10.1038/s41556-018-0108-1.","ista":"Lilja A, Rodilla V, Huyghe M, Hannezo EB, Landragin C, Renaud O, Leroy O, Rulands S, Simons B, Fré S. 2018. Clonal analysis of Notch1-expressing cells reveals the existence of unipotent stem cells that retain long-term plasticity in the embryonic mammary gland. Nature Cell Biology. 20(6), 677–687.","chicago":"Lilja, Anna, Veronica Rodilla, Mathilde Huyghe, Edouard B Hannezo, Camille Landragin, Olivier Renaud, Olivier Leroy, Steffen Rulands, Benjamin Simons, and Silvia Fré. “Clonal Analysis of Notch1-Expressing Cells Reveals the Existence of Unipotent Stem Cells That Retain Long-Term Plasticity in the Embryonic Mammary Gland.” Nature Cell Biology. Nature Publishing Group, 2018. https://doi.org/10.1038/s41556-018-0108-1."},"issue":"6","volume":20,"language":[{"iso":"eng"}],"publication_status":"published","month":"05","intvolume":" 20","scopus_import":"1","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6984964","open_access":"1"}],"oa_version":"Submitted Version","pmid":1,"abstract":[{"text":"Recent lineage tracing studies have revealed that mammary gland homeostasis relies on unipotent stem cells. However, whether and when lineage restriction occurs during embryonic mammary development, and which signals orchestrate cell fate specification, remain unknown. Using a combination of in vivo clonal analysis with whole mount immunofluorescence and mathematical modelling of clonal dynamics, we found that embryonic multipotent mammary cells become lineage-restricted surprisingly early in development, with evidence for unipotency as early as E12.5 and no statistically discernable bipotency after E15.5. To gain insights into the mechanisms governing the switch from multipotency to unipotency, we used gain-of-function Notch1 mice and demonstrated that Notch activation cell autonomously dictates luminal cell fate specification to both embryonic and basally committed mammary cells. These functional studies have important implications for understanding the signals underlying cell plasticity and serve to clarify how reactivation of embryonic programs in adult cells can lead to cancer.","lang":"eng"}],"department":[{"_id":"EdHa"}],"date_updated":"2023-09-11T12:44:08Z","status":"public","article_type":"original","type":"journal_article","_id":"288"},{"article_number":"159","project":[{"grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"short":"T. Auzinger, W. Heidrich, B. Bickel, ACM Transactions on Graphics 37 (2018).","ieee":"T. Auzinger, W. Heidrich, and B. Bickel, “Computational design of nanostructural color for additive manufacturing,” ACM Transactions on Graphics, vol. 37, no. 4. ACM, 2018.","ama":"Auzinger T, Heidrich W, Bickel B. Computational design of nanostructural color for additive manufacturing. ACM Transactions on Graphics. 2018;37(4). doi:10.1145/3197517.3201376","apa":"Auzinger, T., Heidrich, W., & Bickel, B. (2018). Computational design of nanostructural color for additive manufacturing. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3197517.3201376","mla":"Auzinger, Thomas, et al. “Computational Design of Nanostructural Color for Additive Manufacturing.” ACM Transactions on Graphics, vol. 37, no. 4, 159, ACM, 2018, doi:10.1145/3197517.3201376.","ista":"Auzinger T, Heidrich W, Bickel B. 2018. Computational design of nanostructural color for additive manufacturing. ACM Transactions on Graphics. 37(4), 159.","chicago":"Auzinger, Thomas, Wolfgang Heidrich, and Bernd Bickel. “Computational Design of Nanostructural Color for Additive Manufacturing.” ACM Transactions on Graphics. ACM, 2018. https://doi.org/10.1145/3197517.3201376."},"title":"Computational design of nanostructural color for additive manufacturing","article_processing_charge":"No","external_id":{"isi":["000448185000120"]},"author":[{"orcid":"0000-0002-1546-3265","full_name":"Auzinger, Thomas","last_name":"Auzinger","id":"4718F954-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas"},{"full_name":"Heidrich, Wolfgang","last_name":"Heidrich","first_name":"Wolfgang"},{"last_name":"Bickel","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd"}],"acknowledgement":"This work was in part supported by King Abdullah University of Science and Technology Baseline Funding.","oa":1,"quality_controlled":"1","publisher":"ACM","publication":"ACM Transactions on Graphics","day":"01","year":"2018","isi":1,"has_accepted_license":"1","date_created":"2018-12-11T11:45:43Z","doi":"10.1145/3197517.3201376","date_published":"2018-08-01T00:00:00Z","_id":"304","pubrep_id":"1028","status":"public","type":"journal_article","ddc":["000","535","680"],"date_updated":"2023-09-11T12:46:13Z","file_date_updated":"2020-07-14T12:45:59Z","department":[{"_id":"BeBi"}],"oa_version":"Submitted Version","abstract":[{"text":"Additive manufacturing has recently seen drastic improvements in resolution, making it now possible to fabricate features at scales of hundreds or even dozens of nanometers, which previously required very expensive lithographic methods.\r\nAs a result, additive manufacturing now seems poised for optical applications, including those relevant to computer graphics, such as material design, as well as display and imaging applications.\r\n \r\nIn this work, we explore the use of additive manufacturing for generating structural colors, where the structures are designed using a fabrication-aware optimization process.\r\nThis requires a combination of full-wave simulation, a feasible parameterization of the design space, and a tailored optimization procedure.\r\nMany of these components should be re-usable for the design of other optical structures at this scale.\r\n \r\nWe show initial results of material samples fabricated based on our designs.\r\nWhile these suffer from the prototype character of state-of-the-art fabrication hardware, we believe they clearly demonstrate the potential of additive nanofabrication for structural colors and other graphics applications.","lang":"eng"}],"intvolume":" 37","month":"08","alternative_title":["ACM Transactions on Graphics"],"scopus_import":"1","language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-12T10:18:14Z","file_name":"IST-2018-1024-v1+1_NanoStructColor-Auzinger-paper.pdf","creator":"system","date_updated":"2020-07-14T12:45:59Z","file_size":10751684,"file_id":"5334","checksum":"dcdcc955a4c1c6d2599aeebb97d2e7b9","access_level":"open_access","relation":"main_file","content_type":"application/pdf"},{"file_name":"IST-2018-1024-v1+2_NanoStructColor-Auzinger-supplemental.pdf","date_created":"2018-12-12T10:18:15Z","creator":"system","file_size":20755095,"date_updated":"2020-07-14T12:45:59Z","checksum":"cae52b3a8d5e97be84771cd61ea2f75e","file_id":"5335","relation":"main_file","access_level":"open_access","content_type":"application/pdf"},{"file_name":"IST-2018-1024-v1+3_NanoStructColor-Auzinger-image.jpg","date_created":"2018-12-12T10:18:16Z","file_size":2186944,"date_updated":"2020-07-14T12:45:59Z","creator":"system","file_id":"5336","checksum":"76dd90648f75779d3f64e324b6daaffe","content_type":"image/jpeg","relation":"main_file","access_level":"open_access"},{"relation":"main_file","access_level":"open_access","content_type":"application/x-7z-compressed","checksum":"c3a5b775a0ecdb20ccefb8d9646ec140","file_id":"5337","creator":"system","file_size":2734352,"date_updated":"2020-07-14T12:45:59Z","file_name":"IST-2018-1024-v1+4_NanoStructColor-Auzinger-blueprint.7z","date_created":"2018-12-12T10:18:17Z"},{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"dcdcc955a4c1c6d2599aeebb97d2e7b9","file_id":"5338","date_updated":"2020-07-14T12:45:59Z","file_size":10751684,"creator":"system","date_created":"2018-12-12T10:18:18Z","file_name":"IST-2018-1024-v2+1_NanoStructColor-Auzinger-paper.pdf"},{"file_id":"5339","checksum":"76dd90648f75779d3f64e324b6daaffe","access_level":"open_access","relation":"main_file","content_type":"image/jpeg","date_created":"2018-12-12T10:18:19Z","file_name":"IST-2018-1024-v2+3_NanoStructColor-Auzinger-image.jpg","creator":"system","date_updated":"2020-07-14T12:45:59Z","file_size":2186944},{"date_created":"2018-12-12T10:18:20Z","file_name":"IST-2018-1024-v2+4_NanoStructColor-Auzinger-blueprint.7z","date_updated":"2020-07-14T12:45:59Z","file_size":2734352,"creator":"system","checksum":"c3a5b775a0ecdb20ccefb8d9646ec140","file_id":"5340","content_type":"application/x-7z-compressed","access_level":"open_access","relation":"main_file"},{"file_name":"IST-2018-1024-v2+5_NanoStructColor-Auzinger-supplemental.pdf","date_created":"2018-12-12T10:18:21Z","file_size":20755762,"date_updated":"2020-07-14T12:45:59Z","creator":"system","file_id":"5341","checksum":"667e91b686db41e44d855a4fb2137402","content_type":"application/pdf","relation":"main_file","access_level":"open_access"},{"checksum":"dcdcc955a4c1c6d2599aeebb97d2e7b9","file_id":"5342","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2018-1024-v3+1_NanoStructColor-Auzinger-paper.pdf","date_created":"2018-12-12T10:18:22Z","creator":"system","file_size":10751684,"date_updated":"2020-07-14T12:45:59Z"},{"file_name":"IST-2018-1024-v3+3_NanoStructColor-Auzinger-image.jpg","date_created":"2018-12-12T10:18:22Z","creator":"system","file_size":2186944,"date_updated":"2020-07-14T12:45:59Z","checksum":"76dd90648f75779d3f64e324b6daaffe","file_id":"5343","relation":"main_file","access_level":"open_access","content_type":"image/jpeg"},{"access_level":"open_access","relation":"main_file","content_type":"application/x-7z-compressed","checksum":"c3a5b775a0ecdb20ccefb8d9646ec140","file_id":"5344","creator":"system","date_updated":"2020-07-14T12:45:59Z","file_size":2734352,"date_created":"2018-12-12T10:18:23Z","file_name":"IST-2018-1024-v3+4_NanoStructColor-Auzinger-blueprint.7z"},{"file_size":20755762,"date_updated":"2020-07-14T12:45:59Z","creator":"system","file_name":"IST-2018-1024-v3+5_NanoStructColor-Auzinger-supplemental.pdf","date_created":"2018-12-12T10:18:24Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"667e91b686db41e44d855a4fb2137402","file_id":"5345"},{"checksum":"72dce35388fb1aa7953df4d9ae3d02f1","file_id":"5346","access_level":"open_access","relation":"main_file","content_type":"application/vnd.openxmlformats-officedocument.presentationml.presentation","date_created":"2018-12-12T10:18:25Z","file_name":"IST-2018-1024-v3+6_NanoStructColor-Auzinger-presentation.pptx","creator":"system","date_updated":"2020-07-14T12:45:59Z","file_size":69698068}],"publication_status":"published","ec_funded":1,"volume":37,"issue":"4","related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/color-effects-from-transparent-3d-printed-nanostructures/","relation":"press_release"}]}},{"ec_funded":1,"volume":37,"related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/interactive-software-tool-makes-complex-mold-design-simple/","relation":"press_release"}]},"issue":"4","publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_size":104225664,"date_updated":"2020-07-14T12:44:38Z","creator":"system","file_name":"IST-2018-1037-v1+1_CoreCavity-AuthorVersion.pdf","date_created":"2018-12-12T10:18:38Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5360","checksum":"6a5368bc86c4e1a9fcfe588fd1f14ee8"},{"checksum":"3861e693ba47c51f3ec7b7867d573a61","file_id":"5361","content_type":"application/zip","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:18:39Z","file_name":"IST-2018-1037-v1+2_CoreCavity-Supplemental.zip","date_updated":"2020-07-14T12:44:38Z","file_size":377743553,"creator":"system"},{"content_type":"video/vnd.objectvideo","relation":"main_file","access_level":"open_access","file_id":"5362","checksum":"490040c685ed869536e2a18f5a906b94","file_size":162634396,"date_updated":"2020-07-14T12:44:38Z","creator":"system","file_name":"IST-2018-1037-v1+3_CoreCavity-Video.mp4","date_created":"2018-12-12T10:18:41Z"},{"file_size":527972,"date_updated":"2020-07-14T12:44:38Z","creator":"system","file_name":"IST-2018-1037-v1+4_CoreCavity-RepresentativeImage.jpg","date_created":"2018-12-12T10:18:42Z","content_type":"image/jpeg","relation":"main_file","access_level":"open_access","file_id":"5363","checksum":"be7fc8b229adda727419b6504b3b9352"}],"scopus_import":"1","intvolume":" 37","month":"08","abstract":[{"text":"Molding is a popular mass production method, in which the initial expenses for the mold are offset by the low per-unit production cost. However, the physical fabrication constraints of the molding technique commonly restrict the shape of moldable objects. For a complex shape, a decomposition of the object into moldable parts is a common strategy to address these constraints, with plastic model kits being a popular and illustrative example. However, conducting such a decomposition requires considerable expertise, and it depends on the technical aspects of the fabrication technique, as well as aesthetic considerations. We present an interactive technique to create such decompositions for two-piece molding, in which each part of the object is cast between two rigid mold pieces. Given the surface description of an object, we decompose its thin-shell equivalent into moldable parts by first performing a coarse decomposition and then utilizing an active contour model for the boundaries between individual parts. Formulated as an optimization problem, the movement of the contours is guided by an energy reflecting fabrication constraints to ensure the moldability of each part. Simultaneously, the user is provided with editing capabilities to enforce aesthetic guidelines. Our interactive interface provides control of the contour positions by allowing, for example, the alignment of part boundaries with object features. Our technique enables a novel workflow, as it empowers novice users to explore the design space, and it generates fabrication-ready two-piece molds that can be used either for casting or industrial injection molding of free-form objects.","lang":"eng"}],"oa_version":"Submitted Version","file_date_updated":"2020-07-14T12:44:38Z","department":[{"_id":"BeBi"}],"date_updated":"2023-09-11T12:48:09Z","ddc":["004","516","670"],"type":"journal_article","pubrep_id":"1037","status":"public","_id":"12","date_created":"2018-12-11T11:44:09Z","doi":"10.1145/3197517.3201341","date_published":"2018-08-04T00:00:00Z","year":"2018","has_accepted_license":"1","isi":1,"publication":"ACM Transaction on Graphics","day":"04","oa":1,"quality_controlled":"1","publisher":"ACM","external_id":{"isi":["000448185000096"]},"article_processing_charge":"No","publist_id":"8044","author":[{"full_name":"Nakashima, Kazutaka","last_name":"Nakashima","first_name":"Kazutaka"},{"last_name":"Auzinger","full_name":"Auzinger, Thomas","orcid":"0000-0002-1546-3265","id":"4718F954-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas"},{"id":"33F19F16-F248-11E8-B48F-1D18A9856A87","first_name":"Emmanuel","full_name":"Iarussi, Emmanuel","last_name":"Iarussi"},{"full_name":"Zhang, Ran","orcid":"0000-0002-3808-281X","last_name":"Zhang","first_name":"Ran","id":"4DDBCEB0-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Takeo","full_name":"Igarashi, Takeo","last_name":"Igarashi"},{"full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd"}],"title":"CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid molds","citation":{"ista":"Nakashima K, Auzinger T, Iarussi E, Zhang R, Igarashi T, Bickel B. 2018. CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid molds. ACM Transaction on Graphics. 37(4), 135.","chicago":"Nakashima, Kazutaka, Thomas Auzinger, Emmanuel Iarussi, Ran Zhang, Takeo Igarashi, and Bernd Bickel. “CoreCavity: Interactive Shell Decomposition for Fabrication with Two-Piece Rigid Molds.” ACM Transaction on Graphics. ACM, 2018. https://doi.org/10.1145/3197517.3201341.","apa":"Nakashima, K., Auzinger, T., Iarussi, E., Zhang, R., Igarashi, T., & Bickel, B. (2018). CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid molds. ACM Transaction on Graphics. ACM. https://doi.org/10.1145/3197517.3201341","ama":"Nakashima K, Auzinger T, Iarussi E, Zhang R, Igarashi T, Bickel B. CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid molds. ACM Transaction on Graphics. 2018;37(4). doi:10.1145/3197517.3201341","short":"K. Nakashima, T. Auzinger, E. Iarussi, R. Zhang, T. Igarashi, B. Bickel, ACM Transaction on Graphics 37 (2018).","ieee":"K. Nakashima, T. Auzinger, E. Iarussi, R. Zhang, T. Igarashi, and B. Bickel, “CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid molds,” ACM Transaction on Graphics, vol. 37, no. 4. ACM, 2018.","mla":"Nakashima, Kazutaka, et al. “CoreCavity: Interactive Shell Decomposition for Fabrication with Two-Piece Rigid Molds.” ACM Transaction on Graphics, vol. 37, no. 4, 135, ACM, 2018, doi:10.1145/3197517.3201341."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767","call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","_id":"2508E324-B435-11E9-9278-68D0E5697425","grant_number":"642841","name":"Distributed 3D Object Design"}],"article_number":"135"},{"project":[{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"name":"Game Theory","grant_number":"S11407","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"article_number":"555","title":"Crosstalk in concurrent repeated games impedes direct reciprocity and requires stronger levels of forgiveness","article_processing_charge":"No","external_id":{"isi":["000424318200001"]},"publist_id":"7368","author":[{"last_name":"Reiter","orcid":"0000-0002-0170-7353","full_name":"Reiter, Johannes","first_name":"Johannes","id":"4A918E98-F248-11E8-B48F-1D18A9856A87"},{"id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","orcid":"0000-0001-5116-955X","full_name":"Hilbe, Christian","last_name":"Hilbe"},{"first_name":"David","full_name":"Rand, David","last_name":"Rand"},{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Nowak","full_name":"Nowak, Martin","first_name":"Martin"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Reiter J, Hilbe C, Rand D, Chatterjee K, Nowak M. 2018. Crosstalk in concurrent repeated games impedes direct reciprocity and requires stronger levels of forgiveness. Nature Communications. 9(1), 555.","chicago":"Reiter, Johannes, Christian Hilbe, David Rand, Krishnendu Chatterjee, and Martin Nowak. “Crosstalk in Concurrent Repeated Games Impedes Direct Reciprocity and Requires Stronger Levels of Forgiveness.” Nature Communications. Nature Publishing Group, 2018. https://doi.org/10.1038/s41467-017-02721-8.","ama":"Reiter J, Hilbe C, Rand D, Chatterjee K, Nowak M. Crosstalk in concurrent repeated games impedes direct reciprocity and requires stronger levels of forgiveness. Nature Communications. 2018;9(1). doi:10.1038/s41467-017-02721-8","apa":"Reiter, J., Hilbe, C., Rand, D., Chatterjee, K., & Nowak, M. (2018). Crosstalk in concurrent repeated games impedes direct reciprocity and requires stronger levels of forgiveness. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-02721-8","short":"J. Reiter, C. Hilbe, D. Rand, K. Chatterjee, M. Nowak, Nature Communications 9 (2018).","ieee":"J. Reiter, C. Hilbe, D. Rand, K. Chatterjee, and M. Nowak, “Crosstalk in concurrent repeated games impedes direct reciprocity and requires stronger levels of forgiveness,” Nature Communications, vol. 9, no. 1. Nature Publishing Group, 2018.","mla":"Reiter, Johannes, et al. “Crosstalk in Concurrent Repeated Games Impedes Direct Reciprocity and Requires Stronger Levels of Forgiveness.” Nature Communications, vol. 9, no. 1, 555, Nature Publishing Group, 2018, doi:10.1038/s41467-017-02721-8."},"oa":1,"publisher":"Nature Publishing Group","quality_controlled":"1","acknowledgement":"This work was supported by the European Research Council (ERC) start grant 279307: Graph Games (C.K.), Austrian Science Fund (FWF) grant no P23499-N23 (C.K.), FWF\r\nNFN grant no S11407-N23 RiSE/SHiNE (C.K.), Office of Naval Research grant N00014-16-1-2914 (M.A.N.), National Cancer Institute grant CA179991 (M.A.N.) and by the John Templeton Foundation. J.G.R. is supported by an Erwin Schrödinger fellowship\r\n(Austrian Science Fund FWF J-3996). C.H. acknowledges generous support from the\r\nISTFELLOW program. The Program for Evolutionary Dynamics is supported in part by\r\na gift from B Wu and Eric Larson.","date_created":"2018-12-11T11:46:34Z","date_published":"2018-02-07T00:00:00Z","doi":"10.1038/s41467-017-02721-8","publication":"Nature Communications","day":"07","year":"2018","has_accepted_license":"1","isi":1,"pubrep_id":"964","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":"454","file_date_updated":"2020-07-14T12:46:31Z","department":[{"_id":"KrCh"}],"ddc":["004"],"date_updated":"2023-09-11T12:51:03Z","intvolume":" 9","month":"02","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"Direct reciprocity is a mechanism for cooperation among humans. Many of our daily interactions are repeated. We interact repeatedly with our family, friends, colleagues, members of the local and even global community. In the theory of repeated games, it is a tacit assumption that the various games that a person plays simultaneously have no effect on each other. Here we introduce a general framework that allows us to analyze “crosstalk” between a player’s concurrent games. In the presence of crosstalk, the action a person experiences in one game can alter the person’s decision in another. We find that crosstalk impedes the maintenance of cooperation and requires stronger levels of forgiveness. The magnitude of the effect depends on the population structure. In more densely connected social groups, crosstalk has a stronger effect. A harsh retaliator, such as Tit-for-Tat, is unable to counteract crosstalk. The crosstalk framework provides a unified interpretation of direct and upstream reciprocity in the context of repeated games.","lang":"eng"}],"ec_funded":1,"issue":"1","volume":9,"language":[{"iso":"eng"}],"file":[{"file_name":"IST-2018-964-v1+1_2018_Hilbe_Crosstalk_in.pdf","date_created":"2018-12-12T10:09:18Z","creator":"system","file_size":843646,"date_updated":"2020-07-14T12:46:31Z","file_id":"4741","checksum":"b6b90367545b4c615891c960ab0567f1","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"publication_status":"published"},{"project":[{"grant_number":"268548","name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons","_id":"25C0F108-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","grant_number":"692692"},{"call_identifier":"FWF","_id":"25C26B1E-B435-11E9-9278-68D0E5697425","grant_number":"P24909-B24","name":"Mechanisms of transmitter release at GABAergic synapses"},{"name":"The Wittgenstein Prize","grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"external_id":{"isi":["000429192100016"]},"article_processing_charge":"Yes (in subscription journal)","author":[{"last_name":"Hu","full_name":"Hu, Hua","first_name":"Hua","id":"4AC0145C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Roth","full_name":"Roth, Fabian","first_name":"Fabian"},{"id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","first_name":"David H","last_name":"Vandael","orcid":"0000-0001-7577-1676","full_name":"Vandael, David H"},{"first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","last_name":"Jonas"}],"publist_id":"7545","title":"Complementary tuning of Na+ and K+ channel gating underlies fast and energy-efficient action potentials in GABAergic interneuron axons","citation":{"mla":"Hu, Hua, et al. “Complementary Tuning of Na+ and K+ Channel Gating Underlies Fast and Energy-Efficient Action Potentials in GABAergic Interneuron Axons.” Neuron, vol. 98, no. 1, Elsevier, 2018, pp. 156–65, doi:10.1016/j.neuron.2018.02.024.","ieee":"H. Hu, F. Roth, D. H. Vandael, and P. M. Jonas, “Complementary tuning of Na+ and K+ channel gating underlies fast and energy-efficient action potentials in GABAergic interneuron axons,” Neuron, vol. 98, no. 1. Elsevier, pp. 156–165, 2018.","short":"H. Hu, F. Roth, D.H. Vandael, P.M. Jonas, Neuron 98 (2018) 156–165.","ama":"Hu H, Roth F, Vandael DH, Jonas PM. Complementary tuning of Na+ and K+ channel gating underlies fast and energy-efficient action potentials in GABAergic interneuron axons. Neuron. 2018;98(1):156-165. doi:10.1016/j.neuron.2018.02.024","apa":"Hu, H., Roth, F., Vandael, D. H., & Jonas, P. M. (2018). Complementary tuning of Na+ and K+ channel gating underlies fast and energy-efficient action potentials in GABAergic interneuron axons. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2018.02.024","chicago":"Hu, Hua, Fabian Roth, David H Vandael, and Peter M Jonas. “Complementary Tuning of Na+ and K+ Channel Gating Underlies Fast and Energy-Efficient Action Potentials in GABAergic Interneuron Axons.” Neuron. Elsevier, 2018. https://doi.org/10.1016/j.neuron.2018.02.024.","ista":"Hu H, Roth F, Vandael DH, Jonas PM. 2018. Complementary tuning of Na+ and K+ channel gating underlies fast and energy-efficient action potentials in GABAergic interneuron axons. Neuron. 98(1), 156–165."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"publisher":"Elsevier","quality_controlled":"1","page":"156 - 165","date_created":"2018-12-11T11:45:48Z","date_published":"2018-04-04T00:00:00Z","doi":"10.1016/j.neuron.2018.02.024","year":"2018","isi":1,"has_accepted_license":"1","publication":"Neuron","day":"04","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","status":"public","_id":"320","department":[{"_id":"PeJo"}],"file_date_updated":"2020-07-14T12:46:03Z","date_updated":"2023-09-11T12:45:10Z","ddc":["570"],"scopus_import":"1","intvolume":" 98","month":"04","abstract":[{"text":"Fast-spiking, parvalbumin-expressing GABAergic interneurons (PV+-BCs) express a complex machinery of rapid signaling mechanisms, including specialized voltage-gated ion channels to generate brief action potentials (APs). However, short APs are associated with overlapping Na+ and K+ fluxes and are therefore energetically expensive. How the potentially vicious combination of high AP frequency and inefficient spike generation can be reconciled with limited energy supply is presently unclear. To address this question, we performed direct recordings from the PV+-BC axon, the subcellular structure where active conductances for AP initiation and propagation are located. Surprisingly, the energy required for the AP was, on average, only ∼1.6 times the theoretical minimum. High energy efficiency emerged from the combination of fast inactivation of Na+ channels and delayed activation of Kv3-type K+ channels, which minimized ion flux overlap during APs. Thus, the complementary tuning of axonal Na+ and K+ channel gating optimizes both fast signaling properties and metabolic efficiency. Hu et al. demonstrate that action potentials in parvalbumin-expressing GABAergic interneuron axons are energetically efficient, which is highly unexpected given their brief duration. High energy efficiency emerges from the combination of fast inactivation of voltage-gated Na+ channels and delayed activation of Kv3 channels in the axon. ","lang":"eng"}],"oa_version":"Published Version","ec_funded":1,"volume":98,"related_material":{"link":[{"url":"https://ist.ac.at/en/news/a-certain-type-of-neurons-is-more-energy-efficient-than-previously-assumed/","relation":"press_release","description":"News on IST Homepage"}]},"issue":"1","publication_status":"published","language":[{"iso":"eng"}],"file":[{"checksum":"76070f3729f9c603e1080d0151aa2b11","file_id":"5690","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-17T10:37:50Z","file_name":"2018_Neuron_Hu.pdf","creator":"dernst","date_updated":"2020-07-14T12:46:03Z","file_size":3180444}]},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Payne, Pavel, et al. “CRISPR-Based Herd Immunity Can Limit Phage Epidemics in Bacterial Populations.” ELife, vol. 7, e32035, eLife Sciences Publications, 2018, doi:10.7554/eLife.32035.","ieee":"P. Payne, L. Geyrhofer, N. H. Barton, and J. P. Bollback, “CRISPR-based herd immunity can limit phage epidemics in bacterial populations,” eLife, vol. 7. eLife Sciences Publications, 2018.","short":"P. Payne, L. Geyrhofer, N.H. Barton, J.P. Bollback, ELife 7 (2018).","apa":"Payne, P., Geyrhofer, L., Barton, N. H., & Bollback, J. P. (2018). CRISPR-based herd immunity can limit phage epidemics in bacterial populations. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.32035","ama":"Payne P, Geyrhofer L, Barton NH, Bollback JP. CRISPR-based herd immunity can limit phage epidemics in bacterial populations. eLife. 2018;7. doi:10.7554/eLife.32035","chicago":"Payne, Pavel, Lukas Geyrhofer, Nicholas H Barton, and Jonathan P Bollback. “CRISPR-Based Herd Immunity Can Limit Phage Epidemics in Bacterial Populations.” ELife. eLife Sciences Publications, 2018. https://doi.org/10.7554/eLife.32035.","ista":"Payne P, Geyrhofer L, Barton NH, Bollback JP. 2018. CRISPR-based herd immunity can limit phage epidemics in bacterial populations. eLife. 7, e32035."},"title":"CRISPR-based herd immunity can limit phage epidemics in bacterial populations","external_id":{"isi":["000431035800001"]},"article_processing_charge":"No","author":[{"last_name":"Payne","full_name":"Payne, Pavel","orcid":"0000-0002-2711-9453","id":"35F78294-F248-11E8-B48F-1D18A9856A87","first_name":"Pavel"},{"first_name":"Lukas","last_name":"Geyrhofer","full_name":"Geyrhofer, Lukas"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"},{"last_name":"Bollback","full_name":"Bollback, Jonathan P","orcid":"0000-0002-4624-4612","first_name":"Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7400","article_number":"e32035","project":[{"grant_number":"648440","name":"Selective Barriers to Horizontal Gene Transfer","_id":"2578D616-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"publication":"eLife","day":"09","year":"2018","isi":1,"has_accepted_license":"1","date_created":"2018-12-11T11:46:23Z","doi":"10.7554/eLife.32035","date_published":"2018-03-09T00:00:00Z","acknowledgement":"We are grateful to Remy Chait for his help and assistance with establishing our experimental setups and to Tobias Bergmiller for valuable insights into some specific experimental details. We thank Luciano Marraffini for donating us the pCas9 plasmid used in this study. We also want to express our gratitude to Seth Barribeau, Andrea Betancourt, Călin Guet, Mato Lagator, Tiago Paixão and Maroš Pleška for valuable discussions on the manuscript. Finally, we would like to thank the \r\neditors and reviewers for their helpful comments and suggestions.","oa":1,"publisher":"eLife Sciences Publications","quality_controlled":"1","ddc":["576"],"date_updated":"2023-09-11T12:49:17Z","file_date_updated":"2020-07-14T12:46:25Z","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"_id":"423","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"447cf6e680bdc3c01062a8737d876569","file_id":"5689","date_updated":"2020-07-14T12:46:25Z","file_size":3533881,"creator":"dernst","date_created":"2018-12-17T10:36:07Z","file_name":"2018_eLife_Payne.pdf"}],"publication_status":"published","ec_funded":1,"related_material":{"record":[{"id":"9840","status":"public","relation":"research_data"}]},"volume":7,"oa_version":"Published Version","abstract":[{"text":"Herd immunity, a process in which resistant individuals limit the spread of a pathogen among susceptible hosts has been extensively studied in eukaryotes. Even though bacteria have evolved multiple immune systems against their phage pathogens, herd immunity in bacteria remains unexplored. Here we experimentally demonstrate that herd immunity arises during phage epidemics in structured and unstructured Escherichia coli populations consisting of differing frequencies of susceptible and resistant cells harboring CRISPR immunity. In addition, we develop a mathematical model that quantifies how herd immunity is affected by spatial population structure, bacterial growth rate, and phage replication rate. Using our model we infer a general epidemiological rule describing the relative speed of an epidemic in partially resistant spatially structured populations. Our experimental and theoretical findings indicate that herd immunity may be important in bacterial communities, allowing for stable coexistence of bacteria and their phages and the maintenance of polymorphism in bacterial immunity.","lang":"eng"}],"intvolume":" 7","month":"03","scopus_import":"1"},{"author":[{"last_name":"Fulek","orcid":"0000-0001-8485-1774","full_name":"Fulek, Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","first_name":"Radoslav"},{"first_name":"Csaba D.","full_name":"Tóth, Csaba D.","last_name":"Tóth"}],"external_id":{"isi":["000672802500016"],"arxiv":["1808.07608"]},"article_processing_charge":"No","title":"Crossing minimization in perturbed drawings","citation":{"chicago":"Fulek, Radoslav, and Csaba D. Tóth. “Crossing Minimization in Perturbed Drawings,” 11282:229–41. Springer, 2018. https://doi.org/10.1007/978-3-030-04414-5_16.","ista":"Fulek R, Tóth CD. 2018. Crossing minimization in perturbed drawings. Graph Drawing and Network Visualization, LNCS, vol. 11282, 229–241.","mla":"Fulek, Radoslav, and Csaba D. Tóth. Crossing Minimization in Perturbed Drawings. Vol. 11282, Springer, 2018, pp. 229–41, doi:10.1007/978-3-030-04414-5_16.","ama":"Fulek R, Tóth CD. Crossing minimization in perturbed drawings. In: Vol 11282. Springer; 2018:229-241. doi:10.1007/978-3-030-04414-5_16","apa":"Fulek, R., & Tóth, C. D. (2018). Crossing minimization in perturbed drawings (Vol. 11282, pp. 229–241). Presented at the Graph Drawing and Network Visualization, Barcelona, Spain: Springer. https://doi.org/10.1007/978-3-030-04414-5_16","ieee":"R. Fulek and C. D. Tóth, “Crossing minimization in perturbed drawings,” presented at the Graph Drawing and Network Visualization, Barcelona, Spain, 2018, vol. 11282, pp. 229–241.","short":"R. Fulek, C.D. Tóth, in:, Springer, 2018, pp. 229–241."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"229-241","doi":"10.1007/978-3-030-04414-5_16","date_published":"2018-12-18T00:00:00Z","date_created":"2018-12-30T22:59:15Z","isi":1,"year":"2018","day":"18","publisher":"Springer","quality_controlled":"1","oa":1,"department":[{"_id":"UlWa"}],"date_updated":"2023-09-11T12:49:55Z","type":"conference","conference":{"start_date":"2018-09-26","location":"Barcelona, Spain","end_date":"2018-09-28","name":"Graph Drawing and Network Visualization"},"status":"public","_id":"5791","volume":"11282 ","publication_identifier":{"isbn":["9783030044138"]},"publication_status":"published","language":[{"iso":"eng"}],"alternative_title":["LNCS"],"scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1808.07608","open_access":"1"}],"month":"12","abstract":[{"text":"Due to data compression or low resolution, nearby vertices and edges of a graph drawing may be bundled to a common node or arc. We model such a “compromised” drawing by a piecewise linear map φ:G → ℝ. We wish to perturb φ by an arbitrarily small ε>0 into a proper drawing (in which the vertices are distinct points, any two edges intersect in finitely many points, and no three edges have a common interior point) that minimizes the number of crossings. An ε-perturbation, for every ε>0, is given by a piecewise linear map (Formula Presented), where with ||·|| is the uniform norm (i.e., sup norm). We present a polynomial-time solution for this optimization problem when G is a cycle and the map φ has no spurs (i.e., no two adjacent edges are mapped to overlapping arcs). We also show that the problem becomes NP-complete (i) when G is an arbitrary graph and φ has no spurs, and (ii) when φ may have spurs and G is a cycle or a union of disjoint paths.","lang":"eng"}],"oa_version":"Preprint"},{"date_updated":"2023-09-11T12:45:44Z","department":[{"_id":"BjHo"}],"_id":"291","type":"journal_article","status":"public","publication_status":"published","language":[{"iso":"eng"}],"volume":3,"issue":"5","abstract":[{"text":"Over the past decade, the edge of chaos has proven to be a fruitful starting point for investigations of shear flows when the laminar base flow is linearly stable. Numerous computational studies of shear flows demonstrated the existence of states that separate laminar and turbulent regions of the state space. In addition, some studies determined invariant solutions that reside on this edge. In this paper, we study the unstable manifold of one such solution with the aid of continuous symmetry reduction, which we formulate here for the simultaneous quotiening of axial and azimuthal symmetries. Upon our investigation of the unstable manifold, we discover a previously unknown traveling-wave solution on the laminar-turbulent boundary with a relatively complex structure. By means of low-dimensional projections, we visualize different dynamical paths that connect these solutions to the turbulence. Our numerical experiments demonstrate that the laminar-turbulent boundary exhibits qualitatively different regions whose properties are influenced by the nearby invariant solutions.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1802.01918"}],"scopus_import":"1","intvolume":" 3","month":"05","citation":{"ieee":"N. B. Budanur and B. Hof, “Complexity of the laminar-turbulent boundary in pipe flow,” Physical Review Fluids, vol. 3, no. 5. American Physical Society, 2018.","short":"N.B. Budanur, B. Hof, Physical Review Fluids 3 (2018).","apa":"Budanur, N. B., & Hof, B. (2018). Complexity of the laminar-turbulent boundary in pipe flow. Physical Review Fluids. American Physical Society. https://doi.org/10.1103/PhysRevFluids.3.054401","ama":"Budanur NB, Hof B. Complexity of the laminar-turbulent boundary in pipe flow. Physical Review Fluids. 2018;3(5). doi:10.1103/PhysRevFluids.3.054401","mla":"Budanur, Nazmi B., and Björn Hof. “Complexity of the Laminar-Turbulent Boundary in Pipe Flow.” Physical Review Fluids, vol. 3, no. 5, 054401, American Physical Society, 2018, doi:10.1103/PhysRevFluids.3.054401.","ista":"Budanur NB, Hof B. 2018. Complexity of the laminar-turbulent boundary in pipe flow. Physical Review Fluids. 3(5), 054401.","chicago":"Budanur, Nazmi B, and Björn Hof. “Complexity of the Laminar-Turbulent Boundary in Pipe Flow.” Physical Review Fluids. American Physical Society, 2018. https://doi.org/10.1103/PhysRevFluids.3.054401."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"arxiv":["1802.01918"],"isi":["000433426200001"]},"article_processing_charge":"No","author":[{"full_name":"Budanur, Nazmi B","orcid":"0000-0003-0423-5010","last_name":"Budanur","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","first_name":"Nazmi B"},{"first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn"}],"publist_id":"7590","title":"Complexity of the laminar-turbulent boundary in pipe flow","article_number":"054401","year":"2018","isi":1,"publication":"Physical Review Fluids","day":"30","date_created":"2018-12-11T11:45:39Z","date_published":"2018-05-30T00:00:00Z","doi":"10.1103/PhysRevFluids.3.054401","oa":1,"quality_controlled":"1","publisher":"American Physical Society"},{"_id":"58","status":"public","type":"journal_article","date_updated":"2023-09-11T12:48:39Z","department":[{"_id":"HeEd"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Inside a two-dimensional region (``cake""), there are m nonoverlapping tiles of a certain kind (``toppings""). We want to expand the toppings while keeping them nonoverlapping, and possibly add some blank pieces of the same ``certain kind,"" such that the entire cake is covered. How many blanks must we add? We study this question in several cases: (1) The cake and toppings are general polygons. (2) The cake and toppings are convex figures. (3) The cake and toppings are axis-parallel rectangles. (4) The cake is an axis-parallel rectilinear polygon and the toppings are axis-parallel rectangles. In all four cases, we provide tight bounds on the number of blanks."}],"intvolume":" 32","month":"09","main_file_link":[{"url":"https://arxiv.org/abs/1604.00960","open_access":"1"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"issue":"3","volume":32,"project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Akopyan A, Segal Halevi E. 2018. Counting blanks in polygonal arrangements. SIAM Journal on Discrete Mathematics. 32(3), 2242–2257.","chicago":"Akopyan, Arseniy, and Erel Segal Halevi. “Counting Blanks in Polygonal Arrangements.” SIAM Journal on Discrete Mathematics. Society for Industrial and Applied Mathematics , 2018. https://doi.org/10.1137/16M110407X.","apa":"Akopyan, A., & Segal Halevi, E. (2018). Counting blanks in polygonal arrangements. SIAM Journal on Discrete Mathematics. Society for Industrial and Applied Mathematics . https://doi.org/10.1137/16M110407X","ama":"Akopyan A, Segal Halevi E. Counting blanks in polygonal arrangements. SIAM Journal on Discrete Mathematics. 2018;32(3):2242-2257. doi:10.1137/16M110407X","short":"A. Akopyan, E. Segal Halevi, SIAM Journal on Discrete Mathematics 32 (2018) 2242–2257.","ieee":"A. Akopyan and E. Segal Halevi, “Counting blanks in polygonal arrangements,” SIAM Journal on Discrete Mathematics, vol. 32, no. 3. Society for Industrial and Applied Mathematics , pp. 2242–2257, 2018.","mla":"Akopyan, Arseniy, and Erel Segal Halevi. “Counting Blanks in Polygonal Arrangements.” SIAM Journal on Discrete Mathematics, vol. 32, no. 3, Society for Industrial and Applied Mathematics , 2018, pp. 2242–57, doi:10.1137/16M110407X."},"title":"Counting blanks in polygonal arrangements","article_processing_charge":"No","external_id":{"isi":["000450810500036"],"arxiv":["1604.00960"]},"publist_id":"7996","author":[{"last_name":"Akopyan","full_name":"Akopyan, Arseniy","orcid":"0000-0002-2548-617X","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","first_name":"Arseniy"},{"full_name":"Segal Halevi, Erel","last_name":"Segal Halevi","first_name":"Erel"}],"oa":1,"publisher":"Society for Industrial and Applied Mathematics ","quality_controlled":"1","publication":"SIAM Journal on Discrete Mathematics","day":"06","year":"2018","isi":1,"date_created":"2018-12-11T11:44:24Z","date_published":"2018-09-06T00:00:00Z","doi":"10.1137/16M110407X","page":"2242 - 2257"},{"department":[{"_id":"NiBa"},{"_id":"JoBo"}],"title":"Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations","author":[{"id":"35F78294-F248-11E8-B48F-1D18A9856A87","first_name":"Pavel","orcid":"0000-0002-2711-9453","full_name":"Payne, Pavel","last_name":"Payne"},{"full_name":"Geyrhofer, Lukas","last_name":"Geyrhofer","first_name":"Lukas"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton"},{"id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","first_name":"Jonathan P","last_name":"Bollback","orcid":"0000-0002-4624-4612","full_name":"Bollback, Jonathan P"}],"article_processing_charge":"No","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-09-11T12:49:17Z","citation":{"ista":"Payne P, Geyrhofer L, Barton NH, Bollback JP. 2018. Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations, Dryad, 10.5061/dryad.42n44.","chicago":"Payne, Pavel, Lukas Geyrhofer, Nicholas H Barton, and Jonathan P Bollback. “Data from: CRISPR-Based Herd Immunity Limits Phage Epidemics in Bacterial Populations.” Dryad, 2018. https://doi.org/10.5061/dryad.42n44.","short":"P. Payne, L. Geyrhofer, N.H. Barton, J.P. Bollback, (2018).","ieee":"P. Payne, L. Geyrhofer, N. H. Barton, and J. P. Bollback, “Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations.” Dryad, 2018.","apa":"Payne, P., Geyrhofer, L., Barton, N. H., & Bollback, J. P. (2018). Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations. Dryad. https://doi.org/10.5061/dryad.42n44","ama":"Payne P, Geyrhofer L, Barton NH, Bollback JP. Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations. 2018. doi:10.5061/dryad.42n44","mla":"Payne, Pavel, et al. Data from: CRISPR-Based Herd Immunity Limits Phage Epidemics in Bacterial Populations. Dryad, 2018, doi:10.5061/dryad.42n44."},"status":"public","type":"research_data_reference","_id":"9840","doi":"10.5061/dryad.42n44","date_published":"2018-03-12T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"423"}]},"date_created":"2021-08-09T13:10:02Z","day":"12","year":"2018","month":"03","publisher":"Dryad","main_file_link":[{"url":"https://doi.org/10.5061/dryad.42n44","open_access":"1"}],"oa":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Herd immunity, a process in which resistant individuals limit the spread of a pathogen among susceptible hosts has been extensively studied in eukaryotes. Even though bacteria have evolved multiple immune systems against their phage pathogens, herd immunity in bacteria remains unexplored. Here we experimentally demonstrate that herd immunity arises during phage epidemics in structured and unstructured Escherichia coli populations consisting of differing frequencies of susceptible and resistant cells harboring CRISPR immunity. In addition, we develop a mathematical model that quantifies how herd immunity is affected by spatial population structure, bacterial growth rate, and phage replication rate. Using our model we infer a general epidemiological rule describing the relative speed of an epidemic in partially resistant spatially structured populations. Our experimental and theoretical findings indicate that herd immunity may be important in bacterial communities, allowing for stable coexistence of bacteria and their phages and the maintenance of polymorphism in bacterial immunity."}]},{"doi":"10.7554/eLife.32073","date_published":"2018-01-09T00:00:00Z","date_created":"2018-12-11T11:47:31Z","day":"09","publication":"eLife","has_accepted_license":"1","isi":1,"year":"2018","quality_controlled":"1","publisher":"eLife Sciences Publications","oa":1,"title":"Destructive disinfection of infected brood prevents systemic disease spread in ant colonies","author":[{"first_name":"Christopher","id":"3C7F4840-F248-11E8-B48F-1D18A9856A87","last_name":"Pull","orcid":"0000-0003-1122-3982","full_name":"Pull, Christopher"},{"id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","first_name":"Line V","full_name":"Ugelvig, Line V","orcid":"0000-0003-1832-8883","last_name":"Ugelvig"},{"last_name":"Wiesenhofer","full_name":"Wiesenhofer, Florian","first_name":"Florian","id":"39523C54-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Grasse","full_name":"Grasse, Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87","first_name":"Anna V"},{"last_name":"Tragust","full_name":"Tragust, Simon","first_name":"Simon","id":"35A7A418-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Schmitt, Thomas","last_name":"Schmitt","first_name":"Thomas"},{"first_name":"Mark","last_name":"Brown","full_name":"Brown, Mark"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","last_name":"Cremer","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia"}],"publist_id":"7188","article_processing_charge":"Yes","external_id":{"isi":["000419601300001"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ama":"Pull C, Ugelvig LV, Wiesenhofer F, et al. Destructive disinfection of infected brood prevents systemic disease spread in ant colonies. eLife. 2018;7. doi:10.7554/eLife.32073","apa":"Pull, C., Ugelvig, L. V., Wiesenhofer, F., Grasse, A. V., Tragust, S., Schmitt, T., … Cremer, S. (2018). Destructive disinfection of infected brood prevents systemic disease spread in ant colonies. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.32073","ieee":"C. Pull et al., “Destructive disinfection of infected brood prevents systemic disease spread in ant colonies,” eLife, vol. 7. eLife Sciences Publications, 2018.","short":"C. Pull, L.V. Ugelvig, F. Wiesenhofer, A.V. Grasse, S. Tragust, T. Schmitt, M. Brown, S. Cremer, ELife 7 (2018).","mla":"Pull, Christopher, et al. “Destructive Disinfection of Infected Brood Prevents Systemic Disease Spread in Ant Colonies.” ELife, vol. 7, e32073, eLife Sciences Publications, 2018, doi:10.7554/eLife.32073.","ista":"Pull C, Ugelvig LV, Wiesenhofer F, Grasse AV, Tragust S, Schmitt T, Brown M, Cremer S. 2018. Destructive disinfection of infected brood prevents systemic disease spread in ant colonies. eLife. 7, e32073.","chicago":"Pull, Christopher, Line V Ugelvig, Florian Wiesenhofer, Anna V Grasse, Simon Tragust, Thomas Schmitt, Mark Brown, and Sylvia Cremer. “Destructive Disinfection of Infected Brood Prevents Systemic Disease Spread in Ant Colonies.” ELife. eLife Sciences Publications, 2018. https://doi.org/10.7554/eLife.32073."},"project":[{"_id":"25DC711C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects","grant_number":"243071"},{"_id":"25DDF0F0-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Pathogen Detectors Collective disease defence and pathogen detection abilities in ant societies: a chemo-neuro-immunological approach","grant_number":"302004"}],"article_number":"e32073","volume":7,"related_material":{"record":[{"relation":"dissertation_contains","id":"819","status":"public"}]},"ec_funded":1,"file":[{"file_size":1435585,"date_updated":"2020-07-14T12:47:20Z","creator":"system","file_name":"IST-2018-978-v1+1_elife-32073-v1.pdf","date_created":"2018-12-12T10:10:43Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"540f941e8d3530a9441e4affd94f07d7","file_id":"4832"}],"language":[{"iso":"eng"}],"publication_status":"published","month":"01","intvolume":" 7","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Social insects protect their colonies from infectious disease through collective defences that result in social immunity. In ants, workers first try to prevent infection of colony members. Here, we show that if this fails and a pathogen establishes an infection, ants employ an efficient multicomponent behaviour − "destructive disinfection" − to prevent further spread of disease through the colony. Ants specifically target infected pupae during the pathogen's non-contagious incubation period, relying on chemical 'sickness cues' emitted by pupae. They then remove the pupal cocoon, perforate its cuticle and administer antimicrobial poison, which enters the body and prevents pathogen replication from the inside out. Like the immune system of a body that specifically targets and eliminates infected cells, this social immunity measure sacrifices infected brood to stop the pathogen completing its lifecycle, thus protecting the rest of the colony. Hence, the same principles of disease defence apply at different levels of biological organisation."}],"file_date_updated":"2020-07-14T12:47:20Z","department":[{"_id":"SyCr"}],"ddc":["570","590"],"date_updated":"2023-09-11T12:54:26Z","status":"public","pubrep_id":"978","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"616"},{"date_updated":"2023-09-11T12:52:41Z","ddc":["570"],"department":[{"_id":"EdHa"}],"file_date_updated":"2020-07-14T12:44:43Z","_id":"132","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","publication_status":"published","file":[{"checksum":"78d2062b9e3c3b90fe71545aeb6d2f65","file_id":"5694","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2018_DevelopmentalCell_Sznurkowska.pdf","date_created":"2018-12-17T10:49:49Z","creator":"dernst","file_size":8948384,"date_updated":"2020-07-14T12:44:43Z"}],"language":[{"iso":"eng"}],"volume":46,"issue":"3","abstract":[{"lang":"eng","text":"Pancreas development involves a coordinated process in which an early phase of cell segregation is followed by a longer phase of lineage restriction, expansion, and tissue remodeling. By combining clonal tracing and whole-mount reconstruction with proliferation kinetics and single-cell transcriptional profiling, we define the functional basis of pancreas morphogenesis. We show that the large-scale organization of mouse pancreas can be traced to the activity of self-renewing precursors positioned at the termini of growing ducts, which act collectively to drive serial rounds of stochastic ductal bifurcation balanced by termination. During this phase of branching morphogenesis, multipotent precursors become progressively fate-restricted, giving rise to self-renewing acinar-committed precursors that are conveyed with growing ducts, as well as ductal progenitors that expand the trailing ducts and give rise to delaminating endocrine cells. These findings define quantitatively how the functional behavior and lineage progression of precursor pools determine the large-scale patterning of pancreatic sub-compartments."}],"oa_version":"Published Version","scopus_import":"1","month":"08","intvolume":" 46","citation":{"ama":"Sznurkowska M, Hannezo EB, Azzarelli R, et al. Defining lineage potential and fate behavior of precursors during pancreas development. Developmental Cell. 2018;46(3):360-375. doi:10.1016/j.devcel.2018.06.028","apa":"Sznurkowska, M., Hannezo, E. B., Azzarelli, R., Rulands, S., Nestorowa, S., Hindley, C., … Simons, B. (2018). Defining lineage potential and fate behavior of precursors during pancreas development. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2018.06.028","ieee":"M. Sznurkowska et al., “Defining lineage potential and fate behavior of precursors during pancreas development,” Developmental Cell, vol. 46, no. 3. Cell Press, pp. 360–375, 2018.","short":"M. Sznurkowska, E.B. Hannezo, R. Azzarelli, S. Rulands, S. Nestorowa, C. Hindley, J. Nichols, B. Göttgens, M. Huch, A. Philpott, B. Simons, Developmental Cell 46 (2018) 360–375.","mla":"Sznurkowska, Magdalena, et al. “Defining Lineage Potential and Fate Behavior of Precursors during Pancreas Development.” Developmental Cell, vol. 46, no. 3, Cell Press, 2018, pp. 360–75, doi:10.1016/j.devcel.2018.06.028.","ista":"Sznurkowska M, Hannezo EB, Azzarelli R, Rulands S, Nestorowa S, Hindley C, Nichols J, Göttgens B, Huch M, Philpott A, Simons B. 2018. Defining lineage potential and fate behavior of precursors during pancreas development. Developmental Cell. 46(3), 360–375.","chicago":"Sznurkowska, Magdalena, Edouard B Hannezo, Roberta Azzarelli, Steffen Rulands, Sonia Nestorowa, Christopher Hindley, Jennifer Nichols, et al. “Defining Lineage Potential and Fate Behavior of Precursors during Pancreas Development.” Developmental Cell. Cell Press, 2018. https://doi.org/10.1016/j.devcel.2018.06.028."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Magdalena","last_name":"Sznurkowska","full_name":"Sznurkowska, Magdalena"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo"},{"first_name":"Roberta","full_name":"Azzarelli, Roberta","last_name":"Azzarelli"},{"full_name":"Rulands, Steffen","last_name":"Rulands","first_name":"Steffen"},{"first_name":"Sonia","last_name":"Nestorowa","full_name":"Nestorowa, Sonia"},{"first_name":"Christopher","full_name":"Hindley, Christopher","last_name":"Hindley"},{"first_name":"Jennifer","full_name":"Nichols, Jennifer","last_name":"Nichols"},{"full_name":"Göttgens, Berthold","last_name":"Göttgens","first_name":"Berthold"},{"first_name":"Meritxell","last_name":"Huch","full_name":"Huch, Meritxell"},{"first_name":"Anna","full_name":"Philpott, Anna","last_name":"Philpott"},{"first_name":"Benjamin","full_name":"Simons, Benjamin","last_name":"Simons"}],"publist_id":"7791","external_id":{"isi":["000441327300012"]},"article_processing_charge":"No","title":"Defining lineage potential and fate behavior of precursors during pancreas development","has_accepted_license":"1","isi":1,"year":"2018","day":"06","publication":"Developmental Cell","page":"360 - 375","date_published":"2018-08-06T00:00:00Z","doi":"10.1016/j.devcel.2018.06.028","date_created":"2018-12-11T11:44:48Z","acknowledgement":"E.H. is funded by a Junior Research Fellowship from Trinity College, Cam-bridge, a Sir Henry Wellcome Fellowship from the Wellcome Trust, and theBettencourt-Schueller Young Researcher Prize for support.","publisher":"Cell Press","quality_controlled":"1","oa":1},{"publist_id":"8012","author":[{"first_name":"Mara","full_name":"Cucinotta, Mara","last_name":"Cucinotta"},{"first_name":"Silvia","last_name":"Manrique","full_name":"Manrique, Silvia"},{"first_name":"Candela","id":"33A3C818-F248-11E8-B48F-1D18A9856A87","last_name":"Cuesta","full_name":"Cuesta, Candela","orcid":"0000-0003-1923-2410"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","last_name":"Benková","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739"},{"first_name":"Ondřej","last_name":"Novák","full_name":"Novák, Ondřej"},{"first_name":"Lucia","full_name":"Colombo, Lucia","last_name":"Colombo"}],"article_processing_charge":"No","external_id":{"isi":["000448163900015"]},"title":"Cup-shaped Cotyledon1 (CUC1) and CU2 regulate cytokinin homeostasis to determine ovule number in arabidopsis","citation":{"chicago":"Cucinotta, Mara, Silvia Manrique, Candela Cuesta, Eva Benková, Ondřej Novák, and Lucia Colombo. “Cup-Shaped Cotyledon1 (CUC1) and CU2 Regulate Cytokinin Homeostasis to Determine Ovule Number in Arabidopsis.” Journal of Experimental Botany. Oxford University Press, 2018. https://doi.org/10.1093/jxb/ery281.","ista":"Cucinotta M, Manrique S, Cuesta C, Benková E, Novák O, Colombo L. 2018. Cup-shaped Cotyledon1 (CUC1) and CU2 regulate cytokinin homeostasis to determine ovule number in arabidopsis. Journal of Experimental Botany. 69(21), 5169–5176.","mla":"Cucinotta, Mara, et al. “Cup-Shaped Cotyledon1 (CUC1) and CU2 Regulate Cytokinin Homeostasis to Determine Ovule Number in Arabidopsis.” Journal of Experimental Botany, vol. 69, no. 21, Oxford University Press, 2018, pp. 5169–76, doi:10.1093/jxb/ery281.","ieee":"M. Cucinotta, S. Manrique, C. Cuesta, E. Benková, O. Novák, and L. Colombo, “Cup-shaped Cotyledon1 (CUC1) and CU2 regulate cytokinin homeostasis to determine ovule number in arabidopsis,” Journal of Experimental Botany, vol. 69, no. 21. Oxford University Press, pp. 5169–5176, 2018.","short":"M. Cucinotta, S. Manrique, C. Cuesta, E. Benková, O. Novák, L. Colombo, Journal of Experimental Botany 69 (2018) 5169–5176.","ama":"Cucinotta M, Manrique S, Cuesta C, Benková E, Novák O, Colombo L. Cup-shaped Cotyledon1 (CUC1) and CU2 regulate cytokinin homeostasis to determine ovule number in arabidopsis. Journal of Experimental Botany. 2018;69(21):5169-5176. doi:10.1093/jxb/ery281","apa":"Cucinotta, M., Manrique, S., Cuesta, C., Benková, E., Novák, O., & Colombo, L. (2018). Cup-shaped Cotyledon1 (CUC1) and CU2 regulate cytokinin homeostasis to determine ovule number in arabidopsis. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/ery281"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"5169 - 5176","date_published":"2018-07-26T00:00:00Z","doi":"10.1093/jxb/ery281","date_created":"2018-12-11T11:44:19Z","has_accepted_license":"1","isi":1,"year":"2018","day":"26","publication":"Journal of Experimental Botany","quality_controlled":"1","publisher":"Oxford University Press","oa":1,"acknowledgement":"This work was funded by the Ministry of Education, Youth and Sports of the Czech Republic through the National Program of Sustainability (grant no. LO1204).","department":[{"_id":"EvBe"}],"file_date_updated":"2020-07-14T12:46:25Z","date_updated":"2023-09-11T12:52:03Z","ddc":["575"],"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"42","issue":"21","volume":69,"publication_status":"published","file":[{"file_name":"2018_JournalExperimBotany_Cucinotta.pdf","date_created":"2018-12-17T10:44:16Z","file_size":1292128,"date_updated":"2020-07-14T12:46:25Z","creator":"dernst","checksum":"ca3b6711040b1662488aeb3d1f961f13","file_id":"5691","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"07","intvolume":" 69","abstract":[{"text":"Seeds derive from ovules upon fertilization and therefore the total number of ovules determines the final seed yield, a fundamental trait in crop plants. Among the factors that co-ordinate the process of ovule formation, the transcription factors CUP-SHAPED COTYLEDON 1 (CUC1) and CUC2 and the hormone cytokinin (CK) have a particularly prominent role. Indeed, the absence of both CUC1 and CUC2 causes a severe reduction in ovule number, a phenotype that can be rescued by CK treatment. In this study, we combined CK quantification with an integrative genome-wide target identification approach to select Arabidopsis genes regulated by CUCs that are also involved in CK metabolism. We focused our attention on the functional characterization of UDP-GLUCOSYL TRANSFERASE 85A3 (UGT85A3) and UGT73C1, which are up-regulated in the absence of CUC1 and CUC2 and encode enzymes able to catalyse CK inactivation by O-glucosylation. Our results demonstrate a role for these UGTs as a link between CUCs and CK homeostasis, and highlight the importance of CUCs and CKs in the determination of seed yield.","lang":"eng"}],"oa_version":"Published Version"},{"page":"1-11","doi":"10.1016/j.phytochem.2018.02.015","date_published":"2018-06-01T00:00:00Z","date_created":"2018-12-11T11:46:18Z","isi":1,"year":"2018","day":"01","publication":"Phytochemistry","publisher":"Elsevier","quality_controlled":"1","acknowledgement":"This work was supported by the Ministry of Education Youth and Sports, Czech Republic (grant LO1204 from the National Program of Sustainability I and Agricultural Research ) and by Czech Science Foundation grants 16-04184S , 501/10/1450 and 13-39982S and by IGA projects IGA_PrF_2018_033 and IGA_PrF_2018_023 . We would like to thank Jarmila Balonová, Olga Hustáková and Miroslava Šubová for their skillful technical assistance and Mgr. Tomáš Pospíšil, Ph.D. for his measurement of 1 H NMR and analysis of some 2D NMR spectral data. \r\n","author":[{"full_name":"Kubiasová, Karolina","last_name":"Kubiasová","first_name":"Karolina"},{"first_name":"Václav","last_name":"Mik","full_name":"Mik, Václav"},{"full_name":"Nisler, Jaroslav","last_name":"Nisler","first_name":"Jaroslav"},{"full_name":"Hönig, Martin","last_name":"Hönig","first_name":"Martin"},{"last_name":"Husičková","full_name":"Husičková, Alexandra","first_name":"Alexandra"},{"first_name":"Lukáš","last_name":"Spíchal","full_name":"Spíchal, Lukáš"},{"last_name":"Pěkná","full_name":"Pěkná, Zuzana","first_name":"Zuzana"},{"full_name":"Šamajová, Olga","last_name":"Šamajová","first_name":"Olga"},{"full_name":"Doležal, Karel","last_name":"Doležal","first_name":"Karel"},{"last_name":"Plíhal","full_name":"Plíhal, Ondřej","first_name":"Ondřej"},{"last_name":"Benková","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva"},{"full_name":"Strnad, Miroslav","last_name":"Strnad","first_name":"Miroslav"},{"first_name":"Lucie","last_name":"Plíhalová","full_name":"Plíhalová, Lucie"}],"publist_id":"7422","article_processing_charge":"No","external_id":{"isi":["000435623400001"]},"title":"Design, synthesis and perception of fluorescently labeled isoprenoid cytokinins","citation":{"ieee":"K. Kubiasová et al., “Design, synthesis and perception of fluorescently labeled isoprenoid cytokinins,” Phytochemistry, vol. 150. Elsevier, pp. 1–11, 2018.","short":"K. Kubiasová, V. Mik, J. Nisler, M. Hönig, A. Husičková, L. Spíchal, Z. Pěkná, O. Šamajová, K. Doležal, O. Plíhal, E. Benková, M. Strnad, L. Plíhalová, Phytochemistry 150 (2018) 1–11.","ama":"Kubiasová K, Mik V, Nisler J, et al. Design, synthesis and perception of fluorescently labeled isoprenoid cytokinins. Phytochemistry. 2018;150:1-11. doi:10.1016/j.phytochem.2018.02.015","apa":"Kubiasová, K., Mik, V., Nisler, J., Hönig, M., Husičková, A., Spíchal, L., … Plíhalová, L. (2018). Design, synthesis and perception of fluorescently labeled isoprenoid cytokinins. Phytochemistry. Elsevier. https://doi.org/10.1016/j.phytochem.2018.02.015","mla":"Kubiasová, Karolina, et al. “Design, Synthesis and Perception of Fluorescently Labeled Isoprenoid Cytokinins.” Phytochemistry, vol. 150, Elsevier, 2018, pp. 1–11, doi:10.1016/j.phytochem.2018.02.015.","ista":"Kubiasová K, Mik V, Nisler J, Hönig M, Husičková A, Spíchal L, Pěkná Z, Šamajová O, Doležal K, Plíhal O, Benková E, Strnad M, Plíhalová L. 2018. Design, synthesis and perception of fluorescently labeled isoprenoid cytokinins. Phytochemistry. 150, 1–11.","chicago":"Kubiasová, Karolina, Václav Mik, Jaroslav Nisler, Martin Hönig, Alexandra Husičková, Lukáš Spíchal, Zuzana Pěkná, et al. “Design, Synthesis and Perception of Fluorescently Labeled Isoprenoid Cytokinins.” Phytochemistry. Elsevier, 2018. https://doi.org/10.1016/j.phytochem.2018.02.015."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":150,"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","month":"06","intvolume":" 150","abstract":[{"lang":"eng","text":"Isoprenoid cytokinins play a number of crucial roles in the regulation of plant growth and development. To study cytokinin receptor properties in plants, we designed and prepared fluorescent derivatives of 6-[(3-methylbut-2-en-1-yl)amino]purine (N6-isopentenyladenine, iP) with several fluorescent labels attached to the C2 or N9 atom of the purine moiety via a 2- or 6-carbon linker. The fluorescent labels included dansyl (DS), fluorescein (FC), 7-nitrobenzofurazan (NBD), rhodamine B (RhoB), coumarin (Cou), 7-(diethylamino)coumarin (DEAC) and cyanine 5 dye (Cy5). All prepared compounds were screened for affinity for the Arabidopsis thaliana cytokinin receptor (CRE1/AHK4). Although the attachment of the fluorescent labels to iP via the linkers mostly disrupted binding to the receptor, several fluorescent derivatives interacted well. For this reason, three derivatives, two rhodamine B and one 4-chloro-7-nitrobenzofurazan labeled iP were tested for their interaction with CRE1/AHK4 and Zea mays cytokinin receptors in detail. We further showed that the three derivatives were able to activate transcription of cytokinin response regulator ARR5 in Arabidopsis seedlings. The activity of fluorescently labeled cytokinins was compared with corresponding 6-dimethylaminopurine fluorescently labeled negative controls. Selected rhodamine B C2-labeled compounds 17, 18 and 4-chloro-7-nitrobenzofurazan N9-labeled compound 28 and their respective negative controls (19, 20 and 29, respectively) were used for in planta staining experiments in Arabidopsis thaliana cell suspension culture using live cell confocal microscopy."}],"oa_version":"None","department":[{"_id":"EvBe"}],"date_updated":"2023-09-11T12:53:11Z","type":"journal_article","status":"public","_id":"407"},{"article_number":"161122","citation":{"chicago":"Hetterich, Daniel, Norman Yao, Maksym Serbyn, Frank Pollmann, and Björn Trauzettel. “Detection and Characterization of Many-Body Localization in Central Spin Models.” Physical Review B. American Physical Society, 2018. https://doi.org/10.1103/PhysRevB.98.161122.","ista":"Hetterich D, Yao N, Serbyn M, Pollmann F, Trauzettel B. 2018. Detection and characterization of many-body localization in central spin models. Physical Review B. 98(16), 161122.","mla":"Hetterich, Daniel, et al. “Detection and Characterization of Many-Body Localization in Central Spin Models.” Physical Review B, vol. 98, no. 16, 161122, American Physical Society, 2018, doi:10.1103/PhysRevB.98.161122.","ama":"Hetterich D, Yao N, Serbyn M, Pollmann F, Trauzettel B. Detection and characterization of many-body localization in central spin models. Physical Review B. 2018;98(16). doi:10.1103/PhysRevB.98.161122","apa":"Hetterich, D., Yao, N., Serbyn, M., Pollmann, F., & Trauzettel, B. (2018). Detection and characterization of many-body localization in central spin models. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.98.161122","short":"D. Hetterich, N. Yao, M. Serbyn, F. Pollmann, B. Trauzettel, Physical Review B 98 (2018).","ieee":"D. Hetterich, N. Yao, M. Serbyn, F. Pollmann, and B. Trauzettel, “Detection and characterization of many-body localization in central spin models,” Physical Review B, vol. 98, no. 16. American Physical Society, 2018."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"arxiv":["1806.08316"],"isi":["000448596500002"]},"article_processing_charge":"No","publist_id":"8008","author":[{"last_name":"Hetterich","full_name":"Hetterich, Daniel","first_name":"Daniel"},{"full_name":"Yao, Norman","last_name":"Yao","first_name":"Norman"},{"first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym"},{"first_name":"Frank","full_name":"Pollmann, Frank","last_name":"Pollmann"},{"first_name":"Björn","last_name":"Trauzettel","full_name":"Trauzettel, Björn"}],"title":"Detection and characterization of many-body localization in central spin models","acknowledgement":"F.P. acknowledges the sup- port of the DFG Research Unit FOR 1807 through Grants No. PO 1370/2-1 and No. TRR80, the Nanosystems Initiative Munich (NIM) by the German Excellence Initiative, and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 771537). N.Y.Y. acknowledges support from the NSF (PHY-1654740), the ARO STIR program, and a Google research award.","oa":1,"publisher":"American Physical Society","quality_controlled":"1","year":"2018","isi":1,"publication":"Physical Review B","day":"15","date_created":"2018-12-11T11:44:20Z","date_published":"2018-10-15T00:00:00Z","doi":"10.1103/PhysRevB.98.161122","_id":"46","type":"journal_article","article_type":"original","status":"public","date_updated":"2023-09-11T12:55:03Z","department":[{"_id":"MaSe"}],"abstract":[{"text":"We analyze a disordered central spin model, where a central spin interacts equally with each spin in a periodic one-dimensional (1D) random-field Heisenberg chain. If the Heisenberg chain is initially in the many-body localized (MBL) phase, we find that the coupling to the central spin suffices to delocalize the chain for a substantial range of coupling strengths. We calculate the phase diagram of the model and identify the phase boundary between the MBL and ergodic phase. Within the localized phase, the central spin significantly enhances the rate of the logarithmic entanglement growth and its saturation value. We attribute the increase in entanglement entropy to a nonextensive enhancement of magnetization fluctuations induced by the central spin. Finally, we demonstrate that correlation functions of the central spin can be utilized to distinguish between MBL and ergodic phases of the 1D chain. Hence, we propose the use of a central spin as a possible experimental probe to identify the MBL phase.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1806.08316","open_access":"1"}],"scopus_import":"1","intvolume":" 98","month":"10","publication_status":"published","language":[{"iso":"eng"}],"issue":"16","volume":98},{"department":[{"_id":"DaSi"},{"_id":"CaHe"},{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"MiSi"}],"date_updated":"2023-09-11T13:22:13Z","status":"public","article_type":"original","type":"journal_article","_id":"308","ec_funded":1,"issue":"3","volume":45,"related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/cells-change-tension-to-make-tissue-barriers-easier-to-get-through/"}]},"language":[{"iso":"eng"}],"publication_status":"published","intvolume":" 45","month":"05","main_file_link":[{"url":"https://doi.org/10.1016/j.devcel.2018.04.002","open_access":"1"}],"scopus_import":"1","oa_version":"Published Version","pmid":1,"acknowledged_ssus":[{"_id":"SSU"}],"abstract":[{"lang":"eng","text":"Migrating cells penetrate tissue barriers during development, inflammatory responses, and tumor metastasis. We study if migration in vivo in such three-dimensionally confined environments requires changes in the mechanical properties of the surrounding cells using embryonic Drosophila melanogaster hemocytes, also called macrophages, as a model. We find that macrophage invasion into the germband through transient separation of the apposing ectoderm and mesoderm requires cell deformations and reductions in apical tension in the ectoderm. Interestingly, the genetic pathway governing these mechanical shifts acts downstream of the only known tumor necrosis factor superfamily member in Drosophila, Eiger, and its receptor, Grindelwald. Eiger-Grindelwald signaling reduces levels of active Myosin in the germband ectodermal cortex through the localization of a Crumbs complex component, Patj (Pals-1-associated tight junction protein). We therefore elucidate a distinct molecular pathway that controls tissue tension and demonstrate the importance of such regulation for invasive migration in vivo."}],"title":"Drosophila TNF modulates tissue tension in the embryo to facilitate macrophage invasive migration","article_processing_charge":"No","external_id":{"pmid":["29738712"],"isi":["000432461400009"]},"author":[{"last_name":"Ratheesh","full_name":"Ratheesh, Aparna","orcid":"0000-0001-7190-0776","first_name":"Aparna","id":"2F064CFE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Biebl, Julia","last_name":"Biebl","id":"3CCBB46E-F248-11E8-B48F-1D18A9856A87","first_name":"Julia"},{"full_name":"Smutny, Michael","last_name":"Smutny","first_name":"Michael"},{"id":"433253EE-F248-11E8-B48F-1D18A9856A87","first_name":"Jana","full_name":"Veselá, Jana","last_name":"Veselá"},{"full_name":"Papusheva, Ekaterina","last_name":"Papusheva","first_name":"Ekaterina","id":"41DB591E-F248-11E8-B48F-1D18A9856A87"},{"id":"2B819732-F248-11E8-B48F-1D18A9856A87","first_name":"Gabriel","full_name":"Krens, Gabriel","orcid":"0000-0003-4761-5996","last_name":"Krens"},{"last_name":"Kaufmann","orcid":"0000-0001-9735-5315","full_name":"Kaufmann, Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","first_name":"Walter"},{"full_name":"György, Attila","orcid":"0000-0002-1819-198X","last_name":"György","id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87","first_name":"Attila"},{"last_name":"Casano","full_name":"Casano, Alessandra M","orcid":"0000-0002-6009-6804","first_name":"Alessandra M","id":"3DBA3F4E-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-8323-8353","full_name":"Siekhaus, Daria E","last_name":"Siekhaus","first_name":"Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Ratheesh, Aparna, et al. “Drosophila TNF Modulates Tissue Tension in the Embryo to Facilitate Macrophage Invasive Migration.” Developmental Cell, vol. 45, no. 3, Elsevier, 2018, pp. 331–46, doi:10.1016/j.devcel.2018.04.002.","ieee":"A. Ratheesh et al., “Drosophila TNF modulates tissue tension in the embryo to facilitate macrophage invasive migration,” Developmental Cell, vol. 45, no. 3. Elsevier, pp. 331–346, 2018.","short":"A. Ratheesh, J. Bicher, M. Smutny, J. Veselá, E. Papusheva, G. Krens, W. Kaufmann, A. György, A.M. Casano, D.E. Siekhaus, Developmental Cell 45 (2018) 331–346.","apa":"Ratheesh, A., Bicher, J., Smutny, M., Veselá, J., Papusheva, E., Krens, G., … Siekhaus, D. E. (2018). Drosophila TNF modulates tissue tension in the embryo to facilitate macrophage invasive migration. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2018.04.002","ama":"Ratheesh A, Bicher J, Smutny M, et al. Drosophila TNF modulates tissue tension in the embryo to facilitate macrophage invasive migration. Developmental Cell. 2018;45(3):331-346. doi:10.1016/j.devcel.2018.04.002","chicago":"Ratheesh, Aparna, Julia Bicher, Michael Smutny, Jana Veselá, Ekaterina Papusheva, Gabriel Krens, Walter Kaufmann, Attila György, Alessandra M Casano, and Daria E Siekhaus. “Drosophila TNF Modulates Tissue Tension in the Embryo to Facilitate Macrophage Invasive Migration.” Developmental Cell. Elsevier, 2018. https://doi.org/10.1016/j.devcel.2018.04.002.","ista":"Ratheesh A, Bicher J, Smutny M, Veselá J, Papusheva E, Krens G, Kaufmann W, György A, Casano AM, Siekhaus DE. 2018. Drosophila TNF modulates tissue tension in the embryo to facilitate macrophage invasive migration. Developmental Cell. 45(3), 331–346."},"project":[{"call_identifier":"FWF","_id":"253B6E48-B435-11E9-9278-68D0E5697425","grant_number":"P29638","name":"Drosophila TNFa´s Funktion in Immunzellen"},{"name":"Investigating the role of transporters in invasive migration through junctions","grant_number":"334077","_id":"2536F660-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"date_created":"2018-12-11T11:45:44Z","date_published":"2018-05-07T00:00:00Z","doi":"10.1016/j.devcel.2018.04.002","page":"331 - 346","publication":"Developmental Cell","day":"07","year":"2018","isi":1,"oa":1,"quality_controlled":"1","publisher":"Elsevier"},{"type":"journal_article","pubrep_id":"1061","status":"public","_id":"17","department":[{"_id":"BjHo"}],"file_date_updated":"2020-07-14T12:45:12Z","date_updated":"2023-09-11T12:59:28Z","ddc":["532"],"scopus_import":"1","intvolume":" 3","month":"10","abstract":[{"lang":"eng","text":"Creeping flow of polymeric fluid without inertia exhibits elastic instabilities and elastic turbulence accompanied by drag enhancement due to elastic stress produced by flow-stretched polymers. However, in inertia-dominated flow at high Re and low fluid elasticity El, a reduction in turbulent frictional drag is caused by an intricate competition between inertial and elastic stresses. Here we explore the effect of inertia on the stability of viscoelastic flow in a broad range of control parameters El and (Re,Wi). We present the stability diagram of observed flow regimes in Wi-Re coordinates and find that the instabilities' onsets show an unexpectedly nonmonotonic dependence on El. Further, three distinct regions in the diagram are identified based on El. Strikingly, for high-elasticity fluids we discover a complete relaminarization of flow at Reynolds number in the range of 1 to 10, different from a well-known turbulent drag reduction. These counterintuitive effects may be explained by a finite polymer extensibility and a suppression of vorticity at high Wi. Our results call for further theoretical and numerical development to uncover the role of inertial effect on elastic turbulence in a viscoelastic flow."}],"oa_version":"Published Version","ec_funded":1,"volume":3,"issue":"10","publication_status":"published","language":[{"iso":"eng"}],"file":[{"checksum":"e1445be33e8165114e96246275600750","file_id":"4800","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"IST-2018-1061-v1+1_PhysRevFluids.3.103302.pdf","date_created":"2018-12-12T10:10:14Z","file_size":1409040,"date_updated":"2020-07-14T12:45:12Z","creator":"system"}],"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"article_number":"103302 ","article_processing_charge":"No","external_id":{"isi":["000447311500001"]},"author":[{"id":"2A2006B2-F248-11E8-B48F-1D18A9856A87","first_name":"Atul","last_name":"Varshney","orcid":"0000-0002-3072-5999","full_name":"Varshney, Atul"},{"first_name":"Victor","last_name":"Steinberg","full_name":"Steinberg, Victor"}],"publist_id":"8038","title":"Drag enhancement and drag reduction in viscoelastic flow","citation":{"mla":"Varshney, Atul, and Victor Steinberg. “Drag Enhancement and Drag Reduction in Viscoelastic Flow.” Physical Review Fluids, vol. 3, no. 10, 103302, American Physical Society, 2018, doi:10.1103/PhysRevFluids.3.103302.","ama":"Varshney A, Steinberg V. Drag enhancement and drag reduction in viscoelastic flow. Physical Review Fluids. 2018;3(10). doi:10.1103/PhysRevFluids.3.103302","apa":"Varshney, A., & Steinberg, V. (2018). Drag enhancement and drag reduction in viscoelastic flow. Physical Review Fluids. American Physical Society. https://doi.org/10.1103/PhysRevFluids.3.103302","short":"A. Varshney, V. Steinberg, Physical Review Fluids 3 (2018).","ieee":"A. Varshney and V. Steinberg, “Drag enhancement and drag reduction in viscoelastic flow,” Physical Review Fluids, vol. 3, no. 10. American Physical Society, 2018.","chicago":"Varshney, Atul, and Victor Steinberg. “Drag Enhancement and Drag Reduction in Viscoelastic Flow.” Physical Review Fluids. American Physical Society, 2018. https://doi.org/10.1103/PhysRevFluids.3.103302.","ista":"Varshney A, Steinberg V. 2018. Drag enhancement and drag reduction in viscoelastic flow. Physical Review Fluids. 3(10), 103302."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"publisher":"American Physical Society","quality_controlled":"1","date_created":"2018-12-11T11:44:11Z","doi":"10.1103/PhysRevFluids.3.103302","date_published":"2018-10-15T00:00:00Z","year":"2018","has_accepted_license":"1","isi":1,"publication":"Physical Review Fluids","day":"15"},{"publisher":"National Academy of Sciences","quality_controlled":"1","oa":1,"acknowledgement":"This work was supported by the Biotechnology and Biological Sciences Research Council (J.M.J.P., I.F., and P.S.S.), the Engineering and Physical Sciences Research Council (EPSRC) (A.A.G.), and Austrian Science Fund Grant FWF P28844 (to G.T.).","doi":"10.1073/pnas.1716659115","date_published":"2018-06-05T00:00:00Z","date_created":"2018-12-11T11:45:35Z","page":"6088 - 6093","day":"05","publication":"PNAS","isi":1,"year":"2018","project":[{"call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425","grant_number":"P28844-B27","name":"Biophysics of information processing in gene regulation"}],"title":"Distributed and dynamic intracellular organization of extracellular information","author":[{"first_name":"Alejandro","last_name":"Granados","full_name":"Granados, Alejandro"},{"full_name":"Pietsch, Julian","last_name":"Pietsch","first_name":"Julian"},{"last_name":"Cepeda Humerez","full_name":"Cepeda Humerez, Sarah A","id":"3DEE19A4-F248-11E8-B48F-1D18A9856A87","first_name":"Sarah A"},{"full_name":"Farquhar, Isebail","last_name":"Farquhar","first_name":"Isebail"},{"last_name":"Tkacik","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper"},{"first_name":"Peter","full_name":"Swain, Peter","last_name":"Swain"}],"publist_id":"7618","external_id":{"pmid":["29784812"],"isi":["000434114900071"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Granados, Alejandro, Julian Pietsch, Sarah A Cepeda Humerez, Isebail Farquhar, Gašper Tkačik, and Peter Swain. “Distributed and Dynamic Intracellular Organization of Extracellular Information.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1716659115.","ista":"Granados A, Pietsch J, Cepeda Humerez SA, Farquhar I, Tkačik G, Swain P. 2018. Distributed and dynamic intracellular organization of extracellular information. PNAS. 115(23), 6088–6093.","mla":"Granados, Alejandro, et al. “Distributed and Dynamic Intracellular Organization of Extracellular Information.” PNAS, vol. 115, no. 23, National Academy of Sciences, 2018, pp. 6088–93, doi:10.1073/pnas.1716659115.","short":"A. Granados, J. Pietsch, S.A. Cepeda Humerez, I. Farquhar, G. Tkačik, P. Swain, PNAS 115 (2018) 6088–6093.","ieee":"A. Granados, J. Pietsch, S. A. Cepeda Humerez, I. Farquhar, G. Tkačik, and P. Swain, “Distributed and dynamic intracellular organization of extracellular information,” PNAS, vol. 115, no. 23. National Academy of Sciences, pp. 6088–6093, 2018.","ama":"Granados A, Pietsch J, Cepeda Humerez SA, Farquhar I, Tkačik G, Swain P. Distributed and dynamic intracellular organization of extracellular information. PNAS. 2018;115(23):6088-6093. doi:10.1073/pnas.1716659115","apa":"Granados, A., Pietsch, J., Cepeda Humerez, S. A., Farquhar, I., Tkačik, G., & Swain, P. (2018). Distributed and dynamic intracellular organization of extracellular information. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1716659115"},"month":"06","intvolume":" 115","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/early/2017/09/21/192039"}],"oa_version":"Preprint","pmid":1,"abstract":[{"lang":"eng","text":"Although cells respond specifically to environments, how environmental identity is encoded intracellularly is not understood. Here, we study this organization of information in budding yeast by estimating the mutual information between environmental transitions and the dynamics of nuclear translocation for 10 transcription factors. Our method of estimation is general, scalable, and based on decoding from single cells. The dynamics of the transcription factors are necessary to encode the highest amounts of extracellular information, and we show that information is transduced through two channels: Generalists (Msn2/4, Tod6 and Dot6, Maf1, and Sfp1) can encode the nature of multiple stresses, but only if stress is high; specialists (Hog1, Yap1, and Mig1/2) encode one particular stress, but do so more quickly and for a wider range of magnitudes. In particular, Dot6 encodes almost as much information as Msn2, the master regulator of the environmental stress response. Each transcription factor reports differently, and it is only their collective behavior that distinguishes between multiple environmental states. Changes in the dynamics of the localization of transcription factors thus constitute a precise, distributed internal representation of extracellular change. We predict that such multidimensional representations are common in cellular decision-making."}],"volume":115,"issue":"23","related_material":{"record":[{"id":"6473","status":"public","relation":"part_of_dissertation"}]},"language":[{"iso":"eng"}],"publication_status":"published","status":"public","type":"journal_article","article_type":"original","_id":"281","department":[{"_id":"GaTk"}],"date_updated":"2023-09-11T12:58:24Z"},{"date_created":"2018-12-11T11:47:32Z","date_published":"2018-01-04T00:00:00Z","doi":"10.1242/jcs.207696","publication":"Journal of Cell Science","day":"04","year":"2018","isi":1,"oa":1,"publisher":"Company of Biologists","quality_controlled":"1","title":"Distinct roles for plasma membrane PtdIns 4 P and PtdIns 4 5 P2 during yeast receptor mediated endocytosis","external_id":{"pmid":["29192062"],"isi":["000424786900012"]},"article_processing_charge":"No","publist_id":"7184","author":[{"full_name":"Yamamoto, Wataru","last_name":"Yamamoto","first_name":"Wataru"},{"first_name":"Suguru","full_name":"Wada, Suguru","last_name":"Wada"},{"full_name":"Nagano, Makoto","last_name":"Nagano","first_name":"Makoto"},{"first_name":"Kaito","last_name":"Aoshima","full_name":"Aoshima, Kaito"},{"last_name":"Siekhaus","full_name":"Siekhaus, Daria E","orcid":"0000-0001-8323-8353","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","first_name":"Daria E"},{"first_name":"Junko","full_name":"Toshima, Junko","last_name":"Toshima"},{"full_name":"Toshima, Jiro","last_name":"Toshima","first_name":"Jiro"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Yamamoto, Wataru, et al. “Distinct Roles for Plasma Membrane PtdIns 4 P and PtdIns 4 5 P2 during Yeast Receptor Mediated Endocytosis.” Journal of Cell Science, vol. 131, no. 1, jcs207696, Company of Biologists, 2018, doi:10.1242/jcs.207696.","apa":"Yamamoto, W., Wada, S., Nagano, M., Aoshima, K., Siekhaus, D. E., Toshima, J., & Toshima, J. (2018). Distinct roles for plasma membrane PtdIns 4 P and PtdIns 4 5 P2 during yeast receptor mediated endocytosis. Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.207696","ama":"Yamamoto W, Wada S, Nagano M, et al. Distinct roles for plasma membrane PtdIns 4 P and PtdIns 4 5 P2 during yeast receptor mediated endocytosis. Journal of Cell Science. 2018;131(1). doi:10.1242/jcs.207696","ieee":"W. Yamamoto et al., “Distinct roles for plasma membrane PtdIns 4 P and PtdIns 4 5 P2 during yeast receptor mediated endocytosis,” Journal of Cell Science, vol. 131, no. 1. Company of Biologists, 2018.","short":"W. Yamamoto, S. Wada, M. Nagano, K. Aoshima, D.E. Siekhaus, J. Toshima, J. Toshima, Journal of Cell Science 131 (2018).","chicago":"Yamamoto, Wataru, Suguru Wada, Makoto Nagano, Kaito Aoshima, Daria E Siekhaus, Junko Toshima, and Jiro Toshima. “Distinct Roles for Plasma Membrane PtdIns 4 P and PtdIns 4 5 P2 during Yeast Receptor Mediated Endocytosis.” Journal of Cell Science. Company of Biologists, 2018. https://doi.org/10.1242/jcs.207696.","ista":"Yamamoto W, Wada S, Nagano M, Aoshima K, Siekhaus DE, Toshima J, Toshima J. 2018. Distinct roles for plasma membrane PtdIns 4 P and PtdIns 4 5 P2 during yeast receptor mediated endocytosis. Journal of Cell Science. 131(1), jcs207696."},"article_number":"jcs207696","volume":131,"issue":"1","language":[{"iso":"eng"}],"publication_status":"published","intvolume":" 131","month":"01","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/29192062"}],"scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Clathrin-mediated endocytosis requires the coordinated assembly of various endocytic proteins and lipids at the plasma membrane. Accumulating evidence demonstrates a crucial role for phosphatidylinositol-4,5-bisphosphate (PtdIns(4,5)P2) in endocytosis, but specific roles for PtdIns(4)P other than as the biosynthetic precursor of PtdIns(4,5)P2 have not been clarified. In this study we investigated the role of PtdIns(4)P or PtdIns(4,5)P2 in receptor-mediated endocytosis through the construction of temperature-sensitive (ts) mutants for the PI 4-kinases Stt4p and Pik1p and the PtdIns(4) 5-kinase Mss4p. Quantitative analyses of endocytosis revealed that both the stt4(ts)pik1(ts) and mss4(ts) mutants have a severe defect in endocytic internalization. Live-cell imaging of endocytic protein dynamics in stt4(ts)pik1(ts) and mss4(ts) mutants revealed that PtdIns(4)P is required for the recruitment of the alpha-factor receptor Ste2p to clathrin-coated pits whereas PtdIns(4,5)P2 is required for membrane internalization. We also found that the localization to endocytic sites of the ENTH/ANTH domain-bearing clathrin adaptors, Ent1p/Ent2p and Yap1801p/Yap1802p, is significantly impaired in the stt4(ts)pik1(ts) mutant, but not in the mss4(ts) mutant. These results suggest distinct roles in successive steps for PtdIns(4)P and PtdIns(4,5)P2 during receptor-mediated endocytosis."}],"department":[{"_id":"DaSi"}],"date_updated":"2023-09-11T12:57:13Z","status":"public","type":"journal_article","_id":"620"},{"scopus_import":"1","alternative_title":["HSCC Proceedings"],"month":"04","abstract":[{"lang":"eng","text":"We describe a new algorithm for the parametric identification problem for signal temporal logic (STL), stated as follows. Given a densetime real-valued signal w and a parameterized temporal logic formula φ, compute the subset of the parameter space that renders the formula satisfied by the signal. Unlike previous solutions, which were based on search in the parameter space or quantifier elimination, our procedure works recursively on φ and computes the evolution over time of the set of valid parameter assignments. This procedure is similar to that of monitoring or computing the robustness of φ relative to w. Our implementation and experiments demonstrate that this approach can work well in practice."}],"oa_version":"Submitted Version","publication_identifier":{"isbn":["978-1-4503-5642-8 "]},"publication_status":"published","file":[{"date_created":"2020-05-14T12:18:29Z","file_name":"2018_HSCC_Bakhirkin.pdf","date_updated":"2020-07-14T12:45:17Z","file_size":5900421,"creator":"dernst","checksum":"81eabc96430e84336ea88310ac0a1ad0","file_id":"7833","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"type":"conference","conference":{"name":"HSCC: Hybrid Systems: Computation and Control","location":"Porto, Portugal","end_date":"2018-04-13","start_date":"2018-04-11"},"status":"public","_id":"182","file_date_updated":"2020-07-14T12:45:17Z","department":[{"_id":"ToHe"}],"date_updated":"2023-09-11T13:30:51Z","ddc":["000"],"quality_controlled":"1","publisher":"ACM","oa":1,"page":"177 - 186","date_published":"2018-04-11T00:00:00Z","doi":"10.1145/3178126.3178132","date_created":"2018-12-11T11:45:04Z","isi":1,"has_accepted_license":"1","year":"2018","day":"11","publication":"Proceedings of the 21st International Conference on Hybrid Systems","project":[{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"author":[{"first_name":"Alexey","last_name":"Bakhirkin","full_name":"Bakhirkin, Alexey"},{"id":"40960E6E-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","last_name":"Ferrere","orcid":"0000-0001-5199-3143","full_name":"Ferrere, Thomas"},{"full_name":"Maler, Oded","last_name":"Maler","first_name":"Oded"}],"publist_id":"7739","article_processing_charge":"No","external_id":{"isi":["000474781600020"]},"title":"Efficient parametric identification for STL","citation":{"ieee":"A. Bakhirkin, T. Ferrere, and O. Maler, “Efficient parametric identification for STL,” in Proceedings of the 21st International Conference on Hybrid Systems, Porto, Portugal, 2018, pp. 177–186.","short":"A. Bakhirkin, T. Ferrere, O. Maler, in:, Proceedings of the 21st International Conference on Hybrid Systems, ACM, 2018, pp. 177–186.","ama":"Bakhirkin A, Ferrere T, Maler O. Efficient parametric identification for STL. In: Proceedings of the 21st International Conference on Hybrid Systems. ACM; 2018:177-186. doi:10.1145/3178126.3178132","apa":"Bakhirkin, A., Ferrere, T., & Maler, O. (2018). Efficient parametric identification for STL. In Proceedings of the 21st International Conference on Hybrid Systems (pp. 177–186). Porto, Portugal: ACM. https://doi.org/10.1145/3178126.3178132","mla":"Bakhirkin, Alexey, et al. “Efficient Parametric Identification for STL.” Proceedings of the 21st International Conference on Hybrid Systems, ACM, 2018, pp. 177–86, doi:10.1145/3178126.3178132.","ista":"Bakhirkin A, Ferrere T, Maler O. 2018. Efficient parametric identification for STL. Proceedings of the 21st International Conference on Hybrid Systems. HSCC: Hybrid Systems: Computation and Control, HSCC Proceedings, , 177–186.","chicago":"Bakhirkin, Alexey, Thomas Ferrere, and Oded Maler. “Efficient Parametric Identification for STL.” In Proceedings of the 21st International Conference on Hybrid Systems, 177–86. ACM, 2018. https://doi.org/10.1145/3178126.3178132."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"department":[{"_id":"KrCh"}],"date_updated":"2023-09-11T13:23:42Z","type":"conference","conference":{"end_date":"2018-07-12","location":"Oxford, United Kingdom","start_date":"2018-07-09","name":"LICS: Logic in Computer Science"},"status":"public","_id":"143","volume":"F138033","ec_funded":1,"publication_identifier":{"isbn":["978-1-4503-5583-4"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","alternative_title":["ACM/IEEE Symposium on Logic in Computer Science"],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.10985"}],"month":"07","abstract":[{"text":"Vector Addition Systems with States (VASS) provide a well-known and fundamental model for the analysis of concurrent processes, parameterized systems, and are also used as abstract models of programs in resource bound analysis. In this paper we study the problem of obtaining asymptotic bounds on the termination time of a given VASS. In particular, we focus on the practically important case of obtaining polynomial bounds on termination time. Our main contributions are as follows: First, we present a polynomial-time algorithm for deciding whether a given VASS has a linear asymptotic complexity. We also show that if the complexity of a VASS is not linear, it is at least quadratic. Second, we classify VASS according to quantitative properties of their cycles. We show that certain singularities in these properties are the key reason for non-polynomial asymptotic complexity of VASS. In absence of singularities, we show that the asymptotic complexity is always polynomial and of the form Θ(nk), for some integer k d, where d is the dimension of the VASS. We present a polynomial-time algorithm computing the optimal k. For general VASS, the same algorithm, which is based on a complete technique for the construction of ranking functions in VASS, produces a valid lower bound, i.e., a k such that the termination complexity is (nk). Our results are based on new insights into the geometry of VASS dynamics, which hold the potential for further applicability to VASS analysis.","lang":"eng"}],"oa_version":"Preprint","publist_id":"7780","author":[{"full_name":"Brázdil, Tomáš","last_name":"Brázdil","first_name":"Tomáš"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"first_name":"Antonín","full_name":"Kučera, Antonín","last_name":"Kučera"},{"last_name":"Novotny","full_name":"Novotny, Petr","first_name":"Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Dominik","full_name":"Velan, Dominik","last_name":"Velan"},{"last_name":"Zuleger","full_name":"Zuleger, Florian","first_name":"Florian"}],"external_id":{"isi":["000545262800020"]},"article_processing_charge":"No","title":"Efficient algorithms for asymptotic bounds on termination time in VASS","citation":{"chicago":"Brázdil, Tomáš, Krishnendu Chatterjee, Antonín Kučera, Petr Novotný, Dominik Velan, and Florian Zuleger. “Efficient Algorithms for Asymptotic Bounds on Termination Time in VASS,” F138033:185–94. IEEE, 2018. https://doi.org/10.1145/3209108.3209191.","ista":"Brázdil T, Chatterjee K, Kučera A, Novotný P, Velan D, Zuleger F. 2018. Efficient algorithms for asymptotic bounds on termination time in VASS. LICS: Logic in Computer Science, ACM/IEEE Symposium on Logic in Computer Science, vol. F138033, 185–194.","mla":"Brázdil, Tomáš, et al. Efficient Algorithms for Asymptotic Bounds on Termination Time in VASS. Vol. F138033, IEEE, 2018, pp. 185–94, doi:10.1145/3209108.3209191.","ama":"Brázdil T, Chatterjee K, Kučera A, Novotný P, Velan D, Zuleger F. Efficient algorithms for asymptotic bounds on termination time in VASS. In: Vol F138033. IEEE; 2018:185-194. doi:10.1145/3209108.3209191","apa":"Brázdil, T., Chatterjee, K., Kučera, A., Novotný, P., Velan, D., & Zuleger, F. (2018). Efficient algorithms for asymptotic bounds on termination time in VASS (Vol. F138033, pp. 185–194). Presented at the LICS: Logic in Computer Science, Oxford, United Kingdom: IEEE. https://doi.org/10.1145/3209108.3209191","ieee":"T. Brázdil, K. Chatterjee, A. Kučera, P. Novotný, D. Velan, and F. Zuleger, “Efficient algorithms for asymptotic bounds on termination time in VASS,” presented at the LICS: Logic in Computer Science, Oxford, United Kingdom, 2018, vol. F138033, pp. 185–194.","short":"T. Brázdil, K. Chatterjee, A. Kučera, P. Novotný, D. Velan, F. Zuleger, in:, IEEE, 2018, pp. 185–194."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"}],"page":"185 - 194","doi":"10.1145/3209108.3209191","date_published":"2018-07-09T00:00:00Z","date_created":"2018-12-11T11:44:51Z","isi":1,"year":"2018","day":"09","publisher":"IEEE","quality_controlled":"1","oa":1},{"type":"conference","conference":{"name":"CVPR: Conference on Computer Vision and Pattern Recognition","start_date":"2018-06-18","location":"Salt Lake City, UT, USA","end_date":"2018-06-22"},"status":"public","_id":"273","department":[{"_id":"VlKo"}],"date_updated":"2023-09-11T13:24:43Z","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1604.08269","open_access":"1"}],"month":"06","abstract":[{"lang":"eng","text":"The accuracy of information retrieval systems is often measured using complex loss functions such as the average precision (AP) or the normalized discounted cumulative gain (NDCG). Given a set of positive and negative samples, the parameters of a retrieval system can be estimated by minimizing these loss functions. However, the non-differentiability and non-decomposability of these loss functions does not allow for simple gradient based optimization algorithms. This issue is generally circumvented by either optimizing a structured hinge-loss upper bound to the loss function or by using asymptotic methods like the direct-loss minimization framework. Yet, the high computational complexity of loss-augmented inference, which is necessary for both the frameworks, prohibits its use in large training data sets. To alleviate this deficiency, we present a novel quicksort flavored algorithm for a large class of non-decomposable loss functions. We provide a complete characterization of the loss functions that are amenable to our algorithm, and show that it includes both AP and NDCG based loss functions. Furthermore, we prove that no comparison based algorithm can improve upon the computational complexity of our approach asymptotically. We demonstrate the effectiveness of our approach in the context of optimizing the structured hinge loss upper bound of AP and NDCG loss for learning models for a variety of vision tasks. We show that our approach provides significantly better results than simpler decomposable loss functions, while requiring a comparable training time."}],"oa_version":"Preprint","ec_funded":1,"publication_identifier":{"isbn":["9781538664209"]},"publication_status":"published","language":[{"iso":"eng"}],"project":[{"_id":"25FBA906-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice","grant_number":"616160"}],"author":[{"first_name":"Pritish","full_name":"Mohapatra, Pritish","last_name":"Mohapatra"},{"id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87","first_name":"Michal","last_name":"Rolinek","full_name":"Rolinek, Michal"},{"first_name":"C V","last_name":"Jawahar","full_name":"Jawahar, C V"},{"first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kolmogorov, Vladimir","last_name":"Kolmogorov"},{"first_name":"M Pawan","last_name":"Kumar","full_name":"Kumar, M Pawan"}],"external_id":{"arxiv":["1604.08269"],"isi":["000457843603087"]},"article_processing_charge":"No","title":"Efficient optimization for rank-based loss functions","citation":{"mla":"Mohapatra, Pritish, et al. “Efficient Optimization for Rank-Based Loss Functions.” 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2018, pp. 3693–701, doi:10.1109/cvpr.2018.00389.","ama":"Mohapatra P, Rolinek M, Jawahar CV, Kolmogorov V, Kumar MP. Efficient optimization for rank-based loss functions. In: 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition. IEEE; 2018:3693-3701. doi:10.1109/cvpr.2018.00389","apa":"Mohapatra, P., Rolinek, M., Jawahar, C. V., Kolmogorov, V., & Kumar, M. P. (2018). Efficient optimization for rank-based loss functions. In 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition (pp. 3693–3701). Salt Lake City, UT, USA: IEEE. https://doi.org/10.1109/cvpr.2018.00389","ieee":"P. Mohapatra, M. Rolinek, C. V. Jawahar, V. Kolmogorov, and M. P. Kumar, “Efficient optimization for rank-based loss functions,” in 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, Salt Lake City, UT, USA, 2018, pp. 3693–3701.","short":"P. Mohapatra, M. Rolinek, C.V. Jawahar, V. Kolmogorov, M.P. Kumar, in:, 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2018, pp. 3693–3701.","chicago":"Mohapatra, Pritish, Michal Rolinek, C V Jawahar, Vladimir Kolmogorov, and M Pawan Kumar. “Efficient Optimization for Rank-Based Loss Functions.” In 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, 3693–3701. IEEE, 2018. https://doi.org/10.1109/cvpr.2018.00389.","ista":"Mohapatra P, Rolinek M, Jawahar CV, Kolmogorov V, Kumar MP. 2018. Efficient optimization for rank-based loss functions. 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition. CVPR: Conference on Computer Vision and Pattern Recognition, 3693–3701."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"IEEE","quality_controlled":"1","oa":1,"page":"3693-3701","date_published":"2018-06-28T00:00:00Z","doi":"10.1109/cvpr.2018.00389","date_created":"2018-12-11T11:45:33Z","isi":1,"year":"2018","day":"28","publication":"2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition"},{"citation":{"ista":"Zibrov A, Rao P, Kometter C, Li J, Dean C, Taniguchi T, Watanabe K, Serbyn M, Young A. 2018. Emergent dirac gullies and gully-symmetry-breaking quantum hall states in ABA trilayer graphene. Physical Review Letters. 121(16), 167601.","chicago":"Zibrov, Alexander, Peng Rao, Carlos Kometter, Jia Li, Cory Dean, Takashi Taniguchi, Kenji Watanabe, Maksym Serbyn, and Andrea Young. “Emergent Dirac Gullies and Gully-Symmetry-Breaking Quantum Hall States in ABA Trilayer Graphene.” Physical Review Letters. American Physical Society, 2018. https://doi.org/10.1103/PhysRevLett.121.167601.","apa":"Zibrov, A., Rao, P., Kometter, C., Li, J., Dean, C., Taniguchi, T., … Young, A. (2018). Emergent dirac gullies and gully-symmetry-breaking quantum hall states in ABA trilayer graphene. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.121.167601","ama":"Zibrov A, Rao P, Kometter C, et al. Emergent dirac gullies and gully-symmetry-breaking quantum hall states in ABA trilayer graphene. Physical Review Letters. 2018;121(16). doi:10.1103/PhysRevLett.121.167601","short":"A. Zibrov, P. Rao, C. Kometter, J. Li, C. Dean, T. Taniguchi, K. Watanabe, M. Serbyn, A. Young, Physical Review Letters 121 (2018).","ieee":"A. Zibrov et al., “Emergent dirac gullies and gully-symmetry-breaking quantum hall states in ABA trilayer graphene,” Physical Review Letters, vol. 121, no. 16. American Physical Society, 2018.","mla":"Zibrov, Alexander, et al. “Emergent Dirac Gullies and Gully-Symmetry-Breaking Quantum Hall States in ABA Trilayer Graphene.” Physical Review Letters, vol. 121, no. 16, 167601, American Physical Society, 2018, doi:10.1103/PhysRevLett.121.167601."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Alexander","full_name":"Zibrov, Alexander","last_name":"Zibrov"},{"orcid":"0000-0003-1250-0021","full_name":"Peng, Rao","last_name":"Peng","first_name":"Rao","id":"47C23AC6-02D0-11E9-BD0E-99399A5D3DEB"},{"first_name":"Carlos","last_name":"Kometter","full_name":"Kometter, Carlos"},{"full_name":"Li, Jia","last_name":"Li","first_name":"Jia"},{"first_name":"Cory","last_name":"Dean","full_name":"Dean, Cory"},{"first_name":"Takashi","last_name":"Taniguchi","full_name":"Taniguchi, Takashi"},{"first_name":"Kenji","full_name":"Watanabe, Kenji","last_name":"Watanabe"},{"last_name":"Serbyn","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym","first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Young, Andrea","last_name":"Young","first_name":"Andrea"}],"article_processing_charge":"No","external_id":{"arxiv":["1805.01038"],"isi":["000447307500007"]},"title":"Emergent dirac gullies and gully-symmetry-breaking quantum hall states in ABA trilayer graphene","article_number":"167601","isi":1,"year":"2018","day":"19","publication":"Physical Review Letters","doi":"10.1103/PhysRevLett.121.167601","date_published":"2018-10-19T00:00:00Z","date_created":"2018-12-11T11:45:38Z","acknowledgement":"The experimental work at UCSB was funded by the National Science Foundation under Grant No. DMR- 1654186. Work at Columbia was supported by the National Science Foundation under Grant No. DMR- 1507788. K. W. and T. T. acknowledge support from the Elemental Strategy Initiative conducted by the Ministry of Education, Culture, Sports, Science and Technology, Japan, and the Japan Society for the Promotion of Science KAKENHI Grant No. JP15K21722. E. M. S. acknowledges the support of the Elings Fellowship from the California Nanosystems Institute at the University of California, Santa Barbara. A. F. Y. acknowledges the support of the David and Lucile Packard foundation and the Sloan Foundation. Measurements made use of a dilution refrigerator funded through the Major Research Instrumentation program of the U.S. National Science Foundation under Grant No. DMR- 1531389, and the MRL Shared Experimental Facilities, which are supported by the MRSEC Program of the U.S. National Science Foundation under Grant No. DMR- 1720256.","quality_controlled":"1","publisher":"American Physical Society","oa":1,"date_updated":"2023-09-11T13:39:50Z","department":[{"_id":"MaSe"}],"_id":"289","type":"journal_article","article_type":"original","status":"public","publication_status":"published","language":[{"iso":"eng"}],"volume":121,"issue":"16","abstract":[{"lang":"eng","text":"We report on quantum capacitance measurements of high quality, graphite- and hexagonal boron nitride encapsulated Bernal stacked trilayer graphene devices. At zero applied magnetic field, we observe a number of electron density- and electrical displacement-tuned features in the electronic compressibility associated with changes in Fermi surface topology. At high displacement field and low density, strong trigonal warping gives rise to emergent Dirac gullies centered near the corners of the hexagonal Brillouin and related by three fold rotation symmetry. At low magnetic fields of B=1.25~T, the gullies manifest as a change in the degeneracy of the Landau levels from two to three. Weak incompressible states are also observed at integer filling within these triplets Landau levels, which a Hartree-Fock analysis indicates are associated with Coulomb-driven nematic phases that spontaneously break rotation symmetry."}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1805.01038","open_access":"1"}],"month":"10","intvolume":" 121"},{"date_updated":"2023-09-11T13:38:14Z","department":[{"_id":"JoFi"}],"_id":"287","status":"public","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","issue":"8","volume":23,"ec_funded":1,"oa_version":"Submitted Version","pmid":1,"abstract":[{"lang":"eng","text":"In this paper, we discuss biological effects of electromagnetic (EM) fields in the context of cancer biology. In particular, we review the nanomechanical properties of microtubules (MTs), the latter being one of the most successful targets for cancer therapy. We propose an investigation on the coupling of electromagnetic radiation to mechanical vibrations of MTs as an important basis for biological and medical applications. In our opinion, optomechanical methods can accurately monitor and control the mechanical properties of isolated MTs in a liquid environment. Consequently, studying nanomechanical properties of MTs may give useful information for future applications to diagnostic and therapeutic technologies involving non-invasive externally applied physical fields. For example, electromagnetic fields or high intensity ultrasound can be used therapeutically avoiding harmful side effects of chemotherapeutic agents or classical radiation therapy."}],"month":"03","intvolume":" 23","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://www.bioscience.org/2018/v23/af/4651/fulltext.htm"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Salari, Vahid, Shabir Barzanjeh, Michal Cifra, Christoph Simon, Felix Scholkmann, Zahra Alirezaei, and Jack Tuszynski. “Electromagnetic Fields and Optomechanics In Cancer Diagnostics and Treatment.” Frontiers in Bioscience - Landmark. Frontiers in Bioscience, 2018. https://doi.org/10.2741/4651.","ista":"Salari V, Barzanjeh S, Cifra M, Simon C, Scholkmann F, Alirezaei Z, Tuszynski J. 2018. Electromagnetic fields and optomechanics In cancer diagnostics and treatment. Frontiers in Bioscience - Landmark. 23(8), 1391–1406.","mla":"Salari, Vahid, et al. “Electromagnetic Fields and Optomechanics In Cancer Diagnostics and Treatment.” Frontiers in Bioscience - Landmark, vol. 23, no. 8, Frontiers in Bioscience, 2018, pp. 1391–406, doi:10.2741/4651.","apa":"Salari, V., Barzanjeh, S., Cifra, M., Simon, C., Scholkmann, F., Alirezaei, Z., & Tuszynski, J. (2018). Electromagnetic fields and optomechanics In cancer diagnostics and treatment. Frontiers in Bioscience - Landmark. Frontiers in Bioscience. https://doi.org/10.2741/4651","ama":"Salari V, Barzanjeh S, Cifra M, et al. Electromagnetic fields and optomechanics In cancer diagnostics and treatment. Frontiers in Bioscience - Landmark. 2018;23(8):1391-1406. doi:10.2741/4651","ieee":"V. Salari et al., “Electromagnetic fields and optomechanics In cancer diagnostics and treatment,” Frontiers in Bioscience - Landmark, vol. 23, no. 8. Frontiers in Bioscience, pp. 1391–1406, 2018.","short":"V. Salari, S. Barzanjeh, M. Cifra, C. Simon, F. Scholkmann, Z. Alirezaei, J. Tuszynski, Frontiers in Bioscience - Landmark 23 (2018) 1391–1406."},"title":"Electromagnetic fields and optomechanics In cancer diagnostics and treatment","author":[{"full_name":"Salari, Vahid","last_name":"Salari","first_name":"Vahid"},{"full_name":"Barzanjeh, Shabir","orcid":"0000-0003-0415-1423","last_name":"Barzanjeh","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","first_name":"Shabir"},{"full_name":"Cifra, Michal","last_name":"Cifra","first_name":"Michal"},{"full_name":"Simon, Christoph","last_name":"Simon","first_name":"Christoph"},{"full_name":"Scholkmann, Felix","last_name":"Scholkmann","first_name":"Felix"},{"full_name":"Alirezaei, Zahra","last_name":"Alirezaei","first_name":"Zahra"},{"full_name":"Tuszynski, Jack","last_name":"Tuszynski","first_name":"Jack"}],"article_processing_charge":"No","external_id":{"isi":["000439042800001"],"pmid":["29293441"]},"project":[{"call_identifier":"H2020","_id":"258047B6-B435-11E9-9278-68D0E5697425","grant_number":"707438","name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics SUPEREOM"}],"day":"01","publication":"Frontiers in Bioscience - Landmark","isi":1,"year":"2018","date_published":"2018-03-01T00:00:00Z","doi":"10.2741/4651","date_created":"2018-12-11T11:45:37Z","page":"1391 - 1406","acknowledgement":"The work of SB has been supported by the European Unions Horizon 2020 research and innovation program under the Marie Sklodowska Curie grant agreement No MSC-IF 707438 SUPEREOM. JAT gratefully acknowledges funding support from NSERC (Canada) for his research. MC acknowledges support from the Czech Science Foundation, projects 15-17102S and 17-11898S and he participates in COST Action BM1309, CA15211 and bilateral exchange project between Czech and Slovak Academies of Sciences, SAV-15-22.","publisher":"Frontiers in Bioscience","quality_controlled":"1","oa":1},{"quality_controlled":"1","publisher":"ACM","oa":1,"isi":1,"year":"2018","day":"01","publication":"Journal of the ACM","date_published":"2018-01-01T00:00:00Z","doi":"10.1145/3078632","date_created":"2018-12-11T11:46:24Z","article_number":"5","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"citation":{"chicago":"Matoušek, Jiří, Eric Sedgwick, Martin Tancer, and Uli Wagner. “Embeddability in the 3-Sphere Is Decidable.” Journal of the ACM. ACM, 2018. https://doi.org/10.1145/3078632.","ista":"Matoušek J, Sedgwick E, Tancer M, Wagner U. 2018. Embeddability in the 3-Sphere is decidable. Journal of the ACM. 65(1), 5.","mla":"Matoušek, Jiří, et al. “Embeddability in the 3-Sphere Is Decidable.” Journal of the ACM, vol. 65, no. 1, 5, ACM, 2018, doi:10.1145/3078632.","apa":"Matoušek, J., Sedgwick, E., Tancer, M., & Wagner, U. (2018). Embeddability in the 3-Sphere is decidable. Journal of the ACM. ACM. https://doi.org/10.1145/3078632","ama":"Matoušek J, Sedgwick E, Tancer M, Wagner U. Embeddability in the 3-Sphere is decidable. Journal of the ACM. 2018;65(1). doi:10.1145/3078632","ieee":"J. Matoušek, E. Sedgwick, M. Tancer, and U. Wagner, “Embeddability in the 3-Sphere is decidable,” Journal of the ACM, vol. 65, no. 1. ACM, 2018.","short":"J. Matoušek, E. Sedgwick, M. Tancer, U. Wagner, Journal of the ACM 65 (2018)."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"last_name":"Matoušek","full_name":"Matoušek, Jiří","first_name":"Jiří"},{"full_name":"Sedgwick, Eric","last_name":"Sedgwick","first_name":"Eric"},{"full_name":"Tancer, Martin","orcid":"0000-0002-1191-6714","last_name":"Tancer","first_name":"Martin","id":"38AC689C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Wagner","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli"}],"publist_id":"7398","external_id":{"arxiv":["1402.0815"],"isi":["000425685900006"]},"article_processing_charge":"No","title":"Embeddability in the 3-Sphere is decidable","abstract":[{"lang":"eng","text":"We show that the following algorithmic problem is decidable: given a 2-dimensional simplicial complex, can it be embedded (topologically, or equivalently, piecewise linearly) in R3? By a known reduction, it suffices to decide the embeddability of a given triangulated 3-manifold X into the 3-sphere S3. The main step, which allows us to simplify X and recurse, is in proving that if X can be embedded in S3, then there is also an embedding in which X has a short meridian, that is, an essential curve in the boundary of X bounding a disk in S3 \\ X with length bounded by a computable function of the number of tetrahedra of X."}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1402.0815"}],"month":"01","intvolume":" 65","publication_status":"published","language":[{"iso":"eng"}],"issue":"1","related_material":{"record":[{"status":"public","id":"2157","relation":"earlier_version"}]},"volume":65,"ec_funded":1,"_id":"425","article_type":"original","type":"journal_article","status":"public","date_updated":"2023-09-11T13:38:49Z","department":[{"_id":"UlWa"}]},{"citation":{"ista":"Barton NH, Etheridge A. 2018. Establishment in a new habitat by polygenic adaptation. Theoretical Population Biology. 122(7), 110–127.","chicago":"Barton, Nicholas H, and Alison Etheridge. “Establishment in a New Habitat by Polygenic Adaptation.” Theoretical Population Biology. Academic Press, 2018. https://doi.org/10.1016/j.tpb.2017.11.007.","ieee":"N. H. Barton and A. Etheridge, “Establishment in a new habitat by polygenic adaptation,” Theoretical Population Biology, vol. 122, no. 7. Academic Press, pp. 110–127, 2018.","short":"N.H. Barton, A. Etheridge, Theoretical Population Biology 122 (2018) 110–127.","ama":"Barton NH, Etheridge A. Establishment in a new habitat by polygenic adaptation. Theoretical Population Biology. 2018;122(7):110-127. doi:10.1016/j.tpb.2017.11.007","apa":"Barton, N. H., & Etheridge, A. (2018). Establishment in a new habitat by polygenic adaptation. Theoretical Population Biology. Academic Press. https://doi.org/10.1016/j.tpb.2017.11.007","mla":"Barton, Nicholas H., and Alison Etheridge. “Establishment in a New Habitat by Polygenic Adaptation.” Theoretical Population Biology, vol. 122, no. 7, Academic Press, 2018, pp. 110–27, doi:10.1016/j.tpb.2017.11.007."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"7250","author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"},{"first_name":"Alison","full_name":"Etheridge, Alison","last_name":"Etheridge"}],"article_processing_charge":"No","external_id":{"isi":["000440392900014"]},"title":"Establishment in a new habitat by polygenic adaptation","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152"}],"has_accepted_license":"1","isi":1,"year":"2018","day":"01","publication":"Theoretical Population Biology","page":"110-127","date_published":"2018-07-01T00:00:00Z","doi":"10.1016/j.tpb.2017.11.007","date_created":"2018-12-11T11:47:12Z","publisher":"Academic Press","quality_controlled":"1","oa":1,"date_updated":"2023-09-11T13:41:22Z","ddc":["519","576"],"department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:47:09Z","_id":"564","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"status":"public","publication_status":"published","file":[{"file_id":"7199","checksum":"0b96f6db47e3e91b5e7d103b847c239d","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"bartonetheridge.pdf","date_created":"2019-12-21T09:36:39Z","creator":"nbarton","file_size":2287682,"date_updated":"2020-07-14T12:47:09Z"}],"language":[{"iso":"eng"}],"volume":122,"issue":"7","related_material":{"record":[{"id":"9842","status":"public","relation":"research_data"}]},"ec_funded":1,"abstract":[{"text":"Maladapted individuals can only colonise a new habitat if they can evolve a\r\npositive growth rate fast enough to avoid extinction, a process known as evolutionary\r\nrescue. We treat log fitness at low density in the new habitat as a\r\nsingle polygenic trait and thus use the infinitesimal model to follow the evolution\r\nof the growth rate; this assumes that the trait values of offspring of a\r\nsexual union are normally distributed around the mean of the parents’ trait\r\nvalues, with variance that depends only on the parents’ relatedness. The\r\nprobability that a single migrant can establish depends on just two parameters:\r\nthe mean and genetic variance of the trait in the source population.\r\nThe chance of success becomes small if migrants come from a population\r\nwith mean growth rate in the new habitat more than a few standard deviations\r\nbelow zero; this chance depends roughly equally on the probability\r\nthat the initial founder is unusually fit, and on the subsequent increase in\r\ngrowth rate of its offspring as a result of selection. The loss of genetic variation\r\nduring the founding event is substantial, but highly variable. With\r\ncontinued migration at rate M, establishment is inevitable; when migration\r\nis rare, the expected time to establishment decreases inversely with M.\r\nHowever, above a threshold migration rate, the population may be trapped\r\nin a ‘sink’ state, in which adaptation is held back by gene flow; above this\r\nthreshold, the expected time to establishment increases exponentially with M. This threshold behaviour is captured by a deterministic approximation,\r\nwhich assumes a Gaussian distribution of the trait in the founder population\r\nwith mean and variance evolving deterministically. By assuming a constant\r\ngenetic variance, we also develop a diffusion approximation for the joint distribution\r\nof population size and trait mean, which extends to include stabilising\r\nselection and density regulation. Divergence of the population from its\r\nancestors causes partial reproductive isolation, which we measure through\r\nthe reproductive value of migrants into the newly established population.","lang":"eng"}],"oa_version":"Submitted Version","scopus_import":"1","month":"07","intvolume":" 122"},{"author":[{"full_name":"Hilbe, Christian","orcid":"0000-0001-5116-955X","last_name":"Hilbe","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","first_name":"Christian"},{"last_name":"Šimsa","full_name":"Šimsa, Štepán","first_name":"Štepán"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"last_name":"Nowak","full_name":"Nowak, Martin","first_name":"Martin"}],"publist_id":"7764","article_processing_charge":"No","external_id":{"isi":["000438240900054"]},"title":"Evolution of cooperation in stochastic games","citation":{"apa":"Hilbe, C., Šimsa, Š., Chatterjee, K., & Nowak, M. (2018). Evolution of cooperation in stochastic games. Nature. Nature Publishing Group. https://doi.org/10.1038/s41586-018-0277-x","ama":"Hilbe C, Šimsa Š, Chatterjee K, Nowak M. Evolution of cooperation in stochastic games. Nature. 2018;559(7713):246-249. doi:10.1038/s41586-018-0277-x","ieee":"C. Hilbe, Š. Šimsa, K. Chatterjee, and M. Nowak, “Evolution of cooperation in stochastic games,” Nature, vol. 559, no. 7713. Nature Publishing Group, pp. 246–249, 2018.","short":"C. Hilbe, Š. Šimsa, K. Chatterjee, M. Nowak, Nature 559 (2018) 246–249.","mla":"Hilbe, Christian, et al. “Evolution of Cooperation in Stochastic Games.” Nature, vol. 559, no. 7713, Nature Publishing Group, 2018, pp. 246–49, doi:10.1038/s41586-018-0277-x.","ista":"Hilbe C, Šimsa Š, Chatterjee K, Nowak M. 2018. Evolution of cooperation in stochastic games. Nature. 559(7713), 246–249.","chicago":"Hilbe, Christian, Štepán Šimsa, Krishnendu Chatterjee, and Martin Nowak. “Evolution of Cooperation in Stochastic Games.” Nature. Nature Publishing Group, 2018. https://doi.org/10.1038/s41586-018-0277-x."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S11407","name":"Game Theory"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"page":"246 - 249","doi":"10.1038/s41586-018-0277-x","date_published":"2018-07-04T00:00:00Z","date_created":"2018-12-11T11:44:56Z","isi":1,"has_accepted_license":"1","year":"2018","day":"04","publication":"Nature","publisher":"Nature Publishing Group","quality_controlled":"1","oa":1,"acknowledgement":"European Research Council Start Grant 279307, Austrian Science Fund (FWF) grant P23499-N23, \r\nC.H. acknowledges support from the ISTFELLOW programme.","department":[{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:45:02Z","date_updated":"2023-09-11T13:43:22Z","ddc":["000"],"type":"journal_article","status":"public","_id":"157","issue":"7713","volume":559,"related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/engineering-cooperation/","description":"News on IST Homepage"}]},"ec_funded":1,"publication_status":"published","file":[{"file_id":"7049","checksum":"011ab905cf9a410bc2b96f15174d654d","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2018_Nature_Hilbe.pdf","date_created":"2019-11-19T08:09:57Z","creator":"dernst","file_size":2834442,"date_updated":"2020-07-14T12:45:02Z"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"07","intvolume":" 559","abstract":[{"lang":"eng","text":"Social dilemmas occur when incentives for individuals are misaligned with group interests 1-7 . According to the 'tragedy of the commons', these misalignments can lead to overexploitation and collapse of public resources. The resulting behaviours can be analysed with the tools of game theory 8 . The theory of direct reciprocity 9-15 suggests that repeated interactions can alleviate such dilemmas, but previous work has assumed that the public resource remains constant over time. Here we introduce the idea that the public resource is instead changeable and depends on the strategic choices of individuals. An intuitive scenario is that cooperation increases the public resource, whereas defection decreases it. Thus, cooperation allows the possibility of playing a more valuable game with higher payoffs, whereas defection leads to a less valuable game. We analyse this idea using the theory of stochastic games 16-19 and evolutionary game theory. We find that the dependence of the public resource on previous interactions can greatly enhance the propensity for cooperation. For these results, the interaction between reciprocity and payoff feedback is crucial: neither repeated interactions in a constant environment nor single interactions in a changing environment yield similar cooperation rates. Our framework shows which feedbacks between exploitation and environment - either naturally occurring or designed - help to overcome social dilemmas."}],"oa_version":"Submitted Version"},{"year":"2018","isi":1,"has_accepted_license":"1","publication":"Genome Biology and Evolution","day":"01","page":"928 - 938","date_created":"2018-12-11T11:46:10Z","doi":"10.1093/gbe/evy049","date_published":"2018-03-01T00:00:00Z","acknowledgement":"his work was supported by the Deutsche Forschungsgemeinschaft (grant number FR 1411/9-1). This work was supported by the German Research Foundation (DFG) and the Technical University of Munich within the fund- ing programme Open Access Publish\r\nWe thank Goar Frishman for help with the annotation of the\r\nsymbiont status of the organisms and Michael Galperin for\r\nuseful comments. T","oa":1,"quality_controlled":"1","publisher":"Oxford University Press","citation":{"mla":"Hönigschmid, Peter, et al. “Evolutionary Interplay between Symbiotic Relationships and Patterns of Signal Peptide Gain and Loss.” Genome Biology and Evolution, vol. 10, no. 3, Oxford University Press, 2018, pp. 928–38, doi:10.1093/gbe/evy049.","ama":"Hönigschmid P, Bykova N, Schneider R, Ivankov D, Frishman D. Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss. Genome Biology and Evolution. 2018;10(3):928-938. doi:10.1093/gbe/evy049","apa":"Hönigschmid, P., Bykova, N., Schneider, R., Ivankov, D., & Frishman, D. (2018). Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss. Genome Biology and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evy049","ieee":"P. Hönigschmid, N. Bykova, R. Schneider, D. Ivankov, and D. Frishman, “Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss,” Genome Biology and Evolution, vol. 10, no. 3. Oxford University Press, pp. 928–938, 2018.","short":"P. Hönigschmid, N. Bykova, R. Schneider, D. Ivankov, D. Frishman, Genome Biology and Evolution 10 (2018) 928–938.","chicago":"Hönigschmid, Peter, Nadya Bykova, René Schneider, Dmitry Ivankov, and Dmitrij Frishman. “Evolutionary Interplay between Symbiotic Relationships and Patterns of Signal Peptide Gain and Loss.” Genome Biology and Evolution. Oxford University Press, 2018. https://doi.org/10.1093/gbe/evy049.","ista":"Hönigschmid P, Bykova N, Schneider R, Ivankov D, Frishman D. 2018. Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss. Genome Biology and Evolution. 10(3), 928–938."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"isi":["000429483700022"]},"publist_id":"7445","author":[{"full_name":"Hönigschmid, Peter","last_name":"Hönigschmid","first_name":"Peter"},{"last_name":"Bykova","full_name":"Bykova, Nadya","first_name":"Nadya"},{"first_name":"René","last_name":"Schneider","full_name":"Schneider, René"},{"last_name":"Ivankov","full_name":"Ivankov, Dmitry","id":"49FF1036-F248-11E8-B48F-1D18A9856A87","first_name":"Dmitry"},{"last_name":"Frishman","full_name":"Frishman, Dmitrij","first_name":"Dmitrij"}],"title":"Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss","publication_status":"published","language":[{"iso":"eng"}],"file":[{"date_updated":"2020-07-14T12:46:16Z","file_size":691602,"creator":"system","date_created":"2018-12-12T10:08:07Z","file_name":"IST-2018-999-v1+1_2018_Ivankov_Evolutionary_interplay.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"458a7c2c2e79528567edfeb0f326cbe0","file_id":"4667"}],"issue":"3","volume":10,"abstract":[{"lang":"eng","text":"Can orthologous proteins differ in terms of their ability to be secreted? To answer this question, we investigated the distribution of signal peptides within the orthologous groups of Enterobacterales. Parsimony analysis and sequence comparisons revealed a large number of signal peptide gain and loss events, in which signal peptides emerge or disappear in the course of evolution. Signal peptide losses prevail over gains, an effect which is especially pronounced in the transition from the free-living or commensal to the endosymbiotic lifestyle. The disproportionate decline in the number of signal peptide-containing proteins in endosymbionts cannot be explained by the overall reduction of their genomes. Signal peptides can be gained and lost either by acquisition/elimination of the corresponding N-terminal regions or by gradual accumulation of mutations. The evolutionary dynamics of signal peptides in bacterial proteins represents a powerful mechanism of functional diversification."}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 10","month":"03","date_updated":"2023-09-11T13:56:52Z","ddc":["576"],"department":[{"_id":"FyKo"}],"file_date_updated":"2020-07-14T12:46:16Z","_id":"384","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"999","status":"public"},{"department":[{"_id":"NiBa"},{"_id":"ChLa"}],"date_updated":"2023-09-11T13:42:38Z","type":"journal_article","status":"public","_id":"563","issue":"3","related_material":{"record":[{"id":"200","status":"public","relation":"dissertation_contains"}]},"volume":208,"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/205484v1","open_access":"1"}],"month":"03","intvolume":" 208","abstract":[{"text":"In continuous populations with local migration, nearby pairs of individuals have on average more similar genotypes\r\nthan geographically well separated pairs. A barrier to gene flow distorts this classical pattern of isolation by distance. Genetic similarity is decreased for sample pairs on different sides of the barrier and increased for pairs on the same side near the barrier. Here, we introduce an inference scheme that utilizes this signal to detect and estimate the strength of a linear barrier to gene flow in two-dimensions. We use a diffusion approximation to model the effects of a barrier on the geographical spread of ancestry backwards in time. This approach allows us to calculate the chance of recent coalescence and probability of identity by descent. We introduce an inference scheme that fits these theoretical results to the geographical covariance structure of bialleleic genetic markers. It can estimate the strength of the barrier as well as several demographic parameters. We investigate the power of our inference scheme to detect barriers by applying it to a wide range of simulated data. We also showcase an example application to a Antirrhinum majus (snapdragon) flower color hybrid zone, where we do not detect any signal of a strong genome wide barrier to gene flow.","lang":"eng"}],"oa_version":"Preprint","publist_id":"7251","author":[{"first_name":"Harald","id":"417FCFF4-F248-11E8-B48F-1D18A9856A87","full_name":"Ringbauer, Harald","orcid":"0000-0002-4884-9682","last_name":"Ringbauer"},{"first_name":"Alexander","id":"2D157DB6-F248-11E8-B48F-1D18A9856A87","full_name":"Kolesnikov, Alexander","last_name":"Kolesnikov"},{"full_name":"Field, David","last_name":"Field","first_name":"David"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"}],"article_processing_charge":"No","external_id":{"isi":["000426219600025"]},"title":"Estimating barriers to gene flow from distorted isolation-by-distance patterns","citation":{"mla":"Ringbauer, Harald, et al. “Estimating Barriers to Gene Flow from Distorted Isolation-by-Distance Patterns.” Genetics, vol. 208, no. 3, Genetics Society of America, 2018, pp. 1231–45, doi:10.1534/genetics.117.300638.","ieee":"H. Ringbauer, A. Kolesnikov, D. Field, and N. H. Barton, “Estimating barriers to gene flow from distorted isolation-by-distance patterns,” Genetics, vol. 208, no. 3. Genetics Society of America, pp. 1231–1245, 2018.","short":"H. Ringbauer, A. Kolesnikov, D. Field, N.H. Barton, Genetics 208 (2018) 1231–1245.","ama":"Ringbauer H, Kolesnikov A, Field D, Barton NH. Estimating barriers to gene flow from distorted isolation-by-distance patterns. Genetics. 2018;208(3):1231-1245. doi:10.1534/genetics.117.300638","apa":"Ringbauer, H., Kolesnikov, A., Field, D., & Barton, N. H. (2018). Estimating barriers to gene flow from distorted isolation-by-distance patterns. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.117.300638","chicago":"Ringbauer, Harald, Alexander Kolesnikov, David Field, and Nicholas H Barton. “Estimating Barriers to Gene Flow from Distorted Isolation-by-Distance Patterns.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.117.300638.","ista":"Ringbauer H, Kolesnikov A, Field D, Barton NH. 2018. Estimating barriers to gene flow from distorted isolation-by-distance patterns. Genetics. 208(3), 1231–1245."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"1231-1245","date_published":"2018-03-01T00:00:00Z","doi":"10.1534/genetics.117.300638","date_created":"2018-12-11T11:47:12Z","isi":1,"year":"2018","day":"01","publication":"Genetics","publisher":"Genetics Society of America","quality_controlled":"1","oa":1},{"department":[{"_id":"ChWo"}],"file_date_updated":"2020-10-08T08:38:23Z","date_updated":"2023-09-11T14:00:26Z","ddc":["006"],"type":"journal_article","article_type":"original","status":"public","_id":"135","ec_funded":1,"volume":37,"issue":"2","publication_status":"published","publication_identifier":{"issn":["0167-7055"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"8edb90da8a72395eb5d970580e0925b6","file_id":"8627","file_size":54309947,"date_updated":"2020-10-08T08:38:23Z","creator":"wojtan","file_name":"exnbflip.pdf","date_created":"2020-10-08T08:38:23Z"}],"scopus_import":"1","alternative_title":["Eurographics"],"intvolume":" 37","month":"05","abstract":[{"text":"The Fluid Implicit Particle method (FLIP) reduces numerical dissipation by combining particles with grids. To improve performance, the subsequent narrow band FLIP method (NB‐FLIP) uses a FLIP‐based fluid simulation only near the liquid surface and a traditional grid‐based fluid simulation away from the surface. This spatially‐limited FLIP simulation significantly reduces the number of particles and alleviates a computational bottleneck. In this paper, we extend the NB‐FLIP idea even further, by allowing a simulation to transition between a FLIP‐like fluid simulation and a grid‐based simulation in arbitrary locations, not just near the surface. This approach leads to even more savings in memory and computation, because we can concentrate the particles only in areas where they are needed. More importantly, this new method allows us to seamlessly transition to smooth implicit surface geometry wherever the particle‐based simulation is unnecessary. Consequently, our method leads to a practical algorithm for avoiding the noisy surface artifacts associated with particle‐based liquid simulations, while simultaneously maintaining the benefits of a FLIP simulation in regions of dynamic motion.","lang":"eng"}],"oa_version":"Submitted Version","article_processing_charge":"No","external_id":{"isi":["000434085600016"]},"author":[{"last_name":"Sato","full_name":"Sato, Takahiro","first_name":"Takahiro"},{"full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","last_name":"Wojtan","first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Nils","full_name":"Thuerey, Nils","last_name":"Thuerey"},{"first_name":"Takeo","full_name":"Igarashi, Takeo","last_name":"Igarashi"},{"last_name":"Ando","full_name":"Ando, Ryoichi","first_name":"Ryoichi"}],"title":"Extended narrow band FLIP for liquid simulations","citation":{"chicago":"Sato, Takahiro, Chris Wojtan, Nils Thuerey, Takeo Igarashi, and Ryoichi Ando. “Extended Narrow Band FLIP for Liquid Simulations.” Computer Graphics Forum. Wiley, 2018. https://doi.org/10.1111/cgf.13351.","ista":"Sato T, Wojtan C, Thuerey N, Igarashi T, Ando R. 2018. Extended narrow band FLIP for liquid simulations. Computer Graphics Forum. 37(2), 169–177.","mla":"Sato, Takahiro, et al. “Extended Narrow Band FLIP for Liquid Simulations.” Computer Graphics Forum, vol. 37, no. 2, Wiley, 2018, pp. 169–77, doi:10.1111/cgf.13351.","apa":"Sato, T., Wojtan, C., Thuerey, N., Igarashi, T., & Ando, R. (2018). Extended narrow band FLIP for liquid simulations. Computer Graphics Forum. Wiley. https://doi.org/10.1111/cgf.13351","ama":"Sato T, Wojtan C, Thuerey N, Igarashi T, Ando R. Extended narrow band FLIP for liquid simulations. Computer Graphics Forum. 2018;37(2):169-177. doi:10.1111/cgf.13351","short":"T. Sato, C. Wojtan, N. Thuerey, T. Igarashi, R. Ando, Computer Graphics Forum 37 (2018) 169–177.","ieee":"T. Sato, C. Wojtan, N. Thuerey, T. Igarashi, and R. Ando, “Extended narrow band FLIP for liquid simulations,” Computer Graphics Forum, vol. 37, no. 2. Wiley, pp. 169–177, 2018."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"call_identifier":"H2020","_id":"2533E772-B435-11E9-9278-68D0E5697425","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","grant_number":"638176"}],"page":"169 - 177","date_created":"2018-12-11T11:44:49Z","date_published":"2018-05-22T00:00:00Z","doi":"10.1111/cgf.13351","year":"2018","isi":1,"has_accepted_license":"1","publication":"Computer Graphics Forum","day":"22","oa":1,"publisher":"Wiley","quality_controlled":"1"},{"_id":"316","status":"public","article_type":"original","type":"journal_article","date_updated":"2023-09-11T13:57:43Z","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"oa_version":"Preprint","abstract":[{"text":"Self-incompatibility (SI) is a genetically based recognition system that functions to prevent self-fertilization and mating among related plants. An enduring puzzle in SI is how the high diversity observed in nature arises and is maintained. Based on the underlying recognition mechanism, SI can be classified into two main groups: self- and non-self recognition. Most work has focused on diversification within self-recognition systems despite expected differences between the two groups in the evolutionary pathways and outcomes of diversification. Here, we use a deterministic population genetic model and stochastic simulations to investigate how novel S-haplotypes evolve in a gametophytic non-self recognition (SRNase/S Locus F-box (SLF)) SI system. For this model the pathways for diversification involve either the maintenance or breakdown of SI and can vary in the order of mutations of the female (SRNase) and male (SLF) components. We show analytically that diversification can occur with high inbreeding depression and self-pollination, but this varies with evolutionary pathway and level of completeness (which determines the number of potential mating partners in the population), and in general is more likely for lower haplotype number. The conditions for diversification are broader in stochastic simulations of finite population size. However, the number of haplotypes observed under high inbreeding and moderate to high self-pollination is less than that commonly observed in nature. Diversification was observed through pathways that maintain SI as well as through self-compatible intermediates. Yet the lifespan of diversified haplotypes was sensitive to their level of completeness. By examining diversification in a non-self recognition SI system, this model extends our understanding of the evolution and maintenance of haplotype diversity observed in a self recognition system common in flowering plants.","lang":"eng"}],"month":"07","intvolume":" 209","scopus_import":"1","main_file_link":[{"url":"https://www.biorxiv.org/node/80098.abstract","open_access":"1"}],"language":[{"iso":"eng"}],"publication_status":"published","related_material":{"link":[{"url":"https://ist.ac.at/en/news/recognizing-others-but-not-yourself-new-insights-into-the-evolution-of-plant-mating/","relation":"press_release","description":"News on IST Homepage"}],"record":[{"id":"9813","status":"public","relation":"research_data"}]},"volume":209,"issue":"3","ec_funded":1,"project":[{"call_identifier":"FP7","_id":"25B36484-B435-11E9-9278-68D0E5697425","name":"Mating system and the evolutionary dynamics of hybrid zones","grant_number":"329960"},{"name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Bodova, Katarina, et al. “Evolutionary Pathways for the Generation of New Self-Incompatibility Haplotypes in a Non-Self Recognition System.” Genetics, vol. 209, no. 3, Genetics Society of America, 2018, pp. 861–83, doi:10.1534/genetics.118.300748.","short":"K. Bodova, T. Priklopil, D. Field, N.H. Barton, M. Pickup, Genetics 209 (2018) 861–883.","ieee":"K. Bodova, T. Priklopil, D. Field, N. H. Barton, and M. Pickup, “Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system,” Genetics, vol. 209, no. 3. Genetics Society of America, pp. 861–883, 2018.","ama":"Bodova K, Priklopil T, Field D, Barton NH, Pickup M. Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system. Genetics. 2018;209(3):861-883. doi:10.1534/genetics.118.300748","apa":"Bodova, K., Priklopil, T., Field, D., Barton, N. H., & Pickup, M. (2018). Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.118.300748","chicago":"Bodova, Katarina, Tadeas Priklopil, David Field, Nicholas H Barton, and Melinda Pickup. “Evolutionary Pathways for the Generation of New Self-Incompatibility Haplotypes in a Non-Self Recognition System.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.118.300748.","ista":"Bodova K, Priklopil T, Field D, Barton NH, Pickup M. 2018. Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system. Genetics. 209(3), 861–883."},"title":"Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system","author":[{"id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","first_name":"Katarina","full_name":"Bodova, Katarina","orcid":"0000-0002-7214-0171","last_name":"Bodova"},{"last_name":"Priklopil","full_name":"Priklopil, Tadeas","id":"3C869AA0-F248-11E8-B48F-1D18A9856A87","first_name":"Tadeas"},{"orcid":"0000-0002-4014-8478","full_name":"Field, David","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"id":"2C78037E-F248-11E8-B48F-1D18A9856A87","first_name":"Melinda","last_name":"Pickup","orcid":"0000-0001-6118-0541","full_name":"Pickup, Melinda"}],"external_id":{"isi":["000437171700017"]},"article_processing_charge":"No","quality_controlled":"1","publisher":"Genetics Society of America","oa":1,"day":"01","publication":"Genetics","isi":1,"year":"2018","doi":"10.1534/genetics.118.300748","date_published":"2018-07-01T00:00:00Z","date_created":"2018-12-11T11:45:47Z","page":"861-883"},{"article_processing_charge":"No","external_id":{"pmid":["29998472"],"isi":["000443231000002"]},"publist_id":"7730","author":[{"last_name":"Harrison","full_name":"Harrison, Mark","first_name":"Mark"},{"first_name":"Nicolas","last_name":"Arning","full_name":"Arning, Nicolas"},{"first_name":"Lucas","last_name":"Kremer","full_name":"Kremer, Lucas"},{"full_name":"Ylla, Guillem","last_name":"Ylla","first_name":"Guillem"},{"first_name":"Xavier","last_name":"Belles","full_name":"Belles, Xavier"},{"full_name":"Bornberg Bauer, Erich","last_name":"Bornberg Bauer","first_name":"Erich"},{"id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","first_name":"Ann K","full_name":"Huylmans, Ann K","orcid":"0000-0001-8871-4961","last_name":"Huylmans"},{"full_name":"Jongepier, Evelien","last_name":"Jongepier","first_name":"Evelien"},{"full_name":"Puilachs, Maria","last_name":"Puilachs","first_name":"Maria"},{"full_name":"Richards, Stephen","last_name":"Richards","first_name":"Stephen"},{"first_name":"Coby","full_name":"Schal, Coby","last_name":"Schal"}],"title":"Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest","citation":{"mla":"Harrison, Mark, et al. “Expansions of Key Protein Families in the German Cockroach Highlight the Molecular Basis of Its Remarkable Success as a Global Indoor Pest.” Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, vol. 330, Wiley, 2018, pp. 254–64, doi:10.1002/jez.b.22824.","short":"M. Harrison, N. Arning, L. Kremer, G. Ylla, X. Belles, E. Bornberg Bauer, A.K. Huylmans, E. Jongepier, M. Puilachs, S. Richards, C. Schal, Journal of Experimental Zoology Part B: Molecular and Developmental Evolution 330 (2018) 254–264.","ieee":"M. Harrison et al., “Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest,” Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, vol. 330. Wiley, pp. 254–264, 2018.","ama":"Harrison M, Arning N, Kremer L, et al. Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution. 2018;330:254-264. doi:10.1002/jez.b.22824","apa":"Harrison, M., Arning, N., Kremer, L., Ylla, G., Belles, X., Bornberg Bauer, E., … Schal, C. (2018). Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution. Wiley. https://doi.org/10.1002/jez.b.22824","chicago":"Harrison, Mark, Nicolas Arning, Lucas Kremer, Guillem Ylla, Xavier Belles, Erich Bornberg Bauer, Ann K Huylmans, et al. “Expansions of Key Protein Families in the German Cockroach Highlight the Molecular Basis of Its Remarkable Success as a Global Indoor Pest.” Journal of Experimental Zoology Part B: Molecular and Developmental Evolution. Wiley, 2018. https://doi.org/10.1002/jez.b.22824.","ista":"Harrison M, Arning N, Kremer L, Ylla G, Belles X, Bornberg Bauer E, Huylmans AK, Jongepier E, Puilachs M, Richards S, Schal C. 2018. Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution. 330, 254–264."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"publisher":"Wiley","quality_controlled":"1","page":"254-264","date_created":"2018-12-11T11:45:06Z","date_published":"2018-07-11T00:00:00Z","doi":"10.1002/jez.b.22824","year":"2018","isi":1,"publication":"Journal of Experimental Zoology Part B: Molecular and Developmental Evolution","day":"11","type":"journal_article","article_type":"original","status":"public","_id":"190","department":[{"_id":"BeVi"}],"date_updated":"2023-09-11T13:59:54Z","main_file_link":[{"url":"https://onlinelibrary.wiley.com/doi/am-pdf/10.1002/jez.b.22824","open_access":"1"}],"scopus_import":"1","intvolume":" 330","month":"07","abstract":[{"lang":"eng","text":"The German cockroach, Blattella germanica, is a worldwide pest that infests buildings, including homes, restaurants, and hospitals, often living in unsanitary conditions. As a disease vector and producer of allergens, this species has major health and economic impacts on humans. Factors contributing to the success of the German cockroach include its resistance to a broad range of insecticides, immunity to many pathogens, and its ability, as an extreme generalist omnivore, to survive on most food sources. The recently published genome shows that B. germanica has an exceptionally high number of protein coding genes. In this study, we investigate the functions of the 93 significantly expanded gene families with the aim to better understand the success of B. germanica as a major pest despite such inhospitable conditions. We find major expansions in gene families with functions related to the detoxification of insecticides and allelochemicals, defense against pathogens, digestion, sensory perception, and gene regulation. These expansions might have allowed B. germanica to develop multiple resistance mechanisms to insecticides and pathogens, and enabled a broad, flexible diet, thus explaining its success in unsanitary conditions and under recurrent chemical control. The findings and resources presented here provide insights for better understanding molecular mechanisms that will facilitate more effective cockroach control."}],"oa_version":"Submitted Version","pmid":1,"volume":330,"publication_status":"published","language":[{"iso":"eng"}]},{"citation":{"chicago":"Fischer, Julian L, and Günther Grün. “Existence of Positive Solutions to Stochastic Thin-Film Equations.” SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics , 2018. https://doi.org/10.1137/16M1098796.","ista":"Fischer JL, Grün G. 2018. Existence of positive solutions to stochastic thin-film equations. SIAM Journal on Mathematical Analysis. 50(1), 411–455.","mla":"Fischer, Julian L., and Günther Grün. “Existence of Positive Solutions to Stochastic Thin-Film Equations.” SIAM Journal on Mathematical Analysis, vol. 50, no. 1, Society for Industrial and Applied Mathematics , 2018, pp. 411–55, doi:10.1137/16M1098796.","ama":"Fischer JL, Grün G. Existence of positive solutions to stochastic thin-film equations. SIAM Journal on Mathematical Analysis. 2018;50(1):411-455. doi:10.1137/16M1098796","apa":"Fischer, J. L., & Grün, G. (2018). Existence of positive solutions to stochastic thin-film equations. SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics . https://doi.org/10.1137/16M1098796","short":"J.L. Fischer, G. Grün, SIAM Journal on Mathematical Analysis 50 (2018) 411–455.","ieee":"J. L. Fischer and G. Grün, “Existence of positive solutions to stochastic thin-film equations,” SIAM Journal on Mathematical Analysis, vol. 50, no. 1. Society for Industrial and Applied Mathematics , pp. 411–455, 2018."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"7425","author":[{"id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","first_name":"Julian L","last_name":"Fischer","full_name":"Fischer, Julian L","orcid":"0000-0002-0479-558X"},{"first_name":"Günther","full_name":"Grün, Günther","last_name":"Grün"}],"external_id":{"isi":["000426630900015"]},"article_processing_charge":"No","title":"Existence of positive solutions to stochastic thin-film equations","quality_controlled":"1","publisher":"Society for Industrial and Applied Mathematics ","oa":1,"isi":1,"has_accepted_license":"1","year":"2018","day":"30","publication":"SIAM Journal on Mathematical Analysis","page":"411 - 455","doi":"10.1137/16M1098796","date_published":"2018-01-30T00:00:00Z","date_created":"2018-12-11T11:46:17Z","_id":"404","article_type":"original","type":"journal_article","status":"public","date_updated":"2023-09-11T13:59:22Z","ddc":["510"],"file_date_updated":"2020-07-14T12:46:22Z","department":[{"_id":"JuFi"}],"abstract":[{"text":"We construct martingale solutions to stochastic thin-film equations by introducing a (spatial) semidiscretization and establishing convergence. The discrete scheme allows for variants of the energy and entropy estimates in the continuous setting as long as the discrete energy does not exceed certain threshold values depending on the spatial grid size $h$. Using a stopping time argument to prolongate high-energy paths constant in time, arbitrary moments of coupled energy/entropy functionals can be controlled. Having established Hölder regularity of approximate solutions, the convergence proof is then based on compactness arguments---in particular on Jakubowski's generalization of Skorokhod's theorem---weak convergence methods, and recent tools on martingale convergence.\r\n\r\n","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"01","intvolume":" 50","publication_status":"published","file":[{"file_id":"6992","checksum":"89a8eae7c52bb356c04f52b44bff4b5a","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2018_SIAM_Fischer.pdf","date_created":"2019-11-07T12:20:25Z","file_size":557338,"date_updated":"2020-07-14T12:46:22Z","creator":"dernst"}],"language":[{"iso":"eng"}],"issue":"1","volume":50},{"day":"30","year":"2018","date_created":"2021-08-06T13:04:32Z","related_material":{"record":[{"status":"public","id":"316","relation":"used_in_publication"}]},"doi":"10.25386/genetics.6148304.v1","date_published":"2018-04-30T00:00:00Z","oa_version":"Published Version","abstract":[{"text":"File S1 contains figures that clarify the following features: (i) effect of population size on the average number/frequency of SI classes, (ii) changes in the minimal completeness deficit in time for a single class, and (iii) diversification diagrams for all studied pathways, including the summary figure for k = 8. File S2 contains the code required for a stochastic simulation of the SLF system with an example. This file also includes the output in the form of figures and tables.","lang":"eng"}],"month":"04","main_file_link":[{"open_access":"1","url":"https://doi.org/10.25386/genetics.6148304.v1"}],"oa":1,"publisher":"Genetics Society of America","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-09-11T13:57:42Z","citation":{"mla":"Bodova, Katarina, et al. Supplemental Material for Bodova et Al., 2018. Genetics Society of America, 2018, doi:10.25386/genetics.6148304.v1.","ama":"Bodova K, Priklopil T, Field D, Barton NH, Pickup M. Supplemental material for Bodova et al., 2018. 2018. doi:10.25386/genetics.6148304.v1","apa":"Bodova, K., Priklopil, T., Field, D., Barton, N. H., & Pickup, M. (2018). Supplemental material for Bodova et al., 2018. Genetics Society of America. https://doi.org/10.25386/genetics.6148304.v1","ieee":"K. Bodova, T. Priklopil, D. Field, N. H. Barton, and M. Pickup, “Supplemental material for Bodova et al., 2018.” Genetics Society of America, 2018.","short":"K. Bodova, T. Priklopil, D. Field, N.H. Barton, M. Pickup, (2018).","chicago":"Bodova, Katarina, Tadeas Priklopil, David Field, Nicholas H Barton, and Melinda Pickup. “Supplemental Material for Bodova et Al., 2018.” Genetics Society of America, 2018. https://doi.org/10.25386/genetics.6148304.v1.","ista":"Bodova K, Priklopil T, Field D, Barton NH, Pickup M. 2018. Supplemental material for Bodova et al., 2018, Genetics Society of America, 10.25386/genetics.6148304.v1."},"department":[{"_id":"NiBa"},{"_id":"GaTk"}],"title":"Supplemental material for Bodova et al., 2018","article_processing_charge":"No","author":[{"full_name":"Bod'ová, Katarína","orcid":"0000-0002-7214-0171","last_name":"Bod'ová","first_name":"Katarína","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Priklopil, Tadeas","last_name":"Priklopil","first_name":"Tadeas","id":"3C869AA0-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-4014-8478","full_name":"Field, David","last_name":"Field","first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"},{"first_name":"Melinda","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","last_name":"Pickup","full_name":"Pickup, Melinda","orcid":"0000-0001-6118-0541"}],"_id":"9813","status":"public","type":"research_data_reference"},{"type":"journal_article","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"},"status":"public","_id":"5780","department":[{"_id":"FyKo"}],"file_date_updated":"2020-07-14T12:47:11Z","date_updated":"2023-09-11T14:04:05Z","ddc":["580"],"scopus_import":"1","month":"12","intvolume":" 115","abstract":[{"lang":"eng","text":"Bioluminescence is found across the entire tree of life, conferring a spectacular set of visually oriented functions from attracting mates to scaring off predators. Half a dozen different luciferins, molecules that emit light when enzymatically oxidized, are known. However, just one biochemical pathway for luciferin biosynthesis has been described in full, which is found only in bacteria. Here, we report identification of the fungal luciferase and three other key enzymes that together form the biosynthetic cycle of the fungal luciferin from caffeic acid, a simple and widespread metabolite. Introduction of the identified genes into the genome of the yeast Pichia pastoris along with caffeic acid biosynthesis genes resulted in a strain that is autoluminescent in standard media. We analyzed evolution of the enzymes of the luciferin biosynthesis cycle and found that fungal bioluminescence emerged through a series of events that included two independent gene duplications. The retention of the duplicated enzymes of the luciferin pathway in nonluminescent fungi shows that the gene duplication was followed by functional sequence divergence of enzymes of at least one gene in the biosynthetic pathway and suggests that the evolution of fungal bioluminescence proceeded through several closely related stepping stone nonluminescent biochemical reactions with adaptive roles. The availability of a complete eukaryotic luciferin biosynthesis pathway provides several applications in biomedicine and bioengineering."}],"oa_version":"Published Version","issue":"50","volume":115,"publication_identifier":{"issn":["00278424"]},"publication_status":"published","file":[{"file_name":"2018_PNAS_Kotlobay.pdf","date_created":"2019-02-05T15:21:40Z","creator":"dernst","file_size":1271988,"date_updated":"2020-07-14T12:47:11Z","file_id":"5926","checksum":"46b2c12185eb2ddb598f4c7b4bd267bf","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"author":[{"first_name":"Alexey A.","last_name":"Kotlobay","full_name":"Kotlobay, Alexey A."},{"id":"39A7BF80-F248-11E8-B48F-1D18A9856A87","first_name":"Karen","last_name":"Sarkisyan","orcid":"0000-0002-5375-6341","full_name":"Sarkisyan, Karen"},{"last_name":"Mokrushina","full_name":"Mokrushina, Yuliana A.","first_name":"Yuliana A."},{"first_name":"Marina","full_name":"Marcet-Houben, Marina","last_name":"Marcet-Houben"},{"last_name":"Serebrovskaya","full_name":"Serebrovskaya, Ekaterina O.","first_name":"Ekaterina O."},{"last_name":"Markina","full_name":"Markina, Nadezhda M.","first_name":"Nadezhda M."},{"last_name":"Gonzalez Somermeyer","full_name":"Gonzalez Somermeyer, Louisa","orcid":"0000-0001-9139-5383","id":"4720D23C-F248-11E8-B48F-1D18A9856A87","first_name":"Louisa"},{"last_name":"Gorokhovatsky","full_name":"Gorokhovatsky, Andrey Y.","first_name":"Andrey Y."},{"first_name":"Andrey","last_name":"Vvedensky","full_name":"Vvedensky, Andrey"},{"last_name":"Purtov","full_name":"Purtov, Konstantin V.","first_name":"Konstantin V."},{"first_name":"Valentin N.","last_name":"Petushkov","full_name":"Petushkov, Valentin N."},{"full_name":"Rodionova, Natalja S.","last_name":"Rodionova","first_name":"Natalja S."},{"full_name":"Chepurnyh, Tatiana V.","last_name":"Chepurnyh","first_name":"Tatiana V."},{"full_name":"Fakhranurova, Liliia","last_name":"Fakhranurova","first_name":"Liliia"},{"first_name":"Elena B.","full_name":"Guglya, Elena B.","last_name":"Guglya"},{"first_name":"Rustam","last_name":"Ziganshin","full_name":"Ziganshin, Rustam"},{"first_name":"Aleksandra S.","full_name":"Tsarkova, Aleksandra S.","last_name":"Tsarkova"},{"full_name":"Kaskova, Zinaida M.","last_name":"Kaskova","first_name":"Zinaida M."},{"full_name":"Shender, Victoria","last_name":"Shender","first_name":"Victoria"},{"full_name":"Abakumov, Maxim","last_name":"Abakumov","first_name":"Maxim"},{"first_name":"Tatiana O.","full_name":"Abakumova, Tatiana O.","last_name":"Abakumova"},{"last_name":"Povolotskaya","full_name":"Povolotskaya, Inna S.","first_name":"Inna S."},{"last_name":"Eroshkin","full_name":"Eroshkin, Fedor M.","first_name":"Fedor M."},{"first_name":"Andrey G.","full_name":"Zaraisky, Andrey G.","last_name":"Zaraisky"},{"first_name":"Alexander S.","last_name":"Mishin","full_name":"Mishin, Alexander S."},{"last_name":"Dolgov","full_name":"Dolgov, Sergey V.","first_name":"Sergey V."},{"first_name":"Tatiana Y.","last_name":"Mitiouchkina","full_name":"Mitiouchkina, Tatiana Y."},{"first_name":"Eugene P.","last_name":"Kopantzev","full_name":"Kopantzev, Eugene P."},{"full_name":"Waldenmaier, Hans E.","last_name":"Waldenmaier","first_name":"Hans E."},{"first_name":"Anderson G.","last_name":"Oliveira","full_name":"Oliveira, Anderson G."},{"first_name":"Yuichi","full_name":"Oba, Yuichi","last_name":"Oba"},{"first_name":"Ekaterina","full_name":"Barsova, Ekaterina","last_name":"Barsova"},{"first_name":"Ekaterina A.","last_name":"Bogdanova","full_name":"Bogdanova, Ekaterina A."},{"first_name":"Toni","full_name":"Gabaldón, Toni","last_name":"Gabaldón"},{"first_name":"Cassius V.","last_name":"Stevani","full_name":"Stevani, Cassius V."},{"first_name":"Sergey","full_name":"Lukyanov, Sergey","last_name":"Lukyanov"},{"first_name":"Ivan V.","last_name":"Smirnov","full_name":"Smirnov, Ivan V."},{"first_name":"Josef I.","full_name":"Gitelson, Josef I.","last_name":"Gitelson"},{"first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor"},{"first_name":"Ilia V.","last_name":"Yampolsky","full_name":"Yampolsky, Ilia V."}],"article_processing_charge":"No","external_id":{"isi":["000452866000068"]},"title":"Genetically encodable bioluminescent system from fungi","citation":{"chicago":"Kotlobay, Alexey A., Karen Sarkisyan, Yuliana A. Mokrushina, Marina Marcet-Houben, Ekaterina O. Serebrovskaya, Nadezhda M. Markina, Louisa Gonzalez Somermeyer, et al. “Genetically Encodable Bioluminescent System from Fungi.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1803615115.","ista":"Kotlobay AA, Sarkisyan K, Mokrushina YA, Marcet-Houben M, Serebrovskaya EO, Markina NM, Gonzalez Somermeyer L, Gorokhovatsky AY, Vvedensky A, Purtov KV, Petushkov VN, Rodionova NS, Chepurnyh TV, Fakhranurova L, Guglya EB, Ziganshin R, Tsarkova AS, Kaskova ZM, Shender V, Abakumov M, Abakumova TO, Povolotskaya IS, Eroshkin FM, Zaraisky AG, Mishin AS, Dolgov SV, Mitiouchkina TY, Kopantzev EP, Waldenmaier HE, Oliveira AG, Oba Y, Barsova E, Bogdanova EA, Gabaldón T, Stevani CV, Lukyanov S, Smirnov IV, Gitelson JI, Kondrashov F, Yampolsky IV. 2018. Genetically encodable bioluminescent system from fungi. Proceedings of the National Academy of Sciences of the United States of America. 115(50), 12728–12732.","mla":"Kotlobay, Alexey A., et al. “Genetically Encodable Bioluminescent System from Fungi.” Proceedings of the National Academy of Sciences of the United States of America, vol. 115, no. 50, National Academy of Sciences, 2018, pp. 12728–32, doi:10.1073/pnas.1803615115.","apa":"Kotlobay, A. A., Sarkisyan, K., Mokrushina, Y. A., Marcet-Houben, M., Serebrovskaya, E. O., Markina, N. M., … Yampolsky, I. V. (2018). Genetically encodable bioluminescent system from fungi. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1803615115","ama":"Kotlobay AA, Sarkisyan K, Mokrushina YA, et al. Genetically encodable bioluminescent system from fungi. Proceedings of the National Academy of Sciences of the United States of America. 2018;115(50):12728-12732. doi:10.1073/pnas.1803615115","ieee":"A. A. Kotlobay et al., “Genetically encodable bioluminescent system from fungi,” Proceedings of the National Academy of Sciences of the United States of America, vol. 115, no. 50. National Academy of Sciences, pp. 12728–12732, 2018.","short":"A.A. Kotlobay, K. Sarkisyan, Y.A. Mokrushina, M. Marcet-Houben, E.O. Serebrovskaya, N.M. Markina, L. Gonzalez Somermeyer, A.Y. Gorokhovatsky, A. Vvedensky, K.V. Purtov, V.N. Petushkov, N.S. Rodionova, T.V. Chepurnyh, L. Fakhranurova, E.B. Guglya, R. Ziganshin, A.S. Tsarkova, Z.M. Kaskova, V. Shender, M. Abakumov, T.O. Abakumova, I.S. Povolotskaya, F.M. Eroshkin, A.G. Zaraisky, A.S. Mishin, S.V. Dolgov, T.Y. Mitiouchkina, E.P. Kopantzev, H.E. Waldenmaier, A.G. Oliveira, Y. Oba, E. Barsova, E.A. Bogdanova, T. Gabaldón, C.V. Stevani, S. Lukyanov, I.V. Smirnov, J.I. Gitelson, F. Kondrashov, I.V. Yampolsky, Proceedings of the National Academy of Sciences of the United States of America 115 (2018) 12728–12732."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","quality_controlled":"1","publisher":"National Academy of Sciences","oa":1,"page":"12728-12732","doi":"10.1073/pnas.1803615115","date_published":"2018-12-11T00:00:00Z","date_created":"2018-12-23T22:59:18Z","has_accepted_license":"1","isi":1,"year":"2018","day":"11","publication":"Proceedings of the National Academy of Sciences of the United States of America"},{"project":[{"grant_number":"282300","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000429012500073"]},"article_processing_charge":"No","author":[{"last_name":"Salanenka","full_name":"Salanenka, Yuliya","first_name":"Yuliya","id":"46DAAE7E-F248-11E8-B48F-1D18A9856A87"},{"id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","first_name":"Inge","orcid":"0000-0001-7241-2328","full_name":"Verstraeten, Inge","last_name":"Verstraeten"},{"full_name":"Löfke, Christian","last_name":"Löfke","first_name":"Christian"},{"last_name":"Tabata","full_name":"Tabata, Kaori","id":"7DAAEDA4-02D0-11E9-B11A-A5A4D7DFFFD0","first_name":"Kaori"},{"first_name":"Satoshi","full_name":"Naramoto, Satoshi","last_name":"Naramoto"},{"first_name":"Matous","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","last_name":"Glanc","orcid":"0000-0003-0619-7783","full_name":"Glanc, Matous"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7395","title":"Gibberellin DELLA signaling targets the retromer complex to redirect protein trafficking to the plasma membrane","citation":{"chicago":"Salanenka, Yuliya, Inge Verstraeten, Christian Löfke, Kaori Tabata, Satoshi Naramoto, Matous Glanc, and Jiří Friml. “Gibberellin DELLA Signaling Targets the Retromer Complex to Redirect Protein Trafficking to the Plasma Membrane.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1721760115.","ista":"Salanenka Y, Verstraeten I, Löfke C, Tabata K, Naramoto S, Glanc M, Friml J. 2018. Gibberellin DELLA signaling targets the retromer complex to redirect protein trafficking to the plasma membrane. PNAS. 115(14), 3716–3721.","mla":"Salanenka, Yuliya, et al. “Gibberellin DELLA Signaling Targets the Retromer Complex to Redirect Protein Trafficking to the Plasma Membrane.” PNAS, vol. 115, no. 14, National Academy of Sciences, 2018, pp. 3716–21, doi:10.1073/pnas.1721760115.","apa":"Salanenka, Y., Verstraeten, I., Löfke, C., Tabata, K., Naramoto, S., Glanc, M., & Friml, J. (2018). Gibberellin DELLA signaling targets the retromer complex to redirect protein trafficking to the plasma membrane. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1721760115","ama":"Salanenka Y, Verstraeten I, Löfke C, et al. Gibberellin DELLA signaling targets the retromer complex to redirect protein trafficking to the plasma membrane. PNAS. 2018;115(14):3716-3721. doi:10.1073/pnas.1721760115","ieee":"Y. Salanenka et al., “Gibberellin DELLA signaling targets the retromer complex to redirect protein trafficking to the plasma membrane,” PNAS, vol. 115, no. 14. National Academy of Sciences, pp. 3716–3721, 2018.","short":"Y. Salanenka, I. Verstraeten, C. Löfke, K. Tabata, S. Naramoto, M. Glanc, J. Friml, PNAS 115 (2018) 3716–3721."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"quality_controlled":"1","publisher":"National Academy of Sciences","acknowledgement":"We gratefully acknowledge M. Blázquez (Instituto de Biología Molecular y Celular de Plantas), M. Fendrych, C. Cuesta Moliner (Institute of Science and Technology Austria), M. Vanstraelen, M. Nowack (Center for Plant Systems Biology, Ghent), C. Luschnig (Universitat fur Bodenkultur Wien, Vienna), S. Simon (Central European Institute of Technology, Brno), C. Sommerville (Carnegie Institution for Science), and Y. Gu (Penn State University) for making available the materials used in this study;\r\n...funding from the European Research Council (ERC) under the European Union’s Seventh Framework Programme (FP7/2007-2013)/ERC Grant Agreement 282300.\r\nCC BY NC ND","page":" 3716 - 3721","date_created":"2018-12-11T11:46:25Z","date_published":"2018-04-03T00:00:00Z","doi":"10.1073/pnas.1721760115","year":"2018","isi":1,"has_accepted_license":"1","publication":"PNAS","day":"03","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"type":"journal_article","status":"public","_id":"428","department":[{"_id":"JiFr"}],"file_date_updated":"2020-07-14T12:46:26Z","date_updated":"2023-09-11T14:06:34Z","ddc":["580"],"scopus_import":"1","intvolume":" 115","month":"04","abstract":[{"text":"The plant hormone gibberellic acid (GA) is a crucial regulator of growth and development. The main paradigm of GA signaling puts forward transcriptional regulation via the degradation of DELLA transcriptional repressors. GA has also been shown to regulate tropic responses by modulation of the plasma membrane incidence of PIN auxin transporters by an unclear mechanism. Here we uncovered the cellular and molecular mechanisms by which GA redirects protein trafficking and thus regulates cell surface functionality. Photoconvertible reporters revealed that GA balances the protein traffic between the vacuole degradation route and recycling back to the cell surface. Low GA levels promote vacuolar delivery and degradation of multiple cargos, including PIN proteins, whereas high GA levels promote their recycling to the plasma membrane. This GA effect requires components of the retromer complex, such as Sorting Nexin 1 (SNX1) and its interacting, microtubule (MT)-associated protein, the Cytoplasmic Linker-Associated Protein (CLASP1). Accordingly, GA regulates the subcellular distribution of SNX1 and CLASP1, and the intact MT cytoskeleton is essential for the GA effect on trafficking. This GA cellular action occurs through DELLA proteins that regulate the MT and retromer presumably via their interaction partners Prefoldins (PFDs). Our study identified a branching of the GA signaling pathway at the level of DELLA proteins, which, in parallel to regulating transcription, also target by a nontranscriptional mechanism the retromer complex acting at the intersection of the degradation and recycling trafficking routes. By this mechanism, GA can redirect receptors and transporters to the cell surface, thus coregulating multiple processes, including PIN-dependent auxin fluxes during tropic responses.","lang":"eng"}],"oa_version":"Published Version","ec_funded":1,"issue":"14","volume":115,"publication_status":"published","language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"1fcf7223fb8f99559cfa80bd6f24ce44","file_id":"5700","creator":"dernst","date_updated":"2020-07-14T12:46:26Z","file_size":1924101,"date_created":"2018-12-17T12:30:14Z","file_name":"2018_PNAS_Salanenka.pdf"}]},{"file_date_updated":"2020-07-14T12:47:24Z","department":[{"_id":"MaJö"}],"date_updated":"2023-09-11T14:02:55Z","ddc":["570"],"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)"},"article_type":"original","type":"journal_article","status":"public","_id":"62","issue":"1","volume":8,"related_material":{"link":[{"relation":"erratum","url":"http://doi.org/10.1038/s41598-018-36220-7"}]},"publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_size":4141645,"date_updated":"2020-07-14T12:47:24Z","creator":"dernst","file_name":"2018_ScientificReports_Shahbazi.pdf","date_created":"2018-12-17T12:22:24Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5699","checksum":"1a14ae0666b82fbaa04bef110e3f6bf2"}],"scopus_import":"1","intvolume":" 8","month":"09","abstract":[{"text":"Imaging is a dominant strategy for data collection in neuroscience, yielding stacks of images that often scale to gigabytes of data for a single experiment. Machine learning algorithms from computer vision can serve as a pair of virtual eyes that tirelessly processes these images, automatically detecting and identifying microstructures. Unlike learning methods, our Flexible Learning-free Reconstruction of Imaged Neural volumes (FLoRIN) pipeline exploits structure-specific contextual clues and requires no training. This approach generalizes across different modalities, including serially-sectioned scanning electron microscopy (sSEM) of genetically labeled and contrast enhanced processes, spectral confocal reflectance (SCoRe) microscopy, and high-energy synchrotron X-ray microtomography (μCT) of large tissue volumes. We deploy the FLoRIN pipeline on newly published and novel mouse datasets, demonstrating the high biological fidelity of the pipeline’s reconstructions. FLoRIN reconstructions are of sufficient quality for preliminary biological study, for example examining the distribution and morphology of cells or extracting single axons from functional data. Compared to existing supervised learning methods, FLoRIN is one to two orders of magnitude faster and produces high-quality reconstructions that are tolerant to noise and artifacts, as is shown qualitatively and quantitatively.","lang":"eng"}],"oa_version":"Published Version","article_processing_charge":"No","external_id":{"isi":["000445336600015"]},"publist_id":"7992","author":[{"first_name":"Ali","last_name":"Shabazi","full_name":"Shabazi, Ali"},{"first_name":"Jeffery","last_name":"Kinnison","full_name":"Kinnison, Jeffery"},{"first_name":"Rafael","full_name":"Vescovi, Rafael","last_name":"Vescovi"},{"last_name":"Du","full_name":"Du, Ming","first_name":"Ming"},{"first_name":"Robert","last_name":"Hill","full_name":"Hill, Robert"},{"orcid":"0000-0002-3937-1330","full_name":"Jösch, Maximilian A","last_name":"Jösch","first_name":"Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Takeno","full_name":"Takeno, Marc","first_name":"Marc"},{"first_name":"Hongkui","last_name":"Zeng","full_name":"Zeng, Hongkui"},{"full_name":"Da Costa, Nuno","last_name":"Da Costa","first_name":"Nuno"},{"last_name":"Grutzendler","full_name":"Grutzendler, Jaime","first_name":"Jaime"},{"full_name":"Kasthuri, Narayanan","last_name":"Kasthuri","first_name":"Narayanan"},{"full_name":"Scheirer, Walter","last_name":"Scheirer","first_name":"Walter"}],"title":"Flexible learning-free segmentation and reconstruction of neural volumes","citation":{"chicago":"Shabazi, Ali, Jeffery Kinnison, Rafael Vescovi, Ming Du, Robert Hill, Maximilian A Jösch, Marc Takeno, et al. “Flexible Learning-Free Segmentation and Reconstruction of Neural Volumes.” Scientific Reports. Nature Publishing Group, 2018. https://doi.org/10.1038/s41598-018-32628-3.","ista":"Shabazi A, Kinnison J, Vescovi R, Du M, Hill R, Jösch MA, Takeno M, Zeng H, Da Costa N, Grutzendler J, Kasthuri N, Scheirer W. 2018. Flexible learning-free segmentation and reconstruction of neural volumes. Scientific Reports. 8(1), 14247.","mla":"Shabazi, Ali, et al. “Flexible Learning-Free Segmentation and Reconstruction of Neural Volumes.” Scientific Reports, vol. 8, no. 1, 14247, Nature Publishing Group, 2018, doi:10.1038/s41598-018-32628-3.","apa":"Shabazi, A., Kinnison, J., Vescovi, R., Du, M., Hill, R., Jösch, M. A., … Scheirer, W. (2018). Flexible learning-free segmentation and reconstruction of neural volumes. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/s41598-018-32628-3","ama":"Shabazi A, Kinnison J, Vescovi R, et al. Flexible learning-free segmentation and reconstruction of neural volumes. Scientific Reports. 2018;8(1). doi:10.1038/s41598-018-32628-3","short":"A. Shabazi, J. Kinnison, R. Vescovi, M. Du, R. Hill, M.A. Jösch, M. Takeno, H. Zeng, N. Da Costa, J. Grutzendler, N. Kasthuri, W. Scheirer, Scientific Reports 8 (2018).","ieee":"A. Shabazi et al., “Flexible learning-free segmentation and reconstruction of neural volumes,” Scientific Reports, vol. 8, no. 1. Nature Publishing Group, 2018."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_number":"14247","date_created":"2018-12-11T11:44:25Z","doi":"10.1038/s41598-018-32628-3","date_published":"2018-09-24T00:00:00Z","year":"2018","isi":1,"has_accepted_license":"1","publication":"Scientific Reports","day":"24","oa":1,"quality_controlled":"1","publisher":"Nature Publishing Group","acknowledgement":"Equipment was generously donated by the NVIDIA Corporation, and made available by the National Science Foundation (NSF) through grant #CNS-1629914. This research used resources of the Argonne Leadership Computing Facility, which is a DOE Office of Science User Facility supported under Contract DE-AC02-06CH11357."},{"day":"13","publication":"European Journal of Immunology","isi":1,"has_accepted_license":"1","year":"2018","doi":"10.1002/eji.201747358","date_published":"2018-02-13T00:00:00Z","date_created":"2018-12-11T11:46:28Z","page":"1074 - 1077","acknowledgement":"This work was supported by grants of the European Research Council (ERC CoG 724373) and the Austrian Science Fund (FWF) to M.S. We thank the scientific support units at IST Austria for excellent technical support.\r\nWe thank the scientific support units at IST Austria for excellent technical support. ","publisher":"Wiley-Blackwell","quality_controlled":"1","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Leithner, Alexander F, Jörg Renkawitz, Ingrid de Vries, Robert Hauschild, Hans Haecker, and Michael K Sixt. “Fast and Efficient Genetic Engineering of Hematopoietic Precursor Cells for the Study of Dendritic Cell Migration.” European Journal of Immunology. Wiley-Blackwell, 2018. https://doi.org/10.1002/eji.201747358.","ista":"Leithner AF, Renkawitz J, de Vries I, Hauschild R, Haecker H, Sixt MK. 2018. Fast and efficient genetic engineering of hematopoietic precursor cells for the study of dendritic cell migration. European Journal of Immunology. 48(6), 1074–1077.","mla":"Leithner, Alexander F., et al. “Fast and Efficient Genetic Engineering of Hematopoietic Precursor Cells for the Study of Dendritic Cell Migration.” European Journal of Immunology, vol. 48, no. 6, Wiley-Blackwell, 2018, pp. 1074–77, doi:10.1002/eji.201747358.","short":"A.F. Leithner, J. Renkawitz, I. de Vries, R. Hauschild, H. Haecker, M.K. Sixt, European Journal of Immunology 48 (2018) 1074–1077.","ieee":"A. F. Leithner, J. Renkawitz, I. de Vries, R. Hauschild, H. Haecker, and M. K. Sixt, “Fast and efficient genetic engineering of hematopoietic precursor cells for the study of dendritic cell migration,” European Journal of Immunology, vol. 48, no. 6. Wiley-Blackwell, pp. 1074–1077, 2018.","apa":"Leithner, A. F., Renkawitz, J., de Vries, I., Hauschild, R., Haecker, H., & Sixt, M. K. (2018). Fast and efficient genetic engineering of hematopoietic precursor cells for the study of dendritic cell migration. European Journal of Immunology. Wiley-Blackwell. https://doi.org/10.1002/eji.201747358","ama":"Leithner AF, Renkawitz J, de Vries I, Hauschild R, Haecker H, Sixt MK. Fast and efficient genetic engineering of hematopoietic precursor cells for the study of dendritic cell migration. European Journal of Immunology. 2018;48(6):1074-1077. doi:10.1002/eji.201747358"},"title":"Fast and efficient genetic engineering of hematopoietic precursor cells for the study of dendritic cell migration","publist_id":"7386","author":[{"first_name":"Alexander F","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","full_name":"Leithner, Alexander F","orcid":"0000-0002-1073-744X","last_name":"Leithner"},{"last_name":"Renkawitz","orcid":"0000-0003-2856-3369","full_name":"Renkawitz, Jörg","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","first_name":"Jörg"},{"last_name":"De Vries","full_name":"De Vries, Ingrid","first_name":"Ingrid","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hauschild","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Hans","full_name":"Haecker, Hans","last_name":"Haecker"},{"last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K"}],"external_id":{"isi":["000434963700016"]},"article_processing_charge":"Yes (via OA deal)","project":[{"name":"Cellular navigation along spatial gradients","grant_number":"724373","call_identifier":"H2020","_id":"25FE9508-B435-11E9-9278-68D0E5697425"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5044","checksum":"9d5b74cd016505aeb9a4c2d33bbedaeb","file_size":590106,"date_updated":"2020-07-14T12:46:27Z","creator":"system","file_name":"IST-2018-1067-v1+2_Leithner_et_al-2018-European_Journal_of_Immunology.pdf","date_created":"2018-12-12T10:13:56Z"}],"language":[{"iso":"eng"}],"publication_status":"published","issue":"6","volume":48,"ec_funded":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Dendritic cells (DCs) are sentinels of the adaptive immune system that reside in peripheral organs of mammals. Upon pathogen encounter, they undergo maturation and up-regulate the chemokine receptor CCR7 that guides them along gradients of its chemokine ligands CCL19 and 21 to the next draining lymph node. There, DCs present peripherally acquired antigen to naïve T cells, thereby triggering adaptive immunity."}],"acknowledged_ssus":[{"_id":"SSU"}],"month":"02","intvolume":" 48","scopus_import":"1","ddc":["570"],"date_updated":"2023-09-11T14:01:18Z","department":[{"_id":"MiSi"},{"_id":"Bio"}],"file_date_updated":"2020-07-14T12:46:27Z","_id":"437","status":"public","pubrep_id":"1067","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"}},{"date_created":"2018-12-11T11:47:31Z","date_published":"2018-01-01T00:00:00Z","doi":"10.1111/jeb.13211","page":"159 - 171","publication":"Journal of Evolutionary Biology","day":"01","year":"2018","isi":1,"oa":1,"quality_controlled":"1","publisher":"Wiley","acknowledgement":"We would like to thank Susann Wicke for performing the genome-wide SNP/indel analyses, as well as Veronica Alves, Kevin Ferro, Momir Futo, Barbara Hasert, Dafne Maximo, Nora Schulz, Marlene Sroka, and Barth Wieczorek for technical help. We thank Brian Lazzaro for the L. lactis strain and Bruno Lemaitre for the Pseudomonas entomophila strain. We would like to thank two anonymous reviewers for their helpful comments. We are grateful to the Deutsche Forschungsgemeinschaft (DFG) priority programme 1399 ‘Host parasite coevolution’ for funding this project (AR 872/1-1). ","title":"Genotype and diet affect resistance, survival, and fecundity but not fecundity tolerance","external_id":{"pmid":["29150962"],"isi":["000419307000014"]},"article_processing_charge":"No","author":[{"id":"29D0B332-F248-11E8-B48F-1D18A9856A87","first_name":"Megan","last_name":"Kutzer","orcid":"0000-0002-8696-6978","full_name":"Kutzer, Megan"},{"last_name":"Kurtz","full_name":"Kurtz, Joachim","first_name":"Joachim"},{"last_name":"Armitage","full_name":"Armitage, Sophie","first_name":"Sophie"}],"publist_id":"7187","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"short":"M. Kutzer, J. Kurtz, S. Armitage, Journal of Evolutionary Biology 31 (2018) 159–171.","ieee":"M. Kutzer, J. Kurtz, and S. Armitage, “Genotype and diet affect resistance, survival, and fecundity but not fecundity tolerance,” Journal of Evolutionary Biology, vol. 31, no. 1. Wiley, pp. 159–171, 2018.","ama":"Kutzer M, Kurtz J, Armitage S. Genotype and diet affect resistance, survival, and fecundity but not fecundity tolerance. Journal of Evolutionary Biology. 2018;31(1):159-171. doi:10.1111/jeb.13211","apa":"Kutzer, M., Kurtz, J., & Armitage, S. (2018). Genotype and diet affect resistance, survival, and fecundity but not fecundity tolerance. Journal of Evolutionary Biology. Wiley. https://doi.org/10.1111/jeb.13211","mla":"Kutzer, Megan, et al. “Genotype and Diet Affect Resistance, Survival, and Fecundity but Not Fecundity Tolerance.” Journal of Evolutionary Biology, vol. 31, no. 1, Wiley, 2018, pp. 159–71, doi:10.1111/jeb.13211.","ista":"Kutzer M, Kurtz J, Armitage S. 2018. Genotype and diet affect resistance, survival, and fecundity but not fecundity tolerance. Journal of Evolutionary Biology. 31(1), 159–171.","chicago":"Kutzer, Megan, Joachim Kurtz, and Sophie Armitage. “Genotype and Diet Affect Resistance, Survival, and Fecundity but Not Fecundity Tolerance.” Journal of Evolutionary Biology. Wiley, 2018. https://doi.org/10.1111/jeb.13211."},"volume":31,"issue":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1420-9101"],"issn":["1010-061X"]},"intvolume":" 31","month":"01","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/jeb.13211"}],"scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Insects are exposed to a variety of potential pathogens in their environment, many of which can severely impact fitness and health. Consequently, hosts have evolved resistance and tolerance strategies to suppress or cope with infections. Hosts utilizing resistance improve fitness by clearing or reducing pathogen loads, and hosts utilizing tolerance reduce harmful fitness effects per pathogen load. To understand variation in, and selective pressures on, resistance and tolerance, we asked to what degree they are shaped by host genetic background, whether plasticity in these responses depends upon dietary environment, and whether there are interactions between these two factors. Females from ten wild-type Drosophila melanogaster genotypes were kept on high- or low-protein (yeast) diets and infected with one of two opportunistic bacterial pathogens, Lactococcus lactis or Pseudomonas entomophila. We measured host resistance as the inverse of bacterial load in the early infection phase. The relationship (slope) between fly fecundity and individual-level bacteria load provided our fecundity tolerance measure. Genotype and dietary yeast determined host fecundity and strongly affected survival after infection with pathogenic P. entomophila. There was considerable genetic variation in host resistance, a commonly found phenomenon resulting from for example varying resistance costs or frequency-dependent selection. Despite this variation and the reproductive cost of higher P. entomophila loads, fecundity tolerance did not vary across genotypes. The absence of genetic variation in tolerance may suggest that at this early infection stage, fecundity tolerance is fixed or that any evolved tolerance mechanisms are not expressed under these infection conditions."}],"department":[{"_id":"SyCr"}],"date_updated":"2023-09-11T14:06:04Z","status":"public","article_type":"original","type":"journal_article","_id":"617"},{"has_accepted_license":"1","isi":1,"year":"2018","day":"07","publication":"Experimental & Molecular Medicine","doi":"10.1038/s12276-018-0129-7","date_published":"2018-08-07T00:00:00Z","date_created":"2019-01-27T22:59:11Z","quality_controlled":"1","publisher":"Springer Nature","oa":1,"citation":{"chicago":"Tarlungeanu, Dora-Clara, and Gaia Novarino. “Genomics in Neurodevelopmental Disorders: An Avenue to Personalized Medicine.” Experimental & Molecular Medicine. Springer Nature, 2018. https://doi.org/10.1038/s12276-018-0129-7.","ista":"Tarlungeanu D-C, Novarino G. 2018. Genomics in neurodevelopmental disorders: an avenue to personalized medicine. Experimental & Molecular Medicine. 50(8), 100.","mla":"Tarlungeanu, Dora-Clara, and Gaia Novarino. “Genomics in Neurodevelopmental Disorders: An Avenue to Personalized Medicine.” Experimental & Molecular Medicine, vol. 50, no. 8, 100, Springer Nature, 2018, doi:10.1038/s12276-018-0129-7.","ama":"Tarlungeanu D-C, Novarino G. Genomics in neurodevelopmental disorders: an avenue to personalized medicine. Experimental & Molecular Medicine. 2018;50(8). doi:10.1038/s12276-018-0129-7","apa":"Tarlungeanu, D.-C., & Novarino, G. (2018). Genomics in neurodevelopmental disorders: an avenue to personalized medicine. Experimental & Molecular Medicine. Springer Nature. https://doi.org/10.1038/s12276-018-0129-7","ieee":"D.-C. Tarlungeanu and G. Novarino, “Genomics in neurodevelopmental disorders: an avenue to personalized medicine,” Experimental & Molecular Medicine, vol. 50, no. 8. Springer Nature, 2018.","short":"D.-C. Tarlungeanu, G. Novarino, Experimental & Molecular Medicine 50 (2018)."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Dora-Clara","id":"2ABCE612-F248-11E8-B48F-1D18A9856A87","full_name":"Tarlungeanu, Dora-Clara","last_name":"Tarlungeanu"},{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","last_name":"Novarino","full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178"}],"article_processing_charge":"No","external_id":{"pmid":["30089840"],"isi":["000441266700006"]},"title":"Genomics in neurodevelopmental disorders: an avenue to personalized medicine","article_number":"100","publication_identifier":{"issn":["2092-6413"]},"publication_status":"published","file":[{"file_size":1237482,"date_updated":"2020-07-14T12:47:13Z","creator":"dernst","file_name":"2018_EMM_Tarlungeanu.pdf","date_created":"2019-01-28T15:18:02Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5893","checksum":"4498301c8c53097c9a1a8ef990936eb5"}],"language":[{"iso":"eng"}],"volume":50,"issue":"8","abstract":[{"text":"Despite the remarkable number of scientific breakthroughs of the last 100 years, the treatment of neurodevelopmental\r\ndisorders (e.g., autism spectrum disorder, intellectual disability) remains a great challenge. Recent advancements in\r\ngenomics, such as whole-exome or whole-genome sequencing, have enabled scientists to identify numerous\r\nmutations underlying neurodevelopmental disorders. Given the few hundred risk genes that have been discovered,\r\nthe etiological variability and the heterogeneous clinical presentation, the need for genotype — along with phenotype-\r\nbased diagnosis of individual patients has become a requisite. In this review we look at recent advancements in\r\ngenomic analysis and their translation into clinical practice.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","month":"08","intvolume":" 50","date_updated":"2023-09-11T14:04:41Z","ddc":["570"],"department":[{"_id":"GaNo"}],"file_date_updated":"2020-07-14T12:47:13Z","_id":"5888","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public"},{"ddc":["510"],"date_updated":"2023-09-11T14:01:57Z","file_date_updated":"2020-07-14T12:45:55Z","department":[{"_id":"RoSe"}],"_id":"295","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":[{"file_name":"2018_LettMathPhys_Lundholm.pdf","date_created":"2018-12-17T12:14:17Z","file_size":551996,"date_updated":"2020-07-14T12:45:55Z","creator":"dernst","file_id":"5698","checksum":"8beb9632fa41bbd19452f55f31286a31","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"publication_status":"published","issue":"11","volume":108,"ec_funded":1,"oa_version":"Published Version","abstract":[{"text":"We prove upper and lower bounds on the ground-state energy of the ideal two-dimensional anyon gas. Our bounds are extensive in the particle number, as for fermions, and linear in the statistics parameter (Formula presented.). The lower bounds extend to Lieb–Thirring inequalities for all anyons except bosons.","lang":"eng"}],"month":"05","intvolume":" 108","scopus_import":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Lundholm, Douglas, and Robert Seiringer. “Fermionic Behavior of Ideal Anyons.” Letters in Mathematical Physics. Springer, 2018. https://doi.org/10.1007/s11005-018-1091-y.","ista":"Lundholm D, Seiringer R. 2018. Fermionic behavior of ideal anyons. Letters in Mathematical Physics. 108(11), 2523–2541.","mla":"Lundholm, Douglas, and Robert Seiringer. “Fermionic Behavior of Ideal Anyons.” Letters in Mathematical Physics, vol. 108, no. 11, Springer, 2018, pp. 2523–41, doi:10.1007/s11005-018-1091-y.","ieee":"D. Lundholm and R. Seiringer, “Fermionic behavior of ideal anyons,” Letters in Mathematical Physics, vol. 108, no. 11. Springer, pp. 2523–2541, 2018.","short":"D. Lundholm, R. Seiringer, Letters in Mathematical Physics 108 (2018) 2523–2541.","ama":"Lundholm D, Seiringer R. Fermionic behavior of ideal anyons. Letters in Mathematical Physics. 2018;108(11):2523-2541. doi:10.1007/s11005-018-1091-y","apa":"Lundholm, D., & Seiringer, R. (2018). Fermionic behavior of ideal anyons. Letters in Mathematical Physics. Springer. https://doi.org/10.1007/s11005-018-1091-y"},"title":"Fermionic behavior of ideal anyons","author":[{"last_name":"Lundholm","full_name":"Lundholm, Douglas","first_name":"Douglas"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","last_name":"Seiringer"}],"publist_id":"7586","external_id":{"isi":["000446491500008"],"arxiv":["1712.06218"]},"article_processing_charge":"No","project":[{"grant_number":"694227","name":"Analysis of quantum many-body systems","call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"25C878CE-B435-11E9-9278-68D0E5697425","grant_number":"P27533_N27","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems"}],"day":"11","publication":"Letters in Mathematical Physics","isi":1,"has_accepted_license":"1","year":"2018","date_published":"2018-05-11T00:00:00Z","doi":"10.1007/s11005-018-1091-y","date_created":"2018-12-11T11:45:40Z","page":"2523-2541","acknowledgement":"Financial support from the Swedish Research Council, grant no. 2013-4734 (D. L.), the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 694227, R. S.), and by the Austrian Science Fund (FWF), project Nr. P 27533-N27 (R. S.), is gratefully acknowledged.","quality_controlled":"1","publisher":"Springer","oa":1},{"publication":"Current Opinion in Structural Biology","day":"01","year":"2018","isi":1,"date_created":"2018-12-11T11:47:09Z","doi":"10.1016/j.sbi.2017.12.002","date_published":"2018-06-01T00:00:00Z","page":"65 - 74","acknowledgement":"This work was supported by the European Research Council [Starting Grant 306435 ‘JELLY’; to RPR], the Spanish Ministry of Competitiveness and Innovation [MAT2014-54867-R, to RPR], the EPSRC Centre for Doctoral Training in Tissue Engineering and Regenerative Medicine — Innovation in Medical and Biological Engineering [EP/L014823/1, to JCFK], the Royal Society [RG160410, to JCFK], Wings for Life [WFL-UK-008/15, to JCFK] and the European Union, the Operational Programme Research, Development and Education in the framework of the project ‘Centre of Reconstructive Neuroscience’ [CZ.02.1.01/0.0./0.0/15_003/0000419, to JCFK]. AJD would like to thank Arthritis Research UK [16539, 19489] and the MRC [76445, G0900538] for funding his work on GAG–protein interactions.\r\n","oa":1,"quality_controlled":"1","publisher":"Elsevier","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Richter, Ralf, Natalia S. Baranova, Anthony Day, and Jessica Kwok. “Glycosaminoglycans in Extracellular Matrix Organisation: Are Concepts from Soft Matter Physics Key to Understanding the Formation of Perineuronal Nets?” Current Opinion in Structural Biology. Elsevier, 2018. https://doi.org/10.1016/j.sbi.2017.12.002.","ista":"Richter R, Baranova NS, Day A, Kwok J. 2018. Glycosaminoglycans in extracellular matrix organisation: Are concepts from soft matter physics key to understanding the formation of perineuronal nets? Current Opinion in Structural Biology. 50, 65–74.","mla":"Richter, Ralf, et al. “Glycosaminoglycans in Extracellular Matrix Organisation: Are Concepts from Soft Matter Physics Key to Understanding the Formation of Perineuronal Nets?” Current Opinion in Structural Biology, vol. 50, Elsevier, 2018, pp. 65–74, doi:10.1016/j.sbi.2017.12.002.","short":"R. Richter, N.S. Baranova, A. Day, J. Kwok, Current Opinion in Structural Biology 50 (2018) 65–74.","ieee":"R. Richter, N. S. Baranova, A. Day, and J. Kwok, “Glycosaminoglycans in extracellular matrix organisation: Are concepts from soft matter physics key to understanding the formation of perineuronal nets?,” Current Opinion in Structural Biology, vol. 50. Elsevier, pp. 65–74, 2018.","ama":"Richter R, Baranova NS, Day A, Kwok J. Glycosaminoglycans in extracellular matrix organisation: Are concepts from soft matter physics key to understanding the formation of perineuronal nets? Current Opinion in Structural Biology. 2018;50:65-74. doi:10.1016/j.sbi.2017.12.002","apa":"Richter, R., Baranova, N. S., Day, A., & Kwok, J. (2018). Glycosaminoglycans in extracellular matrix organisation: Are concepts from soft matter physics key to understanding the formation of perineuronal nets? Current Opinion in Structural Biology. Elsevier. https://doi.org/10.1016/j.sbi.2017.12.002"},"title":"Glycosaminoglycans in extracellular matrix organisation: Are concepts from soft matter physics key to understanding the formation of perineuronal nets?","external_id":{"isi":["000443661300011"]},"article_processing_charge":"No","author":[{"first_name":"Ralf","last_name":"Richter","full_name":"Richter, Ralf"},{"orcid":"0000-0002-3086-9124","full_name":"Baranova, Natalia","last_name":"Baranova","first_name":"Natalia","id":"38661662-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Anthony","full_name":"Day, Anthony","last_name":"Day"},{"first_name":"Jessica","last_name":"Kwok","full_name":"Kwok, Jessica"}],"publist_id":"7259","language":[{"iso":"eng"}],"publication_status":"published","volume":50,"oa_version":"Submitted Version","abstract":[{"text":"Conventional wisdom has it that proteins fold and assemble into definite structures, and that this defines their function. Glycosaminoglycans (GAGs) are different. In most cases the structures they form have a low degree of order, even when interacting with proteins. Here, we discuss how physical features common to all GAGs — hydrophilicity, charge, linearity and semi-flexibility — underpin the overall properties of GAG-rich matrices. By integrating soft matter physics concepts (e.g. polymer brushes and phase separation) with our molecular understanding of GAG–protein interactions, we can better comprehend how GAG-rich matrices assemble, what their properties are, and how they function. Taking perineuronal nets (PNNs) — a GAG-rich matrix enveloping neurons — as a relevant example, we propose that microphase separation determines the holey PNN anatomy that is pivotal to PNN functions.","lang":"eng"}],"intvolume":" 50","month":"06","main_file_link":[{"url":"http://eprints.whiterose.ac.uk/125524/","open_access":"1"}],"scopus_import":"1","date_updated":"2023-09-11T14:07:03Z","department":[{"_id":"MaLo"}],"_id":"555","status":"public","article_type":"original","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)"},"type":"journal_article","pubrep_id":"969","status":"public","_id":"448","file_date_updated":"2020-07-14T12:46:30Z","department":[{"_id":"BeVi"}],"date_updated":"2023-09-11T14:10:57Z","ddc":["576"],"scopus_import":"1","intvolume":" 2","month":"02","abstract":[{"lang":"eng","text":"Around 150 million years ago, eusocial termites evolved from within the cockroaches, 50 million years before eusocial Hymenoptera, such as bees and ants, appeared. Here, we report the 2-Gb genome of the German cockroach, Blattella germanica, and the 1.3-Gb genome of the drywood termite Cryptotermes secundus. We show evolutionary signatures of termite eusociality by comparing the genomes and transcriptomes of three termites and the cockroach against the background of 16 other eusocial and non-eusocial insects. Dramatic adaptive changes in genes underlying the production and perception of pheromones confirm the importance of chemical communication in the termites. These are accompanied by major changes in gene regulation and the molecular evolution of caste determination. Many of these results parallel molecular mechanisms of eusocial evolution in Hymenoptera. However, the specific solutions are remarkably different, thus revealing a striking case of convergence in one of the major evolutionary transitions in biological complexity."}],"oa_version":"Published Version","related_material":{"record":[{"relation":"research_data","status":"public","id":"9841"}]},"issue":"3","volume":2,"publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_name":"IST-2018-969-v1+1_2018_Huylmans_Hemimetabolous_genomes.pdf","date_created":"2018-12-12T10:09:08Z","creator":"system","file_size":3730583,"date_updated":"2020-07-14T12:46:30Z","file_id":"4731","checksum":"874953136ac125e65f37971d3cabc5b7","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"article_processing_charge":"No","external_id":{"isi":["000426559600026"]},"publist_id":"7375","author":[{"last_name":"Harrison","full_name":"Harrison, Mark","first_name":"Mark"},{"first_name":"Evelien","last_name":"Jongepier","full_name":"Jongepier, Evelien"},{"full_name":"Robertson, Hugh","last_name":"Robertson","first_name":"Hugh"},{"first_name":"Nicolas","last_name":"Arning","full_name":"Arning, Nicolas"},{"first_name":"Tristan","last_name":"Bitard Feildel","full_name":"Bitard Feildel, Tristan"},{"full_name":"Chao, Hsu","last_name":"Chao","first_name":"Hsu"},{"last_name":"Childers","full_name":"Childers, Christopher","first_name":"Christopher"},{"last_name":"Dinh","full_name":"Dinh, Huyen","first_name":"Huyen"},{"first_name":"Harshavardhan","full_name":"Doddapaneni, Harshavardhan","last_name":"Doddapaneni"},{"first_name":"Shannon","full_name":"Dugan, Shannon","last_name":"Dugan"},{"full_name":"Gowin, Johannes","last_name":"Gowin","first_name":"Johannes"},{"last_name":"Greiner","full_name":"Greiner, Carolin","first_name":"Carolin"},{"last_name":"Han","full_name":"Han, Yi","first_name":"Yi"},{"first_name":"Haofu","full_name":"Hu, Haofu","last_name":"Hu"},{"last_name":"Hughes","full_name":"Hughes, Daniel","first_name":"Daniel"},{"full_name":"Huylmans, Ann K","orcid":"0000-0001-8871-4961","last_name":"Huylmans","first_name":"Ann K","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kemena, Karsten","last_name":"Kemena","first_name":"Karsten"},{"full_name":"Kremer, Lukas","last_name":"Kremer","first_name":"Lukas"},{"full_name":"Lee, Sandra","last_name":"Lee","first_name":"Sandra"},{"full_name":"López Ezquerra, Alberto","last_name":"López Ezquerra","first_name":"Alberto"},{"last_name":"Mallet","full_name":"Mallet, Ludovic","first_name":"Ludovic"},{"full_name":"Monroy Kuhn, Jose","last_name":"Monroy Kuhn","first_name":"Jose"},{"full_name":"Moser, Annabell","last_name":"Moser","first_name":"Annabell"},{"first_name":"Shwetha","last_name":"Murali","full_name":"Murali, Shwetha"},{"first_name":"Donna","full_name":"Muzny, Donna","last_name":"Muzny"},{"first_name":"Saria","full_name":"Otani, Saria","last_name":"Otani"},{"first_name":"Maria","full_name":"Piulachs, Maria","last_name":"Piulachs"},{"first_name":"Monica","full_name":"Poelchau, Monica","last_name":"Poelchau"},{"full_name":"Qu, Jiaxin","last_name":"Qu","first_name":"Jiaxin"},{"first_name":"Florentine","last_name":"Schaub","full_name":"Schaub, Florentine"},{"full_name":"Wada Katsumata, Ayako","last_name":"Wada Katsumata","first_name":"Ayako"},{"first_name":"Kim","full_name":"Worley, Kim","last_name":"Worley"},{"first_name":"Qiaolin","full_name":"Xie, Qiaolin","last_name":"Xie"},{"first_name":"Guillem","last_name":"Ylla","full_name":"Ylla, Guillem"},{"first_name":"Michael","full_name":"Poulsen, Michael","last_name":"Poulsen"},{"first_name":"Richard","full_name":"Gibbs, Richard","last_name":"Gibbs"},{"first_name":"Coby","full_name":"Schal, Coby","last_name":"Schal"},{"first_name":"Stephen","full_name":"Richards, Stephen","last_name":"Richards"},{"full_name":"Belles, Xavier","last_name":"Belles","first_name":"Xavier"},{"first_name":"Judith","full_name":"Korb, Judith","last_name":"Korb"},{"last_name":"Bornberg Bauer","full_name":"Bornberg Bauer, Erich","first_name":"Erich"}],"title":"Hemimetabolous genomes reveal molecular basis of termite eusociality","citation":{"mla":"Harrison, Mark, et al. “Hemimetabolous Genomes Reveal Molecular Basis of Termite Eusociality.” Nature Ecology and Evolution, vol. 2, no. 3, Springer Nature, 2018, pp. 557–66, doi:10.1038/s41559-017-0459-1.","ieee":"M. Harrison et al., “Hemimetabolous genomes reveal molecular basis of termite eusociality,” Nature Ecology and Evolution, vol. 2, no. 3. Springer Nature, pp. 557–566, 2018.","short":"M. Harrison, E. Jongepier, H. Robertson, N. Arning, T. Bitard Feildel, H. Chao, C. Childers, H. Dinh, H. Doddapaneni, S. Dugan, J. Gowin, C. Greiner, Y. Han, H. Hu, D. Hughes, A.K. Huylmans, K. Kemena, L. Kremer, S. Lee, A. López Ezquerra, L. Mallet, J. Monroy Kuhn, A. Moser, S. Murali, D. Muzny, S. Otani, M. Piulachs, M. Poelchau, J. Qu, F. Schaub, A. Wada Katsumata, K. Worley, Q. Xie, G. Ylla, M. Poulsen, R. Gibbs, C. Schal, S. Richards, X. Belles, J. Korb, E. Bornberg Bauer, Nature Ecology and Evolution 2 (2018) 557–566.","apa":"Harrison, M., Jongepier, E., Robertson, H., Arning, N., Bitard Feildel, T., Chao, H., … Bornberg Bauer, E. (2018). Hemimetabolous genomes reveal molecular basis of termite eusociality. Nature Ecology and Evolution. Springer Nature. https://doi.org/10.1038/s41559-017-0459-1","ama":"Harrison M, Jongepier E, Robertson H, et al. Hemimetabolous genomes reveal molecular basis of termite eusociality. Nature Ecology and Evolution. 2018;2(3):557-566. doi:10.1038/s41559-017-0459-1","chicago":"Harrison, Mark, Evelien Jongepier, Hugh Robertson, Nicolas Arning, Tristan Bitard Feildel, Hsu Chao, Christopher Childers, et al. “Hemimetabolous Genomes Reveal Molecular Basis of Termite Eusociality.” Nature Ecology and Evolution. Springer Nature, 2018. https://doi.org/10.1038/s41559-017-0459-1.","ista":"Harrison M, Jongepier E, Robertson H, Arning N, Bitard Feildel T, Chao H, Childers C, Dinh H, Doddapaneni H, Dugan S, Gowin J, Greiner C, Han Y, Hu H, Hughes D, Huylmans AK, Kemena K, Kremer L, Lee S, López Ezquerra A, Mallet L, Monroy Kuhn J, Moser A, Murali S, Muzny D, Otani S, Piulachs M, Poelchau M, Qu J, Schaub F, Wada Katsumata A, Worley K, Xie Q, Ylla G, Poulsen M, Gibbs R, Schal C, Richards S, Belles X, Korb J, Bornberg Bauer E. 2018. Hemimetabolous genomes reveal molecular basis of termite eusociality. Nature Ecology and Evolution. 2(3), 557–566."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"publisher":"Springer Nature","quality_controlled":"1","acknowledgement":"We thank O. Niehuis for allowing use of the unpublished E. danica genome, J. Gadau and C. Smith for comments and advice on the manuscript, and J. Schmitz for assistance with analyses and proofreading the manuscript. J.K. thanks Charles Darwin University (Australia), especially S. Garnett and the Horticulture and Aquaculture team, for providing logistic support to collect C. secundus. The Parks and Wildlife Commission, Northern Territory, the Department of the Environment, Water, Heritage and the Arts gave permission to collect (Permit number 36401) and export (Permit WT2010-6997) the termites. USDA is an equal opportunity provider and employer. M.C.H. and E.J. are supported by DFG grant BO2544/11-1 to E.B.-B. J.K. is supported by University of Osnabrück and DFG grant KO1895/16-1. X.B. and M.-D.P. are supported by Spanish Ministerio de Economía y Competitividad (CGL2012-36251 and CGL2015-64727-P to X.B., and CGL2016-76011-R to M.-D.P.), including FEDER funds, and by Catalan Government (2014 SGR 619). C.S. is supported by grants from the US Department of Housing and Urban Development (NCHHU-0017-13), the National Science Foundation (IOS-1557864), the Alfred P. Sloan Foundation (2013-5-35 MBE), the National Institute of Environmental Health Sciences (P30ES025128) to the Center for Human Health and the Environment, and the Blanton J. Whitmire Endowment. M.P. is supported by a Villum Kann Rasmussen Young Investigator Fellowship (VKR10101).","page":"557-566","date_created":"2018-12-11T11:46:32Z","doi":"10.1038/s41559-017-0459-1","date_published":"2018-02-05T00:00:00Z","year":"2018","isi":1,"has_accepted_license":"1","publication":"Nature Ecology and Evolution","day":"05"},{"oa_version":"Published Version","abstract":[{"text":"Escaping local optima is one of the major obstacles to function optimisation. Using the metaphor of a fitness landscape, local optima correspond to hills separated by fitness valleys that have to be overcome. We define a class of fitness valleys of tunable difficulty by considering their length, representing the Hamming path between the two optima and their depth, the drop in fitness. For this function class we present a runtime comparison between stochastic search algorithms using different search strategies. The (1+1) EA is a simple and well-studied evolutionary algorithm that has to jump across the valley to a point of higher fitness because it does not accept worsening moves (elitism). In contrast, the Metropolis algorithm and the Strong Selection Weak Mutation (SSWM) algorithm, a famous process in population genetics, are both able to cross the fitness valley by accepting worsening moves. We show that the runtime of the (1+1) EA depends critically on the length of the valley while the runtimes of the non-elitist algorithms depend crucially on the depth of the valley. Moreover, we show that both SSWM and Metropolis can also efficiently optimise a rugged function consisting of consecutive valleys.","lang":"eng"}],"month":"05","intvolume":" 80","scopus_import":"1","file":[{"date_updated":"2020-07-14T12:47:54Z","file_size":691245,"creator":"system","date_created":"2018-12-12T10:08:14Z","file_name":"IST-2018-1014-v1+1_2018_Paixao_Escape.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"4674","checksum":"7d92f5d7be81e387edeec4f06442791c"}],"language":[{"iso":"eng"}],"publication_status":"published","issue":"5","volume":80,"ec_funded":1,"_id":"723","status":"public","pubrep_id":"1014","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)"},"ddc":["576"],"date_updated":"2023-09-11T14:11:35Z","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"file_date_updated":"2020-07-14T12:47:54Z","quality_controlled":"1","publisher":"Springer","oa":1,"day":"01","publication":"Algorithmica","isi":1,"has_accepted_license":"1","year":"2018","doi":"10.1007/s00453-017-0369-2","date_published":"2018-05-01T00:00:00Z","date_created":"2018-12-11T11:48:09Z","page":"1604 - 1633","project":[{"_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","grant_number":"618091"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Oliveto, Pietro, Tiago Paixao, Jorge Pérez Heredia, Dirk Sudholt, and Barbora Trubenova. “How to Escape Local Optima in Black Box Optimisation When Non Elitism Outperforms Elitism.” Algorithmica. Springer, 2018. https://doi.org/10.1007/s00453-017-0369-2.","ista":"Oliveto P, Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. 2018. How to escape local optima in black box optimisation when non elitism outperforms elitism. Algorithmica. 80(5), 1604–1633.","mla":"Oliveto, Pietro, et al. “How to Escape Local Optima in Black Box Optimisation When Non Elitism Outperforms Elitism.” Algorithmica, vol. 80, no. 5, Springer, 2018, pp. 1604–33, doi:10.1007/s00453-017-0369-2.","ama":"Oliveto P, Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. How to escape local optima in black box optimisation when non elitism outperforms elitism. Algorithmica. 2018;80(5):1604-1633. doi:10.1007/s00453-017-0369-2","apa":"Oliveto, P., Paixao, T., Pérez Heredia, J., Sudholt, D., & Trubenova, B. (2018). How to escape local optima in black box optimisation when non elitism outperforms elitism. Algorithmica. Springer. https://doi.org/10.1007/s00453-017-0369-2","ieee":"P. Oliveto, T. Paixao, J. Pérez Heredia, D. Sudholt, and B. Trubenova, “How to escape local optima in black box optimisation when non elitism outperforms elitism,” Algorithmica, vol. 80, no. 5. Springer, pp. 1604–1633, 2018.","short":"P. Oliveto, T. Paixao, J. Pérez Heredia, D. Sudholt, B. Trubenova, Algorithmica 80 (2018) 1604–1633."},"title":"How to escape local optima in black box optimisation when non elitism outperforms elitism","publist_id":"6957","author":[{"first_name":"Pietro","full_name":"Oliveto, Pietro","last_name":"Oliveto"},{"orcid":"0000-0003-2361-3953","full_name":"Paixao, Tiago","last_name":"Paixao","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","first_name":"Tiago"},{"last_name":"Pérez Heredia","full_name":"Pérez Heredia, Jorge","first_name":"Jorge"},{"full_name":"Sudholt, Dirk","last_name":"Sudholt","first_name":"Dirk"},{"first_name":"Barbora","id":"42302D54-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6873-2967","full_name":"Trubenova, Barbora","last_name":"Trubenova"}],"article_processing_charge":"No","external_id":{"isi":["000428239300010"]}},{"page":"1029 - 1031","doi":"10.1109/TPAMI.2018.2804998","date_published":"2018-05-01T00:00:00Z","date_created":"2018-12-11T11:45:48Z","has_accepted_license":"1","isi":1,"year":"2018","day":"01","publication":"IEEE Transactions on Pattern Analysis and Machine Intelligence","quality_controlled":"1","publisher":"IEEE","oa":1,"author":[{"full_name":"Darrell, Trevor","last_name":"Darrell","first_name":"Trevor"},{"last_name":"Lampert","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sebe, Nico","last_name":"Sebe","first_name":"Nico"},{"first_name":"Ying","last_name":"Wu","full_name":"Wu, Ying"},{"first_name":"Yan","last_name":"Yan","full_name":"Yan, Yan"}],"publist_id":"7544","article_processing_charge":"No","external_id":{"isi":["000428901200001"]},"title":"Guest editors' introduction to the special section on learning with Shared information for computer vision and multimedia analysis","citation":{"mla":"Darrell, Trevor, et al. “Guest Editors’ Introduction to the Special Section on Learning with Shared Information for Computer Vision and Multimedia Analysis.” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 40, no. 5, IEEE, 2018, pp. 1029–31, doi:10.1109/TPAMI.2018.2804998.","ieee":"T. Darrell, C. Lampert, N. Sebe, Y. Wu, and Y. Yan, “Guest editors’ introduction to the special section on learning with Shared information for computer vision and multimedia analysis,” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 40, no. 5. IEEE, pp. 1029–1031, 2018.","short":"T. Darrell, C. Lampert, N. Sebe, Y. Wu, Y. Yan, IEEE Transactions on Pattern Analysis and Machine Intelligence 40 (2018) 1029–1031.","ama":"Darrell T, Lampert C, Sebe N, Wu Y, Yan Y. Guest editors’ introduction to the special section on learning with Shared information for computer vision and multimedia analysis. IEEE Transactions on Pattern Analysis and Machine Intelligence. 2018;40(5):1029-1031. doi:10.1109/TPAMI.2018.2804998","apa":"Darrell, T., Lampert, C., Sebe, N., Wu, Y., & Yan, Y. (2018). Guest editors’ introduction to the special section on learning with Shared information for computer vision and multimedia analysis. IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE. https://doi.org/10.1109/TPAMI.2018.2804998","chicago":"Darrell, Trevor, Christoph Lampert, Nico Sebe, Ying Wu, and Yan Yan. “Guest Editors’ Introduction to the Special Section on Learning with Shared Information for Computer Vision and Multimedia Analysis.” IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE, 2018. https://doi.org/10.1109/TPAMI.2018.2804998.","ista":"Darrell T, Lampert C, Sebe N, Wu Y, Yan Y. 2018. Guest editors’ introduction to the special section on learning with Shared information for computer vision and multimedia analysis. IEEE Transactions on Pattern Analysis and Machine Intelligence. 40(5), 1029–1031."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":40,"issue":"5","publication_status":"published","file":[{"date_created":"2020-05-14T12:50:48Z","file_name":"2018_IEEE_Darrell.pdf","creator":"dernst","date_updated":"2020-07-14T12:46:03Z","file_size":141724,"file_id":"7835","checksum":"b19c75da06faf3291a3ca47dfa50ef63","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"05","intvolume":" 40","abstract":[{"lang":"eng","text":"The twelve papers in this special section focus on learning systems with shared information for computer vision and multimedia communication analysis. In the real world, a realistic setting for computer vision or multimedia recognition problems is that we have some classes containing lots of training data and many classes containing a small amount of training data. Therefore, how to use frequent classes to help learning rare classes for which it is harder to collect the training data is an open question. Learning with shared information is an emerging topic in machine learning, computer vision and multimedia analysis. There are different levels of components that can be shared during concept modeling and machine learning stages, such as sharing generic object parts, sharing attributes, sharing transformations, sharing regularization parameters and sharing training examples, etc. Regarding the specific methods, multi-task learning, transfer learning and deep learning can be seen as using different strategies to share information. These learning with shared information methods are very effective in solving real-world large-scale problems."}],"oa_version":"Published Version","file_date_updated":"2020-07-14T12:46:03Z","department":[{"_id":"ChLa"}],"date_updated":"2023-09-11T14:07:54Z","ddc":["000"],"article_type":"original","type":"journal_article","status":"public","_id":"321"},{"year":"2018","day":"12","related_material":{"record":[{"relation":"used_in_publication","id":"448","status":"public"}]},"date_published":"2018-12-12T00:00:00Z","doi":"10.5061/dryad.51d4r","date_created":"2021-08-09T13:13:48Z","abstract":[{"lang":"eng","text":"Around 150 million years ago, eusocial termites evolved from within the cockroaches, 50 million years before eusocial Hymenoptera, such as bees and ants, appeared. Here, we report the 2-Gb genome of the German cockroach, Blattella germanica, and the 1.3-Gb genome of the drywood termite Cryptotermes secundus. We show evolutionary signatures of termite eusociality by comparing the genomes and transcriptomes of three termites and the cockroach against the background of 16 other eusocial and non-eusocial insects. Dramatic adaptive changes in genes underlying the production and perception of pheromones confirm the importance of chemical communication in the termites. These are accompanied by major changes in gene regulation and the molecular evolution of caste determination. Many of these results parallel molecular mechanisms of eusocial evolution in Hymenoptera. However, the specific solutions are remarkably different, thus revealing a striking case of convergence in one of the major evolutionary transitions in biological complexity."}],"oa_version":"Published Version","publisher":"Dryad","main_file_link":[{"url":"https://doi.org/10.5061/dryad.51d4r","open_access":"1"}],"oa":1,"month":"12","date_updated":"2023-09-11T14:10:56Z","citation":{"ista":"Harrison MC, Jongepier E, Robertson HM, Arning N, Bitard-Feildel T, Chao H, Childers CP, Dinh H, Doddapaneni H, Dugan S, Gowin J, Greiner C, Han Y, Hu H, Hughes DST, Huylmans AK, Kemena C, Kremer LPM, Lee SL, Lopez-Ezquerra A, Mallet L, Monroy-Kuhn JM, Moser A, Murali SC, Muzny DM, Otani S, Piulachs M-D, Poelchau M, Qu J, Schaub F, Wada-Katsumata A, Worley KC, Xie Q, Ylla G, Poulsen M, Gibbs RA, Schal C, Richards S, Belles X, Korb J, Bornberg-Bauer E. 2018. Data from: Hemimetabolous genomes reveal molecular basis of termite eusociality, Dryad, 10.5061/dryad.51d4r.","chicago":"Harrison, Mark C., Evelien Jongepier, Hugh M. Robertson, Nicolas Arning, Tristan Bitard-Feildel, Hsu Chao, Christopher P. Childers, et al. “Data from: Hemimetabolous Genomes Reveal Molecular Basis of Termite Eusociality.” Dryad, 2018. https://doi.org/10.5061/dryad.51d4r.","short":"M.C. Harrison, E. Jongepier, H.M. Robertson, N. Arning, T. Bitard-Feildel, H. Chao, C.P. Childers, H. Dinh, H. Doddapaneni, S. Dugan, J. Gowin, C. Greiner, Y. Han, H. Hu, D.S.T. Hughes, A.K. Huylmans, C. Kemena, L.P.M. Kremer, S.L. Lee, A. Lopez-Ezquerra, L. Mallet, J.M. Monroy-Kuhn, A. Moser, S.C. Murali, D.M. Muzny, S. Otani, M.-D. Piulachs, M. Poelchau, J. Qu, F. Schaub, A. Wada-Katsumata, K.C. Worley, Q. Xie, G. Ylla, M. Poulsen, R.A. Gibbs, C. Schal, S. Richards, X. Belles, J. Korb, E. Bornberg-Bauer, (2018).","ieee":"M. C. Harrison et al., “Data from: Hemimetabolous genomes reveal molecular basis of termite eusociality.” Dryad, 2018.","ama":"Harrison MC, Jongepier E, Robertson HM, et al. Data from: Hemimetabolous genomes reveal molecular basis of termite eusociality. 2018. doi:10.5061/dryad.51d4r","apa":"Harrison, M. C., Jongepier, E., Robertson, H. M., Arning, N., Bitard-Feildel, T., Chao, H., … Bornberg-Bauer, E. (2018). Data from: Hemimetabolous genomes reveal molecular basis of termite eusociality. Dryad. https://doi.org/10.5061/dryad.51d4r","mla":"Harrison, Mark C., et al. Data from: Hemimetabolous Genomes Reveal Molecular Basis of Termite Eusociality. Dryad, 2018, doi:10.5061/dryad.51d4r."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"full_name":"Harrison, Mark C.","last_name":"Harrison","first_name":"Mark C."},{"first_name":"Evelien","last_name":"Jongepier","full_name":"Jongepier, Evelien"},{"first_name":"Hugh M.","last_name":"Robertson","full_name":"Robertson, Hugh M."},{"first_name":"Nicolas","last_name":"Arning","full_name":"Arning, Nicolas"},{"last_name":"Bitard-Feildel","full_name":"Bitard-Feildel, Tristan","first_name":"Tristan"},{"first_name":"Hsu","last_name":"Chao","full_name":"Chao, Hsu"},{"last_name":"Childers","full_name":"Childers, Christopher P.","first_name":"Christopher P."},{"first_name":"Huyen","last_name":"Dinh","full_name":"Dinh, Huyen"},{"first_name":"Harshavardhan","last_name":"Doddapaneni","full_name":"Doddapaneni, Harshavardhan"},{"last_name":"Dugan","full_name":"Dugan, Shannon","first_name":"Shannon"},{"last_name":"Gowin","full_name":"Gowin, Johannes","first_name":"Johannes"},{"first_name":"Carolin","last_name":"Greiner","full_name":"Greiner, Carolin"},{"first_name":"Yi","last_name":"Han","full_name":"Han, Yi"},{"full_name":"Hu, Haofu","last_name":"Hu","first_name":"Haofu"},{"first_name":"Daniel S. T.","last_name":"Hughes","full_name":"Hughes, Daniel S. T."},{"last_name":"Huylmans","orcid":"0000-0001-8871-4961","full_name":"Huylmans, Ann K","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","first_name":"Ann K"},{"last_name":"Kemena","full_name":"Kemena, Carsten","first_name":"Carsten"},{"last_name":"Kremer","full_name":"Kremer, Lukas P. M.","first_name":"Lukas P. M."},{"first_name":"Sandra L.","last_name":"Lee","full_name":"Lee, Sandra L."},{"last_name":"Lopez-Ezquerra","full_name":"Lopez-Ezquerra, Alberto","first_name":"Alberto"},{"first_name":"Ludovic","full_name":"Mallet, Ludovic","last_name":"Mallet"},{"first_name":"Jose M.","full_name":"Monroy-Kuhn, Jose M.","last_name":"Monroy-Kuhn"},{"first_name":"Annabell","last_name":"Moser","full_name":"Moser, Annabell"},{"first_name":"Shwetha C.","last_name":"Murali","full_name":"Murali, Shwetha C."},{"first_name":"Donna M.","last_name":"Muzny","full_name":"Muzny, Donna M."},{"last_name":"Otani","full_name":"Otani, Saria","first_name":"Saria"},{"first_name":"Maria-Dolors","last_name":"Piulachs","full_name":"Piulachs, Maria-Dolors"},{"last_name":"Poelchau","full_name":"Poelchau, Monica","first_name":"Monica"},{"first_name":"Jiaxin","full_name":"Qu, Jiaxin","last_name":"Qu"},{"first_name":"Florentine","full_name":"Schaub, Florentine","last_name":"Schaub"},{"last_name":"Wada-Katsumata","full_name":"Wada-Katsumata, Ayako","first_name":"Ayako"},{"first_name":"Kim C.","full_name":"Worley, Kim C.","last_name":"Worley"},{"last_name":"Xie","full_name":"Xie, Qiaolin","first_name":"Qiaolin"},{"last_name":"Ylla","full_name":"Ylla, Guillem","first_name":"Guillem"},{"first_name":"Michael","last_name":"Poulsen","full_name":"Poulsen, Michael"},{"first_name":"Richard A.","full_name":"Gibbs, Richard A.","last_name":"Gibbs"},{"first_name":"Coby","last_name":"Schal","full_name":"Schal, Coby"},{"last_name":"Richards","full_name":"Richards, Stephen","first_name":"Stephen"},{"first_name":"Xavier","full_name":"Belles, Xavier","last_name":"Belles"},{"first_name":"Judith","full_name":"Korb, Judith","last_name":"Korb"},{"full_name":"Bornberg-Bauer, Erich","last_name":"Bornberg-Bauer","first_name":"Erich"}],"article_processing_charge":"No","department":[{"_id":"BeVi"}],"title":"Data from: Hemimetabolous genomes reveal molecular basis of termite eusociality","_id":"9841","type":"research_data_reference","status":"public"},{"year":"2018","isi":1,"day":"10","page":"14 - 27","date_created":"2018-12-11T11:46:14Z","date_published":"2018-02-10T00:00:00Z","doi":"10.1145/3178487.3178489","quality_controlled":"1","publisher":"ACM","citation":{"ista":"Arbel Raviv M, Brown TA. 2018. Harnessing epoch-based reclamation for efficient range queries. PPoPP: Principles and Practice of Parallel Programming, PPoPP, vol. 53, 14–27.","chicago":"Arbel Raviv, Maya, and Trevor A Brown. “Harnessing Epoch-Based Reclamation for Efficient Range Queries,” 53:14–27. ACM, 2018. https://doi.org/10.1145/3178487.3178489.","ieee":"M. Arbel Raviv and T. A. Brown, “Harnessing epoch-based reclamation for efficient range queries,” presented at the PPoPP: Principles and Practice of Parallel Programming, Vienna, Austria, 2018, vol. 53, no. 1, pp. 14–27.","short":"M. Arbel Raviv, T.A. Brown, in:, ACM, 2018, pp. 14–27.","apa":"Arbel Raviv, M., & Brown, T. A. (2018). Harnessing epoch-based reclamation for efficient range queries (Vol. 53, pp. 14–27). Presented at the PPoPP: Principles and Practice of Parallel Programming, Vienna, Austria: ACM. https://doi.org/10.1145/3178487.3178489","ama":"Arbel Raviv M, Brown TA. Harnessing epoch-based reclamation for efficient range queries. In: Vol 53. ACM; 2018:14-27. doi:10.1145/3178487.3178489","mla":"Arbel Raviv, Maya, and Trevor A. Brown. Harnessing Epoch-Based Reclamation for Efficient Range Queries. Vol. 53, no. 1, ACM, 2018, pp. 14–27, doi:10.1145/3178487.3178489."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000446161100002"]},"article_processing_charge":"No","publist_id":"7430","author":[{"first_name":"Maya","full_name":"Arbel Raviv, Maya","last_name":"Arbel Raviv"},{"first_name":"Trevor A","id":"3569F0A0-F248-11E8-B48F-1D18A9856A87","full_name":"Brown, Trevor A","last_name":"Brown"}],"title":"Harnessing epoch-based reclamation for efficient range queries","publication_status":"published","publication_identifier":{"isbn":["978-1-4503-4982-6"]},"language":[{"iso":"eng"}],"issue":"1","volume":53,"abstract":[{"text":"Concurrent sets with range query operations are highly desirable in applications such as in-memory databases. However, few set implementations offer range queries. Known techniques for augmenting data structures with range queries (or operations that can be used to build range queries) have numerous problems that limit their usefulness. For example, they impose high overhead or rely heavily on garbage collection. In this work, we show how to augment data structures with highly efficient range queries, without relying on garbage collection. We identify a property of epoch-based memory reclamation algorithms that makes them ideal for implementing range queries, and produce three algorithms, which use locks, transactional memory and lock-free techniques, respectively. Our algorithms are applicable to more data structures than previous work, and are shown to be highly efficient on a large scale Intel system. ","lang":"eng"}],"oa_version":"None","alternative_title":["PPoPP"],"scopus_import":"1","intvolume":" 53","month":"02","date_updated":"2023-09-11T14:10:25Z","department":[{"_id":"DaAl"}],"_id":"397","conference":{"location":"Vienna, Austria","end_date":"2018-02-28","start_date":"2018-02-24","name":"PPoPP: Principles and Practice of Parallel Programming"},"type":"conference","status":"public"},{"status":"public","type":"journal_article","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":"32","department":[{"_id":"SaSi"}],"file_date_updated":"2020-07-14T12:46:03Z","ddc":["570"],"date_updated":"2023-09-11T14:13:32Z","month":"10","intvolume":" 25","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"The functional role of AMPA receptor (AMPAR)-mediated synaptic signaling between neurons and oligodendrocyte precursor cells (OPCs) remains enigmatic. We modified the properties of AMPARs at axon-OPC synapses in the mouse corpus callosum in vivo during the peak of myelination by targeting the GluA2 subunit. Expression of the unedited (Ca2+ permeable) or the pore-dead GluA2 subunit of AMPARs triggered proliferation of OPCs and reduced their differentiation into oligodendrocytes. Expression of the cytoplasmic C-terminal (GluA2(813-862)) of the GluA2 subunit (C-tail), a modification designed to affect the interaction between GluA2 and AMPAR-binding proteins and to perturb trafficking of GluA2-containing AMPARs, decreased the differentiation of OPCs without affecting their proliferation. These findings suggest that ionotropic and non-ionotropic properties of AMPARs in OPCs, as well as specific aspects of AMPAR-mediated signaling at axon-OPC synapses in the mouse corpus callosum, are important for balancing the response of OPCs to proliferation and differentiation cues. In the brain, oligodendrocyte precursor cells (OPCs) receive glutamatergic AMPA-receptor-mediated synaptic input from neurons. Chen et al. show that modifying AMPA-receptor properties at axon-OPC synapses alters proliferation and differentiation of OPCs. This expands the traditional view of synaptic transmission by suggesting neurons also use synapses to modulate behavior of glia."}],"issue":"4","volume":25,"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"5703","checksum":"d9f74277fd57176e04732707d575cf08","creator":"dernst","file_size":4461997,"date_updated":"2020-07-14T12:46:03Z","file_name":"2018_CellReports_Chen.pdf","date_created":"2018-12-17T12:42:57Z"}],"language":[{"iso":"eng"}],"publication_status":"published","title":"In Vivo regulation of Oligodendrocyte processor cell proliferation and differentiation by the AMPA-receptor Subunit GluA2","author":[{"full_name":"Chen, Ting","last_name":"Chen","first_name":"Ting"},{"first_name":"Bartosz","last_name":"Kula","full_name":"Kula, Bartosz"},{"orcid":"0000-0002-4002-4686","full_name":"Nagy, Balint","last_name":"Nagy","id":"30F830CE-02D1-11E9-9BAA-DAF4881429F2","first_name":"Balint"},{"first_name":"Ruxandra","full_name":"Barzan, Ruxandra","last_name":"Barzan"},{"first_name":"Andrea","full_name":"Gall, Andrea","last_name":"Gall"},{"full_name":"Ehrlich, Ingrid","last_name":"Ehrlich","first_name":"Ingrid"},{"first_name":"Maria","full_name":"Kukley, Maria","last_name":"Kukley"}],"publist_id":"8023","external_id":{"isi":["000448219500005"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Chen, Ting, et al. “In Vivo Regulation of Oligodendrocyte Processor Cell Proliferation and Differentiation by the AMPA-Receptor Subunit GluA2.” Cell Reports, vol. 25, no. 4, Elsevier, 2018, p. 852–861.e7, doi:10.1016/j.celrep.2018.09.066.","short":"T. Chen, B. Kula, B. Nagy, R. Barzan, A. Gall, I. Ehrlich, M. Kukley, Cell Reports 25 (2018) 852–861.e7.","ieee":"T. Chen et al., “In Vivo regulation of Oligodendrocyte processor cell proliferation and differentiation by the AMPA-receptor Subunit GluA2,” Cell Reports, vol. 25, no. 4. Elsevier, p. 852–861.e7, 2018.","apa":"Chen, T., Kula, B., Nagy, B., Barzan, R., Gall, A., Ehrlich, I., & Kukley, M. (2018). In Vivo regulation of Oligodendrocyte processor cell proliferation and differentiation by the AMPA-receptor Subunit GluA2. Cell Reports. Elsevier. https://doi.org/10.1016/j.celrep.2018.09.066","ama":"Chen T, Kula B, Nagy B, et al. In Vivo regulation of Oligodendrocyte processor cell proliferation and differentiation by the AMPA-receptor Subunit GluA2. Cell Reports. 2018;25(4):852-861.e7. doi:10.1016/j.celrep.2018.09.066","chicago":"Chen, Ting, Bartosz Kula, Balint Nagy, Ruxandra Barzan, Andrea Gall, Ingrid Ehrlich, and Maria Kukley. “In Vivo Regulation of Oligodendrocyte Processor Cell Proliferation and Differentiation by the AMPA-Receptor Subunit GluA2.” Cell Reports. Elsevier, 2018. https://doi.org/10.1016/j.celrep.2018.09.066.","ista":"Chen T, Kula B, Nagy B, Barzan R, Gall A, Ehrlich I, Kukley M. 2018. In Vivo regulation of Oligodendrocyte processor cell proliferation and differentiation by the AMPA-receptor Subunit GluA2. Cell Reports. 25(4), 852–861.e7."},"quality_controlled":"1","publisher":"Elsevier","oa":1,"acknowledgement":"This work was supported by Deutsche Forschungsgemeinschaft (DFG) grant KU2569/1-1 (to M.K.); DFG project EXC307Centre for Integrative Neuroscience (CIN), including grant Pool Project 2011-12 (jointly to M.K. and I.E.); and the Charitable Hertie Foundation (to I.E.). CIN is an Excellence Cluster funded by the DFG within the framework of the Excellence Initiative for 2008–2018. M.K. is supported by the Tistou & Charlotte Kerstan Foundation.","date_published":"2018-10-23T00:00:00Z","doi":"10.1016/j.celrep.2018.09.066","date_created":"2018-12-11T11:44:16Z","page":"852 - 861.e7","day":"23","publication":"Cell Reports","isi":1,"has_accepted_license":"1","year":"2018"},{"date_updated":"2023-09-11T14:12:06Z","ddc":["570"],"department":[{"_id":"MiSi"}],"file_date_updated":"2020-07-14T12:47:09Z","_id":"5672","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"type":"journal_article","status":"public","publication_status":"published","publication_identifier":{"issn":["00221007"]},"language":[{"iso":"eng"}],"file":[{"file_name":"2018_JournalExperMed_Reversat.pdf","date_created":"2019-02-06T08:49:52Z","creator":"dernst","file_size":1216437,"date_updated":"2020-07-14T12:47:09Z","file_id":"5931","checksum":"687beea1d64c213f4cb9e3c29ec11a14","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"issue":"12","volume":215,"abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 215","month":"11","citation":{"short":"A. Reversat, M.K. Sixt, Journal of Experimental Medicine 215 (2018) 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","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.","ista":"Reversat A, Sixt MK. 2018. IgM’s exit route. Journal of Experimental Medicine. 215(12), 2959–2961.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"isi":["000451920600002"]},"author":[{"id":"35B76592-F248-11E8-B48F-1D18A9856A87","first_name":"Anne","full_name":"Reversat, Anne","orcid":"0000-0003-0666-8928","last_name":"Reversat"},{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K"}],"title":"IgM's exit route","year":"2018","isi":1,"has_accepted_license":"1","publication":"Journal of Experimental Medicine","day":"20","page":"2959-2961","date_created":"2018-12-16T22:59:18Z","date_published":"2018-11-20T00:00:00Z","doi":"10.1084/jem.20181934","oa":1,"publisher":"Rockefeller University Press","quality_controlled":"1"},{"quality_controlled":"1","publisher":"Elsevier","scopus_import":"1","intvolume":" 13","month":"05","abstract":[{"text":"Objective: To report long-term results after Pipeline Embolization Device (PED) implantation, characterize complex and standard aneurysms comprehensively, and introduce a modified flow disruption scale. Methods: We retrospectively reviewed a consecutive series of 40 patients harboring 59 aneurysms treated with 54 PEDs. Aneurysm complexity was assessed using our proposed classification. Immediate angiographic results were analyzed using previously published grading scales and our novel flow disruption scale. Results: According to our new definition, 46 (78%) aneurysms were classified as complex. Most PED interventions were performed in the paraophthalmic and cavernous internal carotid artery segments. Excellent neurologic outcome (modified Rankin Scale 0 and 1) was observed in 94% of patients. Our data showed low permanent procedure-related mortality (0%) and morbidity (3%) rates. Long-term angiographic follow-up showed complete occlusion in 81% and near-total obliteration in a further 14%. Complete obliteration after deployment of a single PED was achieved in all standard aneurysms with 1-year follow-up. Our new scale was an independent predictor of aneurysm occlusion in a multivariable analysis. All aneurysms with a high flow disruption grade showed complete occlusion at follow-up regardless of PED number or aneurysm complexity. Conclusions: Treatment with the PED should be recognized as a primary management strategy for a highly selected cohort with predominantly complex intracranial aneurysms. We further show that a priori assessment of aneurysm complexity and our new postinterventional angiographic flow disruption scale predict occlusion probability and may help to determine the adequate number of per-aneurysm devices.","lang":"eng"}],"oa_version":"None","page":"e568-e578","date_created":"2018-12-11T11:46:15Z","date_published":"2018-05-01T00:00:00Z","doi":"10.1016/j.wneu.2018.02.096","volume":13,"publication_status":"published","year":"2018","isi":1,"language":[{"iso":"eng"}],"publication":"World Neurosurgery","day":"01","type":"journal_article","status":"public","_id":"398","external_id":{"isi":["000432942700070"]},"article_processing_charge":"No","author":[{"full_name":"Dodier, Philippe","last_name":"Dodier","first_name":"Philippe"},{"first_name":"Josa","full_name":"Frischer, Josa","last_name":"Frischer"},{"last_name":"Wang","full_name":"Wang, Wei","first_name":"Wei"},{"id":"4718F954-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","full_name":"Auzinger, Thomas","orcid":"0000-0002-1546-3265","last_name":"Auzinger"},{"last_name":"Mallouhi","full_name":"Mallouhi, Ammar","first_name":"Ammar"},{"first_name":"Wolfgang","full_name":"Serles, Wolfgang","last_name":"Serles"},{"first_name":"Andreas","last_name":"Gruber","full_name":"Gruber, Andreas"},{"last_name":"Knosp","full_name":"Knosp, Engelbert","first_name":"Engelbert"},{"full_name":"Bavinzski, Gerhard","last_name":"Bavinzski","first_name":"Gerhard"}],"publist_id":"7431","title":"Immediate flow disruption as a prognostic factor after flow diverter treatment long term experience with the pipeline embolization device","department":[{"_id":"BeBi"}],"citation":{"mla":"Dodier, Philippe, et al. “Immediate Flow Disruption as a Prognostic Factor after Flow Diverter Treatment Long Term Experience with the Pipeline Embolization Device.” World Neurosurgery, vol. 13, Elsevier, 2018, pp. e568–78, doi:10.1016/j.wneu.2018.02.096.","ieee":"P. Dodier et al., “Immediate flow disruption as a prognostic factor after flow diverter treatment long term experience with the pipeline embolization device,” World Neurosurgery, vol. 13. Elsevier, pp. e568–e578, 2018.","short":"P. Dodier, J. Frischer, W. Wang, T. Auzinger, A. Mallouhi, W. Serles, A. Gruber, E. Knosp, G. Bavinzski, World Neurosurgery 13 (2018) e568–e578.","apa":"Dodier, P., Frischer, J., Wang, W., Auzinger, T., Mallouhi, A., Serles, W., … Bavinzski, G. (2018). Immediate flow disruption as a prognostic factor after flow diverter treatment long term experience with the pipeline embolization device. World Neurosurgery. Elsevier. https://doi.org/10.1016/j.wneu.2018.02.096","ama":"Dodier P, Frischer J, Wang W, et al. Immediate flow disruption as a prognostic factor after flow diverter treatment long term experience with the pipeline embolization device. World Neurosurgery. 2018;13:e568-e578. doi:10.1016/j.wneu.2018.02.096","chicago":"Dodier, Philippe, Josa Frischer, Wei Wang, Thomas Auzinger, Ammar Mallouhi, Wolfgang Serles, Andreas Gruber, Engelbert Knosp, and Gerhard Bavinzski. “Immediate Flow Disruption as a Prognostic Factor after Flow Diverter Treatment Long Term Experience with the Pipeline Embolization Device.” World Neurosurgery. Elsevier, 2018. https://doi.org/10.1016/j.wneu.2018.02.096.","ista":"Dodier P, Frischer J, Wang W, Auzinger T, Mallouhi A, Serles W, Gruber A, Knosp E, Bavinzski G. 2018. Immediate flow disruption as a prognostic factor after flow diverter treatment long term experience with the pipeline embolization device. World Neurosurgery. 13, e568–e578."},"date_updated":"2023-09-11T14:12:33Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"title":"Incircular nets and confocal conics","article_processing_charge":"No","external_id":{"isi":["000423197800019"]},"publist_id":"7363","author":[{"orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy","last_name":"Akopyan","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","first_name":"Arseniy"},{"last_name":"Bobenko","full_name":"Bobenko, Alexander","first_name":"Alexander"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Akopyan A, Bobenko A. 2018. Incircular nets and confocal conics. Transactions of the American Mathematical Society. 370(4), 2825–2854.","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.","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","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","short":"A. Akopyan, A. Bobenko, Transactions of the American Mathematical Society 370 (2018) 2825–2854.","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.","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."},"oa":1,"quality_controlled":"1","publisher":"American Mathematical Society","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]","date_created":"2018-12-11T11:46:35Z","date_published":"2018-04-01T00:00:00Z","doi":"10.1090/tran/7292","page":"2825 - 2854","publication":"Transactions of the American Mathematical Society","day":"01","year":"2018","isi":1,"status":"public","type":"journal_article","_id":"458","department":[{"_id":"HeEd"}],"date_updated":"2023-09-11T14:19:12Z","intvolume":" 370","month":"04","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1602.04637"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"lang":"eng","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."}],"ec_funded":1,"volume":370,"issue":"4","language":[{"iso":"eng"}],"publication_status":"published"},{"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","publisher":"Elsevier","quality_controlled":"1","day":"01","publication":"Journal of Insect Physiology","isi":1,"year":"2018","doi":"10.1016/j.jinsphys.2017.12.003","date_published":"2018-05-01T00:00:00Z","date_created":"2018-12-11T11:46:25Z","page":"284-290","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","short":"S. Metzler, A. Schrempf, J. Heinze, Journal of Insect Physiology 107 (2018) 284–290.","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.","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."},"title":"Individual- and ejaculate-specific sperm traits in ant males","author":[{"full_name":"Metzler, Sina","orcid":"0000-0002-9547-2494","last_name":"Metzler","first_name":"Sina","id":"48204546-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Alexandra","full_name":"Schrempf, Alexandra","last_name":"Schrempf"},{"full_name":"Heinze, Jürgen","last_name":"Heinze","first_name":"Jürgen"}],"publist_id":"7397","external_id":{"isi":["000434751100034"]},"article_processing_charge":"No","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","language":[{"iso":"eng"}],"publication_status":"published","volume":107,"_id":"426","status":"public","type":"journal_article","date_updated":"2023-09-12T07:43:26Z","department":[{"_id":"SyCr"}]},{"doi":"10.1007/978-3-030-04612-5_2","date_published":"2018-11-21T00:00:00Z","date_created":"2018-12-30T22:59:14Z","page":"21-36","day":"21","isi":1,"year":"2018","publisher":"Springer","quality_controlled":"1","oa":1,"title":"Infinite-duration poorman-bidding games","author":[{"last_name":"Avni","full_name":"Avni, Guy","orcid":"0000-0001-5588-8287","first_name":"Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Ibsen-Jensen","full_name":"Ibsen-Jensen, Rasmus","orcid":"0000-0003-4783-0389","id":"3B699956-F248-11E8-B48F-1D18A9856A87","first_name":"Rasmus"}],"article_processing_charge":"No","external_id":{"isi":["000865933000002"],"arxiv":["1804.04372"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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.","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","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","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."},"project":[{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z211","name":"The Wittgenstein Prize"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"_id":"264B3912-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Formal Methods meets Algorithmic Game Theory","grant_number":"M02369"}],"volume":11316,"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9783030046118"],"issn":["03029743"]},"month":"11","intvolume":" 11316","alternative_title":["LNCS"],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.04372"}],"oa_version":"Preprint","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"}],"department":[{"_id":"ToHe"}],"date_updated":"2023-09-12T07:44:01Z","status":"public","type":"conference","conference":{"start_date":"2018-12-15","location":"Oxford, UK","end_date":"2018-12-17","name":"14th International Conference on Web and Internet Economics, WINE"},"_id":"5788"},{"department":[{"_id":"FlSc"}],"date_updated":"2023-09-12T07:44:37Z","article_type":"original","type":"journal_article","status":"public","_id":"150","issue":"7719","volume":560,"related_material":{"link":[{"url":"https://doi.org/10.1038/s41586-018-0505-4","relation":"erratum"}]},"publication_status":"published","publication_identifier":{"eissn":["1476-4687"]},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6242333/","open_access":"1"}],"scopus_import":"1","intvolume":" 560","month":"08","abstract":[{"lang":"eng","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."}],"pmid":1,"oa_version":"Submitted Version","external_id":{"pmid":["30158708"],"isi":["000442483400046"]},"article_processing_charge":"No","author":[{"first_name":"Robert","last_name":"Dick","full_name":"Dick, Robert"},{"last_name":"Zadrozny","full_name":"Zadrozny, Kaneil K","first_name":"Kaneil K"},{"first_name":"Chaoyi","last_name":"Xu","full_name":"Xu, Chaoyi"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","last_name":"Schur","full_name":"Schur, Florian","orcid":"0000-0003-4790-8078"},{"last_name":"Lyddon","full_name":"Lyddon, Terri D","first_name":"Terri D"},{"last_name":"Ricana","full_name":"Ricana, Clifton L","first_name":"Clifton L"},{"full_name":"Wagner, Jonathan M","last_name":"Wagner","first_name":"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"},{"last_name":"Johnson","full_name":"Johnson, Marc C","first_name":"Marc C"},{"first_name":"Owen","last_name":"Pornillos","full_name":"Pornillos, Owen"},{"last_name":"Vogt","full_name":"Vogt, Volker","first_name":"Volker"}],"title":"Inositol phosphates are assembly co-factors for HIV-1","citation":{"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.","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.","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.","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.","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","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","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"509–512","date_created":"2018-12-11T11:44:53Z","date_published":"2018-08-29T00:00:00Z","doi":"10.1038/s41586-018-0396-4","year":"2018","isi":1,"publication":"Nature","day":"29","oa":1,"quality_controlled":"1","publisher":"Nature Publishing Group"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","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.","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.","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"},"title":"Introduction to tropical series and wave dynamic on them","external_id":{"isi":["000438818400007"],"arxiv":["1706.03062"]},"article_processing_charge":"No","author":[{"last_name":"Kalinin","full_name":"Kalinin, Nikita","first_name":"Nikita"},{"last_name":"Shkolnikov","full_name":"Shkolnikov, Mikhail","orcid":"0000-0002-4310-178X","first_name":"Mikhail","id":"35084A62-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7576","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,"publisher":"AIMS","quality_controlled":"1","publication":"Discrete and Continuous Dynamical Systems- Series A","day":"01","year":"2018","isi":1,"date_created":"2018-12-11T11:45:43Z","doi":"10.3934/dcds.2018120","date_published":"2018-06-01T00:00:00Z","page":"2827 - 2849","_id":"303","status":"public","type":"journal_article","date_updated":"2023-09-12T07:45:37Z","department":[{"_id":"TaHa"}],"oa_version":"Submitted Version","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."}],"intvolume":" 38","month":"06","main_file_link":[{"url":"https://arxiv.org/abs/1706.03062","open_access":"1"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","issue":"6","volume":38},{"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"}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1806.02185","open_access":"1"}],"month":"06","intvolume":" 31","publication_identifier":{"isbn":["9781510884472"],"eissn":["1049-5258"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":31,"_id":"14202","type":"conference","conference":{"name":"NeurIPS: Neural Information Processing Systems","start_date":"2018-12-03","end_date":"2018-12-08","location":"Montreal, Canada"},"status":"public","date_updated":"2023-09-13T07:38:24Z","extern":"1","department":[{"_id":"FrLo"}],"publisher":"Neural Information Processing Systems Foundation","quality_controlled":"1","oa":1,"year":"2018","day":"06","publication":"Advances in Neural Information Processing Systems","date_published":"2018-06-06T00:00:00Z","date_created":"2023-08-22T14:15:40Z","citation":{"mla":"Locatello, Francesco, et al. “Boosting Black Box Variational Inference.” Advances in Neural Information Processing Systems, vol. 31, Neural Information Processing Systems Foundation, 2018.","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.","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.","short":"F. Locatello, G. Dresdner, R. Khanna, I. Valera, G. Rätsch, in:, Advances in Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2018.","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.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco","last_name":"Locatello","full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683"},{"last_name":"Dresdner","full_name":"Dresdner, Gideon","first_name":"Gideon"},{"first_name":"Rajiv","full_name":"Khanna, Rajiv","last_name":"Khanna"},{"first_name":"Isabel","last_name":"Valera","full_name":"Valera, Isabel"},{"first_name":"Gunnar","full_name":"Rätsch, Gunnar","last_name":"Rätsch"}],"external_id":{"arxiv":["1806.02185"]},"article_processing_charge":"No","title":"Boosting black box variational inference"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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.","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.","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.","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.","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.","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.","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."},"title":"Boosting variational inference: An optimization perspective","article_processing_charge":"No","external_id":{"arxiv":["1708.01733"]},"author":[{"full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683","last_name":"Locatello","first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4"},{"last_name":"Khanna","full_name":"Khanna, Rajiv","first_name":"Rajiv"},{"full_name":"Ghosh, Joydeep","last_name":"Ghosh","first_name":"Joydeep"},{"full_name":"Rätsch, Gunnar","last_name":"Rätsch","first_name":"Gunnar"}],"publication":"Proceedings of the 21st International Conference on Artificial Intelligence and Statistics","day":"15","year":"2018","date_created":"2023-08-22T14:15:20Z","date_published":"2018-04-15T00:00:00Z","page":"464-472","oa":1,"publisher":"ML Research Press","quality_controlled":"1","extern":"1","date_updated":"2023-09-13T07:52:40Z","department":[{"_id":"FrLo"}],"_id":"14201","status":"public","conference":{"location":"Playa Blanca, Lanzarote","end_date":"2018-04-11","start_date":"2018-04-09","name":"AISTATS: Conference on Artificial Intelligence and Statistics"},"type":"conference","language":[{"iso":"eng"}],"publication_status":"published","volume":84,"oa_version":"Preprint","abstract":[{"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.","lang":"eng"}],"intvolume":" 84","month":"04","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1708.01733"}],"scopus_import":"1","alternative_title":["PMLR"]},{"date_published":"2018-06-06T00:00:00Z","date_created":"2023-08-22T14:12:48Z","day":"06","publication":"International Conference on Learning Representations","language":[{"iso":"eng"}],"year":"2018","publication_status":"published","month":"06","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1806.02199","open_access":"1"}],"oa":1,"oa_version":"Preprint","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"}],"title":"SOM-VAE: Interpretable discrete representation learning on time series","department":[{"_id":"FrLo"}],"author":[{"first_name":"Vincent","full_name":"Fortuin, Vincent","last_name":"Fortuin"},{"last_name":"Hüser","full_name":"Hüser, Matthias","first_name":"Matthias"},{"last_name":"Locatello","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco"},{"last_name":"Strathmann","full_name":"Strathmann, Heiko","first_name":"Heiko"},{"first_name":"Gunnar","last_name":"Rätsch","full_name":"Rätsch, Gunnar"}],"article_processing_charge":"No","external_id":{"arxiv":["1806.02199"]},"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-09-13T06:35:12Z","citation":{"mla":"Fortuin, Vincent, et al. “SOM-VAE: Interpretable Discrete Representation Learning on Time Series.” International Conference on Learning Representations, 2018.","short":"V. Fortuin, M. Hüser, F. Locatello, H. Strathmann, G. Rätsch, in:, International Conference on Learning Representations, 2018.","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.","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.","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."},"status":"public","type":"conference","conference":{"start_date":"2019-05-06","location":"New Orleans, LA, United States","end_date":"2019-05-09","name":"ICLR: International Conference on Learning Representations"},"_id":"14198"},{"author":[{"last_name":"Yurtsever","full_name":"Yurtsever, Alp","first_name":"Alp"},{"full_name":"Fercoq, Olivier","last_name":"Fercoq","first_name":"Olivier"},{"first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco"},{"full_name":"Cevher, Volkan","last_name":"Cevher","first_name":"Volkan"}],"article_processing_charge":"No","external_id":{"arxiv":["1804.08544"]},"title":"A conditional gradient framework for composite convex minimization with applications to semidefinite programming","citation":{"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.","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.","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.","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.","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.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publisher":"ML Research Press","oa":1,"page":"5727-5736","date_published":"2018-07-15T00:00:00Z","date_created":"2023-08-22T14:16:01Z","year":"2018","day":"15","publication":"Proceedings of the 35th International Conference on Machine Learning","type":"conference","conference":{"name":"ICML: International Conference on Machine Learning","start_date":"2018-07-10","location":"Stockholm, Sweden","end_date":"2018-07-15"},"status":"public","_id":"14203","department":[{"_id":"FrLo"}],"date_updated":"2023-09-13T08:13:39Z","extern":"1","alternative_title":["PMLR"],"main_file_link":[{"url":"https://arxiv.org/abs/1804.08544","open_access":"1"}],"month":"07","intvolume":" 80","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":"Preprint","volume":80,"publication_status":"published","language":[{"iso":"eng"}]},{"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.","ista":"Sachdeva H, Barton NH. 2018. Introgression of a block of genome under infinitesimal selection. Genetics. 209(4), 1279–1303.","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.","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","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.","short":"H. Sachdeva, N.H. Barton, Genetics 209 (2018) 1279–1303."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"last_name":"Sachdeva","full_name":"Sachdeva, Himani","first_name":"Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"publist_id":"7617","external_id":{"isi":["000440014100020"]},"article_processing_charge":"No","title":"Introgression of a block of genome under infinitesimal selection","publisher":"Genetics Society of America","quality_controlled":"1","oa":1,"isi":1,"year":"2018","day":"01","publication":"Genetics","page":"1279 - 1303","date_published":"2018-08-01T00:00:00Z","doi":"10.1534/genetics.118.301018","date_created":"2018-12-11T11:45:36Z","_id":"282","type":"journal_article","status":"public","date_updated":"2023-09-13T08:22:32Z","department":[{"_id":"NiBa"}],"abstract":[{"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.","lang":"eng"}],"oa_version":"Submitted Version","scopus_import":"1","main_file_link":[{"url":"https://www.biorxiv.org/content/early/2017/11/30/227082","open_access":"1"}],"month":"08","intvolume":" 209","publication_status":"published","language":[{"iso":"eng"}],"volume":209,"issue":"4"},{"oa":1,"publisher":"IEEE","quality_controlled":"1","year":"2018","isi":1,"day":"16","date_created":"2018-12-11T11:44:40Z","doi":"10.1109/ISIT.2018.8437654","date_published":"2018-08-16T00:00:00Z","citation":{"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.","short":"M. Obremski, M. Skórski, in:, IEEE, 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.","ama":"Obremski M, Skórski M. Inverted leftover hash lemma. In: Vol 2018. IEEE; 2018. doi:10.1109/ISIT.2018.8437654","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"isi":["000448139300368"]},"author":[{"first_name":"Marciej","last_name":"Obremski","full_name":"Obremski, Marciej"},{"first_name":"Maciej","id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","full_name":"Skorski, Maciej","last_name":"Skorski"}],"publist_id":"7946","title":"Inverted leftover hash lemma","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."}],"oa_version":"Submitted Version","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2017/507"}],"scopus_import":"1","alternative_title":["ISIT Proceedings"],"intvolume":" 2018","month":"08","publication_status":"published","language":[{"iso":"eng"}],"volume":2018,"_id":"108","conference":{"name":"ISIT: International Symposium on Information Theory","location":"Vail, CO, USA","end_date":"2018-06-22","start_date":"2018-06-17 "},"type":"conference","status":"public","date_updated":"2023-09-13T08:23:18Z","department":[{"_id":"KrPi"}]},{"oa_version":"Preprint","abstract":[{"lang":"eng","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."}],"month":"07","intvolume":" 80","alternative_title":["PMLR"],"scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1803.09539","open_access":"1"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":80,"_id":"14204","status":"public","type":"conference","extern":"1","date_updated":"2023-09-13T08:19:05Z","department":[{"_id":"FrLo"}],"publisher":"ML Research Press","quality_controlled":"1","oa":1,"day":"01","publication":"Proceedings of the 35th International Conference on Machine Learning","year":"2018","date_published":"2018-07-01T00:00:00Z","date_created":"2023-08-22T14:16:25Z","page":"3198-3207","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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.","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.","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.","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."},"title":"On matching pursuit and coordinate descent","author":[{"first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello","full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683"},{"first_name":"Anant","last_name":"Raj","full_name":"Raj, Anant"},{"last_name":"Karimireddy","full_name":"Karimireddy, Sai Praneeth","first_name":"Sai Praneeth"},{"first_name":"Gunnar","full_name":"Rätsch, Gunnar","last_name":"Rätsch"},{"first_name":"Bernhard","full_name":"Schölkopf, Bernhard","last_name":"Schölkopf"},{"last_name":"Stich","full_name":"Stich, Sebastian U.","first_name":"Sebastian U."},{"last_name":"Jaggi","full_name":"Jaggi, Martin","first_name":"Martin"}],"article_processing_charge":"No","external_id":{"arxiv":["1803.09539"]}},{"status":"public","type":"conference","conference":{"start_date":"2018-07-14","end_date":"2018-07-17","location":"Oxford, UK","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)"},"_id":"160","department":[{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:45:04Z","ddc":["000"],"date_updated":"2023-09-13T08:45:09Z","month":"07","intvolume":" 10981","scopus_import":"1","alternative_title":["LNCS"],"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"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8332"}]},"volume":10981,"file":[{"file_size":1603844,"date_updated":"2020-07-14T12:45:04Z","creator":"dernst","file_name":"2018_LNCS_Kragl.pdf","date_created":"2018-12-17T12:52:12Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"c64fff560fe5a7532ec10626ad1c215e","file_id":"5705"}],"language":[{"iso":"eng"}],"publication_status":"published","project":[{"grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"}],"title":"Layered Concurrent Programs","publist_id":"7761","author":[{"last_name":"Kragl","full_name":"Kragl, Bernhard","orcid":"0000-0001-7745-9117","id":"320FC952-F248-11E8-B48F-1D18A9856A87","first_name":"Bernhard"},{"first_name":"Shaz","last_name":"Qadeer","full_name":"Qadeer, Shaz"}],"article_processing_charge":"No","external_id":{"isi":["000491481600005"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","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","ama":"Kragl B, Qadeer S. Layered Concurrent Programs. In: Vol 10981. Springer; 2018:79-102. doi: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.","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.","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."},"publisher":"Springer","quality_controlled":"1","oa":1,"date_published":"2018-07-18T00:00:00Z","doi":"10.1007/978-3-319-96145-3_5","date_created":"2018-12-11T11:44:57Z","page":"79 - 102","day":"18","isi":1,"has_accepted_license":"1","year":"2018"},{"author":[{"first_name":"Zhen","last_name":"Gao","full_name":"Gao, Zhen"},{"full_name":"Daneva, Anna","last_name":"Daneva","first_name":"Anna"},{"last_name":"Salanenka","full_name":"Salanenka, Yuliya","first_name":"Yuliya","id":"46DAAE7E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Matthias","last_name":"Van Durme","full_name":"Van Durme, Matthias"},{"first_name":"Marlies","last_name":"Huysmans","full_name":"Huysmans, Marlies"},{"full_name":"Lin, Zongcheng","last_name":"Lin","first_name":"Zongcheng"},{"full_name":"De Winter, Freya","last_name":"De Winter","first_name":"Freya"},{"last_name":"Vanneste","full_name":"Vanneste, Steffen","first_name":"Steffen"},{"first_name":"Mansour","full_name":"Karimi, Mansour","last_name":"Karimi"},{"full_name":"Van De Velde, Jan","last_name":"Van De Velde","first_name":"Jan"},{"last_name":"Vandepoele","full_name":"Vandepoele, Klaas","first_name":"Klaas"},{"last_name":"Van De Walle","full_name":"Van De Walle, Davy","first_name":"Davy"},{"first_name":"Koen","full_name":"Dewettinck, Koen","last_name":"Dewettinck"},{"first_name":"Bart","last_name":"Lambrecht","full_name":"Lambrecht, Bart"},{"first_name":"Moritz","last_name":"Nowack","full_name":"Nowack, Moritz"}],"publist_id":"7619","external_id":{"isi":["000435571000017"]},"article_processing_charge":"No","title":"KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis","citation":{"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.","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.","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.","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.","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"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","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.).","page":"365 - 375","date_published":"2018-05-28T00:00:00Z","doi":"10.1038/s41477-018-0160-7","date_created":"2018-12-11T11:45:35Z","isi":1,"year":"2018","day":"28","publication":"Nature Plants","type":"journal_article","status":"public","_id":"280","department":[{"_id":"JiFr"}],"date_updated":"2023-09-13T08:24:17Z","scopus_import":"1","month":"05","intvolume":" 4","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."}],"oa_version":"None","issue":"6","volume":4,"publication_status":"published","language":[{"iso":"eng"}]},{"title":"Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains","publist_id":"7317","author":[{"orcid":"0000-0003-3768-877X","full_name":"Tomasek, Kathrin","last_name":"Tomasek","first_name":"Kathrin","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-5396-4346","full_name":"Bergmiller, Tobias","last_name":"Bergmiller","first_name":"Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","last_name":"Guet","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["000425715100006"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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","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","short":"K. Tomasek, T. Bergmiller, C.C. Guet, Journal of Biotechnology 268 (2018) 40–52.","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.","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.","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."},"date_published":"2018-02-20T00:00:00Z","doi":"10.1016/j.jbiotec.2018.01.008","date_created":"2018-12-11T11:46:50Z","page":"40 - 52","day":"20","publication":"Journal of Biotechnology","isi":1,"year":"2018","quality_controlled":"1","publisher":"Elsevier","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","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","month":"02","intvolume":" 268","scopus_import":"1","oa_version":"None","acknowledged_ssus":[{"_id":"Bio"}],"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."}]},{"oa":1,"quality_controlled":"1","publisher":"Public Library of Science","publication":"PLoS Biology","day":"16","year":"2018","isi":1,"has_accepted_license":"1","date_created":"2018-12-11T11:44:32Z","date_published":"2018-08-16T00:00:00Z","doi":"10.1371/journal.pbio.2005971","article_number":"2005971","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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","short":"W. Chaudhry, M. Pleska, N. Shah, H. Weiss, I. Mccall, J. Meyer, A. Gupta, C.C. Guet, B. Levin, PLoS Biology 16 (2018).","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.","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.","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.","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."},"title":"Leaky resistance and the conditions for the existence of lytic bacteriophage","article_processing_charge":"Yes","external_id":{"isi":["000443383300024"]},"publist_id":"7972","author":[{"last_name":"Chaudhry","full_name":"Chaudhry, Waqas","first_name":"Waqas"},{"full_name":"Pleska, Maros","orcid":"0000-0001-7460-7479","last_name":"Pleska","id":"4569785E-F248-11E8-B48F-1D18A9856A87","first_name":"Maros"},{"first_name":"Nilang","full_name":"Shah, Nilang","last_name":"Shah"},{"last_name":"Weiss","full_name":"Weiss, Howard","first_name":"Howard"},{"last_name":"Mccall","full_name":"Mccall, Ingrid","first_name":"Ingrid"},{"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","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","last_name":"Guet"},{"full_name":"Levin, Bruce","last_name":"Levin","first_name":"Bruce"}],"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"}],"intvolume":" 16","month":"08","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"file_id":"5706","checksum":"527076f78265cd4ea192cd1569851587","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-17T12:55:31Z","file_name":"2018_Plos_Chaudhry.pdf","creator":"dernst","date_updated":"2020-07-14T12:48:10Z","file_size":4007095}],"publication_status":"published","related_material":{"record":[{"status":"public","id":"9810","relation":"research_data"}]},"volume":16,"issue":"8","_id":"82","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","ddc":["570"],"date_updated":"2023-09-13T08:45:41Z","department":[{"_id":"CaGu"}],"file_date_updated":"2020-07-14T12:48:10Z"},{"article_number":"89","project":[{"name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767","call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425"}],"citation":{"ista":"Umetani N, Bickel B. 2018. Learning three-dimensional flow for interactive aerodynamic design. ACM Trans. Graph. 37(4), 89.","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.","short":"N. Umetani, B. Bickel, ACM Trans. Graph. 37 (2018).","ieee":"N. Umetani and B. Bickel, “Learning three-dimensional flow for interactive aerodynamic design,” ACM Trans. Graph., vol. 37, no. 4. ACM, 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","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Nobuyuki","last_name":"Umetani","full_name":"Umetani, Nobuyuki"},{"last_name":"Bickel","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd"}],"publist_id":"8053","article_processing_charge":"No","external_id":{"isi":["000448185000050"]},"title":"Learning three-dimensional flow for interactive aerodynamic design","publisher":"ACM","quality_controlled":"1","oa":1,"isi":1,"has_accepted_license":"1","year":"2018","day":"04","publication":"ACM Trans. Graph.","doi":"10.1145/3197517.3201325","date_published":"2018-08-04T00:00:00Z","date_created":"2018-12-11T11:44:06Z","_id":"4","type":"journal_article","status":"public","pubrep_id":"1049","date_updated":"2023-09-13T08:46:15Z","ddc":["003","004"],"department":[{"_id":"BeBi"}],"file_date_updated":"2020-07-14T12:46:22Z","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."}],"oa_version":"Submitted Version","scopus_import":"1","month":"08","intvolume":" 37","publication_status":"published","file":[{"file_id":"5216","checksum":"7a2243668f215821bc6aecad0320079a","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:16:28Z","file_name":"IST-2018-1049-v1+1_2018_sigg_Learning3DAerodynamics.pdf","date_updated":"2020-07-14T12:46:22Z","file_size":22803163,"creator":"system"}],"language":[{"iso":"eng"}],"volume":37,"related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/new-interactive-machine-learning-tool-makes-car-designs-more-aerodynamic/","relation":"press_release"}]},"issue":"4","ec_funded":1},{"citation":{"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.","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.","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","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","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.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000474781600022"]},"article_processing_charge":"No","publist_id":"7738","author":[{"full_name":"Bartocci, Ezio","last_name":"Bartocci","first_name":"Ezio"},{"first_name":"Thomas","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5199-3143","full_name":"Ferrere, Thomas","last_name":"Ferrere"},{"first_name":"Niveditha","last_name":"Manjunath","full_name":"Manjunath, Niveditha"},{"last_name":"Nickovic","full_name":"Nickovic, Dejan","first_name":"Dejan"}],"title":"Localizing faults in simulink/stateflow models with STL","project":[{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"}],"year":"2018","isi":1,"day":"11","page":"197 - 206","date_created":"2018-12-11T11:45:04Z","date_published":"2018-04-11T00:00:00Z","doi":"10.1145/3178126.3178131","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.","quality_controlled":"1","publisher":"Association for Computing Machinery, Inc","date_updated":"2023-09-13T08:48:46Z","department":[{"_id":"ToHe"}],"_id":"183","conference":{"name":"HSCC: Hybrid Systems: Computation and Control","start_date":"2018-04-11","location":"Porto, Portugal","end_date":"2018-04-13"},"type":"conference","status":"public","publication_status":"published","language":[{"iso":"eng"}],"abstract":[{"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.","lang":"eng"}],"oa_version":"None","alternative_title":["HSCC Proceedings"],"scopus_import":"1","month":"04"}]