[{"type":"conference","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","main_file_link":[{"open_access":"1","url":"https://hal.inria.fr/hal-01367181"}],"day":"10","month":"10","conference":{"location":"San Francisco, CA, USA","end_date":"2016-10-12","name":"MIG: Motion in Games","start_date":"2016-10-10"},"author":[{"last_name":"Manteaux","full_name":"Manteaux, Pierre","first_name":"Pierre"},{"last_name":"Vimont","first_name":"Ulysse","full_name":"Vimont, Ulysse"},{"first_name":"Christopher J","full_name":"Wojtan, Christopher J","last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546"},{"first_name":"Damien","full_name":"Rohmer, Damien","last_name":"Rohmer"},{"full_name":"Cani, Marie","first_name":"Marie","last_name":"Cani"}],"publication":"Proceedings of the 9th International Conference on Motion in Games ","language":[{"iso":"eng"}],"has_accepted_license":"1","scopus_import":"1","title":"Space-time sculpting of liquid animation","article_processing_charge":"No","date_updated":"2023-02-21T09:49:49Z","oa":1,"quality_controlled":"1","department":[{"_id":"ChWo"}],"date_published":"2016-10-10T00:00:00Z","publisher":"ACM","project":[{"_id":"2533E772-B435-11E9-9278-68D0E5697425","grant_number":"638176","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","call_identifier":"H2020"}],"abstract":[{"lang":"eng","text":"We propose an interactive sculpting system for seamlessly editing pre-computed animations of liquid, without the need for any resimulation. The input is a sequence of meshes without correspondences representing the liquid surface over time. Our method enables the efficient selection of consistent space-time parts of this animation, such as moving waves or droplets, which we call space-time features. Once selected, a feature can be copied, edited, or duplicated and then pasted back anywhere in space and time in the same or in another liquid animation sequence. Our method circumvents tedious user interactions by automatically computing the spatial and temporal ranges of the selected feature. We also provide space-time shape editing tools for non-uniform scaling, rotation, trajectory changes, and temporal editing to locally speed up or slow down motion. Using our tools, the user can edit and progressively refine any input simulation result, possibly using a library of precomputed space-time features extracted from other animations. In contrast to the trial-and-error loop usually required to edit animation results through the tuning of indirect simulation parameters, our method gives the user full control over the edited space-time behaviors. © 2016 Copyright held by the owner/author(s)."}],"ddc":["004"],"publication_status":"published","doi":"10.1145/2994258.2994261","_id":"1136","article_number":"2994261","ec_funded":1,"citation":{"ista":"Manteaux P, Vimont U, Wojtan C, Rohmer D, Cani M. 2016. Space-time sculpting of liquid animation. Proceedings of the 9th International Conference on Motion in Games . MIG: Motion in Games, 2994261.","mla":"Manteaux, Pierre, et al. “Space-Time Sculpting of Liquid Animation.” <i>Proceedings of the 9th International Conference on Motion in Games </i>, 2994261, ACM, 2016, doi:<a href=\"https://doi.org/10.1145/2994258.2994261\">10.1145/2994258.2994261</a>.","chicago":"Manteaux, Pierre, Ulysse Vimont, Chris Wojtan, Damien Rohmer, and Marie Cani. “Space-Time Sculpting of Liquid Animation.” In <i>Proceedings of the 9th International Conference on Motion in Games </i>. ACM, 2016. <a href=\"https://doi.org/10.1145/2994258.2994261\">https://doi.org/10.1145/2994258.2994261</a>.","ieee":"P. Manteaux, U. Vimont, C. Wojtan, D. Rohmer, and M. Cani, “Space-time sculpting of liquid animation,” in <i>Proceedings of the 9th International Conference on Motion in Games </i>, San Francisco, CA, USA, 2016.","ama":"Manteaux P, Vimont U, Wojtan C, Rohmer D, Cani M. Space-time sculpting of liquid animation. In: <i>Proceedings of the 9th International Conference on Motion in Games </i>. ACM; 2016. doi:<a href=\"https://doi.org/10.1145/2994258.2994261\">10.1145/2994258.2994261</a>","short":"P. Manteaux, U. Vimont, C. Wojtan, D. Rohmer, M. Cani, in:, Proceedings of the 9th International Conference on Motion in Games , ACM, 2016.","apa":"Manteaux, P., Vimont, U., Wojtan, C., Rohmer, D., &#38; Cani, M. (2016). Space-time sculpting of liquid animation. In <i>Proceedings of the 9th International Conference on Motion in Games </i>. San Francisco, CA, USA: ACM. <a href=\"https://doi.org/10.1145/2994258.2994261\">https://doi.org/10.1145/2994258.2994261</a>"},"publist_id":"6222","date_created":"2018-12-11T11:50:20Z","year":"2016","acknowledgement":"This work was partly supported by the starting grant BigSplash, as well as the advanced grant EXPRESSIVE from the European Research Council (ERC-2014-StG 638176 , and ERC-2011-ADG 20110209)."},{"article_type":"original","_id":"1137","doi":"10.1038/ni.3575","year":"2016","publist_id":"6221","citation":{"apa":"Salzer, E., Çaǧdaş, D., Hons, M., Mace, E., Garncarz, W., Petronczki, O., … Boztug, K. (2016). RASGRP1 deficiency causes immunodeficiency with impaired cytoskeletal dynamics. <i>Nature Immunology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ni.3575\">https://doi.org/10.1038/ni.3575</a>","ama":"Salzer E, Çaǧdaş D, Hons M, et al. RASGRP1 deficiency causes immunodeficiency with impaired cytoskeletal dynamics. <i>Nature Immunology</i>. 2016;17(12):1352-1360. doi:<a href=\"https://doi.org/10.1038/ni.3575\">10.1038/ni.3575</a>","ieee":"E. Salzer <i>et al.</i>, “RASGRP1 deficiency causes immunodeficiency with impaired cytoskeletal dynamics,” <i>Nature Immunology</i>, vol. 17, no. 12. Nature Publishing Group, pp. 1352–1360, 2016.","short":"E. Salzer, D. Çaǧdaş, M. Hons, E. Mace, W. Garncarz, O. Petronczki, R. Platzer, L. Pfajfer, I. Bilic, S. Ban, K. Willmann, M. Mukherjee, V. Supper, H. Hsu, P. Banerjee, P. Sinha, F. Mcclanahan, G. Zlabinger, W. Pickl, J. Gribben, H. Stockinger, K. Bennett, J. Huppa, L. Dupré, Ö. Sanal, U. Jäger, M.K. Sixt, I. Tezcan, J. Orange, K. Boztug, Nature Immunology 17 (2016) 1352–1360.","chicago":"Salzer, Elisabeth, Deniz Çaǧdaş, Miroslav Hons, Emily Mace, Wojciech Garncarz, Oezlem Petronczki, René Platzer, et al. “RASGRP1 Deficiency Causes Immunodeficiency with Impaired Cytoskeletal Dynamics.” <i>Nature Immunology</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/ni.3575\">https://doi.org/10.1038/ni.3575</a>.","ista":"Salzer E, Çaǧdaş D, Hons M, Mace E, Garncarz W, Petronczki O, Platzer R, Pfajfer L, Bilic I, Ban S, Willmann K, Mukherjee M, Supper V, Hsu H, Banerjee P, Sinha P, Mcclanahan F, Zlabinger G, Pickl W, Gribben J, Stockinger H, Bennett K, Huppa J, Dupré L, Sanal Ö, Jäger U, Sixt MK, Tezcan I, Orange J, Boztug K. 2016. RASGRP1 deficiency causes immunodeficiency with impaired cytoskeletal dynamics. Nature Immunology. 17(12), 1352–1360.","mla":"Salzer, Elisabeth, et al. “RASGRP1 Deficiency Causes Immunodeficiency with Impaired Cytoskeletal Dynamics.” <i>Nature Immunology</i>, vol. 17, no. 12, Nature Publishing Group, 2016, pp. 1352–60, doi:<a href=\"https://doi.org/10.1038/ni.3575\">10.1038/ni.3575</a>."},"date_created":"2018-12-11T11:50:21Z","date_published":"2016-12-01T00:00:00Z","publisher":"Nature Publishing Group","volume":17,"quality_controlled":"1","page":"1352 - 1360","department":[{"_id":"MiSi"}],"publication_status":"published","abstract":[{"text":"RASGRP1 is an important guanine nucleotide exchange factor and activator of the RAS-MAPK pathway following T cell antigen receptor (TCR) signaling. The consequences of RASGRP1 mutations in humans are unknown. In a patient with recurrent bacterial and viral infections, born to healthy consanguineous parents, we used homozygosity mapping and exome sequencing to identify a biallelic stop-gain variant in RASGRP1. This variant segregated perfectly with the disease and has not been reported in genetic databases. RASGRP1 deficiency was associated in T cells and B cells with decreased phosphorylation of the extracellular-signal-regulated serine kinase ERK, which was restored following expression of wild-type RASGRP1. RASGRP1 deficiency also resulted in defective proliferation, activation and motility of T cells and B cells. RASGRP1-deficient natural killer (NK) cells exhibited impaired cytotoxicity with defective granule convergence and actin accumulation. Interaction proteomics identified the dynein light chain DYNLL1 as interacting with RASGRP1, which links RASGRP1 to cytoskeletal dynamics. RASGRP1-deficient cells showed decreased activation of the GTPase RhoA. Treatment with lenalidomide increased RhoA activity and reversed the migration and activation defects of RASGRP1-deficient lymphocytes.","lang":"eng"}],"external_id":{"pmid":["27776107"]},"language":[{"iso":"eng"}],"publication":"Nature Immunology","article_processing_charge":"No","issue":"12","date_updated":"2021-01-12T06:48:33Z","oa":1,"title":"RASGRP1 deficiency causes immunodeficiency with impaired cytoskeletal dynamics","intvolume":"        17","scopus_import":1,"type":"journal_article","status":"public","pmid":1,"author":[{"last_name":"Salzer","first_name":"Elisabeth","full_name":"Salzer, Elisabeth"},{"last_name":"Çaǧdaş","full_name":"Çaǧdaş, Deniz","first_name":"Deniz"},{"full_name":"Hons, Miroslav","first_name":"Miroslav","orcid":"0000-0002-6625-3348","last_name":"Hons","id":"4167FE56-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Mace, Emily","first_name":"Emily","last_name":"Mace"},{"last_name":"Garncarz","first_name":"Wojciech","full_name":"Garncarz, Wojciech"},{"last_name":"Petronczki","full_name":"Petronczki, Oezlem","first_name":"Oezlem"},{"last_name":"Platzer","full_name":"Platzer, René","first_name":"René"},{"last_name":"Pfajfer","first_name":"Laurène","full_name":"Pfajfer, Laurène"},{"last_name":"Bilic","first_name":"Ivan","full_name":"Bilic, Ivan"},{"first_name":"Sol","full_name":"Ban, Sol","last_name":"Ban"},{"full_name":"Willmann, Katharina","first_name":"Katharina","last_name":"Willmann"},{"first_name":"Malini","full_name":"Mukherjee, Malini","last_name":"Mukherjee"},{"full_name":"Supper, Verena","first_name":"Verena","last_name":"Supper"},{"last_name":"Hsu","first_name":"Hsiangting","full_name":"Hsu, Hsiangting"},{"first_name":"Pinaki","full_name":"Banerjee, Pinaki","last_name":"Banerjee"},{"full_name":"Sinha, Papiya","first_name":"Papiya","last_name":"Sinha"},{"last_name":"Mcclanahan","first_name":"Fabienne","full_name":"Mcclanahan, Fabienne"},{"full_name":"Zlabinger, Gerhard","first_name":"Gerhard","last_name":"Zlabinger"},{"full_name":"Pickl, Winfried","first_name":"Winfried","last_name":"Pickl"},{"last_name":"Gribben","full_name":"Gribben, John","first_name":"John"},{"full_name":"Stockinger, Hannes","first_name":"Hannes","last_name":"Stockinger"},{"last_name":"Bennett","first_name":"Keiryn","full_name":"Bennett, Keiryn"},{"last_name":"Huppa","full_name":"Huppa, Johannes","first_name":"Johannes"},{"first_name":"Loï̈C","full_name":"Dupré, Loï̈C","last_name":"Dupré"},{"first_name":"Özden","full_name":"Sanal, Özden","last_name":"Sanal"},{"last_name":"Jäger","full_name":"Jäger, Ulrich","first_name":"Ulrich"},{"last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K","full_name":"Sixt, Michael K"},{"full_name":"Tezcan, Ilhan","first_name":"Ilhan","last_name":"Tezcan"},{"first_name":"Jordan","full_name":"Orange, Jordan","last_name":"Orange"},{"first_name":"Kaan","full_name":"Boztug, Kaan","last_name":"Boztug"}],"month":"12","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6400263"}],"oa_version":"Submitted Version","day":"01"},{"conference":{"start_date":"2016-07-05","name":"LICS: Logic in Computer Science","end_date":"2016-07-08","location":"New York, NY, USA"},"month":"07","day":"05","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1604.06764"}],"oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"full_name":"Henzinger, Thomas A","first_name":"Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","last_name":"Otop","full_name":"Otop, Jan","first_name":"Jan"}],"arxiv":1,"type":"conference","status":"public","scopus_import":1,"date_updated":"2021-01-12T06:48:34Z","oa":1,"title":"Quantitative automata under probabilistic semantics","publication":"Proceedings of the 31st Annual ACM/IEEE Symposium","language":[{"iso":"eng"}],"external_id":{"arxiv":["1604.06764"]},"abstract":[{"lang":"eng","text":"Automata with monitor counters, where the transitions do not depend on counter values, and nested weighted automata are two expressive automata-theoretic frameworks for quantitative properties. For a well-studied and wide class of quantitative functions, we establish that automata with monitor counters and nested weighted automata are equivalent. We study for the first time such quantitative automata under probabilistic semantics. We show that several problems that are undecidable for the classical questions of emptiness and universality become decidable under the probabilistic semantics. We present a complete picture of decidability for such automata, and even an almost-complete picture of computational complexity, for the probabilistic questions we consider. © 2016 ACM."}],"publication_status":"published","publisher":"IEEE","date_published":"2016-07-05T00:00:00Z","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"page":"76 - 85","quality_controlled":"1","project":[{"grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Reactive Modeling"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF","name":"The Wittgenstein Prize"},{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification"}],"ec_funded":1,"acknowledgement":"This research was funded in part by the European Research Council (ERC) under grant agreement 267989 (QUAREM), by the Austrian Science Fund (FWF) projects S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award), FWF Grant No P23499- N23, FWF NFN Grant No S114","year":"2016","citation":{"ista":"Chatterjee K, Henzinger TA, Otop J. 2016. Quantitative automata under probabilistic semantics. Proceedings of the 31st Annual ACM/IEEE Symposium. LICS: Logic in Computer Science, 76–85.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Quantitative Automata under Probabilistic Semantics.” In <i>Proceedings of the 31st Annual ACM/IEEE Symposium</i>, 76–85. IEEE, 2016. <a href=\"https://doi.org/10.1145/2933575.2933588\">https://doi.org/10.1145/2933575.2933588</a>.","mla":"Chatterjee, Krishnendu, et al. “Quantitative Automata under Probabilistic Semantics.” <i>Proceedings of the 31st Annual ACM/IEEE Symposium</i>, IEEE, 2016, pp. 76–85, doi:<a href=\"https://doi.org/10.1145/2933575.2933588\">10.1145/2933575.2933588</a>.","ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, “Quantitative automata under probabilistic semantics,” in <i>Proceedings of the 31st Annual ACM/IEEE Symposium</i>, New York, NY, USA, 2016, pp. 76–85.","ama":"Chatterjee K, Henzinger TA, Otop J. Quantitative automata under probabilistic semantics. In: <i>Proceedings of the 31st Annual ACM/IEEE Symposium</i>. IEEE; 2016:76-85. doi:<a href=\"https://doi.org/10.1145/2933575.2933588\">10.1145/2933575.2933588</a>","short":"K. Chatterjee, T.A. Henzinger, J. Otop, in:, Proceedings of the 31st Annual ACM/IEEE Symposium, IEEE, 2016, pp. 76–85.","apa":"Chatterjee, K., Henzinger, T. A., &#38; Otop, J. (2016). Quantitative automata under probabilistic semantics. In <i>Proceedings of the 31st Annual ACM/IEEE Symposium</i> (pp. 76–85). New York, NY, USA: IEEE. <a href=\"https://doi.org/10.1145/2933575.2933588\">https://doi.org/10.1145/2933575.2933588</a>"},"date_created":"2018-12-11T11:50:21Z","publist_id":"6220","doi":"10.1145/2933575.2933588","_id":"1138"},{"intvolume":"        27","date_created":"2018-12-11T11:50:21Z","citation":{"apa":"Düllberg, C. F., Cade, N., &#38; Surrey, T. (2016). Microtubule aging probed by microfluidics assisted tubulin washout. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1091/mbc.E16-07-0548\">https://doi.org/10.1091/mbc.E16-07-0548</a>","chicago":"Düllberg, Christian F, Nicholas Cade, and Thomas Surrey. “Microtubule Aging Probed by Microfluidics Assisted Tubulin Washout.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2016. <a href=\"https://doi.org/10.1091/mbc.E16-07-0548\">https://doi.org/10.1091/mbc.E16-07-0548</a>.","mla":"Düllberg, Christian F., et al. “Microtubule Aging Probed by Microfluidics Assisted Tubulin Washout.” <i>Molecular Biology and Evolution</i>, vol. 27, no. 22, Oxford University Press, 2016, pp. 3563–73, doi:<a href=\"https://doi.org/10.1091/mbc.E16-07-0548\">10.1091/mbc.E16-07-0548</a>.","ista":"Düllberg CF, Cade N, Surrey T. 2016. Microtubule aging probed by microfluidics assisted tubulin washout. Molecular Biology and Evolution. 27(22), 3563–3573.","ieee":"C. F. Düllberg, N. Cade, and T. Surrey, “Microtubule aging probed by microfluidics assisted tubulin washout,” <i>Molecular Biology and Evolution</i>, vol. 27, no. 22. Oxford University Press, pp. 3563–3573, 2016.","ama":"Düllberg CF, Cade N, Surrey T. Microtubule aging probed by microfluidics assisted tubulin washout. <i>Molecular Biology and Evolution</i>. 2016;27(22):3563-3573. doi:<a href=\"https://doi.org/10.1091/mbc.E16-07-0548\">10.1091/mbc.E16-07-0548</a>","short":"C.F. Düllberg, N. Cade, T. Surrey, Molecular Biology and Evolution 27 (2016) 3563–3573."},"title":"Microtubule aging probed by microfluidics assisted tubulin washout","publist_id":"6218","article_processing_charge":"No","issue":"22","year":"2016","date_updated":"2021-01-12T06:48:34Z","doi":"10.1091/mbc.E16-07-0548","publication":"Molecular Biology and Evolution","_id":"1139","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Microtubules switch stochastically between phases of growth and shrinkage. The molecular mechanism responsible for the end of a growth phase, an event called catastrophe, is still not understood. The probability for a catastrophe to occur increases with microtubule age, putting constraints on the possible molecular mechanism of catastrophe induction. Here we used microfluidics-Assisted fast tubulin washout experiments to induce microtubule depolymerization in a controlled manner at different times after the start of growth. We found that aging can also be observed in this assay, providing valuable new constraints against which theoretical models of catastrophe induction can be tested. We found that the data can be quantitatively well explained by a simple kinetic threshold model that assumes an age-dependent broadening of the protective cap at the microtubule end as a result of an evolving tapered end structure; this leads to a decrease of the cap density and its stability. This analysis suggests an intuitive picture of the role of morphological changes of the protective cap for the age dependence of microtubule stability."}],"day":"07","oa_version":"None","month":"11","publication_status":"published","author":[{"orcid":"0000-0001-6335-9748","id":"459064DC-F248-11E8-B48F-1D18A9856A87","last_name":"Düllberg","first_name":"Christian F","full_name":"Düllberg, Christian F"},{"first_name":"Nicholas","full_name":"Cade, Nicholas","last_name":"Cade"},{"first_name":"Thomas","full_name":"Surrey, Thomas","last_name":"Surrey"}],"volume":27,"page":"3563 - 3573","extern":"1","date_published":"2016-11-07T00:00:00Z","type":"journal_article","status":"public","publisher":"Oxford University Press"},{"article_processing_charge":"No","oa":1,"date_updated":"2025-06-02T08:53:44Z","title":"Model and objective separation with conditional lower bounds: disjunction is harder than conjunction","scopus_import":"1","language":[{"iso":"eng"}],"publication":"Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science","arxiv":1,"author":[{"last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"full_name":"Dvoák, Wolfgang","first_name":"Wolfgang","last_name":"Dvoák"},{"last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","first_name":"Monika H","full_name":"Henzinger, Monika H"},{"last_name":"Loitzenbauer","first_name":"Veronika","full_name":"Loitzenbauer, Veronika"}],"month":"07","conference":{"start_date":"2016-07-05","name":"LICS: Logic in Computer Science","end_date":"2016-07-08","location":"New York, NY, USA"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1602.02670","open_access":"1"}],"day":"05","status":"public","type":"conference","alternative_title":["Proceedings Symposium on Logic in Computer Science"],"year":"2016","acknowledgement":"K.  C.,  M.  H.,  and  W.  D.  are  partially  supported  by  the  Vienna\r\nScience and Technology Fund (WWTF) through project ICT15-003.\r\nK. C. is partially supported by the Austrian Science Fund (FWF)\r\nNFN Grant No S11407-N23 (RiSE/SHiNE) and an ERC Start grant\r\n(279307: Graph Games). For W. D., M. H., and V. L. the research\r\nleading to these results has received funding from the European\r\nResearch Council under the European Union’s Seventh Framework\r\nProgramme (FP/2007-2013) / ERC Grant Agreement no. 340506.","date_created":"2018-12-11T11:50:22Z","citation":{"apa":"Chatterjee, K., Dvoák, W., Henzinger, M. H., &#38; Loitzenbauer, V. (2016). Model and objective separation with conditional lower bounds: disjunction is harder than conjunction. In <i>Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science</i> (pp. 197–206). New York, NY, USA: IEEE. <a href=\"https://doi.org/10.1145/2933575.2935304\">https://doi.org/10.1145/2933575.2935304</a>","ista":"Chatterjee K, Dvoák W, Henzinger MH, Loitzenbauer V. 2016. Model and objective separation with conditional lower bounds: disjunction is harder than conjunction. Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science. LICS: Logic in Computer Science, Proceedings Symposium on Logic in Computer Science, , 197–206.","mla":"Chatterjee, Krishnendu, et al. “Model and Objective Separation with Conditional Lower Bounds: Disjunction Is Harder than Conjunction.” <i>Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science</i>, IEEE, 2016, pp. 197–206, doi:<a href=\"https://doi.org/10.1145/2933575.2935304\">10.1145/2933575.2935304</a>.","chicago":"Chatterjee, Krishnendu, Wolfgang Dvoák, Monika H Henzinger, and Veronika Loitzenbauer. “Model and Objective Separation with Conditional Lower Bounds: Disjunction Is Harder than Conjunction.” In <i>Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science</i>, 197–206. IEEE, 2016. <a href=\"https://doi.org/10.1145/2933575.2935304\">https://doi.org/10.1145/2933575.2935304</a>.","short":"K. Chatterjee, W. Dvoák, M.H. Henzinger, V. Loitzenbauer, in:, Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science, IEEE, 2016, pp. 197–206.","ama":"Chatterjee K, Dvoák W, Henzinger MH, Loitzenbauer V. Model and objective separation with conditional lower bounds: disjunction is harder than conjunction. In: <i>Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science</i>. IEEE; 2016:197-206. doi:<a href=\"https://doi.org/10.1145/2933575.2935304\">10.1145/2933575.2935304</a>","ieee":"K. Chatterjee, W. Dvoák, M. H. Henzinger, and V. Loitzenbauer, “Model and objective separation with conditional lower bounds: disjunction is harder than conjunction,” in <i>Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science</i>, New York, NY, USA, 2016, pp. 197–206."},"publist_id":"6219","_id":"1140","doi":"10.1145/2933575.2935304","publication_status":"published","abstract":[{"text":"Given a model of a system and an objective, the model-checking question asks whether the model satisfies the objective. We study polynomial-time problems in two classical models, graphs and Markov Decision Processes (MDPs), with respect to several fundamental -regular objectives, e.g., Rabin and Streett objectives. For many of these problems the best-known upper bounds are quadratic or cubic, yet no super-linear lower bounds are known. In this work our contributions are two-fold: First, we present several improved algorithms, and second, we present the first conditional super-linear lower bounds based on widely believed assumptions about the complexity of CNF-SAT and combinatorial Boolean matrix multiplication. A separation result for two models with respect to an objective means a conditional lower bound for one model that is strictly higher than the existing upper bound for the other model, and similarly for two objectives with respect to a model. Our results establish the following separation results: (1) A separation of models (graphs and MDPs) for disjunctive queries of reachability and Büchi objectives. (2) Two kinds of separations of objectives, both for graphs and MDPs, namely, (2a) the separation of dual objectives such as Streett/Rabin objectives, and (2b) the separation of conjunction and disjunction of multiple objectives of the same type such as safety, Büchi, and coBüchi. In summary, our results establish the first model and objective separation results for graphs and MDPs for various classical -regular objectives. Quite strikingly, we establish conditional lower bounds for the disjunction of objectives that are strictly higher than the existing upper bounds for the conjunction of the same objectives. © 2016 ACM.","lang":"eng"}],"external_id":{"arxiv":["1602.02670"]},"project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"}],"date_published":"2016-07-05T00:00:00Z","publisher":"IEEE","quality_controlled":"1","department":[{"_id":"KrCh"}],"page":"197 - 206"},{"publication":"Journal of Computational Science","doi":"10.1016/j.jocs.2016.03.004","language":[{"iso":"eng"}],"_id":"1141","intvolume":"        17","scopus_import":1,"year":"2016","issue":"1","date_updated":"2021-01-12T06:48:35Z","acknowledgement":"The work presented in this paper was partially supported by Polish National Science Centre grant nos. DEC-2012/05/N/ST6/03433 and DEC-2011/03/B/ST6/01393. Radosław Łazarz was supported by Polish National Science Centre grant no. DEC-2013/10/M/ST6/00531.","title":"Hierarchic genetic strategy with maturing as a generic tool for multiobjective optimization","publist_id":"6217","citation":{"apa":"Łazarz, R., Idzik, M., Gądek, K., &#38; Gajda-Zagorska, E. P. (2016). Hierarchic genetic strategy with maturing as a generic tool for multiobjective optimization. <i>Journal of Computational Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jocs.2016.03.004\">https://doi.org/10.1016/j.jocs.2016.03.004</a>","ieee":"R. Łazarz, M. Idzik, K. Gądek, and E. P. Gajda-Zagorska, “Hierarchic genetic strategy with maturing as a generic tool for multiobjective optimization,” <i>Journal of Computational Science</i>, vol. 17, no. 1. Elsevier, pp. 249–260, 2016.","ama":"Łazarz R, Idzik M, Gądek K, Gajda-Zagorska EP. Hierarchic genetic strategy with maturing as a generic tool for multiobjective optimization. <i>Journal of Computational Science</i>. 2016;17(1):249-260. doi:<a href=\"https://doi.org/10.1016/j.jocs.2016.03.004\">10.1016/j.jocs.2016.03.004</a>","short":"R. Łazarz, M. Idzik, K. Gądek, E.P. Gajda-Zagorska, Journal of Computational Science 17 (2016) 249–260.","mla":"Łazarz, Radosław, et al. “Hierarchic Genetic Strategy with Maturing as a Generic Tool for Multiobjective Optimization.” <i>Journal of Computational Science</i>, vol. 17, no. 1, Elsevier, 2016, pp. 249–60, doi:<a href=\"https://doi.org/10.1016/j.jocs.2016.03.004\">10.1016/j.jocs.2016.03.004</a>.","chicago":"Łazarz, Radosław, Michał Idzik, Konrad Gądek, and Ewa P Gajda-Zagorska. “Hierarchic Genetic Strategy with Maturing as a Generic Tool for Multiobjective Optimization.” <i>Journal of Computational Science</i>. Elsevier, 2016. <a href=\"https://doi.org/10.1016/j.jocs.2016.03.004\">https://doi.org/10.1016/j.jocs.2016.03.004</a>.","ista":"Łazarz R, Idzik M, Gądek K, Gajda-Zagorska EP. 2016. Hierarchic genetic strategy with maturing as a generic tool for multiobjective optimization. Journal of Computational Science. 17(1), 249–260."},"date_created":"2018-12-11T11:50:22Z","type":"journal_article","status":"public","date_published":"2016-11-01T00:00:00Z","publisher":"Elsevier","volume":17,"quality_controlled":"1","page":"249 - 260","department":[{"_id":"ChWo"}],"month":"11","abstract":[{"text":"In this paper we introduce the Multiobjective Optimization Hierarchic Genetic Strategy with maturing (MO-mHGS), a meta-algorithm that performs evolutionary optimization in a hierarchy of populations. The maturing mechanism improves growth and reduces redundancy. The performance of MO-mHGS with selected state-of-the-art multiobjective evolutionary algorithms as internal algorithms is analysed on benchmark problems and their modifications for which single fitness evaluation time depends on the solution accuracy. We compare the proposed algorithm with the Island Model Genetic Algorithm as well as with single-deme methods, and discuss the impact of internal algorithms on the MO-mHGS meta-algorithm. © 2016 Elsevier B.V.","lang":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"None","day":"01","author":[{"full_name":"Łazarz, Radosław","first_name":"Radosław","last_name":"Łazarz"},{"last_name":"Idzik","first_name":"Michał","full_name":"Idzik, Michał"},{"first_name":"Konrad","full_name":"Gądek, Konrad","last_name":"Gądek"},{"full_name":"Gajda-Zagorska, Ewa P","first_name":"Ewa P","id":"47794CF0-F248-11E8-B48F-1D18A9856A87","last_name":"Gajda-Zagorska"}],"publication_status":"published"},{"type":"journal_article","status":"public","author":[{"last_name":"Martins","first_name":"Rui","full_name":"Martins, Rui"},{"last_name":"Maier","first_name":"Julia","full_name":"Maier, Julia"},{"last_name":"Gorki","first_name":"Anna","full_name":"Gorki, Anna"},{"last_name":"Huber","first_name":"Kilian","full_name":"Huber, Kilian"},{"full_name":"Sharif, Omar","first_name":"Omar","last_name":"Sharif"},{"full_name":"Starkl, Philipp","first_name":"Philipp","last_name":"Starkl"},{"first_name":"Simona","full_name":"Saluzzo, Simona","last_name":"Saluzzo"},{"last_name":"Quattrone","full_name":"Quattrone, Federica","first_name":"Federica"},{"first_name":"Riem","full_name":"Gawish, Riem","last_name":"Gawish"},{"full_name":"Lakovits, Karin","first_name":"Karin","last_name":"Lakovits"},{"last_name":"Aichinger","first_name":"Michael","full_name":"Aichinger, Michael"},{"last_name":"Radic Sarikas","first_name":"Branka","full_name":"Radic Sarikas, Branka"},{"last_name":"Lardeau","first_name":"Charles","full_name":"Lardeau, Charles"},{"first_name":"Anastasiya","full_name":"Hladik, Anastasiya","last_name":"Hladik"},{"last_name":"Korosec","full_name":"Korosec, Ana","first_name":"Ana"},{"full_name":"Brown, Markus","first_name":"Markus","last_name":"Brown","id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Kari","full_name":"Vaahtomeri, Kari","id":"368EE576-F248-11E8-B48F-1D18A9856A87","last_name":"Vaahtomeri","orcid":"0000-0001-7829-3518"},{"first_name":"Michelle","full_name":"Duggan, Michelle","id":"2EDEA62C-F248-11E8-B48F-1D18A9856A87","last_name":"Duggan"},{"last_name":"Kerjaschki","first_name":"Dontscho","full_name":"Kerjaschki, Dontscho"},{"last_name":"Esterbauer","full_name":"Esterbauer, Harald","first_name":"Harald"},{"last_name":"Colinge","full_name":"Colinge, Jacques","first_name":"Jacques"},{"first_name":"Stephanie","full_name":"Eisenbarth, Stephanie","last_name":"Eisenbarth"},{"first_name":"Thomas","full_name":"Decker, Thomas","last_name":"Decker"},{"first_name":"Keiryn","full_name":"Bennett, Keiryn","last_name":"Bennett"},{"first_name":"Stefan","full_name":"Kubicek, Stefan","last_name":"Kubicek"},{"last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K","full_name":"Sixt, Michael K"},{"first_name":"Giulio","full_name":"Superti Furga, Giulio","last_name":"Superti Furga"},{"last_name":"Knapp","first_name":"Sylvia","full_name":"Knapp, Sylvia"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","day":"01","oa_version":"Submitted Version","main_file_link":[{"url":"https://ora.ox.ac.uk/objects/uuid:f53a464e-1e5b-4f08-a7d8-b6749b852b9d","open_access":"1"}],"month":"12","language":[{"iso":"eng"}],"publication":"Nature Immunology","title":"Heme drives hemolysis-induced susceptibility to infection via disruption of phagocyte functions","issue":"12","oa":1,"date_updated":"2021-01-12T06:48:36Z","scopus_import":1,"intvolume":"        17","volume":17,"quality_controlled":"1","page":"1361 - 1372","department":[{"_id":"MiSi"},{"_id":"PeJo"}],"date_published":"2016-12-01T00:00:00Z","publisher":"Nature Publishing Group","publication_status":"published","abstract":[{"lang":"eng","text":"Hemolysis drives susceptibility to bacterial infections and predicts poor outcome from sepsis. These detrimental effects are commonly considered to be a consequence of heme-iron serving as a nutrient for bacteria. We employed a Gram-negative sepsis model and found that elevated heme levels impaired the control of bacterial proliferation independently of heme-iron acquisition by pathogens. Heme strongly inhibited phagocytosis and the migration of human and mouse phagocytes by disrupting actin cytoskeletal dynamics via activation of the GTP-binding Rho family protein Cdc42 by the guanine nucleotide exchange factor DOCK8. A chemical screening approach revealed that quinine effectively prevented heme effects on the cytoskeleton, restored phagocytosis and improved survival in sepsis. These mechanistic insights provide potential therapeutic targets for patients with sepsis or hemolytic disorders."}],"_id":"1142","doi":"10.1038/ni.3590","citation":{"short":"R. Martins, J. Maier, A. Gorki, K. Huber, O. Sharif, P. Starkl, S. Saluzzo, F. Quattrone, R. Gawish, K. Lakovits, M. Aichinger, B. Radic Sarikas, C. Lardeau, A. Hladik, A. Korosec, M. Brown, K. Vaahtomeri, M. Duggan, D. Kerjaschki, H. Esterbauer, J. Colinge, S. Eisenbarth, T. Decker, K. Bennett, S. Kubicek, M.K. Sixt, G. Superti Furga, S. Knapp, Nature Immunology 17 (2016) 1361–1372.","ama":"Martins R, Maier J, Gorki A, et al. Heme drives hemolysis-induced susceptibility to infection via disruption of phagocyte functions. <i>Nature Immunology</i>. 2016;17(12):1361-1372. doi:<a href=\"https://doi.org/10.1038/ni.3590\">10.1038/ni.3590</a>","ieee":"R. Martins <i>et al.</i>, “Heme drives hemolysis-induced susceptibility to infection via disruption of phagocyte functions,” <i>Nature Immunology</i>, vol. 17, no. 12. Nature Publishing Group, pp. 1361–1372, 2016.","ista":"Martins R, Maier J, Gorki A, Huber K, Sharif O, Starkl P, Saluzzo S, Quattrone F, Gawish R, Lakovits K, Aichinger M, Radic Sarikas B, Lardeau C, Hladik A, Korosec A, Brown M, Vaahtomeri K, Duggan M, Kerjaschki D, Esterbauer H, Colinge J, Eisenbarth S, Decker T, Bennett K, Kubicek S, Sixt MK, Superti Furga G, Knapp S. 2016. Heme drives hemolysis-induced susceptibility to infection via disruption of phagocyte functions. Nature Immunology. 17(12), 1361–1372.","chicago":"Martins, Rui, Julia Maier, Anna Gorki, Kilian Huber, Omar Sharif, Philipp Starkl, Simona Saluzzo, et al. “Heme Drives Hemolysis-Induced Susceptibility to Infection via Disruption of Phagocyte Functions.” <i>Nature Immunology</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/ni.3590\">https://doi.org/10.1038/ni.3590</a>.","mla":"Martins, Rui, et al. “Heme Drives Hemolysis-Induced Susceptibility to Infection via Disruption of Phagocyte Functions.” <i>Nature Immunology</i>, vol. 17, no. 12, Nature Publishing Group, 2016, pp. 1361–72, doi:<a href=\"https://doi.org/10.1038/ni.3590\">10.1038/ni.3590</a>.","apa":"Martins, R., Maier, J., Gorki, A., Huber, K., Sharif, O., Starkl, P., … Knapp, S. (2016). Heme drives hemolysis-induced susceptibility to infection via disruption of phagocyte functions. <i>Nature Immunology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ni.3590\">https://doi.org/10.1038/ni.3590</a>"},"date_created":"2018-12-11T11:50:22Z","publist_id":"6216","year":"2016","acknowledgement":"Y. Fukui (Medical Institute of Bioregulation, Kyushu University) and J. Stein (Theodor Kocher Institute, University of Bern) are acknowledged for providing the DOCK8 deficient bone marrow. and H. Häcker (St. Judes Children's Research Hospital) for providing the ERHBD-HoxB8-encoding retroviral construct. pSpCas9(BB)-2a-Puro (PX459) was a gift from F. Zhang (Massachusetts Institute of Technology) (Addgene plasmid # 48139) and pGRG36 was a gift from N. Craig (Johns Hopkins University School of Medicine) (Addgene plasmid # 16666). LifeAct-GFP-encoding retrovirus was kindly provided by A. Leithner (Institute of Science and Technology Austria). pSIM8 and TKC E. coli were gifts from D.L. Court (Center for Cancer Research, National Cancer Institute). We acknowledge M. Gröger and S. Rauscher for excellent technical support (Core imaging facility, Medical University of Vienna). We thank D.P. Barlow and L.R. Cheever for critical reading of the manuscript. This work was supported by the Austrian Academy of Sciences, the Science Fund of the Austrian National Bank (14107) and the Austrian Science Fund FWF (I1620-B22) in the Infect-ERA framework (to S.Knapp)."},{"doi":"10.2140/apde.2016.9.459","_id":"1143","ec_funded":1,"publist_id":"6215","date_created":"2018-12-11T11:50:23Z","citation":{"apa":"Nam, P., Rougerie, N., &#38; Seiringer, R. (2016). Ground states of large bosonic systems: The gross Pitaevskii limit revisited. <i>Analysis and PDE</i>. Mathematical Sciences Publishers. <a href=\"https://doi.org/10.2140/apde.2016.9.459\">https://doi.org/10.2140/apde.2016.9.459</a>","short":"P. Nam, N. Rougerie, R. Seiringer, Analysis and PDE 9 (2016) 459–485.","ama":"Nam P, Rougerie N, Seiringer R. Ground states of large bosonic systems: The gross Pitaevskii limit revisited. <i>Analysis and PDE</i>. 2016;9(2):459-485. doi:<a href=\"https://doi.org/10.2140/apde.2016.9.459\">10.2140/apde.2016.9.459</a>","ieee":"P. Nam, N. Rougerie, and R. Seiringer, “Ground states of large bosonic systems: The gross Pitaevskii limit revisited,” <i>Analysis and PDE</i>, vol. 9, no. 2. Mathematical Sciences Publishers, pp. 459–485, 2016.","chicago":"Nam, Phan, Nicolas Rougerie, and Robert Seiringer. “Ground States of Large Bosonic Systems: The Gross Pitaevskii Limit Revisited.” <i>Analysis and PDE</i>. Mathematical Sciences Publishers, 2016. <a href=\"https://doi.org/10.2140/apde.2016.9.459\">https://doi.org/10.2140/apde.2016.9.459</a>.","mla":"Nam, Phan, et al. “Ground States of Large Bosonic Systems: The Gross Pitaevskii Limit Revisited.” <i>Analysis and PDE</i>, vol. 9, no. 2, Mathematical Sciences Publishers, 2016, pp. 459–85, doi:<a href=\"https://doi.org/10.2140/apde.2016.9.459\">10.2140/apde.2016.9.459</a>.","ista":"Nam P, Rougerie N, Seiringer R. 2016. Ground states of large bosonic systems: The gross Pitaevskii limit revisited. Analysis and PDE. 9(2), 459–485."},"year":"2016","volume":9,"quality_controlled":"1","department":[{"_id":"RoSe"}],"page":"459 - 485","date_published":"2016-03-24T00:00:00Z","publisher":"Mathematical Sciences Publishers","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"abstract":[{"text":"We study the ground state of a dilute Bose gas in a scaling limit where the Gross-Pitaevskii functional emerges. This is a repulsive nonlinear Schrödinger functional whose quartic term is proportional to the scattering length of the interparticle interaction potential. We propose a new derivation of this limit problem, with a method that bypasses some of the technical difficulties that previous derivations had to face. The new method is based on a combination of Dyson\\'s lemma, the quantum de Finetti theorem and a second moment estimate for ground states of the effective Dyson Hamiltonian. It applies equally well to the case where magnetic fields or rotation are present.","lang":"eng"}],"publication_status":"published","publication":"Analysis and PDE","language":[{"iso":"eng"}],"scopus_import":1,"intvolume":"         9","title":"Ground states of large bosonic systems: The gross Pitaevskii limit revisited","issue":"2","oa":1,"date_updated":"2021-01-12T06:48:36Z","type":"journal_article","status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1503.07061"}],"oa_version":"Preprint","day":"24","month":"03","author":[{"last_name":"Nam","id":"404092F4-F248-11E8-B48F-1D18A9856A87","first_name":"Phan","full_name":"Nam, Phan"},{"last_name":"Rougerie","first_name":"Nicolas","full_name":"Rougerie, Nicolas"},{"first_name":"Robert","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer"}]},{"date_published":"2016-11-07T00:00:00Z","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","publisher":"Cell Press","quality_controlled":"1","volume":9,"department":[{"_id":"JiFr"}],"page":"1504 - 1519","project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"ddc":["581"],"abstract":[{"lang":"eng","text":"Auxin directs plant ontogenesis via differential accumulation within tissues depending largely on the activity of PIN proteins that mediate auxin efflux from cells and its directional cell-to-cell transport. Regardless of the developmental importance of PINs, the structure of these transporters is poorly characterized. Here, we present experimental data concerning protein topology of plasma membrane-localized PINs. Utilizing approaches based on pH-dependent quenching of fluorescent reporters combined with immunolocalization techniques, we mapped the membrane topology of PINs and further cross-validated our results using available topology modeling software. We delineated the topology of PIN1 with two transmembrane (TM) bundles of five α-helices linked by a large intracellular loop and a C-terminus positioned outside the cytoplasm. Using constraints derived from our experimental data, we also provide an updated position of helical regions generating a verisimilitude model of PIN1. Since the canonical long PINs show a high degree of conservation in TM domains and auxin transport capacity has been demonstrated for Arabidopsis representatives of this group, this empirically enhanced topological model of PIN1 will be an important starting point for further studies on PIN structure–function relationships. In addition, we have established protocols that can be used to probe the topology of other plasma membrane proteins in plants. © 2016 The Authors"}],"publication_status":"published","doi":"10.1016/j.molp.2016.08.010","_id":"1145","file_date_updated":"2018-12-12T10:13:22Z","ec_funded":1,"year":"2016","acknowledgement":"This research has been financially supported by the Ministry of Education, Youth and Sports of the Czech Republic under the project CEITEC 2020 (LQ1601) (T.N., M.Z., M.P., J.H.), Czech Science Foundation (13-40637S [J.F., M.Z.], 13-39982S [J.H.]); Research Foundation Flanders (Grant number FWO09/PDO/196) (S.V.) and the European Research Council (project ERC-2011-StG-20101109-PSDP) (J.F.). We thank David G. Robinson and Ranjan Swarup for sharing published material; Maria Šimášková, Mamoona Khan, Eva Benková for technical assistance; and R. Tejos, J. Kleine-Vehn, and E. Feraru for helpful discussions.","publist_id":"6213","date_created":"2018-12-11T11:50:23Z","citation":{"short":"T. Nodzyński, S. Vanneste, M. Zwiewka, M. Pernisová, J. Hejátko, J. Friml, Molecular Plant 9 (2016) 1504–1519.","ieee":"T. Nodzyński, S. Vanneste, M. Zwiewka, M. Pernisová, J. Hejátko, and J. Friml, “Enquiry into the topology of plasma membrane localized PIN auxin transport components,” <i>Molecular Plant</i>, vol. 9, no. 11. Cell Press, pp. 1504–1519, 2016.","ama":"Nodzyński T, Vanneste S, Zwiewka M, Pernisová M, Hejátko J, Friml J. Enquiry into the topology of plasma membrane localized PIN auxin transport components. <i>Molecular Plant</i>. 2016;9(11):1504-1519. doi:<a href=\"https://doi.org/10.1016/j.molp.2016.08.010\">10.1016/j.molp.2016.08.010</a>","ista":"Nodzyński T, Vanneste S, Zwiewka M, Pernisová M, Hejátko J, Friml J. 2016. Enquiry into the topology of plasma membrane localized PIN auxin transport components. Molecular Plant. 9(11), 1504–1519.","chicago":"Nodzyński, Tomasz, Steffen Vanneste, Marta Zwiewka, Markéta Pernisová, Jan Hejátko, and Jiří Friml. “Enquiry into the Topology of Plasma Membrane Localized PIN Auxin Transport Components.” <i>Molecular Plant</i>. Cell Press, 2016. <a href=\"https://doi.org/10.1016/j.molp.2016.08.010\">https://doi.org/10.1016/j.molp.2016.08.010</a>.","mla":"Nodzyński, Tomasz, et al. “Enquiry into the Topology of Plasma Membrane Localized PIN Auxin Transport Components.” <i>Molecular Plant</i>, vol. 9, no. 11, Cell Press, 2016, pp. 1504–19, doi:<a href=\"https://doi.org/10.1016/j.molp.2016.08.010\">10.1016/j.molp.2016.08.010</a>.","apa":"Nodzyński, T., Vanneste, S., Zwiewka, M., Pernisová, M., Hejátko, J., &#38; Friml, J. (2016). Enquiry into the topology of plasma membrane localized PIN auxin transport components. <i>Molecular Plant</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.molp.2016.08.010\">https://doi.org/10.1016/j.molp.2016.08.010</a>"},"type":"journal_article","status":"public","month":"11","file":[{"relation":"main_file","file_size":5005876,"access_level":"open_access","content_type":"application/pdf","creator":"system","date_created":"2018-12-12T10:13:22Z","date_updated":"2018-12-12T10:13:22Z","file_id":"5004","file_name":"IST-2017-746-v1+1_1-s2.0-S1674205216301915-main.pdf"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","day":"07","author":[{"last_name":"Nodzyński","full_name":"Nodzyński, Tomasz","first_name":"Tomasz"},{"first_name":"Steffen","full_name":"Vanneste, Steffen","last_name":"Vanneste"},{"full_name":"Zwiewka, Marta","first_name":"Marta","last_name":"Zwiewka"},{"first_name":"Markéta","full_name":"Pernisová, Markéta","last_name":"Pernisová"},{"last_name":"Hejátko","first_name":"Jan","full_name":"Hejátko, Jan"},{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","first_name":"Jirí"}],"publication":"Molecular Plant","language":[{"iso":"eng"}],"scopus_import":1,"has_accepted_license":"1","intvolume":"         9","issue":"11","oa":1,"pubrep_id":"746","date_updated":"2021-01-12T06:48:37Z","title":"Enquiry into the topology of plasma membrane localized PIN auxin transport components"},{"status":"public","type":"journal_article","file":[{"file_name":"IST-2017-745-v1+1_srep35955.pdf","file_id":"4752","date_updated":"2018-12-12T10:09:28Z","date_created":"2018-12-12T10:09:28Z","creator":"system","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_size":1587544}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","day":"08","month":"11","author":[{"full_name":"Balla, Jozef","first_name":"Jozef","last_name":"Balla"},{"full_name":"Medved'Ová, Zuzana","first_name":"Zuzana","last_name":"Medved'Ová"},{"first_name":"Petr","full_name":"Kalousek, Petr","last_name":"Kalousek"},{"last_name":"Matiješčuková","first_name":"Natálie","full_name":"Matiješčuková, Natálie"},{"full_name":"Friml, Jirí","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596"},{"last_name":"Reinöhl","full_name":"Reinöhl, Vilém","first_name":"Vilém"},{"first_name":"Stanislav","full_name":"Procházka, Stanislav","last_name":"Procházka"}],"publication":"Scientific Reports","language":[{"iso":"eng"}],"scopus_import":1,"intvolume":"         6","has_accepted_license":"1","title":"Auxin flow mediated competition between axillary buds to restore apical dominance","date_updated":"2021-01-12T06:48:38Z","oa":1,"pubrep_id":"745","volume":6,"quality_controlled":"1","department":[{"_id":"JiFr"}],"date_published":"2016-11-08T00:00:00Z","publisher":"Nature Publishing Group","abstract":[{"lang":"eng","text":"Apical dominance is one of the fundamental developmental phenomena in plant biology, which determines the overall architecture of aerial plant parts. Here we show apex decapitation activated competition for dominance in adjacent upper and lower axillary buds. A two-nodal-bud pea (Pisum sativum L.) was used as a model system to monitor and assess auxin flow, auxin transport channels, and dormancy and initiation status of axillary buds. Auxin flow was manipulated by lateral stem wounds or chemically by auxin efflux inhibitors 2,3,5-triiodobenzoic acid (TIBA), 1-N-naphtylphtalamic acid (NPA), or protein synthesis inhibitor cycloheximide (CHX) treatments, which served to interfere with axillary bud competition. Redirecting auxin flow to different points influenced which bud formed the outgrowing and dominant shoot. The obtained results proved that competition between upper and lower axillary buds as secondary auxin sources is based on the same auxin canalization principle that operates between the shoot apex and axillary bud. © The Author(s) 2016."}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["581"],"publication_status":"published","doi":"10.1038/srep35955","_id":"1147","file_date_updated":"2018-12-12T10:09:28Z","article_number":"35955","citation":{"apa":"Balla, J., Medved’Ová, Z., Kalousek, P., Matiješčuková, N., Friml, J., Reinöhl, V., &#38; Procházka, S. (2016). Auxin flow mediated competition between axillary buds to restore apical dominance. <i>Scientific Reports</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/srep35955\">https://doi.org/10.1038/srep35955</a>","ama":"Balla J, Medved’Ová Z, Kalousek P, et al. Auxin flow mediated competition between axillary buds to restore apical dominance. <i>Scientific Reports</i>. 2016;6. doi:<a href=\"https://doi.org/10.1038/srep35955\">10.1038/srep35955</a>","ieee":"J. Balla <i>et al.</i>, “Auxin flow mediated competition between axillary buds to restore apical dominance,” <i>Scientific Reports</i>, vol. 6. Nature Publishing Group, 2016.","short":"J. Balla, Z. Medved’Ová, P. Kalousek, N. Matiješčuková, J. Friml, V. Reinöhl, S. Procházka, Scientific Reports 6 (2016).","mla":"Balla, Jozef, et al. “Auxin Flow Mediated Competition between Axillary Buds to Restore Apical Dominance.” <i>Scientific Reports</i>, vol. 6, 35955, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/srep35955\">10.1038/srep35955</a>.","ista":"Balla J, Medved’Ová Z, Kalousek P, Matiješčuková N, Friml J, Reinöhl V, Procházka S. 2016. Auxin flow mediated competition between axillary buds to restore apical dominance. Scientific Reports. 6, 35955.","chicago":"Balla, Jozef, Zuzana Medved’Ová, Petr Kalousek, Natálie Matiješčuková, Jiří Friml, Vilém Reinöhl, and Stanislav Procházka. “Auxin Flow Mediated Competition between Axillary Buds to Restore Apical Dominance.” <i>Scientific Reports</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/srep35955\">https://doi.org/10.1038/srep35955</a>."},"date_created":"2018-12-11T11:50:24Z","publist_id":"6211","year":"2016","acknowledgement":"This research was carried out under the project CEITEC 2020 (LQ1601) with financial support from the Ministry of Education, Youth and Sports of the Czech Republic under the National Sustainability Programme II., supported by the project “CEITEC–Central European Institute of Technology” (CZ.1.05/1.1.00/02.0068) and the Agronomy faculty grant from Mendel University “IGA AF MENDELU” (IP 14/2013)."},{"intvolume":"       149","scopus_import":1,"date_updated":"2023-02-23T10:08:46Z","title":"Adaptive moment closure for parameter inference of biochemical reaction networks","publication":"Biosystems","language":[{"iso":"eng"}],"month":"11","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","oa_version":"None","author":[{"last_name":"Schilling","full_name":"Schilling, Christian","first_name":"Christian"},{"full_name":"Bogomolov, Sergiy","first_name":"Sergiy","orcid":"0000-0002-0686-0365","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","last_name":"Bogomolov"},{"orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A","first_name":"Thomas A"},{"last_name":"Podelski","first_name":"Andreas","full_name":"Podelski, Andreas"},{"full_name":"Ruess, Jakob","first_name":"Jakob","id":"4A245D00-F248-11E8-B48F-1D18A9856A87","last_name":"Ruess","orcid":"0000-0003-1615-3282"}],"status":"public","type":"journal_article","related_material":{"record":[{"status":"public","id":"1658","relation":"earlier_version"}]},"ec_funded":1,"year":"2016","acknowledgement":"This work is based on the CMSB 2015 paper “Adaptive moment closure for parameter inference of biochemical reaction networks” (Bogomolov et al., 2015). The work was partly supported by the German Research Foundation (DFG) as part of the Transregional Collaborative Research Center “Automatic Verification and Analysis of Complex Systems” (SFB/TR 14 AVACS1), by the European Research Council (ERC) under grant 267989 (QUAREM) and by the Austrian Science Fund (FWF) under grants S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award). J.R. acknowledges support from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. 291734.","publist_id":"6210","citation":{"apa":"Schilling, C., Bogomolov, S., Henzinger, T. A., Podelski, A., &#38; Ruess, J. (2016). Adaptive moment closure for parameter inference of biochemical reaction networks. <i>Biosystems</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.biosystems.2016.07.005\">https://doi.org/10.1016/j.biosystems.2016.07.005</a>","short":"C. Schilling, S. Bogomolov, T.A. Henzinger, A. Podelski, J. Ruess, Biosystems 149 (2016) 15–25.","ama":"Schilling C, Bogomolov S, Henzinger TA, Podelski A, Ruess J. Adaptive moment closure for parameter inference of biochemical reaction networks. <i>Biosystems</i>. 2016;149:15-25. doi:<a href=\"https://doi.org/10.1016/j.biosystems.2016.07.005\">10.1016/j.biosystems.2016.07.005</a>","ieee":"C. Schilling, S. Bogomolov, T. A. Henzinger, A. Podelski, and J. Ruess, “Adaptive moment closure for parameter inference of biochemical reaction networks,” <i>Biosystems</i>, vol. 149. Elsevier, pp. 15–25, 2016.","mla":"Schilling, Christian, et al. “Adaptive Moment Closure for Parameter Inference of Biochemical Reaction Networks.” <i>Biosystems</i>, vol. 149, Elsevier, 2016, pp. 15–25, doi:<a href=\"https://doi.org/10.1016/j.biosystems.2016.07.005\">10.1016/j.biosystems.2016.07.005</a>.","ista":"Schilling C, Bogomolov S, Henzinger TA, Podelski A, Ruess J. 2016. Adaptive moment closure for parameter inference of biochemical reaction networks. Biosystems. 149, 15–25.","chicago":"Schilling, Christian, Sergiy Bogomolov, Thomas A Henzinger, Andreas Podelski, and Jakob Ruess. “Adaptive Moment Closure for Parameter Inference of Biochemical Reaction Networks.” <i>Biosystems</i>. Elsevier, 2016. <a href=\"https://doi.org/10.1016/j.biosystems.2016.07.005\">https://doi.org/10.1016/j.biosystems.2016.07.005</a>."},"date_created":"2018-12-11T11:50:24Z","doi":"10.1016/j.biosystems.2016.07.005","_id":"1148","abstract":[{"text":"Continuous-time Markov chain (CTMC) models have become a central tool for understanding the dynamics of complex reaction networks and the importance of stochasticity in the underlying biochemical processes. When such models are employed to answer questions in applications, in order to ensure that the model provides a sufficiently accurate representation of the real system, it is of vital importance that the model parameters are inferred from real measured data. This, however, is often a formidable task and all of the existing methods fail in one case or the other, usually because the underlying CTMC model is high-dimensional and computationally difficult to analyze. The parameter inference methods that tend to scale best in the dimension of the CTMC are based on so-called moment closure approximations. However, there exists a large number of different moment closure approximations and it is typically hard to say a priori which of the approximations is the most suitable for the inference procedure. Here, we propose a moment-based parameter inference method that automatically chooses the most appropriate moment closure method. Accordingly, contrary to existing methods, the user is not required to be experienced in moment closure techniques. In addition to that, our method adaptively changes the approximation during the parameter inference to ensure that always the best approximation is used, even in cases where different approximations are best in different regions of the parameter space. © 2016 Elsevier Ireland Ltd","lang":"eng"}],"publication_status":"published","date_published":"2016-11-01T00:00:00Z","publisher":"Elsevier","quality_controlled":"1","volume":149,"department":[{"_id":"ToHe"},{"_id":"GaTk"}],"page":"15 - 25","project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","name":"Quantitative Reactive Modeling","call_identifier":"FP7"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}]},{"ec_funded":1,"intvolume":"       107","scopus_import":1,"publist_id":"6209","date_created":"2018-12-11T11:50:25Z","citation":{"chicago":"Miyaji, Tomoyuki, Pawel Pilarczyk, Marcio Gameiro, Hiroshi Kokubu, and Konstantin Mischaikow. “A Study of Rigorous ODE Integrators for Multi Scale Set Oriented Computations.” <i>Applied Numerical Mathematics</i>. Elsevier, 2016. <a href=\"https://doi.org/10.1016/j.apnum.2016.04.005\">https://doi.org/10.1016/j.apnum.2016.04.005</a>.","mla":"Miyaji, Tomoyuki, et al. “A Study of Rigorous ODE Integrators for Multi Scale Set Oriented Computations.” <i>Applied Numerical Mathematics</i>, vol. 107, Elsevier, 2016, pp. 34–47, doi:<a href=\"https://doi.org/10.1016/j.apnum.2016.04.005\">10.1016/j.apnum.2016.04.005</a>.","ista":"Miyaji T, Pilarczyk P, Gameiro M, Kokubu H, Mischaikow K. 2016. A study of rigorous ODE integrators for multi scale set oriented computations. Applied Numerical Mathematics. 107, 34–47.","short":"T. Miyaji, P. Pilarczyk, M. Gameiro, H. Kokubu, K. Mischaikow, Applied Numerical Mathematics 107 (2016) 34–47.","ama":"Miyaji T, Pilarczyk P, Gameiro M, Kokubu H, Mischaikow K. A study of rigorous ODE integrators for multi scale set oriented computations. <i>Applied Numerical Mathematics</i>. 2016;107:34-47. doi:<a href=\"https://doi.org/10.1016/j.apnum.2016.04.005\">10.1016/j.apnum.2016.04.005</a>","ieee":"T. Miyaji, P. Pilarczyk, M. Gameiro, H. Kokubu, and K. Mischaikow, “A study of rigorous ODE integrators for multi scale set oriented computations,” <i>Applied Numerical Mathematics</i>, vol. 107. Elsevier, pp. 34–47, 2016.","apa":"Miyaji, T., Pilarczyk, P., Gameiro, M., Kokubu, H., &#38; Mischaikow, K. (2016). A study of rigorous ODE integrators for multi scale set oriented computations. <i>Applied Numerical Mathematics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.apnum.2016.04.005\">https://doi.org/10.1016/j.apnum.2016.04.005</a>"},"title":"A study of rigorous ODE integrators for multi scale set oriented computations","date_updated":"2021-01-12T06:48:38Z","acknowledgement":"MG was partially supported by FAPESP grants 2013/07460-7 and 2010/00875-9, and by CNPq grants 305860/2013-5 and 306453/2009-6, Brazil. The work of HK was partially supported by Grant-in-Aid for Scientific Research (Nos.24654022, 25287029), Ministry of Education, Science, Technology, Culture and Sports, Japan. KM was supported by NSF grants NSF-DMS-0835621, 0915019, 1125174, 1248071, and contracts from AFOSR and DARPA. TM was supported by Grant-in-Aid for JSPS Fellows No. 245312. A part of the research of TM and HK was also supported by JST, CREST.\r\n\r\nResearch conducted by PP has received funding from Fundo Europeu de Desenvolvimento Regional (FEDER) through COMPETE – Programa Operacional Factores de Competitividade (POFC) and from the Portuguese national funds through Fundação para a Ciência e a Tecnologia (FCT) in the framework of the research project FCOMP-01-0124-FEDER-010645 (Ref. FCT PTDC/MAT/098871/2008); from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement No. 622033; and from the same sources as HK.\r\n\r\nThe authors express their gratitude to the Department of Mathematics of Kyoto University for making their server available for conducting the computations described in the paper, and to the reviewers for helpful comments that contributed towards increasing the quality of the paper.","year":"2016","doi":"10.1016/j.apnum.2016.04.005","publication":"Applied Numerical Mathematics","_id":"1149","language":[{"iso":"eng"}],"oa_version":"None","day":"01","abstract":[{"text":"We study the usefulness of two most prominent publicly available rigorous ODE integrators: one provided by the CAPD group (capd.ii.uj.edu.pl), the other based on the COSY Infinity project (cosyinfinity.org). Both integrators are capable of handling entire sets of initial conditions and provide tight rigorous outer enclosures of the images under a time-T map. We conduct extensive benchmark computations using the well-known Lorenz system, and compare the computation time against the final accuracy achieved. We also discuss the effect of a few technical parameters, such as the order of the numerical integration method, the value of T, and the phase space resolution. We conclude that COSY may provide more precise results due to its ability of avoiding the variable dependency problem. However, the overall cost of computations conducted using CAPD is typically lower, especially when intervals of parameters are involved. Moreover, access to COSY is limited (registration required) and the rigorous ODE integrators are not publicly available, while CAPD is an open source free software project. Therefore, we recommend the latter integrator for this kind of computations. Nevertheless, proper choice of the various integration parameters turns out to be of even greater importance than the choice of the integrator itself. © 2016 IMACS. Published by Elsevier B.V. All rights reserved.","lang":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","month":"09","author":[{"last_name":"Miyaji","full_name":"Miyaji, Tomoyuki","first_name":"Tomoyuki"},{"first_name":"Pawel","full_name":"Pilarczyk, Pawel","last_name":"Pilarczyk","id":"3768D56A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Marcio","full_name":"Gameiro, Marcio","last_name":"Gameiro"},{"last_name":"Kokubu","full_name":"Kokubu, Hiroshi","first_name":"Hiroshi"},{"last_name":"Mischaikow","first_name":"Konstantin","full_name":"Mischaikow, Konstantin"}],"publication_status":"published","page":"34 - 47","department":[{"_id":"HeEd"}],"volume":107,"quality_controlled":"1","publisher":"Elsevier","type":"journal_article","status":"public","date_published":"2016-09-01T00:00:00Z","project":[{"name":"Persistent Homology - Images, Data and Maps","call_identifier":"FP7","_id":"255F06BE-B435-11E9-9278-68D0E5697425","grant_number":"622033"}]},{"publication_status":"published","author":[{"full_name":"Renkawitz, Jörg","first_name":"Jörg","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","last_name":"Renkawitz","orcid":"0000-0003-2856-3369"},{"full_name":"Sixt, Michael K","first_name":"Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"When neutrophils infiltrate a site of inflammation, they have to stop at the right place to exert their effector function. In this issue of Developmental Cell, Wang et al. (2016) show that neutrophils sense reactive oxygen species via the TRPM2 channel to arrest migration at their target site. © 2016 Elsevier Inc.","lang":"eng"}],"oa_version":"None","day":"12","month":"09","volume":38,"quality_controlled":"1","department":[{"_id":"MiSi"}],"page":"448 - 450","date_published":"2016-09-12T00:00:00Z","status":"public","type":"journal_article","publisher":"Cell Press","title":"A Radical Break Restraining Neutrophil Migration","citation":{"apa":"Renkawitz, J., &#38; Sixt, M. K. (2016). A Radical Break Restraining Neutrophil Migration. <i>Developmental Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.devcel.2016.08.017\">https://doi.org/10.1016/j.devcel.2016.08.017</a>","chicago":"Renkawitz, Jörg, and Michael K Sixt. “A Radical Break Restraining Neutrophil Migration.” <i>Developmental Cell</i>. Cell Press, 2016. <a href=\"https://doi.org/10.1016/j.devcel.2016.08.017\">https://doi.org/10.1016/j.devcel.2016.08.017</a>.","mla":"Renkawitz, Jörg, and Michael K. Sixt. “A Radical Break Restraining Neutrophil Migration.” <i>Developmental Cell</i>, vol. 38, no. 5, Cell Press, 2016, pp. 448–50, doi:<a href=\"https://doi.org/10.1016/j.devcel.2016.08.017\">10.1016/j.devcel.2016.08.017</a>.","ista":"Renkawitz J, Sixt MK. 2016. A Radical Break Restraining Neutrophil Migration. Developmental Cell. 38(5), 448–450.","ama":"Renkawitz J, Sixt MK. A Radical Break Restraining Neutrophil Migration. <i>Developmental Cell</i>. 2016;38(5):448-450. doi:<a href=\"https://doi.org/10.1016/j.devcel.2016.08.017\">10.1016/j.devcel.2016.08.017</a>","ieee":"J. Renkawitz and M. K. Sixt, “A Radical Break Restraining Neutrophil Migration,” <i>Developmental Cell</i>, vol. 38, no. 5. Cell Press, pp. 448–450, 2016.","short":"J. Renkawitz, M.K. Sixt, Developmental Cell 38 (2016) 448–450."},"publist_id":"6208","date_created":"2018-12-11T11:50:25Z","issue":"5","year":"2016","date_updated":"2021-01-12T06:48:39Z","scopus_import":1,"intvolume":"        38","_id":"1150","language":[{"iso":"eng"}],"doi":"10.1016/j.devcel.2016.08.017","publication":"Developmental Cell"},{"pmid":1,"type":"journal_article","status":"public","month":"10","day":"15","oa_version":"Published Version","file":[{"file_id":"5882","file_name":"2016_GeneDev_Simonini.pdf","success":1,"date_updated":"2019-01-25T09:32:55Z","date_created":"2019-01-25T09:32:55Z","creator":"dernst","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_size":1419263}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Simonini, Sara","first_name":"Sara","last_name":"Simonini"},{"first_name":"Joyita","full_name":"Deb, Joyita","last_name":"Deb"},{"last_name":"Moubayidin","first_name":"Laila","full_name":"Moubayidin, Laila"},{"last_name":"Stephenson","first_name":"Pauline","full_name":"Stephenson, Pauline"},{"last_name":"Valluru","first_name":"Manoj","full_name":"Valluru, Manoj"},{"first_name":"Alejandra","full_name":"Freire Rios, Alejandra","last_name":"Freire Rios"},{"last_name":"Sorefan","full_name":"Sorefan, Karim","first_name":"Karim"},{"first_name":"Dolf","full_name":"Weijers, Dolf","last_name":"Weijers"},{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","first_name":"Jirí"},{"full_name":"Östergaard, Lars","first_name":"Lars","last_name":"Östergaard"}],"publication":"Genes and Development","language":[{"iso":"eng"}],"has_accepted_license":"1","scopus_import":1,"intvolume":"        30","oa":1,"date_updated":"2021-01-12T06:48:39Z","issue":"20","title":"A noncanonical auxin sensing mechanism is required for organ morphogenesis in arabidopsis","publisher":"Cold Spring Harbor Laboratory Press","date_published":"2016-10-15T00:00:00Z","page":"2286 - 2296","department":[{"_id":"JiFr"}],"quality_controlled":"1","volume":30,"ddc":["570"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"external_id":{"pmid":["27898393"]},"abstract":[{"text":"Tissue patterning in multicellular organisms is the output of precise spatio–temporal regulation of gene expression coupled with changes in hormone dynamics. In plants, the hormone auxin regulates growth and development at every stage of a plant’s life cycle. Auxin signaling occurs through binding of the auxin molecule to a TIR1/AFB F-box ubiquitin ligase, allowing interaction with Aux/IAA transcriptional repressor proteins. These are subsequently ubiquitinated and degraded via the 26S proteasome, leading to derepression of auxin response factors (ARFs). How auxin is able to elicit such a diverse range of developmental responses through a single signaling module has not yet been resolved. Here we present an alternative auxin-sensing mechanism in which the ARF ARF3/ETTIN controls gene expression through interactions with process-specific transcription factors. This noncanonical hormonesensing mechanism exhibits strong preference for the naturally occurring auxin indole 3-acetic acid (IAA) and is important for coordinating growth and patterning in diverse developmental contexts such as gynoecium morphogenesis, lateral root emergence, ovule development, and primary branch formation. Disrupting this IAA-sensing ability induces morphological aberrations with consequences for plant fitness. Therefore, our findings introduce a novel transcription factor-based mechanism of hormone perception in plants. © 2016 Simonini et al.","lang":"eng"}],"publication_status":"published","doi":"10.1101/gad.285361.116","file_date_updated":"2019-01-25T09:32:55Z","_id":"1151","acknowledgement":"We thank Norwich Research Park Bioimaging, Grant Calder, Roy\r\nDunford, Caroline Smith, Paul Thomas, and Mark Youles for\r\ntechnical support; Charlie Scutt, Alejandro Ferrando, and George\r\nLomonossoff for plasmids; Toshiro Ito for seeds; Brendan Davies\r\nand Barry Causier for the REGIA library; and Mark Buttner,\r\nSimona Masiero, Fabio Rossi, Doris Wagner, and Jun Xiao for\r\nhelp and material. We are also grateful to Stefano Bencivenga,\r\nMarie Brüser, Friederike Jantzen, Lukasz Langowski, Xinran Li,\r\nand Nicola Stacey for discussions and helpful comments on the\r\nmanuscript. This work was supported by grants BB/M004112/1\r\nand BB/I017232/1 (Crop Improvement Research Club) to L.Ø.\r\nfrom the Biotechnological and Biological Sciences Research\r\nCouncil, and Institute Strategic Programme grant (BB/J004553/\r\n1) to the John Innes Centre. S.S., J.D., and L.Ø conceived the ex-\r\nperiments. ","year":"2016","citation":{"apa":"Simonini, S., Deb, J., Moubayidin, L., Stephenson, P., Valluru, M., Freire Rios, A., … Östergaard, L. (2016). A noncanonical auxin sensing mechanism is required for organ morphogenesis in arabidopsis. <i>Genes and Development</i>. Cold Spring Harbor Laboratory Press. <a href=\"https://doi.org/10.1101/gad.285361.116\">https://doi.org/10.1101/gad.285361.116</a>","chicago":"Simonini, Sara, Joyita Deb, Laila Moubayidin, Pauline Stephenson, Manoj Valluru, Alejandra Freire Rios, Karim Sorefan, Dolf Weijers, Jiří Friml, and Lars Östergaard. “A Noncanonical Auxin Sensing Mechanism Is Required for Organ Morphogenesis in Arabidopsis.” <i>Genes and Development</i>. Cold Spring Harbor Laboratory Press, 2016. <a href=\"https://doi.org/10.1101/gad.285361.116\">https://doi.org/10.1101/gad.285361.116</a>.","ista":"Simonini S, Deb J, Moubayidin L, Stephenson P, Valluru M, Freire Rios A, Sorefan K, Weijers D, Friml J, Östergaard L. 2016. A noncanonical auxin sensing mechanism is required for organ morphogenesis in arabidopsis. Genes and Development. 30(20), 2286–2296.","mla":"Simonini, Sara, et al. “A Noncanonical Auxin Sensing Mechanism Is Required for Organ Morphogenesis in Arabidopsis.” <i>Genes and Development</i>, vol. 30, no. 20, Cold Spring Harbor Laboratory Press, 2016, pp. 2286–96, doi:<a href=\"https://doi.org/10.1101/gad.285361.116\">10.1101/gad.285361.116</a>.","short":"S. Simonini, J. Deb, L. Moubayidin, P. Stephenson, M. Valluru, A. Freire Rios, K. Sorefan, D. Weijers, J. Friml, L. Östergaard, Genes and Development 30 (2016) 2286–2296.","ieee":"S. Simonini <i>et al.</i>, “A noncanonical auxin sensing mechanism is required for organ morphogenesis in arabidopsis,” <i>Genes and Development</i>, vol. 30, no. 20. Cold Spring Harbor Laboratory Press, pp. 2286–2296, 2016.","ama":"Simonini S, Deb J, Moubayidin L, et al. A noncanonical auxin sensing mechanism is required for organ morphogenesis in arabidopsis. <i>Genes and Development</i>. 2016;30(20):2286-2296. doi:<a href=\"https://doi.org/10.1101/gad.285361.116\">10.1101/gad.285361.116</a>"},"date_created":"2018-12-11T11:50:25Z","publist_id":"6207"},{"project":[{"name":"Hormonal cross-talk in plant organogenesis","call_identifier":"FP7","_id":"253FCA6A-B435-11E9-9278-68D0E5697425","grant_number":"207362"}],"quality_controlled":"1","volume":28,"page":"2464 - 2477","department":[{"_id":"EvBe"},{"_id":"JiFr"}],"date_published":"2016-10-01T00:00:00Z","publisher":"American Society of Plant Biologists","publication_status":"published","abstract":[{"lang":"eng","text":"Differential cell growth enables flexible organ bending in the presence of environmental signals such as light or gravity. A prominent example of the developmental processes based on differential cell growth is the formation of the apical hook that protects the fragile shoot apical meristem when it breaks through the soil during germination. Here, we combined in silico and in vivo approaches to identify a minimal mechanism producing auxin gradient-guided differential growth during the establishment of the apical hook in the model plant Arabidopsis thaliana. Computer simulation models based on experimental data demonstrate that asymmetric expression of the PIN-FORMED auxin efflux carrier at the concave (inner) versus convex (outer) side of the hook suffices to establish an auxin maximum in the epidermis at the concave side of the apical hook. Furthermore, we propose a mechanism that translates this maximum into differential growth, and thus curvature, of the apical hook. Through a combination of experimental and in silico computational approaches, we have identified the individual contributions of differential cell elongation and proliferation to defining the apical hook and reveal the role of auxin-ethylene crosstalk in balancing these two processes. © 2016 American Society of Plant Biologists. All rights reserved."}],"_id":"1153","doi":"10.1105/tpc.15.00569","date_created":"2018-12-11T11:50:26Z","citation":{"chicago":"Žádníková, Petra, Krzysztof T Wabnik, Anas Abuzeineh, Marçal Gallemí, Dominique Van Der Straeten, Richard Smith, Dirk Inze, Jiří Friml, Przemysław Prusinkiewicz, and Eva Benková. “A Model of Differential Growth Guided Apical Hook Formation in Plants.” <i>Plant Cell</i>. American Society of Plant Biologists, 2016. <a href=\"https://doi.org/10.1105/tpc.15.00569\">https://doi.org/10.1105/tpc.15.00569</a>.","mla":"Žádníková, Petra, et al. “A Model of Differential Growth Guided Apical Hook Formation in Plants.” <i>Plant Cell</i>, vol. 28, no. 10, American Society of Plant Biologists, 2016, pp. 2464–77, doi:<a href=\"https://doi.org/10.1105/tpc.15.00569\">10.1105/tpc.15.00569</a>.","ista":"Žádníková P, Wabnik KT, Abuzeineh A, Gallemí M, Van Der Straeten D, Smith R, Inze D, Friml J, Prusinkiewicz P, Benková E. 2016. A model of differential growth guided apical hook formation in plants. Plant Cell. 28(10), 2464–2477.","short":"P. Žádníková, K.T. Wabnik, A. Abuzeineh, M. Gallemí, D. Van Der Straeten, R. Smith, D. Inze, J. Friml, P. Prusinkiewicz, E. Benková, Plant Cell 28 (2016) 2464–2477.","ama":"Žádníková P, Wabnik KT, Abuzeineh A, et al. A model of differential growth guided apical hook formation in plants. <i>Plant Cell</i>. 2016;28(10):2464-2477. doi:<a href=\"https://doi.org/10.1105/tpc.15.00569\">10.1105/tpc.15.00569</a>","ieee":"P. Žádníková <i>et al.</i>, “A model of differential growth guided apical hook formation in plants,” <i>Plant Cell</i>, vol. 28, no. 10. American Society of Plant Biologists, pp. 2464–2477, 2016.","apa":"Žádníková, P., Wabnik, K. T., Abuzeineh, A., Gallemí, M., Van Der Straeten, D., Smith, R., … Benková, E. (2016). A model of differential growth guided apical hook formation in plants. <i>Plant Cell</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1105/tpc.15.00569\">https://doi.org/10.1105/tpc.15.00569</a>"},"publist_id":"6205","year":"2016","acknowledgement":"We thank Martine De Cock and Annick Bleys for help in preparing the manuscript, Daniel Van Damme for sharing material and stimulating discussion, and Rudiger Simon for support during revision of the manuscript.\r\nThis work was supported by grants from the European Research Council (StartingIndependentResearchGrantERC-2007-Stg-207362-HCPO)and the Czech Science Foundation (GACR CZ.1.07/2.3.00/20.0043) to E.B.\r\nand Natural Sciences and Engineering Research Council of Canada Discovery Grant 2014-05325 to P.P. K.W. acknowledges funding from a Human Frontier Science Program Long-Term Fellowship (LT-000209-2014).","ec_funded":1,"type":"journal_article","status":"public","author":[{"full_name":"Žádníková, Petra","first_name":"Petra","last_name":"Žádníková"},{"id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","last_name":"Wabnik","orcid":"0000-0001-7263-0560","first_name":"Krzysztof T","full_name":"Wabnik, Krzysztof T"},{"last_name":"Abuzeineh","first_name":"Anas","full_name":"Abuzeineh, Anas"},{"first_name":"Marçal","full_name":"Gallemí, Marçal","last_name":"Gallemí"},{"last_name":"Van Der Straeten","first_name":"Dominique","full_name":"Van Der Straeten, Dominique"},{"full_name":"Smith, Richard","first_name":"Richard","last_name":"Smith"},{"full_name":"Inze, Dirk","first_name":"Dirk","last_name":"Inze"},{"first_name":"Jirí","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Prusinkiewicz","full_name":"Prusinkiewicz, Przemysław","first_name":"Przemysław"},{"last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","first_name":"Eva","full_name":"Benková, Eva"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","day":"01","oa_version":"Submitted Version","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5134968/","open_access":"1"}],"month":"10","language":[{"iso":"eng"}],"publication":"Plant Cell","title":"A model of differential growth guided apical hook formation in plants","issue":"10","date_updated":"2021-01-12T06:48:40Z","oa":1,"intvolume":"        28","scopus_import":1},{"publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["579"],"abstract":[{"lang":"eng","text":"Cellular locomotion is a central hallmark of eukaryotic life. It is governed by cell-extrinsic molecular factors, which can either emerge in the soluble phase or as immobilized, often adhesive ligands. To encode for direction, every cue must be present as a spatial or temporal gradient. Here, we developed a microfluidic chamber that allows measurement of cell migration in combined response to surface immobilized and soluble molecular gradients. As a proof of principle we study the response of dendritic cells to their major guidance cues, chemokines. The majority of data on chemokine gradient sensing is based on in vitro studies employing soluble gradients. Despite evidence suggesting that in vivo chemokines are often immobilized to sugar residues, limited information is available how cells respond to immobilized chemokines. We tracked migration of dendritic cells towards immobilized gradients of the chemokine CCL21 and varying superimposed soluble gradients of CCL19. Differential migratory patterns illustrate the potential of our setup to quantitatively study the competitive response to both types of gradients. Beyond chemokines our approach is broadly applicable to alternative systems of chemo- and haptotaxis such as cells migrating along gradients of adhesion receptor ligands vs. any soluble cue. \r\n"}],"project":[{"_id":"25A603A2-B435-11E9-9278-68D0E5697425","grant_number":"281556","call_identifier":"FP7","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)"},{"call_identifier":"FWF","name":"Cytoskeletal force generation and transduction of leukocytes (FWF)","grant_number":"Y 564-B12","_id":"25A8E5EA-B435-11E9-9278-68D0E5697425"}],"date_published":"2016-11-07T00:00:00Z","publisher":"Nature Publishing Group","quality_controlled":"1","volume":6,"department":[{"_id":"MiSi"},{"_id":"NanoFab"},{"_id":"Bio"},{"_id":"ToBo"}],"year":"2016","acknowledgement":"This work was supported by the Swiss National Science Foundation (Ambizione fellowship; PZ00P3-154733 to M.M.), the Swiss Multiple Sclerosis Society (research support to M.M.), a fellowship from the Boehringer Ingelheim Fonds (BIF) to J.S., the European Research Council (grant ERC GA 281556) and a START award from the Austrian Science Foundation (FWF) to M.S. #BioimagingFacility","publist_id":"6204","date_created":"2018-12-11T11:50:27Z","citation":{"chicago":"Schwarz, Jan, Veronika Bierbaum, Jack Merrin, Tino Frank, Robert Hauschild, Mark Tobias Bollenbach, Savaş Tay, Michael K Sixt, and Matthias Mehling. “A Microfluidic Device for Measuring Cell Migration towards Substrate Bound and Soluble Chemokine Gradients.” <i>Scientific Reports</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/srep36440\">https://doi.org/10.1038/srep36440</a>.","mla":"Schwarz, Jan, et al. “A Microfluidic Device for Measuring Cell Migration towards Substrate Bound and Soluble Chemokine Gradients.” <i>Scientific Reports</i>, vol. 6, 36440, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/srep36440\">10.1038/srep36440</a>.","ista":"Schwarz J, Bierbaum V, Merrin J, Frank T, Hauschild R, Bollenbach MT, Tay S, Sixt MK, Mehling M. 2016. A microfluidic device for measuring cell migration towards substrate bound and soluble chemokine gradients. Scientific Reports. 6, 36440.","ama":"Schwarz J, Bierbaum V, Merrin J, et al. A microfluidic device for measuring cell migration towards substrate bound and soluble chemokine gradients. <i>Scientific Reports</i>. 2016;6. doi:<a href=\"https://doi.org/10.1038/srep36440\">10.1038/srep36440</a>","ieee":"J. Schwarz <i>et al.</i>, “A microfluidic device for measuring cell migration towards substrate bound and soluble chemokine gradients,” <i>Scientific Reports</i>, vol. 6. Nature Publishing Group, 2016.","short":"J. Schwarz, V. Bierbaum, J. Merrin, T. Frank, R. Hauschild, M.T. Bollenbach, S. Tay, M.K. Sixt, M. Mehling, Scientific Reports 6 (2016).","apa":"Schwarz, J., Bierbaum, V., Merrin, J., Frank, T., Hauschild, R., Bollenbach, M. T., … Mehling, M. (2016). A microfluidic device for measuring cell migration towards substrate bound and soluble chemokine gradients. <i>Scientific Reports</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/srep36440\">https://doi.org/10.1038/srep36440</a>"},"article_number":"36440","ec_funded":1,"_id":"1154","file_date_updated":"2018-12-12T10:09:32Z","doi":"10.1038/srep36440","author":[{"last_name":"Schwarz","id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","full_name":"Schwarz, Jan","first_name":"Jan"},{"id":"3FD04378-F248-11E8-B48F-1D18A9856A87","last_name":"Bierbaum","full_name":"Bierbaum, Veronika","first_name":"Veronika"},{"orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87","last_name":"Merrin","full_name":"Merrin, Jack","first_name":"Jack"},{"first_name":"Tino","full_name":"Frank, Tino","last_name":"Frank"},{"first_name":"Robert","full_name":"Hauschild, Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","orcid":"0000-0001-9843-3522"},{"orcid":"0000-0003-4398-476X","last_name":"Bollenbach","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","full_name":"Bollenbach, Mark Tobias","first_name":"Mark Tobias"},{"last_name":"Tay","full_name":"Tay, Savaş","first_name":"Savaş"},{"full_name":"Sixt, Michael K","first_name":"Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Mehling, Matthias","first_name":"Matthias","id":"3C23B994-F248-11E8-B48F-1D18A9856A87","last_name":"Mehling","orcid":"0000-0001-8599-1226"}],"month":"11","file":[{"file_size":2353456,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","creator":"system","date_created":"2018-12-12T10:09:32Z","date_updated":"2018-12-12T10:09:32Z","file_id":"4756","file_name":"IST-2017-744-v1+1_srep36440.pdf"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","day":"07","type":"journal_article","status":"public","pubrep_id":"744","oa":1,"date_updated":"2021-01-12T06:48:41Z","title":"A microfluidic device for measuring cell migration towards substrate bound and soluble chemokine gradients","intvolume":"         6","has_accepted_license":"1","scopus_import":1,"language":[{"iso":"eng"}],"publication":"Scientific Reports"},{"date_published":"2016-12-01T00:00:00Z","status":"public","type":"journal_article","publisher":"Springer","quality_controlled":0,"volume":20,"page":"815 - 829","extern":1,"month":"12","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"abstract":[{"text":"Let k, n, and r be positive integers with k &lt; n and r≤⌊nk⌋. We determine the facets of the r-stable n, k-hypersimplex. As a result, it turns out that the r-stable n, k-hypersimplex has exactly 2n facets for every r&lt;⌊nk⌋. We then utilize the equations of the facets to study when the r-stable hypersimplex is Gorenstein. For every k &gt; 0 we identify an infinite collection of Gorenstein r-stable hypersimplices, consequently expanding the collection of r-stable hypersimplices known to have unimodal Ehrhart δ-vectors.","lang":"eng"}],"day":"01","author":[{"full_name":"Hibi, Takayugi","first_name":"Takayugi","last_name":"Hibi"},{"last_name":"Solus","id":"2AADA620-F248-11E8-B48F-1D18A9856A87","full_name":"Liam Solus","first_name":"Liam T"}],"publication_status":"published","publication":"Annals of Combinatorics","doi":"10.1007/s00026-016-0325-x","_id":"1156","intvolume":"        20","year":"2016","issue":"4","date_updated":"2021-01-12T06:48:43Z","acknowledgement":"Liam Solus was supported by a 2014 National Science Foundation/Japan Society for the Promotion of Science East Asia and Pacific Summer Institute Fellowship. \nOpen access funding provided by IST Austria.","date_created":"2018-12-11T11:50:27Z","title":"Facets of the r-stable (n, k)-hypersimplex","publist_id":"6202","citation":{"apa":"Hibi, T., &#38; Solus, L. T. (2016). Facets of the r-stable (n, k)-hypersimplex. <i>Annals of Combinatorics</i>. Springer. <a href=\"https://doi.org/10.1007/s00026-016-0325-x\">https://doi.org/10.1007/s00026-016-0325-x</a>","ieee":"T. Hibi and L. T. Solus, “Facets of the r-stable (n, k)-hypersimplex,” <i>Annals of Combinatorics</i>, vol. 20, no. 4. Springer, pp. 815–829, 2016.","ama":"Hibi T, Solus LT. Facets of the r-stable (n, k)-hypersimplex. <i>Annals of Combinatorics</i>. 2016;20(4):815-829. doi:<a href=\"https://doi.org/10.1007/s00026-016-0325-x\">10.1007/s00026-016-0325-x</a>","short":"T. Hibi, L.T. Solus, Annals of Combinatorics 20 (2016) 815–829.","mla":"Hibi, Takayugi, and Liam T. Solus. “Facets of the R-Stable (n, k)-Hypersimplex.” <i>Annals of Combinatorics</i>, vol. 20, no. 4, Springer, 2016, pp. 815–29, doi:<a href=\"https://doi.org/10.1007/s00026-016-0325-x\">10.1007/s00026-016-0325-x</a>.","ista":"Hibi T, Solus LT. 2016. Facets of the r-stable (n, k)-hypersimplex. Annals of Combinatorics. 20(4), 815–829.","chicago":"Hibi, Takayugi, and Liam T Solus. “Facets of the R-Stable (n, k)-Hypersimplex.” <i>Annals of Combinatorics</i>. Springer, 2016. <a href=\"https://doi.org/10.1007/s00026-016-0325-x\">https://doi.org/10.1007/s00026-016-0325-x</a>."}},{"_id":"1157","doi":"10.1214/16-AAP1193","acknowledgement":"We thank Horng-Tzer Yau for numerous discussions and remarks. We are grateful to Ben Adlam, Jinho Baik, Zhigang Bao, Paul Bourgade, László Erd ̋os, Iain Johnstone and Antti Knowles for comments. We are also grate-\r\nful to the anonymous referee for carefully reading our manuscript and suggesting several improvements.","year":"2016","citation":{"chicago":"Lee, Ji, and Kevin Schnelli. “Tracy-Widom Distribution for the Largest Eigenvalue of Real Sample Covariance Matrices with General Population.” <i>Annals of Applied Probability</i>. Institute of Mathematical Statistics, 2016. <a href=\"https://doi.org/10.1214/16-AAP1193\">https://doi.org/10.1214/16-AAP1193</a>.","mla":"Lee, Ji, and Kevin Schnelli. “Tracy-Widom Distribution for the Largest Eigenvalue of Real Sample Covariance Matrices with General Population.” <i>Annals of Applied Probability</i>, vol. 26, no. 6, Institute of Mathematical Statistics, 2016, pp. 3786–839, doi:<a href=\"https://doi.org/10.1214/16-AAP1193\">10.1214/16-AAP1193</a>.","ista":"Lee J, Schnelli K. 2016. Tracy-widom distribution for the largest eigenvalue of real sample covariance matrices with general population. Annals of Applied Probability. 26(6), 3786–3839.","ieee":"J. Lee and K. Schnelli, “Tracy-widom distribution for the largest eigenvalue of real sample covariance matrices with general population,” <i>Annals of Applied Probability</i>, vol. 26, no. 6. Institute of Mathematical Statistics, pp. 3786–3839, 2016.","ama":"Lee J, Schnelli K. Tracy-widom distribution for the largest eigenvalue of real sample covariance matrices with general population. <i>Annals of Applied Probability</i>. 2016;26(6):3786-3839. doi:<a href=\"https://doi.org/10.1214/16-AAP1193\">10.1214/16-AAP1193</a>","short":"J. Lee, K. Schnelli, Annals of Applied Probability 26 (2016) 3786–3839.","apa":"Lee, J., &#38; Schnelli, K. (2016). Tracy-widom distribution for the largest eigenvalue of real sample covariance matrices with general population. <i>Annals of Applied Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/16-AAP1193\">https://doi.org/10.1214/16-AAP1193</a>"},"publist_id":"6201","date_created":"2018-12-11T11:50:27Z","ec_funded":1,"project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804","name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7"}],"publisher":"Institute of Mathematical Statistics","date_published":"2016-12-15T00:00:00Z","department":[{"_id":"LaEr"}],"page":"3786 - 3839","volume":26,"quality_controlled":"1","publication_status":"published","abstract":[{"lang":"eng","text":"We consider sample covariance matrices of the form Q = ( σ1/2X)(σ1/2X)∗, where the sample X is an M ×N random matrix whose entries are real independent random variables with variance 1/N and whereσ is an M × M positive-definite deterministic matrix. We analyze the asymptotic fluctuations of the largest rescaled eigenvalue of Q when both M and N tend to infinity with N/M →d ϵ (0,∞). For a large class of populations σ in the sub-critical regime, we show that the distribution of the largest rescaled eigenvalue of Q is given by the type-1 Tracy-Widom distribution under the additional assumptions that (1) either the entries of X are i.i.d. Gaussians or (2) that σ is diagonal and that the entries of X have a sub-exponential decay."}],"language":[{"iso":"eng"}],"publication":"Annals of Applied Probability","oa":1,"date_updated":"2021-01-12T06:48:43Z","issue":"6","title":"Tracy-widom distribution for the largest eigenvalue of real sample covariance matrices with general population","scopus_import":1,"intvolume":"        26","type":"journal_article","status":"public","author":[{"full_name":"Lee, Ji","first_name":"Ji","last_name":"Lee"},{"last_name":"Schnelli","id":"434AD0AE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0954-3231","full_name":"Schnelli, Kevin","first_name":"Kevin"}],"month":"12","day":"15","oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1409.4979"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"publication_status":"published","external_id":{"arxiv":["1606.07435"]},"abstract":[{"lang":"eng","text":"We present new results from the widest narrow-band survey search for Lyα emitters at z = 5.7, just after reionization. We survey a total of 7 deg2 spread over the COSMOS, UDS and SA22 fields. We find over 11 000 line emitters, out of which 514 are robust Lyα candidates at z = 5.7 within a volume of 6.3 × 106 Mpc3. Our Lyα emitters span a wide range in Lyα luminosities, from faint to bright (LLyα ∼ 1042.5–44 erg s−1) and rest-frame equivalent widths (EW0 ∼ 25–1000 Å) in a single, homogeneous data set. By combining all our fields, we find that the faint end slope of the z = 5.7 Lyα luminosity function is very steep, with α=−2.3+0.4−0.3⁠. We also present an updated z = 6.6 Lyα luminosity function, based on comparable volumes and obtained with the same methods, which we directly compare with that at z = 5.7. We find a significant decline of the number density of faint Lyα emitters from z = 5.7 to 6.6 (by 0.5 ± 0.1 dex), but no evolution at the bright end/no evolution in L*. Faint Lyα emitters at z = 6.6 show much more extended haloes than those at z = 5.7, suggesting that neutral Hydrogen plays an important role, increasing the scattering and leading to observations missing faint Lyα emission within the epoch of reionization. Altogether, our results suggest that we are observing patchy reionization which happens first around the brightest Lyα emitters, allowing the number densities of those sources to remain unaffected by the increase of neutral Hydrogen fraction from z ∼ 5 to 7."}],"publisher":"Oxford University Press","date_published":"2016-12-01T00:00:00Z","page":"1678-1691","extern":"1","quality_controlled":"1","volume":463,"acknowledgement":"We thank the anonymous referee for useful and constructive comments and suggestions which greatly improved the quality and clarity of our work. The authors acknowledge financial support from the Netherlands Organisation for Scientific research (NWO) through a Veni fellowship. SS and DS acknowledge funding from FCT through an FCT Investigator Starting Grant and Start-up Grant (IF/01154/2012/CP0189/CT0010). SS also acknowledges support from FCT through the research grants UID/FIS/04434/2013 and PTDC/FIS-AST/2194/2012. JM acknowledges a Huygens PhD fellowship from Leiden University. Based on observations with the Subaru Telescope (Program IDs: S05B-027, S06A-025, S06B-010, S07A-013, S07B-008, S08B-008, S09A-017, S14A-086). Based on observations made with ESO Telescopes at the La Silla Paranal Observatory under programme ID 294.A-5018. Based on observations obtained with MegaPrime/Megacam, a joint project of CFHT and CEA/IRFU, at the Canada–France–Hawaii Telescope (CFHT) which is operated by the National Research Council (NRC) of Canada, the Institut National des Science de l’Univers of the Centre National de la Recherche Scientifique (CNRS) of France, and the University of Hawaii. This work is based in part on data products produced at TERAPIX available at the Canadian Astronomy Data Centre as part of the Canada–France–Hawaii Telescope Legacy Survey, a collaborative project of NRC and CNRS. Based on data products from observations made with ESO Telescopes at the La Silla Paranal Observatory under ESO programme ID 179.A-2005 and on data products produced by TERAPIX and the Cambridge Astronomy Survey Unit on behalf of the UltraVISTA consortium. We are grateful to the CFHTLS, COSMOS-UltraVISTA, UKIDSS, SXDF and COSMOS survey teams. Without these legacy surveys, this research would have been impossible. The authors wish to recognize and acknowledge the very significant cultural role and reverence that the summit of Mauna Kea has always had within the indigenous Hawaiian community. We are most fortunate to have the opportunity to conduct and explore observations from this mountain. Finally, the authors acknowledge the unique value of the publicly available programming language PYTHON, including the NUMPY, PYFITS, MATPLOTLIB, SCIPY and ASTROPY (Astropy Collaboration et al.","year":"2016","date_created":"2022-07-13T10:08:20Z","citation":{"ama":"Santos S, Sobral D, Matthee JJ. The Lyα luminosity function at z= 5.7–6.6 and the steep drop of the faint end: Implications for reionization. <i>Monthly Notices of the Royal Astronomical Society</i>. 2016;463(2):1678-1691. doi:<a href=\"https://doi.org/10.1093/mnras/stw2076\">10.1093/mnras/stw2076</a>","ieee":"S. Santos, D. Sobral, and J. J. Matthee, “The Lyα luminosity function at z= 5.7–6.6 and the steep drop of the faint end: Implications for reionization,” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 463, no. 2. Oxford University Press, pp. 1678–1691, 2016.","short":"S. Santos, D. Sobral, J.J. Matthee, Monthly Notices of the Royal Astronomical Society 463 (2016) 1678–1691.","mla":"Santos, Sérgio, et al. “The Lyα Luminosity Function at Z= 5.7–6.6 and the Steep Drop of the Faint End: Implications for Reionization.” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 463, no. 2, Oxford University Press, 2016, pp. 1678–91, doi:<a href=\"https://doi.org/10.1093/mnras/stw2076\">10.1093/mnras/stw2076</a>.","chicago":"Santos, Sérgio, David Sobral, and Jorryt J Matthee. “The Lyα Luminosity Function at Z= 5.7–6.6 and the Steep Drop of the Faint End: Implications for Reionization.” <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press, 2016. <a href=\"https://doi.org/10.1093/mnras/stw2076\">https://doi.org/10.1093/mnras/stw2076</a>.","ista":"Santos S, Sobral D, Matthee JJ. 2016. The Lyα luminosity function at z= 5.7–6.6 and the steep drop of the faint end: Implications for reionization. Monthly Notices of the Royal Astronomical Society. 463(2), 1678–1691.","apa":"Santos, S., Sobral, D., &#38; Matthee, J. J. (2016). The Lyα luminosity function at z= 5.7–6.6 and the steep drop of the faint end: Implications for reionization. <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/mnras/stw2076\">https://doi.org/10.1093/mnras/stw2076</a>"},"keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: high-redshift","galaxies: luminosity function","mass function","cosmology: observations","dark ages","reionization","first stars"],"_id":"11574","article_type":"original","doi":"10.1093/mnras/stw2076","author":[{"last_name":"Santos","full_name":"Santos, Sérgio","first_name":"Sérgio"},{"last_name":"Sobral","first_name":"David","full_name":"Sobral, David"},{"id":"7439a258-f3c0-11ec-9501-9df22fe06720","last_name":"Matthee","orcid":"0000-0003-2871-127X","full_name":"Matthee, Jorryt J","first_name":"Jorryt J"}],"arxiv":1,"publication_identifier":{"issn":["0035-8711"],"eissn":["1365-2966"]},"month":"12","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1606.07435"}],"day":"01","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","status":"public","oa":1,"date_updated":"2022-08-19T08:09:54Z","issue":"2","article_processing_charge":"No","title":"The Lyα luminosity function at z= 5.7–6.6 and the steep drop of the faint end: Implications for reionization","intvolume":"       463","scopus_import":"1","language":[{"iso":"eng"}],"publication":"Monthly Notices of the Royal Astronomical Society"},{"scopus_import":"1","intvolume":"       459","issue":"3","article_processing_charge":"No","date_updated":"2022-08-19T08:12:07Z","oa":1,"title":"The Fundamental Plane of star formation in galaxies revealed by the EAGLE hydrodynamical simulations","publication":"Monthly Notices of the Royal Astronomical Society","language":[{"iso":"eng"}],"month":"07","publication_identifier":{"issn":["0035-8711"],"eissn":["1365-2966"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1510.08067"}],"oa_version":"Preprint","arxiv":1,"author":[{"last_name":"Lagos","full_name":"Lagos, Claudia del P.","first_name":"Claudia del P."},{"last_name":"Theuns","full_name":"Theuns, Tom","first_name":"Tom"},{"last_name":"Schaye","full_name":"Schaye, Joop","first_name":"Joop"},{"last_name":"Furlong","full_name":"Furlong, Michelle","first_name":"Michelle"},{"first_name":"Richard G.","full_name":"Bower, Richard G.","last_name":"Bower"},{"last_name":"Schaller","full_name":"Schaller, Matthieu","first_name":"Matthieu"},{"full_name":"Crain, Robert A.","first_name":"Robert A.","last_name":"Crain"},{"first_name":"James W.","full_name":"Trayford, James W.","last_name":"Trayford"},{"first_name":"Jorryt J","full_name":"Matthee, Jorryt J","last_name":"Matthee","id":"7439a258-f3c0-11ec-9501-9df22fe06720","orcid":"0000-0003-2871-127X"}],"type":"journal_article","status":"public","year":"2016","acknowledgement":"We thank Luca Cortese, Matt Bothwell, Paola Santini and Tim Davis for providing observational data sets, and Aaron Robotham, Luca Cortese and Barbara Catinella for useful discussions. CdPL is funded by a Discovery Early Career Researcher Award (DE150100618). CdPL also thanks the MERAC Foundation for a Postdoctoral Research Award. This work used the DiRAC Data Centric system at Durham University, operated by the Institute for Computational Cosmology on behalf of the STFC DiRAC HPC Facility (www.dirac.ac.uk). This equipment was funded by BIS National E-infrastructure capital grant ST/K00042X/1, STFC capital grant ST/H008519/1, and STFC DiRAC Operations grant ST/K003267/1 and Durham University. DiRAC is part of the National E-Infrastructure. Support was also received via the Interuniversity Attraction Poles Programme initiated by the Belgian Science Policy Office ([AP P7/08 CHARM]), the National Science Foundation under grant no. NSF PHY11-25915, and the UK Science and Technology Facilities Council (grant numbers ST/F001166/1 and ST/I000976/1) via rolling and consolidating grants awarded to the ICC. The research was supported in part by the European Research Council under the European Union‘s Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement 278594-GasAroundGalaxies.","keyword":["Space and Planetary Science","Astronomy and Astrophysics  stars: formation","ISM: evolution","galaxies: evolution","galaxies: formation","galaxies: ISM"],"date_created":"2022-07-13T10:21:24Z","citation":{"mla":"Lagos, Claudia del P., et al. “The Fundamental Plane of Star Formation in Galaxies Revealed by the EAGLE Hydrodynamical Simulations.” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 459, no. 3, Oxford University Press, 2016, pp. 2632–50, doi:<a href=\"https://doi.org/10.1093/mnras/stw717\">10.1093/mnras/stw717</a>.","ista":"Lagos C del P, Theuns T, Schaye J, Furlong M, Bower RG, Schaller M, Crain RA, Trayford JW, Matthee JJ. 2016. The Fundamental Plane of star formation in galaxies revealed by the EAGLE hydrodynamical simulations. Monthly Notices of the Royal Astronomical Society. 459(3), 2632–2650.","chicago":"Lagos, Claudia del P., Tom Theuns, Joop Schaye, Michelle Furlong, Richard G. Bower, Matthieu Schaller, Robert A. Crain, James W. Trayford, and Jorryt J Matthee. “The Fundamental Plane of Star Formation in Galaxies Revealed by the EAGLE Hydrodynamical Simulations.” <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press, 2016. <a href=\"https://doi.org/10.1093/mnras/stw717\">https://doi.org/10.1093/mnras/stw717</a>.","ama":"Lagos C del P, Theuns T, Schaye J, et al. The Fundamental Plane of star formation in galaxies revealed by the EAGLE hydrodynamical simulations. <i>Monthly Notices of the Royal Astronomical Society</i>. 2016;459(3):2632-2650. doi:<a href=\"https://doi.org/10.1093/mnras/stw717\">10.1093/mnras/stw717</a>","ieee":"C. del P. Lagos <i>et al.</i>, “The Fundamental Plane of star formation in galaxies revealed by the EAGLE hydrodynamical simulations,” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 459, no. 3. Oxford University Press, pp. 2632–2650, 2016.","short":"C. del P. Lagos, T. Theuns, J. Schaye, M. Furlong, R.G. Bower, M. Schaller, R.A. Crain, J.W. Trayford, J.J. Matthee, Monthly Notices of the Royal Astronomical Society 459 (2016) 2632–2650.","apa":"Lagos, C. del P., Theuns, T., Schaye, J., Furlong, M., Bower, R. G., Schaller, M., … Matthee, J. J. (2016). The Fundamental Plane of star formation in galaxies revealed by the EAGLE hydrodynamical simulations. <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/mnras/stw717\">https://doi.org/10.1093/mnras/stw717</a>"},"doi":"10.1093/mnras/stw717","article_type":"original","_id":"11575","abstract":[{"lang":"eng","text":"We investigate correlations between different physical properties of star-forming galaxies in the ‘Evolution and Assembly of GaLaxies and their Environments’ (EAGLE) cosmological hydrodynamical simulation suite over the redshift range 0 ≤ z ≤ 4.5. A principal component analysis reveals that neutral gas fraction (fgas,neutral), stellar mass (Mstellar) and star formation rate (SFR) account for most of the variance seen in the population, with galaxies tracing a two-dimensional, nearly flat, surface in the three-dimensional space of fgas, neutral–Mstellar–SFR with little scatter. The location of this plane varies little with redshift, whereas galaxies themselves move along the plane as their fgas, neutral and SFR drop with redshift. The positions of galaxies along the plane are highly correlated with gas metallicity. The metallicity can therefore be robustly predicted from fgas, neutral, or from the Mstellar and SFR. We argue that the appearance of this ‘Fundamental Plane of star formation’ is a consequence of self-regulation, with the plane's curvature set by the dependence of the SFR on gas density and metallicity. We analyse a large compilation of observations spanning the redshift range 0 ≲ z ≲ 3, and find that such a plane is also present in the data. The properties of the observed Fundamental Plane of star formation are in good agreement with EAGLE's predictions."}],"external_id":{"arxiv":["1510.08067"]},"publication_status":"published","date_published":"2016-07-01T00:00:00Z","publisher":"Oxford University Press","quality_controlled":"1","volume":459,"page":"2632-2650","extern":"1"}]