[{"publication_identifier":{"issn":["03036898"]},"status":"public","publication_status":"published","author":[{"first_name":"Abraham","full_name":"Martin Del Campo Sanchez, Abraham","last_name":"Martin Del Campo Sanchez"},{"first_name":"Sarah A","id":"3DEE19A4-F248-11E8-B48F-1D18A9856A87","last_name":"Cepeda Humerez","full_name":"Cepeda Humerez, Sarah A"},{"id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","first_name":"Caroline","full_name":"Uhler, Caroline","last_name":"Uhler","orcid":"0000-0002-7008-0216"}],"title":"Exact goodness-of-fit testing for the Ising model","_id":"2016","issue":"2","abstract":[{"text":"The Ising model is one of the simplest and most famous models of interacting systems. It was originally proposed to model ferromagnetic interactions in statistical physics and is now widely used to model spatial processes in many areas such as ecology, sociology, and genetics, usually without testing its goodness-of-fit. Here, we propose an exact goodness-of-fit test for the finite-lattice Ising model. The theory of Markov bases has been developed in algebraic statistics for exact goodness-of-fit testing using a Monte Carlo approach. However, this beautiful theory has fallen short of its promise for applications, because finding a Markov basis is usually computationally intractable. We develop a Monte Carlo method for exact goodness-of-fit testing for the Ising model which avoids computing a Markov basis and also leads to a better connectivity of the Markov chain and hence to a faster convergence. We show how this method can be applied to analyze the spatial organization of receptors on the cell membrane.","lang":"eng"}],"doi":"10.1111/sjos.12251","arxiv":1,"volume":44,"article_processing_charge":"No","day":"01","citation":{"chicago":"Martin Del Campo Sanchez, Abraham, Sarah A Cepeda Humerez, and Caroline Uhler. “Exact Goodness-of-Fit Testing for the Ising Model.” <i>Scandinavian Journal of Statistics</i>. Wiley-Blackwell, 2017. <a href=\"https://doi.org/10.1111/sjos.12251\">https://doi.org/10.1111/sjos.12251</a>.","mla":"Martin Del Campo Sanchez, Abraham, et al. “Exact Goodness-of-Fit Testing for the Ising Model.” <i>Scandinavian Journal of Statistics</i>, vol. 44, no. 2, Wiley-Blackwell, 2017, pp. 285–306, doi:<a href=\"https://doi.org/10.1111/sjos.12251\">10.1111/sjos.12251</a>.","ieee":"A. Martin Del Campo Sanchez, S. A. Cepeda Humerez, and C. Uhler, “Exact goodness-of-fit testing for the Ising model,” <i>Scandinavian Journal of Statistics</i>, vol. 44, no. 2. Wiley-Blackwell, pp. 285–306, 2017.","apa":"Martin Del Campo Sanchez, A., Cepeda Humerez, S. A., &#38; Uhler, C. (2017). Exact goodness-of-fit testing for the Ising model. <i>Scandinavian Journal of Statistics</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/sjos.12251\">https://doi.org/10.1111/sjos.12251</a>","ista":"Martin Del Campo Sanchez A, Cepeda Humerez SA, Uhler C. 2017. Exact goodness-of-fit testing for the Ising model. Scandinavian Journal of Statistics. 44(2), 285–306.","short":"A. Martin Del Campo Sanchez, S.A. Cepeda Humerez, C. Uhler, Scandinavian Journal of Statistics 44 (2017) 285–306.","ama":"Martin Del Campo Sanchez A, Cepeda Humerez SA, Uhler C. Exact goodness-of-fit testing for the Ising model. <i>Scandinavian Journal of Statistics</i>. 2017;44(2):285-306. doi:<a href=\"https://doi.org/10.1111/sjos.12251\">10.1111/sjos.12251</a>"},"month":"06","oa_version":"Preprint","publication":"Scandinavian Journal of Statistics","date_updated":"2023-09-19T15:13:27Z","related_material":{"record":[{"id":"6473","relation":"part_of_dissertation","status":"public"}]},"page":"285 - 306","oa":1,"year":"2017","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1410.1242"}],"intvolume":"        44","publisher":"Wiley-Blackwell","isi":1,"quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","department":[{"_id":"GaTk"}],"publist_id":"5060","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"arxiv":["1410.1242"],"isi":["000400985000001"]},"date_published":"2017-06-01T00:00:00Z","scopus_import":"1","date_created":"2018-12-11T11:55:13Z"},{"abstract":[{"text":"Restriction-modification (RM) represents the simplest and possibly the most widespread mechanism of self/non-self discrimination in nature. In order to provide bacteria with immunity against bacteriophages and other parasitic genetic elements, RM systems rely on a balance between two enzymes: the restriction enzyme, which cleaves non-self DNA at specific restriction sites, and the modification enzyme, which tags the host’s DNA as self and thus protects it from cleavage. In this thesis, I use population and single-cell level experiments in combination with mathematical modeling to study different aspects of the interplay between RM systems, bacteria and bacteriophages. First, I analyze how mutations in phage restriction sites affect the probability of phage escape – an inherently stochastic process, during which phages accidently get modified instead of restricted. Next, I use single-cell experiments to show that RM systems can, with a low probability, attack the genome of their bacterial host and that this primitive form of autoimmunity leads to a tradeoff between the evolutionary cost and benefit of RM systems. Finally, I investigate the nature of interactions between bacteria, RM systems and temperate bacteriophages to find that, as a consequence of phage escape and its impact on population dynamics, RM systems can promote acquisition of symbiotic bacteriophages, rather than limit it. The results presented here uncover new fundamental biological properties of RM systems and highlight their importance in the ecology and evolution of bacteria, bacteriophages and their interactions.","lang":"eng"}],"doi":"10.15479/AT:ISTA:th_916","title":"Biology of restriction-modification systems at the single-cell and population level","supervisor":[{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","full_name":"Guet, Calin C","last_name":"Guet","orcid":"0000-0001-6220-2052"}],"author":[{"orcid":"0000-0001-7460-7479","first_name":"Maros","id":"4569785E-F248-11E8-B48F-1D18A9856A87","last_name":"Pleska","full_name":"Pleska, Maros"}],"_id":"202","publication_status":"published","acknowledgement":"During my PhD studies, I received help from many people, all of which unfortunately cannot be listed here. I thank them deeply and hope that I never made them regret their kindness.\r\nI would like to express my deepest gratitude to Călin Guet, who went far beyond his responsibilities as an advisor and was to me also a great mentor and a friend. Călin never questioned my potential or lacked compassion and I cannot thank him enough for cultivating in me an independent scientist. I was amazed by his ability to recognize the most fascinating scientific problems in objects of study that others would find mundane. I hope I adopted at least a fraction of this ability.\r\nI will be forever grateful to Bruce Levin for all his support and especially for giving me the best possible example of how one can practice excellent science with humor and style. Working with Bruce was a true privilege.\r\nI thank Jonathan Bollback and Gašper Tkačik for serving in my PhD committee and the Austrian Academy of Science for funding my PhD research via the DOC fellowship.\r\nI thank all our lab members: Tobias Bergmiller for his guidance, especially in the first years of my research, and for being a good friend throughout; Remy Chait for staying in the lab at unreasonable hours and for the good laughs at bad jokes we shared; Anna Staron for supportively listening to my whines whenever I had to run a gel; Magdalena Steinrück for her pioneering work in the lab; Kathrin Tomasek for keeping the entropic forces in check and for her FACS virtuosity; Isabella Tomanek for always being nice to me, no matter how much bench space I took from her.\r\nI thank all my collaborators: Reiko Okura and Yuichi Wakamoto for performing and analyzing the microfluidic experiments; Long Qian and Edo Kussell for their bioinformatics analysis; Dominik Refardt for the λ kan phage; Moritz for his help with the mathematical modeling. I thank Fabienne Jesse for her tireless editorial work on all our manuscripts.\r\nFinally, I would like to thank my family and especially my wife Edita, who sacrificed a lot so that I can pursue my goals and dreams.\r\n","status":"public","publication_identifier":{"issn":["2663-337X"]},"project":[{"grant_number":"24210","_id":"251D65D8-B435-11E9-9278-68D0E5697425","name":"Effects of Stochasticity on the Function of Restriction-Modi cation Systems at the Single-Cell Level (DOC Fellowship)"}],"oa_version":"Published Version","citation":{"chicago":"Pleska, Maros. “Biology of Restriction-Modification Systems at the Single-Cell and Population Level.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:th_916\">https://doi.org/10.15479/AT:ISTA:th_916</a>.","mla":"Pleska, Maros. <i>Biology of Restriction-Modification Systems at the Single-Cell and Population Level</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_916\">10.15479/AT:ISTA:th_916</a>.","ama":"Pleska M. Biology of restriction-modification systems at the single-cell and population level. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_916\">10.15479/AT:ISTA:th_916</a>","short":"M. Pleska, Biology of Restriction-Modification Systems at the Single-Cell and Population Level, Institute of Science and Technology Austria, 2017.","ista":"Pleska M. 2017. Biology of restriction-modification systems at the single-cell and population level. Institute of Science and Technology Austria.","apa":"Pleska, M. (2017). <i>Biology of restriction-modification systems at the single-cell and population level</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_916\">https://doi.org/10.15479/AT:ISTA:th_916</a>","ieee":"M. Pleska, “Biology of restriction-modification systems at the single-cell and population level,” Institute of Science and Technology Austria, 2017."},"pubrep_id":"916","day":"01","file_date_updated":"2020-07-14T12:45:24Z","month":"10","ddc":["576","579"],"has_accepted_license":"1","article_processing_charge":"No","degree_awarded":"PhD","file":[{"file_name":"IST-2018-916-v1+3_2017_Pleska_Maros_Thesis.pdf","creator":"system","file_size":18569590,"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"33cfb59674e91f82e3738396d3fb3776","date_updated":"2020-07-14T12:45:24Z","file_id":"4710","date_created":"2018-12-12T10:08:48Z"},{"access_level":"closed","checksum":"dcc239968decb233e7f98cf1083d8c26","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2020-07-14T12:45:24Z","file_name":"2017_Pleska_Maros_Thesis.docx","relation":"source_file","file_size":2801649,"creator":"dernst","file_id":"6204","date_created":"2019-04-05T08:33:14Z"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"alternative_title":["ISTA Thesis"],"year":"2017","oa":1,"related_material":{"record":[{"id":"1243","status":"public","relation":"part_of_dissertation"},{"id":"561","status":"public","relation":"part_of_dissertation"},{"id":"457","relation":"part_of_dissertation","status":"public"}]},"page":"126","date_updated":"2023-09-15T12:04:56Z","date_published":"2017-10-01T00:00:00Z","date_created":"2018-12-11T11:45:10Z","department":[{"_id":"CaGu"}],"publist_id":"7711","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"type":"dissertation","publisher":"Institute of Science and Technology Austria"},{"day":"01","citation":{"ama":"Shi L, Hof B, Rampp M, Avila M. Hydrodynamic turbulence in quasi Keplerian rotating flows. <i>Physics of Fluids</i>. 2017;29(4). doi:<a href=\"https://doi.org/10.1063/1.4981525\">10.1063/1.4981525</a>","short":"L. Shi, B. Hof, M. Rampp, M. Avila, Physics of Fluids 29 (2017).","ista":"Shi L, Hof B, Rampp M, Avila M. 2017. Hydrodynamic turbulence in quasi Keplerian rotating flows. Physics of Fluids. 29(4), 044107.","ieee":"L. Shi, B. Hof, M. Rampp, and M. Avila, “Hydrodynamic turbulence in quasi Keplerian rotating flows,” <i>Physics of Fluids</i>, vol. 29, no. 4. American Institute of Physics, 2017.","apa":"Shi, L., Hof, B., Rampp, M., &#38; Avila, M. (2017). Hydrodynamic turbulence in quasi Keplerian rotating flows. <i>Physics of Fluids</i>. American Institute of Physics. <a href=\"https://doi.org/10.1063/1.4981525\">https://doi.org/10.1063/1.4981525</a>","chicago":"Shi, Liang, Björn Hof, Markus Rampp, and Marc Avila. “Hydrodynamic Turbulence in Quasi Keplerian Rotating Flows.” <i>Physics of Fluids</i>. American Institute of Physics, 2017. <a href=\"https://doi.org/10.1063/1.4981525\">https://doi.org/10.1063/1.4981525</a>.","mla":"Shi, Liang, et al. “Hydrodynamic Turbulence in Quasi Keplerian Rotating Flows.” <i>Physics of Fluids</i>, vol. 29, no. 4, 044107, American Institute of Physics, 2017, doi:<a href=\"https://doi.org/10.1063/1.4981525\">10.1063/1.4981525</a>."},"month":"04","oa_version":"Submitted Version","volume":29,"author":[{"last_name":"Shi","full_name":"Shi, Liang","first_name":"Liang"},{"full_name":"Hof, Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","orcid":"0000-0003-2057-2754"},{"last_name":"Rampp","full_name":"Rampp, Markus","first_name":"Markus"},{"last_name":"Avila","full_name":"Avila, Marc","first_name":"Marc"}],"title":"Hydrodynamic turbulence in quasi Keplerian rotating flows","_id":"662","issue":"4","abstract":[{"lang":"eng","text":"We report a direct-numerical-simulation study of the Taylor-Couette flow in the quasi-Keplerian regime at shear Reynolds numbers up to (105). Quasi-Keplerian rotating flow has been investigated for decades as a simplified model system to study the origin of turbulence in accretion disks that is not fully understood. The flow in this study is axially periodic and thus the experimental end-wall effects on the stability of the flow are avoided. Using optimal linear perturbations as initial conditions, our simulations find no sustained turbulence: the strong initial perturbations distort the velocity profile and trigger turbulence that eventually decays."}],"doi":"10.1063/1.4981525","publication_identifier":{"issn":["10706631"]},"project":[{"grant_number":"SFB 963  TP A8","_id":"2511D90C-B435-11E9-9278-68D0E5697425","name":"Astrophysical instability of currents and turbulences"}],"status":"public","publication_status":"published","department":[{"_id":"BjHo"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"7072","date_published":"2017-04-01T00:00:00Z","scopus_import":1,"date_created":"2018-12-11T11:47:47Z","intvolume":"        29","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1703.01714"}],"publisher":"American Institute of Physics","type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","oa":1,"year":"2017","publication":"Physics of Fluids","date_updated":"2021-01-12T08:08:15Z","article_number":"044107"},{"quality_controlled":"1","type":"conference","language":[{"iso":"eng"}],"publisher":"ACM","scopus_import":1,"date_created":"2018-12-11T11:47:47Z","date_published":"2017-04-01T00:00:00Z","publist_id":"7067","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"ToHe"}],"page":"163 - 172","date_updated":"2021-01-12T08:08:17Z","publication":"Proceedings of the 20th International Conference on Hybrid Systems","year":"2017","oa":1,"has_accepted_license":"1","file":[{"file_name":"IST-2017-817-v1+1_p163-kong.pdf","file_size":1650530,"relation":"main_file","creator":"system","access_level":"open_access","content_type":"application/pdf","checksum":"b7667434cbf5b5f0ade3bea1dbe5bf63","date_updated":"2020-07-14T12:47:34Z","file_id":"4873","date_created":"2018-12-12T10:11:20Z"}],"conference":{"name":"HSCC: Hybrid Systems Computation and Control ","start_date":"2017-04-18","location":"Pittsburgh, PA, United States","end_date":"2017-04-20"},"oa_version":"Submitted Version","month":"04","ddc":["000"],"file_date_updated":"2020-07-14T12:47:34Z","day":"01","pubrep_id":"817","citation":{"chicago":"Kong, Hui, Sergiy Bogomolov, Christian Schilling, Yu Jiang, and Thomas A Henzinger. “Safety Verification of Nonlinear Hybrid Systems Based on Invariant Clusters.” In <i>Proceedings of the 20th International Conference on Hybrid Systems</i>, 163–72. ACM, 2017. <a href=\"https://doi.org/10.1145/3049797.3049814\">https://doi.org/10.1145/3049797.3049814</a>.","mla":"Kong, Hui, et al. “Safety Verification of Nonlinear Hybrid Systems Based on Invariant Clusters.” <i>Proceedings of the 20th International Conference on Hybrid Systems</i>, ACM, 2017, pp. 163–72, doi:<a href=\"https://doi.org/10.1145/3049797.3049814\">10.1145/3049797.3049814</a>.","apa":"Kong, H., Bogomolov, S., Schilling, C., Jiang, Y., &#38; Henzinger, T. A. (2017). Safety verification of nonlinear hybrid systems based on invariant clusters. In <i>Proceedings of the 20th International Conference on Hybrid Systems</i> (pp. 163–172). Pittsburgh, PA, United States: ACM. <a href=\"https://doi.org/10.1145/3049797.3049814\">https://doi.org/10.1145/3049797.3049814</a>","ieee":"H. Kong, S. Bogomolov, C. Schilling, Y. Jiang, and T. A. Henzinger, “Safety verification of nonlinear hybrid systems based on invariant clusters,” in <i>Proceedings of the 20th International Conference on Hybrid Systems</i>, Pittsburgh, PA, United States, 2017, pp. 163–172.","short":"H. Kong, S. Bogomolov, C. Schilling, Y. Jiang, T.A. Henzinger, in:, Proceedings of the 20th International Conference on Hybrid Systems, ACM, 2017, pp. 163–172.","ista":"Kong H, Bogomolov S, Schilling C, Jiang Y, Henzinger TA. 2017. Safety verification of nonlinear hybrid systems based on invariant clusters. Proceedings of the 20th International Conference on Hybrid Systems. HSCC: Hybrid Systems Computation and Control , 163–172.","ama":"Kong H, Bogomolov S, Schilling C, Jiang Y, Henzinger TA. Safety verification of nonlinear hybrid systems based on invariant clusters. In: <i>Proceedings of the 20th International Conference on Hybrid Systems</i>. ACM; 2017:163-172. doi:<a href=\"https://doi.org/10.1145/3049797.3049814\">10.1145/3049797.3049814</a>"},"status":"public","publication_status":"published","publication_identifier":{"isbn":["978-145034590-3"]},"doi":"10.1145/3049797.3049814","abstract":[{"text":"In this paper, we propose an approach to automatically compute invariant clusters for nonlinear semialgebraic hybrid systems. An invariant cluster for an ordinary differential equation (ODE) is a multivariate polynomial invariant g(u→, x→) = 0, parametric in u→, which can yield an infinite number of concrete invariants by assigning different values to u→ so that every trajectory of the system can be overapproximated precisely by the intersection of a group of concrete invariants. For semialgebraic systems, which involve ODEs with multivariate polynomial right-hand sides, given a template multivariate polynomial g(u→, x→), an invariant cluster can be obtained by first computing the remainder of the Lie derivative of g(u→, x→) divided by g(u→, x→) and then solving the system of polynomial equations obtained from the coefficients of the remainder. Based on invariant clusters and sum-of-squares (SOS) programming, we present a new method for the safety verification of hybrid systems. Experiments on nonlinear benchmark systems from biology and control theory show that our approach is efficient. ","lang":"eng"}],"_id":"663","author":[{"full_name":"Kong, Hui","last_name":"Kong","id":"3BDE25AA-F248-11E8-B48F-1D18A9856A87","first_name":"Hui","orcid":"0000-0002-3066-6941"},{"last_name":"Bogomolov","full_name":"Bogomolov, Sergiy","first_name":"Sergiy","orcid":"0000-0002-0686-0365"},{"first_name":"Christian","full_name":"Schilling, Christian","last_name":"Schilling"},{"first_name":"Yu","last_name":"Jiang","full_name":"Jiang, Yu"},{"last_name":"Henzinger","full_name":"Henzinger, Thomas A","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724"}],"title":"Safety verification of nonlinear hybrid systems based on invariant clusters"},{"publication":"Immunity","publication_identifier":{"issn":["10747613"]},"date_updated":"2024-03-25T23:30:05Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"6947"}]},"status":"public","publication_status":"published","page":"519 - 520","title":"The dynamic cytokine niche","author":[{"orcid":"0000-0003-3470-6119","id":"3A8E7F24-F248-11E8-B48F-1D18A9856A87","first_name":"Frank P","full_name":"Assen, Frank P","last_name":"Assen"},{"orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K"}],"_id":"664","abstract":[{"lang":"eng","text":"Immune cells communicate using cytokine signals, but the quantitative rules of this communication aren't clear. In this issue of Immunity, Oyler-Yaniv et al. (2017) suggest that the distribution of a cytokine within a lymphatic organ is primarily governed by the local density of cells consuming it."}],"year":"2017","issue":"4","doi":"10.1016/j.immuni.2017.04.006","publisher":"Cell Press","intvolume":"        46","volume":46,"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","citation":{"mla":"Assen, Frank P., and Michael K. Sixt. “The Dynamic Cytokine Niche.” <i>Immunity</i>, vol. 46, no. 4, Cell Press, 2017, pp. 519–20, doi:<a href=\"https://doi.org/10.1016/j.immuni.2017.04.006\">10.1016/j.immuni.2017.04.006</a>.","chicago":"Assen, Frank P, and Michael K Sixt. “The Dynamic Cytokine Niche.” <i>Immunity</i>. Cell Press, 2017. <a href=\"https://doi.org/10.1016/j.immuni.2017.04.006\">https://doi.org/10.1016/j.immuni.2017.04.006</a>.","short":"F.P. Assen, M.K. Sixt, Immunity 46 (2017) 519–520.","ama":"Assen FP, Sixt MK. The dynamic cytokine niche. <i>Immunity</i>. 2017;46(4):519-520. doi:<a href=\"https://doi.org/10.1016/j.immuni.2017.04.006\">10.1016/j.immuni.2017.04.006</a>","ista":"Assen FP, Sixt MK. 2017. The dynamic cytokine niche. Immunity. 46(4), 519–520.","apa":"Assen, F. P., &#38; Sixt, M. K. (2017). The dynamic cytokine niche. <i>Immunity</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.immuni.2017.04.006\">https://doi.org/10.1016/j.immuni.2017.04.006</a>","ieee":"F. P. Assen and M. K. Sixt, “The dynamic cytokine niche,” <i>Immunity</i>, vol. 46, no. 4. Cell Press, pp. 519–520, 2017."},"day":"18","department":[{"_id":"MiSi"}],"publist_id":"7065","month":"04","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_published":"2017-04-18T00:00:00Z","oa_version":"None","date_created":"2018-12-11T11:47:47Z","scopus_import":1},{"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","intvolume":"       356","publisher":"American Association for the Advancement of Science","scopus_import":1,"date_created":"2018-12-11T11:47:48Z","date_published":"2017-04-21T00:00:00Z","publist_id":"7064","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"CaGu"},{"_id":"GaTk"},{"_id":"Bio"}],"article_type":"original","page":"311 - 315","related_material":{"record":[{"id":"5560","relation":"popular_science","status":"public"}]},"date_updated":"2024-02-21T13:49:00Z","publication":"Science","year":"2017","article_processing_charge":"No","volume":356,"oa_version":"None","month":"04","day":"21","citation":{"chicago":"Bergmiller, Tobias, Anna M Andersson, Kathrin Tomasek, Enrique Balleza, Daniel Kiviet, Robert Hauschild, Gašper Tkačik, and Calin C Guet. “Biased Partitioning of the Multidrug Efflux Pump AcrAB TolC Underlies Long Lived Phenotypic Heterogeneity.” <i>Science</i>. American Association for the Advancement of Science, 2017. <a href=\"https://doi.org/10.1126/science.aaf4762\">https://doi.org/10.1126/science.aaf4762</a>.","mla":"Bergmiller, Tobias, et al. “Biased Partitioning of the Multidrug Efflux Pump AcrAB TolC Underlies Long Lived Phenotypic Heterogeneity.” <i>Science</i>, vol. 356, no. 6335, American Association for the Advancement of Science, 2017, pp. 311–15, doi:<a href=\"https://doi.org/10.1126/science.aaf4762\">10.1126/science.aaf4762</a>.","ama":"Bergmiller T, Andersson AM, Tomasek K, et al. Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity. <i>Science</i>. 2017;356(6335):311-315. doi:<a href=\"https://doi.org/10.1126/science.aaf4762\">10.1126/science.aaf4762</a>","ista":"Bergmiller T, Andersson AM, Tomasek K, Balleza E, Kiviet D, Hauschild R, Tkačik G, Guet CC. 2017. Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity. Science. 356(6335), 311–315.","short":"T. Bergmiller, A.M. Andersson, K. Tomasek, E. Balleza, D. Kiviet, R. Hauschild, G. Tkačik, C.C. Guet, Science 356 (2017) 311–315.","apa":"Bergmiller, T., Andersson, A. M., Tomasek, K., Balleza, E., Kiviet, D., Hauschild, R., … Guet, C. C. (2017). Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.aaf4762\">https://doi.org/10.1126/science.aaf4762</a>","ieee":"T. Bergmiller <i>et al.</i>, “Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity,” <i>Science</i>, vol. 356, no. 6335. American Association for the Advancement of Science, pp. 311–315, 2017."},"status":"public","publication_status":"published","project":[{"call_identifier":"FWF","name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"issn":["00368075"]},"doi":"10.1126/science.aaf4762","issue":"6335","abstract":[{"lang":"eng","text":"The molecular mechanisms underlying phenotypic variation in isogenic bacterial populations remain poorly understood.We report that AcrAB-TolC, the main multidrug efflux pump of Escherichia coli, exhibits a strong partitioning bias for old cell poles by a segregation mechanism that is mediated by ternary AcrAB-TolC complex formation. Mother cells inheriting old poles are phenotypically distinct and display increased drug efflux activity relative to daughters. Consequently, we find systematic and long-lived growth differences between mother and daughter cells in the presence of subinhibitory drug concentrations. A simple model for biased partitioning predicts a population structure of long-lived and highly heterogeneous phenotypes. This straightforward mechanism of generating sustained growth rate differences at subinhibitory antibiotic concentrations has implications for understanding the emergence of multidrug resistance in bacteria."}],"_id":"665","author":[{"orcid":"0000-0001-5396-4346","full_name":"Bergmiller, Tobias","last_name":"Bergmiller","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias"},{"orcid":"0000-0003-2912-6769","id":"2B8A40DA-F248-11E8-B48F-1D18A9856A87","first_name":"Anna M","full_name":"Andersson, Anna M","last_name":"Andersson"},{"first_name":"Kathrin","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","last_name":"Tomasek","full_name":"Tomasek, Kathrin","orcid":"0000-0003-3768-877X"},{"full_name":"Balleza, Enrique","last_name":"Balleza","first_name":"Enrique"},{"first_name":"Daniel","last_name":"Kiviet","full_name":"Kiviet, Daniel"},{"first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522"},{"orcid":"0000-0002-6699-1455","last_name":"Tkacik","full_name":"Tkacik, Gasper","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","full_name":"Guet, Calin C","last_name":"Guet","orcid":"0000-0001-6220-2052"}],"title":"Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity"},{"project":[{"name":"Optimality principles in responses to antibiotics","call_identifier":"FP7","_id":"25E83C2C-B435-11E9-9278-68D0E5697425","grant_number":"303507"},{"_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","grant_number":"P27201-B22","name":"Revealing the mechanisms underlying drug interactions","call_identifier":"FWF"},{"name":"Revealing the fundamental limits of cell growth","grant_number":"RGP0042/2013","_id":"25EB3A80-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"issn":["24054712"]},"ec_funded":1,"status":"public","publication_status":"published","_id":"666","author":[{"first_name":"Karin","id":"39B66846-F248-11E8-B48F-1D18A9856A87","last_name":"Mitosch","full_name":"Mitosch, Karin"},{"last_name":"Rieckh","full_name":"Rieckh, Georg","first_name":"Georg","id":"34DA8BD6-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Tobias","last_name":"Bollenbach","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias"}],"title":"Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment","doi":"10.1016/j.cels.2017.03.001","issue":"4","abstract":[{"lang":"eng","text":"Antibiotics elicit drastic changes in microbial gene expression, including the induction of stress response genes. While certain stress responses are known to “cross-protect” bacteria from other stressors, it is unclear whether cellular responses to antibiotics have a similar protective role. By measuring the genome-wide transcriptional response dynamics of Escherichia coli to four antibiotics, we found that trimethoprim induces a rapid acid stress response that protects bacteria from subsequent exposure to acid. Combining microfluidics with time-lapse imaging to monitor survival and acid stress response in single cells revealed that the noisy expression of the acid resistance operon gadBC correlates with single-cell survival. Cells with higher gadBC expression following trimethoprim maintain higher intracellular pH and survive the acid stress longer. The seemingly random single-cell survival under acid stress can therefore be predicted from gadBC expression and rationalized in terms of GadB/C molecular function. Overall, we provide a roadmap for identifying the molecular mechanisms of single-cell cross-protection between antibiotics and other stressors."}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"file":[{"file_id":"5041","date_created":"2018-12-12T10:13:54Z","date_updated":"2020-07-14T12:47:35Z","access_level":"open_access","content_type":"application/pdf","checksum":"04ff20011c3d9a601c514aa999a5fe1a","file_name":"IST-2017-901-v1+1_1-s2.0-S2405471217300868-main.pdf","creator":"system","file_size":2438660,"relation":"main_file"}],"article_processing_charge":"Yes (in subscription journal)","volume":4,"has_accepted_license":"1","month":"04","file_date_updated":"2020-07-14T12:47:35Z","ddc":["576","610"],"day":"26","citation":{"chicago":"Mitosch, Karin, Georg Rieckh, and Mark Tobias Bollenbach. “Noisy Response to Antibiotic Stress Predicts Subsequent Single Cell Survival in an Acidic Environment.” <i>Cell Systems</i>. Cell Press, 2017. <a href=\"https://doi.org/10.1016/j.cels.2017.03.001\">https://doi.org/10.1016/j.cels.2017.03.001</a>.","mla":"Mitosch, Karin, et al. “Noisy Response to Antibiotic Stress Predicts Subsequent Single Cell Survival in an Acidic Environment.” <i>Cell Systems</i>, vol. 4, no. 4, Cell Press, 2017, pp. 393–403, doi:<a href=\"https://doi.org/10.1016/j.cels.2017.03.001\">10.1016/j.cels.2017.03.001</a>.","apa":"Mitosch, K., Rieckh, G., &#38; Bollenbach, M. T. (2017). Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment. <i>Cell Systems</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cels.2017.03.001\">https://doi.org/10.1016/j.cels.2017.03.001</a>","ieee":"K. Mitosch, G. Rieckh, and M. T. Bollenbach, “Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment,” <i>Cell Systems</i>, vol. 4, no. 4. Cell Press, pp. 393–403, 2017.","ama":"Mitosch K, Rieckh G, Bollenbach MT. Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment. <i>Cell Systems</i>. 2017;4(4):393-403. doi:<a href=\"https://doi.org/10.1016/j.cels.2017.03.001\">10.1016/j.cels.2017.03.001</a>","ista":"Mitosch K, Rieckh G, Bollenbach MT. 2017. Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment. Cell Systems. 4(4), 393–403.","short":"K. Mitosch, G. Rieckh, M.T. Bollenbach, Cell Systems 4 (2017) 393–403."},"pubrep_id":"901","oa_version":"Published Version","date_updated":"2023-09-07T12:00:25Z","publication":"Cell Systems","page":"393 - 403","related_material":{"record":[{"id":"818","status":"public","relation":"dissertation_contains"}]},"oa":1,"year":"2017","intvolume":"         4","publisher":"Cell Press","quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"7061","department":[{"_id":"ToBo"},{"_id":"GaTk"}],"scopus_import":1,"date_created":"2018-12-11T11:47:48Z","date_published":"2017-04-26T00:00:00Z"},{"date_updated":"2021-01-12T08:08:30Z","publication":"Science Translational Medicine","publication_identifier":{"issn":["19466234"]},"article_number":"2786","publication_status":"published","status":"public","_id":"667","author":[{"orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia"}],"title":"The antisocial side of antibiotics","doi":"10.1126/scitranslmed.aan2786","issue":"387","year":"2017","abstract":[{"lang":"eng","text":"Perinatal exposure to penicillin may result in longlasting gut and behavioral changes."}],"intvolume":"         9","publisher":"American Association for the Advancement of Science","type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"volume":9,"month":"04","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"7060","day":"26","department":[{"_id":"GaNo"}],"citation":{"short":"G. Novarino, Science Translational Medicine 9 (2017).","ama":"Novarino G. The antisocial side of antibiotics. <i>Science Translational Medicine</i>. 2017;9(387). doi:<a href=\"https://doi.org/10.1126/scitranslmed.aan2786\">10.1126/scitranslmed.aan2786</a>","ista":"Novarino G. 2017. The antisocial side of antibiotics. Science Translational Medicine. 9(387), 2786.","apa":"Novarino, G. (2017). The antisocial side of antibiotics. <i>Science Translational Medicine</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/scitranslmed.aan2786\">https://doi.org/10.1126/scitranslmed.aan2786</a>","ieee":"G. Novarino, “The antisocial side of antibiotics,” <i>Science Translational Medicine</i>, vol. 9, no. 387. American Association for the Advancement of Science, 2017.","mla":"Novarino, Gaia. “The Antisocial Side of Antibiotics.” <i>Science Translational Medicine</i>, vol. 9, no. 387, 2786, American Association for the Advancement of Science, 2017, doi:<a href=\"https://doi.org/10.1126/scitranslmed.aan2786\">10.1126/scitranslmed.aan2786</a>.","chicago":"Novarino, Gaia. “The Antisocial Side of Antibiotics.” <i>Science Translational Medicine</i>. American Association for the Advancement of Science, 2017. <a href=\"https://doi.org/10.1126/scitranslmed.aan2786\">https://doi.org/10.1126/scitranslmed.aan2786</a>."},"scopus_import":1,"oa_version":"None","date_created":"2018-12-11T11:47:48Z","date_published":"2017-04-26T00:00:00Z"},{"publisher":"IEEE","arxiv":1,"main_file_link":[{"url":"https://arxiv.org/abs/1705.05497","open_access":"1"}],"quality_controlled":"1","type":"conference","language":[{"iso":"eng"}],"citation":{"mla":"Hashemi, Seyyed Ali, et al. “Partitioned List Decoding of Polar Codes: Analysis and Improvement of Finite Length Performance.” <i>2017 IEEE Global Communications Conference</i>, IEEE, 2017, pp. 1–7, doi:<a href=\"https://doi.org/10.1109/glocom.2017.8254940\">10.1109/glocom.2017.8254940</a>.","chicago":"Hashemi, Seyyed Ali, Marco Mondelli, Hamed Hassani, Ruediger Urbanke, and Warren Gross. “Partitioned List Decoding of Polar Codes: Analysis and Improvement of Finite Length Performance.” In <i>2017 IEEE Global Communications Conference</i>, 1–7. IEEE, 2017. <a href=\"https://doi.org/10.1109/glocom.2017.8254940\">https://doi.org/10.1109/glocom.2017.8254940</a>.","ieee":"S. A. Hashemi, M. Mondelli, H. Hassani, R. Urbanke, and W. Gross, “Partitioned list decoding of polar codes: Analysis and improvement of finite length performance,” in <i>2017 IEEE Global Communications Conference</i>, Singapore, Singapore, 2017, pp. 1–7.","apa":"Hashemi, S. A., Mondelli, M., Hassani, H., Urbanke, R., &#38; Gross, W. (2017). Partitioned list decoding of polar codes: Analysis and improvement of finite length performance. In <i>2017 IEEE Global Communications Conference</i> (pp. 1–7). Singapore, Singapore: IEEE. <a href=\"https://doi.org/10.1109/glocom.2017.8254940\">https://doi.org/10.1109/glocom.2017.8254940</a>","ista":"Hashemi SA, Mondelli M, Hassani H, Urbanke R, Gross W. 2017. Partitioned list decoding of polar codes: Analysis and improvement of finite length performance. 2017 IEEE Global Communications Conference. GLOBECOM: Global Communications Conference, 1–7.","short":"S.A. Hashemi, M. Mondelli, H. Hassani, R. Urbanke, W. Gross, in:, 2017 IEEE Global Communications Conference, IEEE, 2017, pp. 1–7.","ama":"Hashemi SA, Mondelli M, Hassani H, Urbanke R, Gross W. Partitioned list decoding of polar codes: Analysis and improvement of finite length performance. In: <i>2017 IEEE Global Communications Conference</i>. IEEE; 2017:1-7. doi:<a href=\"https://doi.org/10.1109/glocom.2017.8254940\">10.1109/glocom.2017.8254940</a>"},"day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"12","external_id":{"arxiv":["1705.05497"]},"date_published":"2017-12-01T00:00:00Z","extern":"1","oa_version":"Preprint","date_created":"2019-07-24T13:55:25Z","conference":{"location":"Singapore, Singapore","start_date":"2017-12-04","end_date":"2017-12-08","name":"GLOBECOM: Global Communications Conference"},"publication":"2017 IEEE Global Communications Conference","date_updated":"2021-01-12T08:08:34Z","status":"public","publication_status":"published","page":"1-7","oa":1,"title":"Partitioned list decoding of polar codes: Analysis and improvement of finite length performance","author":[{"last_name":"Hashemi","full_name":"Hashemi, Seyyed Ali","first_name":"Seyyed Ali"},{"orcid":"0000-0002-3242-7020","id":"27EB676C-8706-11E9-9510-7717E6697425","first_name":"Marco","full_name":"Mondelli, Marco","last_name":"Mondelli"},{"full_name":"Hassani, Hamed","last_name":"Hassani","first_name":"Hamed"},{"last_name":"Urbanke","full_name":"Urbanke, Ruediger","first_name":"Ruediger"},{"first_name":"Warren","full_name":"Gross, Warren","last_name":"Gross"}],"_id":"6679","abstract":[{"text":"Polar codes represent one of the major recent breakthroughs in coding theory and, because of their attractive features, they have been selected for the incoming 5G standard. As such, a lot of attention has been devoted to the development of decoding algorithms with good error performance and efficient hardware implementation. One of the leading candidates in this regard is represented by successive-cancellation list (SCL) decoding. However, its hardware implementation requires a large amount of memory. Recently, a partitioned SCL (PSCL) decoder has been proposed to significantly reduce the memory consumption [1]. In this paper, we examine the paradigm of PSCL decoding from both theoretical and practical standpoints: (i) by changing the construction of the code, we are able to improve the performance at no additional computational, latency or memory cost, (ii) we present an optimal scheme to allocate cyclic redundancy checks (CRCs), and (iii) we provide an upper bound on the list size that allows MAP performance.","lang":"eng"}],"year":"2017","doi":"10.1109/glocom.2017.8254940"},{"publication_identifier":{"issn":["00219258"]},"publication_status":"published","status":"public","title":"Multiple roles of filopodial dynamics in particle capture and phagocytosis and phenotypes of Cdc42 and Myo10 deletion","author":[{"full_name":"Horsthemke, Markus","last_name":"Horsthemke","first_name":"Markus"},{"first_name":"Anne","last_name":"Bachg","full_name":"Bachg, Anne"},{"first_name":"Katharina","full_name":"Groll, Katharina","last_name":"Groll"},{"first_name":"Sven","full_name":"Moyzio, Sven","last_name":"Moyzio"},{"first_name":"Barbara","full_name":"Müther, Barbara","last_name":"Müther"},{"full_name":"Hemkemeyer, Sandra","last_name":"Hemkemeyer","first_name":"Sandra"},{"full_name":"Wedlich Söldner, Roland","last_name":"Wedlich Söldner","first_name":"Roland"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","full_name":"Sixt, Michael K","last_name":"Sixt","orcid":"0000-0002-6620-9179"},{"full_name":"Tacke, Sebastian","last_name":"Tacke","first_name":"Sebastian"},{"full_name":"Bähler, Martin","last_name":"Bähler","first_name":"Martin"},{"first_name":"Peter","last_name":"Hanley","full_name":"Hanley, Peter"}],"_id":"668","abstract":[{"lang":"eng","text":"Macrophage filopodia, finger-like membrane protrusions, were first implicated in phagocytosis more than 100 years ago, but little is still known about the involvement of these actin-dependent structures in particle clearance. Using spinning disk confocal microscopy to image filopodial dynamics in mouse resident Lifeact-EGFP macrophages, we show that filopodia, or filopodia-like structures, support pathogen clearance by multiple means. Filopodia supported the phagocytic uptake of bacterial (Escherichia coli) particles by (i) capturing along the filopodial shaft and surfing toward the cell body, the most common mode of capture; (ii) capturing via the tip followed by retraction; (iii) combinations of surfing and retraction; or (iv) sweeping actions. In addition, filopodia supported the uptake of zymosan (Saccharomyces cerevisiae) particles by (i) providing fixation, (ii) capturing at the tip and filopodia-guided actin anterograde flow with phagocytic cup formation, and (iii) the rapid growth of new protrusions. To explore the role of filopodia-inducing Cdc42, we generated myeloid-restricted Cdc42 knock-out mice. Cdc42-deficient macrophages exhibited rapid phagocytic cup kinetics, but reduced particle clearance, which could be explained by the marked rounded-up morphology of these cells. Macrophages lacking Myo10, thought to act downstream of Cdc42, had normal morphology, motility, and phagocytic cup formation, but displayed markedly reduced filopodia formation. In conclusion, live-cell imaging revealed multiple mechanisms involving macrophage filopodia in particle capture and engulfment. Cdc42 is not critical for filopodia or phagocytic cup formation, but plays a key role in driving macrophage lamellipodial spreading."}],"issue":"17","doi":"10.1074/jbc.M116.766923","file":[{"date_created":"2019-10-24T15:25:42Z","file_id":"6971","relation":"main_file","creator":"dernst","file_size":5647880,"file_name":"2017_JBC_Horsthemke.pdf","date_updated":"2020-07-14T12:47:37Z","content_type":"application/pdf","checksum":"d488162874326a4bb056065fa549dc4a","access_level":"open_access"}],"has_accepted_license":"1","volume":292,"citation":{"mla":"Horsthemke, Markus, et al. “Multiple Roles of Filopodial Dynamics in Particle Capture and Phagocytosis and Phenotypes of Cdc42 and Myo10 Deletion.” <i>Journal of Biological Chemistry</i>, vol. 292, no. 17, American Society for Biochemistry and Molecular Biology, 2017, pp. 7258–73, doi:<a href=\"https://doi.org/10.1074/jbc.M116.766923\">10.1074/jbc.M116.766923</a>.","chicago":"Horsthemke, Markus, Anne Bachg, Katharina Groll, Sven Moyzio, Barbara Müther, Sandra Hemkemeyer, Roland Wedlich Söldner, et al. “Multiple Roles of Filopodial Dynamics in Particle Capture and Phagocytosis and Phenotypes of Cdc42 and Myo10 Deletion.” <i>Journal of Biological Chemistry</i>. American Society for Biochemistry and Molecular Biology, 2017. <a href=\"https://doi.org/10.1074/jbc.M116.766923\">https://doi.org/10.1074/jbc.M116.766923</a>.","ieee":"M. Horsthemke <i>et al.</i>, “Multiple roles of filopodial dynamics in particle capture and phagocytosis and phenotypes of Cdc42 and Myo10 deletion,” <i>Journal of Biological Chemistry</i>, vol. 292, no. 17. American Society for Biochemistry and Molecular Biology, pp. 7258–7273, 2017.","apa":"Horsthemke, M., Bachg, A., Groll, K., Moyzio, S., Müther, B., Hemkemeyer, S., … Hanley, P. (2017). Multiple roles of filopodial dynamics in particle capture and phagocytosis and phenotypes of Cdc42 and Myo10 deletion. <i>Journal of Biological Chemistry</i>. American Society for Biochemistry and Molecular Biology. <a href=\"https://doi.org/10.1074/jbc.M116.766923\">https://doi.org/10.1074/jbc.M116.766923</a>","ama":"Horsthemke M, Bachg A, Groll K, et al. Multiple roles of filopodial dynamics in particle capture and phagocytosis and phenotypes of Cdc42 and Myo10 deletion. <i>Journal of Biological Chemistry</i>. 2017;292(17):7258-7273. doi:<a href=\"https://doi.org/10.1074/jbc.M116.766923\">10.1074/jbc.M116.766923</a>","short":"M. Horsthemke, A. Bachg, K. Groll, S. Moyzio, B. Müther, S. Hemkemeyer, R. Wedlich Söldner, M.K. Sixt, S. Tacke, M. Bähler, P. Hanley, Journal of Biological Chemistry 292 (2017) 7258–7273.","ista":"Horsthemke M, Bachg A, Groll K, Moyzio S, Müther B, Hemkemeyer S, Wedlich Söldner R, Sixt MK, Tacke S, Bähler M, Hanley P. 2017. Multiple roles of filopodial dynamics in particle capture and phagocytosis and phenotypes of Cdc42 and Myo10 deletion. Journal of Biological Chemistry. 292(17), 7258–7273."},"day":"28","month":"04","ddc":["570"],"file_date_updated":"2020-07-14T12:47:37Z","oa_version":"Published Version","publication":"Journal of Biological Chemistry","date_updated":"2021-01-12T08:08:34Z","page":"7258 - 7273","article_type":"original","oa":1,"year":"2017","publisher":"American Society for Biochemistry and Molecular Biology","intvolume":"       292","quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","department":[{"_id":"MiSi"}],"publist_id":"7059","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2017-04-28T00:00:00Z","date_created":"2018-12-11T11:47:49Z","scopus_import":1},{"oa_version":"Submitted Version","citation":{"mla":"Synek, Lukáš, et al. “EXO70C2 Is a Key Regulatory Factor for Optimal Tip Growth of Pollen.” <i>Plant Physiology</i>, vol. 174, no. 1, American Society of Plant Biologists, 2017, pp. 223–40, doi:<a href=\"https://doi.org/10.1104/pp.16.01282\">10.1104/pp.16.01282</a>.","chicago":"Synek, Lukáš, Nemanja Vukašinović, Ivan Kulich, Michal Hála, Klára Aldorfová, Matyas Fendrych, and Viktor Žárský. “EXO70C2 Is a Key Regulatory Factor for Optimal Tip Growth of Pollen.” <i>Plant Physiology</i>. American Society of Plant Biologists, 2017. <a href=\"https://doi.org/10.1104/pp.16.01282\">https://doi.org/10.1104/pp.16.01282</a>.","ama":"Synek L, Vukašinović N, Kulich I, et al. EXO70C2 is a key regulatory factor for optimal tip growth of pollen. <i>Plant Physiology</i>. 2017;174(1):223-240. doi:<a href=\"https://doi.org/10.1104/pp.16.01282\">10.1104/pp.16.01282</a>","short":"L. Synek, N. Vukašinović, I. Kulich, M. Hála, K. Aldorfová, M. Fendrych, V. Žárský, Plant Physiology 174 (2017) 223–240.","ista":"Synek L, Vukašinović N, Kulich I, Hála M, Aldorfová K, Fendrych M, Žárský V. 2017. EXO70C2 is a key regulatory factor for optimal tip growth of pollen. Plant Physiology. 174(1), 223–240.","apa":"Synek, L., Vukašinović, N., Kulich, I., Hála, M., Aldorfová, K., Fendrych, M., &#38; Žárský, V. (2017). EXO70C2 is a key regulatory factor for optimal tip growth of pollen. <i>Plant Physiology</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1104/pp.16.01282\">https://doi.org/10.1104/pp.16.01282</a>","ieee":"L. Synek <i>et al.</i>, “EXO70C2 is a key regulatory factor for optimal tip growth of pollen,” <i>Plant Physiology</i>, vol. 174, no. 1. American Society of Plant Biologists, pp. 223–240, 2017."},"day":"01","month":"05","pmid":1,"ddc":["580"],"file_date_updated":"2020-07-14T12:47:37Z","has_accepted_license":"1","article_processing_charge":"No","volume":174,"file":[{"file_id":"7041","date_created":"2019-11-18T16:16:18Z","access_level":"open_access","content_type":"application/pdf","checksum":"97155acc6aa5f0d0a78e0589a932fe02","date_updated":"2020-07-14T12:47:37Z","file_name":"2017_PlantPhysio_Synek.pdf","file_size":2176903,"relation":"main_file","creator":"dernst"}],"abstract":[{"lang":"eng","text":"The exocyst, a eukaryotic tethering complex, coregulates targeted exocytosis as an effector of small GTPases in polarized cell growth. In land plants, several exocyst subunits are encoded by double or triple paralogs, culminating in tens of EXO70 paralogs. Out of 23 Arabidopsis thaliana EXO70 isoforms, we analyzed seven isoforms expressed in pollen. Genetic and microscopic analyses of single mutants in EXO70A2, EXO70C1, EXO70C2, EXO70F1, EXO70H3, EXO70H5, and EXO70H6 genes revealed that only a loss-of-function EXO70C2 allele resulted in a significant male-specific transmission defect (segregation 40%:51%:9%) due to aberrant pollen tube growth. Mutant pollen tubes grown in vitro exhibited an enhanced growth rate and a decreased thickness of the tip cell wall, causing tip bursts. However, exo70C2 pollen tubes could frequently recover and restart their speedy elongation, resulting in a repetitive stop-and-go growth dynamics. A pollenspecific depletion of the closest paralog, EXO70C1, using artificial microRNA in the exo70C2 mutant background, resulted in a complete pollen-specific transmission defect, suggesting redundant functions of EXO70C1 and EXO70C2. Both EXO70C1 and EXO70C2, GFP tagged and expressed under the control of their native promoters, localized in the cytoplasm of pollen grains, pollen tubes, and also root trichoblast cells. The expression of EXO70C2-GFP complemented the aberrant growth of exo70C2 pollen tubes. The absent EXO70C2 interactions with core exocyst subunits in the yeast two-hybrid assay, cytoplasmic localization, and genetic effect suggest an unconventional EXO70 function possibly as a regulator of exocytosis outside the exocyst complex. In conclusion, EXO70C2 is a novel factor contributing to the regulation of optimal tip growth of Arabidopsis pollen tubes. "}],"issue":"1","doi":"10.1104/pp.16.01282","title":"EXO70C2 is a key regulatory factor for optimal tip growth of pollen","author":[{"first_name":"Lukáš","full_name":"Synek, Lukáš","last_name":"Synek"},{"last_name":"Vukašinović","full_name":"Vukašinović, Nemanja","first_name":"Nemanja"},{"first_name":"Ivan","full_name":"Kulich, Ivan","last_name":"Kulich"},{"last_name":"Hála","full_name":"Hála, Michal","first_name":"Michal"},{"first_name":"Klára","full_name":"Aldorfová, Klára","last_name":"Aldorfová"},{"orcid":"0000-0002-9767-8699","id":"43905548-F248-11E8-B48F-1D18A9856A87","first_name":"Matyas","full_name":"Fendrych, Matyas","last_name":"Fendrych"},{"first_name":"Viktor","full_name":"Žárský, Viktor","last_name":"Žárský"}],"_id":"669","status":"public","publication_status":"published","publication_identifier":{"issn":["00320889"]},"date_published":"2017-05-01T00:00:00Z","external_id":{"pmid":["28356503"]},"date_created":"2018-12-11T11:47:49Z","scopus_import":1,"department":[{"_id":"JiFr"}],"publist_id":"7058","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"publisher":"American Society of Plant Biologists","intvolume":"       174","year":"2017","oa":1,"page":"223 - 240","article_type":"original","publication":"Plant Physiology","date_updated":"2021-01-12T08:08:35Z"},{"citation":{"ama":"Schreck C, Rohmer D, Hahmann S. Interactive paper tearing. <i>Computer Graphics Forum</i>. 2017;36(2):95-106. doi:<a href=\"https://doi.org/10.1111/cgf.13110\">10.1111/cgf.13110</a>","short":"C. Schreck, D. Rohmer, S. Hahmann, Computer Graphics Forum 36 (2017) 95–106.","ista":"Schreck C, Rohmer D, Hahmann S. 2017. Interactive paper tearing. Computer Graphics Forum. 36(2), 95–106.","ieee":"C. Schreck, D. Rohmer, and S. Hahmann, “Interactive paper tearing,” <i>Computer Graphics Forum</i>, vol. 36, no. 2. Wiley, pp. 95–106, 2017.","apa":"Schreck, C., Rohmer, D., &#38; Hahmann, S. (2017). Interactive paper tearing. <i>Computer Graphics Forum</i>. Wiley. <a href=\"https://doi.org/10.1111/cgf.13110\">https://doi.org/10.1111/cgf.13110</a>","mla":"Schreck, Camille, et al. “Interactive Paper Tearing.” <i>Computer Graphics Forum</i>, vol. 36, no. 2, Wiley, 2017, pp. 95–106, doi:<a href=\"https://doi.org/10.1111/cgf.13110\">10.1111/cgf.13110</a>.","chicago":"Schreck, Camille, Damien Rohmer, and Stefanie Hahmann. “Interactive Paper Tearing.” <i>Computer Graphics Forum</i>. Wiley, 2017. <a href=\"https://doi.org/10.1111/cgf.13110\">https://doi.org/10.1111/cgf.13110</a>."},"day":"01","month":"05","ddc":["000"],"oa_version":"Published Version","article_processing_charge":"No","volume":36,"title":"Interactive paper tearing","author":[{"first_name":"Camille","id":"2B14B676-F248-11E8-B48F-1D18A9856A87","last_name":"Schreck","full_name":"Schreck, Camille"},{"first_name":"Damien","last_name":"Rohmer","full_name":"Rohmer, Damien"},{"first_name":"Stefanie","last_name":"Hahmann","full_name":"Hahmann, Stefanie"}],"_id":"670","abstract":[{"lang":"eng","text":"We propose an efficient method to model paper tearing in the context of interactive modeling. The method uses geometrical information to automatically detect potential starting points of tears. We further introduce a new hybrid geometrical and physical-based method to compute the trajectory of tears while procedurally synthesizing high resolution details of the tearing path using a texture based approach. The results obtained are compared with real paper and with previous studies on the expected geometric paths of paper that tears."}],"issue":"2","doi":"10.1111/cgf.13110","publication_identifier":{"issn":["01677055"]},"project":[{"grant_number":"P 24352-N23","_id":"25357BD2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Deep Pictures: Creating Visual and Haptic Vector Images"}],"publication_status":"published","status":"public","department":[{"_id":"ChWo"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"7056","date_published":"2017-05-01T00:00:00Z","date_created":"2018-12-11T11:47:49Z","scopus_import":1,"publisher":"Wiley","intvolume":"        36","main_file_link":[{"url":"https://hal.inria.fr/hal-01647113/file/eg_2017_schreck_paper_tearing.pdf","open_access":"1"}],"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","oa":1,"year":"2017","publication":"Computer Graphics Forum","date_updated":"2021-01-12T08:08:37Z","page":"95 - 106","article_type":"original"},{"intvolume":"       114","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5422766/","open_access":"1"}],"publisher":"National Academy of Sciences","language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","department":[{"_id":"KrCh"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"7053","external_id":{"pmid":["28420786"]},"date_published":"2017-05-02T00:00:00Z","scopus_import":1,"date_created":"2018-12-11T11:47:50Z","publication":"PNAS","date_updated":"2021-01-12T08:08:37Z","page":"4715 - 4720","oa":1,"year":"2017","article_processing_charge":"Yes (in subscription journal)","volume":114,"day":"02","citation":{"mla":"Hilbe, Christian, et al. “Memory-n Strategies of Direct Reciprocity.” <i>PNAS</i>, vol. 114, no. 18, National Academy of Sciences, 2017, pp. 4715–20, doi:<a href=\"https://doi.org/10.1073/pnas.1621239114\">10.1073/pnas.1621239114</a>.","chicago":"Hilbe, Christian, Vaquero Martinez, Krishnendu Chatterjee, and Martin Nowak. “Memory-n Strategies of Direct Reciprocity.” <i>PNAS</i>. National Academy of Sciences, 2017. <a href=\"https://doi.org/10.1073/pnas.1621239114\">https://doi.org/10.1073/pnas.1621239114</a>.","ista":"Hilbe C, Martinez V, Chatterjee K, Nowak M. 2017. Memory-n strategies of direct reciprocity. PNAS. 114(18), 4715–4720.","short":"C. Hilbe, V. Martinez, K. Chatterjee, M. Nowak, PNAS 114 (2017) 4715–4720.","ama":"Hilbe C, Martinez V, Chatterjee K, Nowak M. Memory-n strategies of direct reciprocity. <i>PNAS</i>. 2017;114(18):4715-4720. doi:<a href=\"https://doi.org/10.1073/pnas.1621239114\">10.1073/pnas.1621239114</a>","ieee":"C. Hilbe, V. Martinez, K. Chatterjee, and M. Nowak, “Memory-n strategies of direct reciprocity,” <i>PNAS</i>, vol. 114, no. 18. National Academy of Sciences, pp. 4715–4720, 2017.","apa":"Hilbe, C., Martinez, V., Chatterjee, K., &#38; Nowak, M. (2017). Memory-n strategies of direct reciprocity. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1621239114\">https://doi.org/10.1073/pnas.1621239114</a>"},"pmid":1,"month":"05","oa_version":"Published Version","publication_identifier":{"issn":["00278424"]},"project":[{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Game Theory"}],"status":"public","publication_status":"published","ec_funded":1,"author":[{"orcid":"0000-0001-5116-955X","full_name":"Hilbe, Christian","last_name":"Hilbe","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","first_name":"Christian"},{"full_name":"Martinez, Vaquero","last_name":"Martinez","first_name":"Vaquero"},{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X"},{"first_name":"Martin","last_name":"Nowak","full_name":"Nowak, Martin"}],"title":"Memory-n strategies of direct reciprocity","_id":"671","issue":"18","abstract":[{"lang":"eng","text":"Humans routinely use conditionally cooperative strategies when interacting in repeated social dilemmas. They are more likely to cooperate if others cooperated before, and are ready to retaliate if others defected. To capture the emergence of reciprocity, most previous models consider subjects who can only choose from a restricted set of representative strategies, or who react to the outcome of the very last round only. As players memorize more rounds, the dimension of the strategy space increases exponentially. This increasing computational complexity renders simulations for individuals with higher cognitive abilities infeasible, especially if multiplayer interactions are taken into account. Here, we take an axiomatic approach instead. We propose several properties that a robust cooperative strategy for a repeated multiplayer dilemma should have. These properties naturally lead to a unique class of cooperative strategies, which contains the classical Win-Stay Lose-Shift rule as a special case. A comprehensive numerical analysis for the prisoner's dilemma and for the public goods game suggests that strategies of this class readily evolve across various memory-n spaces. Our results reveal that successful strategies depend not only on how cooperative others were in the past but also on the respective context of cooperation."}],"doi":"10.1073/pnas.1621239114"},{"publication_status":"published","status":"public","ec_funded":1,"publication_identifier":{"issn":["22111247"]},"project":[{"_id":"25A603A2-B435-11E9-9278-68D0E5697425","grant_number":"281556","call_identifier":"FP7","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)"},{"_id":"25A8E5EA-B435-11E9-9278-68D0E5697425","grant_number":"Y 564-B12","name":"Cytoskeletal force generation and transduction of leukocytes (FWF)","call_identifier":"FWF"}],"abstract":[{"text":"Trafficking cells frequently transmigrate through epithelial and endothelial monolayers. How monolayers cooperate with the penetrating cells to support their transit is poorly understood. We studied dendritic cell (DC) entry into lymphatic capillaries as a model system for transendothelial migration. We find that the chemokine CCL21, which is the decisive guidance cue for intravasation, mainly localizes in the trans-Golgi network and intracellular vesicles of lymphatic endothelial cells. Upon DC transmigration, these Golgi deposits disperse and CCL21 becomes extracellularly enriched at the sites of endothelial cell-cell junctions. When we reconstitute the transmigration process in vitro, we find that secretion of CCL21-positive vesicles is triggered by a DC contact-induced calcium signal, and selective calcium chelation in lymphatic endothelium attenuates transmigration. Altogether, our data demonstrate a chemokine-mediated feedback between DCs and lymphatic endothelium, which facilitates transendothelial migration.","lang":"eng"}],"issue":"5","doi":"10.1016/j.celrep.2017.04.027","title":"Locally triggered release of the chemokine CCL21 promotes dendritic cell transmigration across lymphatic endothelia","author":[{"orcid":"0000-0001-7829-3518","first_name":"Kari","id":"368EE576-F248-11E8-B48F-1D18A9856A87","last_name":"Vaahtomeri","full_name":"Vaahtomeri, Kari"},{"last_name":"Brown","full_name":"Brown, Markus","first_name":"Markus","id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hauschild, Robert","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","orcid":"0000-0001-9843-3522"},{"first_name":"Ingrid","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","last_name":"De Vries","full_name":"De Vries, Ingrid"},{"id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander F","full_name":"Leithner, Alexander F","last_name":"Leithner"},{"full_name":"Mehling, Matthias","last_name":"Mehling","id":"3C23B994-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias","orcid":"0000-0001-8599-1226"},{"id":"3F99E422-F248-11E8-B48F-1D18A9856A87","first_name":"Walter","full_name":"Kaufmann, Walter","last_name":"Kaufmann","orcid":"0000-0001-9735-5315"},{"orcid":"0000-0002-6620-9179","last_name":"Sixt","full_name":"Sixt, Michael K","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"_id":"672","has_accepted_license":"1","volume":19,"article_processing_charge":"Yes","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"file":[{"file_id":"5109","date_created":"2018-12-12T10:14:54Z","file_name":"IST-2017-900-v1+1_1-s2.0-S2211124717305211-main.pdf","relation":"main_file","creator":"system","file_size":2248814,"access_level":"open_access","content_type":"application/pdf","checksum":"8fdddaab1f1d76a6ec9ca94dcb6b07a2","date_updated":"2020-07-14T12:47:38Z"}],"oa_version":"Published Version","pubrep_id":"900","citation":{"chicago":"Vaahtomeri, Kari, Markus Brown, Robert Hauschild, Ingrid de Vries, Alexander F Leithner, Matthias Mehling, Walter Kaufmann, and Michael K Sixt. “Locally Triggered Release of the Chemokine CCL21 Promotes Dendritic Cell Transmigration across Lymphatic Endothelia.” <i>Cell Reports</i>. Cell Press, 2017. <a href=\"https://doi.org/10.1016/j.celrep.2017.04.027\">https://doi.org/10.1016/j.celrep.2017.04.027</a>.","mla":"Vaahtomeri, Kari, et al. “Locally Triggered Release of the Chemokine CCL21 Promotes Dendritic Cell Transmigration across Lymphatic Endothelia.” <i>Cell Reports</i>, vol. 19, no. 5, Cell Press, 2017, pp. 902–09, doi:<a href=\"https://doi.org/10.1016/j.celrep.2017.04.027\">10.1016/j.celrep.2017.04.027</a>.","apa":"Vaahtomeri, K., Brown, M., Hauschild, R., de Vries, I., Leithner, A. F., Mehling, M., … Sixt, M. K. (2017). Locally triggered release of the chemokine CCL21 promotes dendritic cell transmigration across lymphatic endothelia. <i>Cell Reports</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.celrep.2017.04.027\">https://doi.org/10.1016/j.celrep.2017.04.027</a>","ieee":"K. Vaahtomeri <i>et al.</i>, “Locally triggered release of the chemokine CCL21 promotes dendritic cell transmigration across lymphatic endothelia,” <i>Cell Reports</i>, vol. 19, no. 5. Cell Press, pp. 902–909, 2017.","ama":"Vaahtomeri K, Brown M, Hauschild R, et al. Locally triggered release of the chemokine CCL21 promotes dendritic cell transmigration across lymphatic endothelia. <i>Cell Reports</i>. 2017;19(5):902-909. doi:<a href=\"https://doi.org/10.1016/j.celrep.2017.04.027\">10.1016/j.celrep.2017.04.027</a>","ista":"Vaahtomeri K, Brown M, Hauschild R, de Vries I, Leithner AF, Mehling M, Kaufmann W, Sixt MK. 2017. Locally triggered release of the chemokine CCL21 promotes dendritic cell transmigration across lymphatic endothelia. Cell Reports. 19(5), 902–909.","short":"K. Vaahtomeri, M. Brown, R. Hauschild, I. de Vries, A.F. Leithner, M. Mehling, W. Kaufmann, M.K. Sixt, Cell Reports 19 (2017) 902–909."},"day":"02","file_date_updated":"2020-07-14T12:47:38Z","ddc":["570"],"month":"05","page":"902 - 909","publication":"Cell Reports","date_updated":"2023-02-23T12:50:09Z","year":"2017","oa":1,"quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"publisher":"Cell Press","intvolume":"        19","date_published":"2017-05-02T00:00:00Z","date_created":"2018-12-11T11:47:50Z","scopus_import":1,"department":[{"_id":"MiSi"},{"_id":"Bio"},{"_id":"EM-Fac"}],"publist_id":"7052","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"day":"15","citation":{"short":"M. Mondelli, S.H. Hassani, R. Urbanke, in:, 2017 IEEE International Symposium on Information Theory , IEEE, 2017, pp. 1853–1857.","ama":"Mondelli M, Hassani SH, Urbanke R. Construction of polar codes with sublinear complexity. In: <i>2017 IEEE International Symposium on Information Theory </i>. IEEE; 2017:1853-1857. doi:<a href=\"https://doi.org/10.1109/isit.2017.8006850\">10.1109/isit.2017.8006850</a>","ista":"Mondelli M, Hassani SH, Urbanke R. 2017. Construction of polar codes with sublinear complexity. 2017 IEEE International Symposium on Information Theory . ISIT: International Symposium on Information Theory, 1853–1857.","apa":"Mondelli, M., Hassani, S. H., &#38; Urbanke, R. (2017). Construction of polar codes with sublinear complexity. In <i>2017 IEEE International Symposium on Information Theory </i> (pp. 1853–1857). Aachen, Germany: IEEE. <a href=\"https://doi.org/10.1109/isit.2017.8006850\">https://doi.org/10.1109/isit.2017.8006850</a>","ieee":"M. Mondelli, S. H. Hassani, and R. Urbanke, “Construction of polar codes with sublinear complexity,” in <i>2017 IEEE International Symposium on Information Theory </i>, Aachen, Germany, 2017, pp. 1853–1857.","mla":"Mondelli, Marco, et al. “Construction of Polar Codes with Sublinear Complexity.” <i>2017 IEEE International Symposium on Information Theory </i>, IEEE, 2017, pp. 1853–57, doi:<a href=\"https://doi.org/10.1109/isit.2017.8006850\">10.1109/isit.2017.8006850</a>.","chicago":"Mondelli, Marco, S. Hamed Hassani, and Rudiger Urbanke. “Construction of Polar Codes with Sublinear Complexity.” In <i>2017 IEEE International Symposium on Information Theory </i>, 1853–57. IEEE, 2017. <a href=\"https://doi.org/10.1109/isit.2017.8006850\">https://doi.org/10.1109/isit.2017.8006850</a>."},"month":"06","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","external_id":{"arxiv":["1612.05295"]},"date_published":"2017-06-15T00:00:00Z","conference":{"start_date":"2017-06-25","location":"Aachen, Germany","end_date":"2017-06-30","name":"ISIT: International Symposium on Information Theory"},"oa_version":"Preprint","date_created":"2019-07-30T07:14:18Z","main_file_link":[{"url":"https://arxiv.org/abs/1612.05295","open_access":"1"}],"arxiv":1,"publisher":"IEEE","type":"conference","quality_controlled":"1","language":[{"iso":"eng"}],"author":[{"orcid":"0000-0002-3242-7020","id":"27EB676C-8706-11E9-9510-7717E6697425","first_name":"Marco","full_name":"Mondelli, Marco","last_name":"Mondelli"},{"first_name":"S. Hamed","full_name":"Hassani, S. Hamed","last_name":"Hassani"},{"first_name":"Rudiger","last_name":"Urbanke","full_name":"Urbanke, Rudiger"}],"title":"Construction of polar codes with sublinear complexity","oa":1,"_id":"6729","year":"2017","abstract":[{"lang":"eng","text":"Consider the problem of constructing a polar code of block length N for the transmission over a given channel W. Typically this requires to compute the reliability of all the N synthetic channels and then to include those that are sufficiently reliable. However, we know from [1], [2] that there is a partial order among the synthetic channels. Hence, it is natural to ask whether we can exploit it to reduce the computational burden of the construction problem. We show that, if we take advantage of the partial order [1], [2], we can construct a polar code by computing the reliability of roughly N/ log 3/2 N synthetic channels. Such a set of synthetic channels is universal, in the sense that it allows one to construct polar codes for any W, and it can be identified by solving a maximum matching problem on a bipartite graph. Our proof technique consists in reducing the construction problem to the problem of computing the maximum cardinality of an antichain for a suitable partially ordered set. As such, this method is general and it can be used to further improve the complexity of the construction problem in case a new partial order on the synthetic channels of polar codes is discovered."}],"doi":"10.1109/isit.2017.8006850","publication":"2017 IEEE International Symposium on Information Theory ","publication_identifier":{"isbn":["9781509040964"],"eissn":["2157-8117"]},"date_updated":"2023-02-23T12:49:08Z","publication_status":"published","status":"public","related_material":{"record":[{"relation":"later_version","status":"public","id":"6663"}]},"page":"1853-1857"},{"oa_version":"Submitted Version","citation":{"ista":"Altmeyer S, Lueptow R. 2017. Wave propagation reversal for wavy vortices in wide gap counter rotating cylindrical Couette flow. Physical Review E. 95(5), 053103.","ama":"Altmeyer S, Lueptow R. Wave propagation reversal for wavy vortices in wide gap counter rotating cylindrical Couette flow. <i>Physical Review E</i>. 2017;95(5). doi:<a href=\"https://doi.org/10.1103/PhysRevE.95.053103\">10.1103/PhysRevE.95.053103</a>","short":"S. Altmeyer, R. Lueptow, Physical Review E 95 (2017).","ieee":"S. Altmeyer and R. Lueptow, “Wave propagation reversal for wavy vortices in wide gap counter rotating cylindrical Couette flow,” <i>Physical Review E</i>, vol. 95, no. 5. American Physical Society, 2017.","apa":"Altmeyer, S., &#38; Lueptow, R. (2017). Wave propagation reversal for wavy vortices in wide gap counter rotating cylindrical Couette flow. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevE.95.053103\">https://doi.org/10.1103/PhysRevE.95.053103</a>","chicago":"Altmeyer, Sebastian, and Richard Lueptow. “Wave Propagation Reversal for Wavy Vortices in Wide Gap Counter Rotating Cylindrical Couette Flow.” <i>Physical Review E</i>. American Physical Society, 2017. <a href=\"https://doi.org/10.1103/PhysRevE.95.053103\">https://doi.org/10.1103/PhysRevE.95.053103</a>.","mla":"Altmeyer, Sebastian, and Richard Lueptow. “Wave Propagation Reversal for Wavy Vortices in Wide Gap Counter Rotating Cylindrical Couette Flow.” <i>Physical Review E</i>, vol. 95, no. 5, 053103, American Physical Society, 2017, doi:<a href=\"https://doi.org/10.1103/PhysRevE.95.053103\">10.1103/PhysRevE.95.053103</a>."},"day":"10","month":"05","volume":95,"article_processing_charge":"No","abstract":[{"lang":"eng","text":"We present a numerical study of wavy supercritical cylindrical Couette flow between counter-rotating cylinders in which the wavy pattern propagates either prograde with the inner cylinder or retrograde opposite the rotation of the inner cylinder. The wave propagation reversals from prograde to retrograde and vice versa occur at distinct values of the inner cylinder Reynolds number when the associated frequency of the wavy instability vanishes. The reversal occurs for both twofold and threefold symmetric wavy vortices. Moreover, the wave propagation reversal only occurs for sufficiently strong counter-rotation. The flow pattern reversal appears to be intrinsic in the system as either periodic boundary conditions or fixed end wall boundary conditions for different system sizes always result in the wave propagation reversal. We present a detailed bifurcation sequence and parameter space diagram with respect to retrograde behavior of wavy flows. The retrograde propagation of the instability occurs when the inner Reynolds number is about two times the outer Reynolds number. The mechanism for the retrograde propagation is associated with the inviscidly unstable region near the inner cylinder and the direction of the global average azimuthal velocity. Flow dynamics, spatio-temporal behavior, global mean angular velocity, and torque of the flow with the wavy pattern are explored."}],"issue":"5","doi":"10.1103/PhysRevE.95.053103","title":"Wave propagation reversal for wavy vortices in wide gap counter rotating cylindrical Couette flow","author":[{"full_name":"Altmeyer, Sebastian","last_name":"Altmeyer","id":"2EE67FDC-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian","orcid":"0000-0001-5964-0203"},{"first_name":"Richard","last_name":"Lueptow","full_name":"Lueptow, Richard"}],"_id":"673","publication_status":"published","status":"public","publication_identifier":{"issn":["2470-0045"]},"date_published":"2017-05-10T00:00:00Z","date_created":"2018-12-11T11:47:50Z","scopus_import":"1","department":[{"_id":"BjHo"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"7049","language":[{"iso":"eng"}],"type":"journal_article","publisher":"American Physical Society","main_file_link":[{"url":"https://arxiv.org/pdf/physics/0505164.pdf","open_access":"1"}],"intvolume":"        95","year":"2017","oa":1,"article_number":"053103","publication":"Physical Review E","date_updated":"2023-10-10T13:30:03Z"},{"month":"07","day":"01","citation":{"mla":"Kudekar, Shrinivas, et al. “Reed–Muller Codes Achieve Capacity on Erasure Channels.” <i>IEEE Transactions on Information Theory</i>, vol. 63, no. 7, IEEE, 2017, pp. 4298–316, doi:<a href=\"https://doi.org/10.1109/tit.2017.2673829\">10.1109/tit.2017.2673829</a>.","chicago":"Kudekar, Shrinivas, Santhosh Kumar, Marco Mondelli, Henry D. Pfister, Eren Sasoglu, and Ridiger L. Urbanke. “Reed–Muller Codes Achieve Capacity on Erasure Channels.” <i>IEEE Transactions on Information Theory</i>. IEEE, 2017. <a href=\"https://doi.org/10.1109/tit.2017.2673829\">https://doi.org/10.1109/tit.2017.2673829</a>.","short":"S. Kudekar, S. Kumar, M. Mondelli, H.D. Pfister, E. Sasoglu, R.L. Urbanke, IEEE Transactions on Information Theory 63 (2017) 4298–4316.","ama":"Kudekar S, Kumar S, Mondelli M, Pfister HD, Sasoglu E, Urbanke RL. Reed–Muller codes achieve capacity on erasure channels. <i>IEEE Transactions on Information Theory</i>. 2017;63(7):4298-4316. doi:<a href=\"https://doi.org/10.1109/tit.2017.2673829\">10.1109/tit.2017.2673829</a>","ista":"Kudekar S, Kumar S, Mondelli M, Pfister HD, Sasoglu E, Urbanke RL. 2017. Reed–Muller codes achieve capacity on erasure channels. IEEE Transactions on Information Theory. 63(7), 4298–4316.","ieee":"S. Kudekar, S. Kumar, M. Mondelli, H. D. Pfister, E. Sasoglu, and R. L. Urbanke, “Reed–Muller codes achieve capacity on erasure channels,” <i>IEEE Transactions on Information Theory</i>, vol. 63, no. 7. IEEE, pp. 4298–4316, 2017.","apa":"Kudekar, S., Kumar, S., Mondelli, M., Pfister, H. D., Sasoglu, E., &#38; Urbanke, R. L. (2017). Reed–Muller codes achieve capacity on erasure channels. <i>IEEE Transactions on Information Theory</i>. IEEE. <a href=\"https://doi.org/10.1109/tit.2017.2673829\">https://doi.org/10.1109/tit.2017.2673829</a>"},"oa_version":"Preprint","arxiv":1,"volume":63,"_id":"6730","author":[{"last_name":"Kudekar","full_name":"Kudekar, Shrinivas","first_name":"Shrinivas"},{"full_name":"Kumar, Santhosh","last_name":"Kumar","first_name":"Santhosh"},{"orcid":"0000-0002-3242-7020","id":"27EB676C-8706-11E9-9510-7717E6697425","first_name":"Marco","full_name":"Mondelli, Marco","last_name":"Mondelli"},{"last_name":"Pfister","full_name":"Pfister, Henry D.","first_name":"Henry D."},{"first_name":"Eren","full_name":"Sasoglu, Eren","last_name":"Sasoglu"},{"first_name":"Ridiger L.","full_name":"Urbanke, Ridiger L.","last_name":"Urbanke"}],"title":"Reed–Muller codes achieve capacity on erasure channels","doi":"10.1109/tit.2017.2673829","issue":"7","abstract":[{"lang":"eng","text":"We introduce a new approach to proving that a sequence of deterministic linear codes achieves capacity on an erasure channel under maximum a posteriori decoding. Rather than relying on the precise structure of the codes, our method exploits code symmetry. In particular, the technique applies to any sequence of linear codes where the blocklengths are strictly increasing, the code rates converge, and the permutation group of each code is doubly transitive. In other words, we show that symmetry alone implies near-optimal performance. An important consequence of this result is that a sequence of Reed-Muller codes with increasing block length and converging rate achieves capacity. This possibility has been suggested previously in the literature but it has only been proven for cases where the limiting code rate is 0 or 1. Moreover, these results extend naturally to all affine-invariant codes and, thus, to extended primitive narrow-sense BCH codes. This also resolves, in the affirmative, the existence question for capacity-achieving sequences of binary cyclic codes. The primary tools used in the proof are the sharp threshold property for symmetric monotone Boolean functions and the area theorem for extrinsic information transfer functions."}],"publication_identifier":{"issn":["0018-9448"],"eissn":["1557-9654"]},"publication_status":"published","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2019-07-30T07:18:11Z","external_id":{"arxiv":["1601.04689"]},"date_published":"2017-07-01T00:00:00Z","extern":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1601.04689"}],"intvolume":"        63","publisher":"IEEE","language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","oa":1,"year":"2017","date_updated":"2021-01-12T08:08:43Z","publication":"IEEE Transactions on Information Theory","page":"4298-4316"},{"date_created":"2019-07-31T05:56:58Z","oa_version":"Preprint","conference":{"start_date":"2017-03-19","location":"San Francisco, CA, USA","end_date":"2017-03-22","name":"WCNCW: Wireless communications and networking conference workshops"},"date_published":"2017-05-04T00:00:00Z","extern":"1","external_id":{"arxiv":["1611.01199"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"05","citation":{"apa":"Mondelli, M., Hassani, H., Maric, I., Hui, D., &#38; Hong, S.-N. (2017). Capacity-achieving rate-compatible polar codes for general channels. In <i>2017 IEEE Wireless Communications and Networking Conference Workshops </i>. San Francisco, CA, USA: IEEE. <a href=\"https://doi.org/10.1109/wcncw.2017.7919107\">https://doi.org/10.1109/wcncw.2017.7919107</a>","ieee":"M. Mondelli, H. Hassani, I. Maric, D. Hui, and S.-N. Hong, “Capacity-achieving rate-compatible polar codes for general channels,” in <i>2017 IEEE Wireless Communications and Networking Conference Workshops </i>, San Francisco, CA, USA, 2017.","ista":"Mondelli M, Hassani H, Maric I, Hui D, Hong S-N. 2017. Capacity-achieving rate-compatible polar codes for general channels. 2017 IEEE Wireless Communications and Networking Conference Workshops . WCNCW: Wireless communications and networking conference workshops, 7919107.","ama":"Mondelli M, Hassani H, Maric I, Hui D, Hong S-N. Capacity-achieving rate-compatible polar codes for general channels. In: <i>2017 IEEE Wireless Communications and Networking Conference Workshops </i>. IEEE; 2017. doi:<a href=\"https://doi.org/10.1109/wcncw.2017.7919107\">10.1109/wcncw.2017.7919107</a>","short":"M. Mondelli, H. Hassani, I. Maric, D. Hui, S.-N. Hong, in:, 2017 IEEE Wireless Communications and Networking Conference Workshops , IEEE, 2017.","chicago":"Mondelli, Marco, Hamed Hassani, Ivana Maric, Dennis Hui, and Song-Nam Hong. “Capacity-Achieving Rate-Compatible Polar Codes for General Channels.” In <i>2017 IEEE Wireless Communications and Networking Conference Workshops </i>. IEEE, 2017. <a href=\"https://doi.org/10.1109/wcncw.2017.7919107\">https://doi.org/10.1109/wcncw.2017.7919107</a>.","mla":"Mondelli, Marco, et al. “Capacity-Achieving Rate-Compatible Polar Codes for General Channels.” <i>2017 IEEE Wireless Communications and Networking Conference Workshops </i>, 7919107, IEEE, 2017, doi:<a href=\"https://doi.org/10.1109/wcncw.2017.7919107\">10.1109/wcncw.2017.7919107</a>."},"day":"04","language":[{"iso":"eng"}],"type":"conference","quality_controlled":"1","publisher":"IEEE","arxiv":1,"main_file_link":[{"url":"https://arxiv.org/abs/1611.01199","open_access":"1"}],"doi":"10.1109/wcncw.2017.7919107","abstract":[{"text":"We present a rate-compatible polar coding scheme that achieves the capacity of any family of channels. Our solution generalizes the previous results [1], [2] that provide capacity-achieving rate-compatible polar codes for a degraded family of channels. The motivation for our extension comes from the fact that in many practical scenarios, e.g., MIMO systems and non-Gaussian interference, the channels cannot be ordered by degradation. The main technical contribution of this paper consists in removing the degradation condition. To do so, we exploit the ideas coming from the construction of universal polar codes. Our scheme possesses the usual attractive features of polar codes: low complexity code construction, encoding, and decoding; super-polynomial scaling of the error probability with the block length; and absence of error floors. On the negative side, the scaling of the gap to capacity with the block length is slower than in standard polar codes, and we prove an upper bound on the scaling exponent.","lang":"eng"}],"year":"2017","_id":"6731","title":"Capacity-achieving rate-compatible polar codes for general channels","oa":1,"author":[{"first_name":"Marco","id":"27EB676C-8706-11E9-9510-7717E6697425","last_name":"Mondelli","full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020"},{"full_name":"Hassani, Hamed","last_name":"Hassani","first_name":"Hamed"},{"first_name":"Ivana","last_name":"Maric","full_name":"Maric, Ivana"},{"last_name":"Hui","full_name":"Hui, Dennis","first_name":"Dennis"},{"first_name":"Song-Nam","full_name":"Hong, Song-Nam","last_name":"Hong"}],"article_number":"7919107","publication_status":"published","status":"public","date_updated":"2021-01-12T08:08:43Z","publication":"2017 IEEE Wireless Communications and Networking Conference Workshops ","publication_identifier":{"isbn":["9781509059089"]}},{"publist_id":"7050","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"MiSi"},{"_id":"Bio"},{"_id":"NanoFab"}],"scopus_import":1,"date_created":"2018-12-11T11:47:51Z","date_published":"2017-05-09T00:00:00Z","intvolume":"        27","publisher":"Cell Press","language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","year":"2017","date_updated":"2023-02-23T12:50:44Z","publication":"Current Biology","page":"1314 - 1325","month":"05","day":"09","citation":{"ista":"Schwarz J, Bierbaum V, Vaahtomeri K, Hauschild R, Brown M, de Vries I, Leithner AF, Reversat A, Merrin J, Tarrant T, Bollenbach MT, Sixt MK. 2017. Dendritic cells interpret haptotactic chemokine gradients in a manner governed by signal to noise ratio and dependent on GRK6. Current Biology. 27(9), 1314–1325.","ama":"Schwarz J, Bierbaum V, Vaahtomeri K, et al. Dendritic cells interpret haptotactic chemokine gradients in a manner governed by signal to noise ratio and dependent on GRK6. <i>Current Biology</i>. 2017;27(9):1314-1325. doi:<a href=\"https://doi.org/10.1016/j.cub.2017.04.004\">10.1016/j.cub.2017.04.004</a>","short":"J. Schwarz, V. Bierbaum, K. Vaahtomeri, R. Hauschild, M. Brown, I. de Vries, A.F. Leithner, A. Reversat, J. Merrin, T. Tarrant, M.T. Bollenbach, M.K. Sixt, Current Biology 27 (2017) 1314–1325.","ieee":"J. Schwarz <i>et al.</i>, “Dendritic cells interpret haptotactic chemokine gradients in a manner governed by signal to noise ratio and dependent on GRK6,” <i>Current Biology</i>, vol. 27, no. 9. Cell Press, pp. 1314–1325, 2017.","apa":"Schwarz, J., Bierbaum, V., Vaahtomeri, K., Hauschild, R., Brown, M., de Vries, I., … Sixt, M. K. (2017). Dendritic cells interpret haptotactic chemokine gradients in a manner governed by signal to noise ratio and dependent on GRK6. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2017.04.004\">https://doi.org/10.1016/j.cub.2017.04.004</a>","chicago":"Schwarz, Jan, Veronika Bierbaum, Kari Vaahtomeri, Robert Hauschild, Markus Brown, Ingrid de Vries, Alexander F Leithner, et al. “Dendritic Cells Interpret Haptotactic Chemokine Gradients in a Manner Governed by Signal to Noise Ratio and Dependent on GRK6.” <i>Current Biology</i>. Cell Press, 2017. <a href=\"https://doi.org/10.1016/j.cub.2017.04.004\">https://doi.org/10.1016/j.cub.2017.04.004</a>.","mla":"Schwarz, Jan, et al. “Dendritic Cells Interpret Haptotactic Chemokine Gradients in a Manner Governed by Signal to Noise Ratio and Dependent on GRK6.” <i>Current Biology</i>, vol. 27, no. 9, Cell Press, 2017, pp. 1314–25, doi:<a href=\"https://doi.org/10.1016/j.cub.2017.04.004\">10.1016/j.cub.2017.04.004</a>."},"oa_version":"None","volume":27,"_id":"674","author":[{"first_name":"Jan","id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","last_name":"Schwarz","full_name":"Schwarz, Jan"},{"id":"3FD04378-F248-11E8-B48F-1D18A9856A87","first_name":"Veronika","full_name":"Bierbaum, Veronika","last_name":"Bierbaum"},{"orcid":"0000-0001-7829-3518","last_name":"Vaahtomeri","full_name":"Vaahtomeri, Kari","first_name":"Kari","id":"368EE576-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"},{"id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87","first_name":"Markus","full_name":"Brown, Markus","last_name":"Brown"},{"first_name":"Ingrid","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","last_name":"De Vries","full_name":"De Vries, Ingrid"},{"full_name":"Leithner, Alexander F","last_name":"Leithner","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander F"},{"orcid":"0000-0003-0666-8928","first_name":"Anne","id":"35B76592-F248-11E8-B48F-1D18A9856A87","last_name":"Reversat","full_name":"Reversat, Anne"},{"orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack","last_name":"Merrin","id":"4515C308-F248-11E8-B48F-1D18A9856A87","first_name":"Jack"},{"first_name":"Teresa","last_name":"Tarrant","full_name":"Tarrant, Teresa"},{"first_name":"Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach","full_name":"Bollenbach, Tobias","orcid":"0000-0003-4398-476X"},{"orcid":"0000-0002-6620-9179","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","full_name":"Sixt, Michael K"}],"title":"Dendritic cells interpret haptotactic chemokine gradients in a manner governed by signal to noise ratio and dependent on GRK6","doi":"10.1016/j.cub.2017.04.004","issue":"9","abstract":[{"text":"Navigation of cells along gradients of guidance cues is a determining step in many developmental and immunological processes. Gradients can either be soluble or immobilized to tissues as demonstrated for the haptotactic migration of dendritic cells (DCs) toward higher concentrations of immobilized chemokine CCL21. To elucidate how gradient characteristics govern cellular response patterns, we here introduce an in vitro system allowing to track migratory responses of DCs to precisely controlled immobilized gradients of CCL21. We find that haptotactic sensing depends on the absolute CCL21 concentration and local steepness of the gradient, consistent with a scenario where DC directionality is governed by the signal-to-noise ratio of CCL21 binding to the receptor CCR7. We find that the conditions for optimal DC guidance are perfectly provided by the CCL21 gradients we measure in vivo. Furthermore, we find that CCR7 signal termination by the G-protein-coupled receptor kinase 6 (GRK6) is crucial for haptotactic but dispensable for chemotactic CCL21 gradient sensing in vitro and confirm those observations in vivo. These findings suggest that stable, tissue-bound CCL21 gradients as sustainable “roads” ensure optimal guidance in vivo.","lang":"eng"}],"project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"},{"call_identifier":"FWF","name":"Cytoskeletal force generation and transduction of leukocytes (FWF)","_id":"25A8E5EA-B435-11E9-9278-68D0E5697425","grant_number":"Y 564-B12"}],"publication_identifier":{"issn":["09609822"]},"ec_funded":1,"status":"public","publication_status":"published"},{"status":"public","publication_status":"published","doi":"10.1364/OL.42.001931","issue":"10","abstract":[{"lang":"eng","text":"We report the enhancement of infrared absorption of chemisorbed carbon monoxide on platinum in the gap of plasmonic nanoantennas. Our method is based on the self-assembled formation of platinum nanoislands on nanoscopic dipole antenna arrays manufactured via electron beam lithography. We employ systematic variations of the plasmonic antenna resonance to precisely couple to the molecular stretch vibration of carbon monoxide adsorbed on the platinum nanoislands. Ultimately, we reach more than 1500-fold infrared absorption enhancements, allowing for an ultrasensitive detection of a monolayer of chemisorbed carbon monoxide. The developed procedure can be adapted to other metal adsorbents and molecular species and could be utilized for coverage sensing in surface catalytic reactions. "}],"_id":"675","author":[{"first_name":"Johannes","last_name":"Haase","full_name":"Haase, Johannes"},{"first_name":"Salvatore","id":"38ED402E-F248-11E8-B48F-1D18A9856A87","last_name":"Bagiante","full_name":"Bagiante, Salvatore","orcid":"0000-0002-0122-9603"},{"full_name":"Sigg, Hans","last_name":"Sigg","first_name":"Hans"},{"first_name":"Jeroen","full_name":"Van Bokhoven, Jeroen","last_name":"Van Bokhoven"}],"title":"Surface enhanced infrared absorption of chemisorbed carbon monoxide using plasmonic nanoantennas","volume":42,"article_processing_charge":"No","oa_version":"None","month":"05","ddc":["530"],"day":"15","citation":{"chicago":"Haase, Johannes, Salvatore Bagiante, Hans Sigg, and Jeroen Van Bokhoven. “Surface Enhanced Infrared Absorption of Chemisorbed Carbon Monoxide Using Plasmonic Nanoantennas.” <i>Optics Letters</i>. Optica Publishing Group, 2017. <a href=\"https://doi.org/10.1364/OL.42.001931\">https://doi.org/10.1364/OL.42.001931</a>.","mla":"Haase, Johannes, et al. “Surface Enhanced Infrared Absorption of Chemisorbed Carbon Monoxide Using Plasmonic Nanoantennas.” <i>Optics Letters</i>, vol. 42, no. 10, Optica Publishing Group, 2017, pp. 1931–34, doi:<a href=\"https://doi.org/10.1364/OL.42.001931\">10.1364/OL.42.001931</a>.","apa":"Haase, J., Bagiante, S., Sigg, H., &#38; Van Bokhoven, J. (2017). Surface enhanced infrared absorption of chemisorbed carbon monoxide using plasmonic nanoantennas. <i>Optics Letters</i>. Optica Publishing Group. <a href=\"https://doi.org/10.1364/OL.42.001931\">https://doi.org/10.1364/OL.42.001931</a>","ieee":"J. Haase, S. Bagiante, H. Sigg, and J. Van Bokhoven, “Surface enhanced infrared absorption of chemisorbed carbon monoxide using plasmonic nanoantennas,” <i>Optics Letters</i>, vol. 42, no. 10. Optica Publishing Group, pp. 1931–1934, 2017.","ista":"Haase J, Bagiante S, Sigg H, Van Bokhoven J. 2017. Surface enhanced infrared absorption of chemisorbed carbon monoxide using plasmonic nanoantennas. Optics Letters. 42(10), 1931–1934.","short":"J. Haase, S. Bagiante, H. Sigg, J. Van Bokhoven, Optics Letters 42 (2017) 1931–1934.","ama":"Haase J, Bagiante S, Sigg H, Van Bokhoven J. Surface enhanced infrared absorption of chemisorbed carbon monoxide using plasmonic nanoantennas. <i>Optics Letters</i>. 2017;42(10):1931-1934. doi:<a href=\"https://doi.org/10.1364/OL.42.001931\">10.1364/OL.42.001931</a>"},"article_type":"original","page":"1931 - 1934","date_updated":"2023-10-17T12:16:02Z","publication":"Optics Letters","year":"2017","quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","intvolume":"        42","publisher":"Optica Publishing Group","scopus_import":"1","date_created":"2018-12-11T11:47:51Z","date_published":"2017-05-15T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"7048","department":[{"_id":"NanoFab"}]}]