[{"quality_controlled":"1","editor":[{"last_name":"Toth","first_name":"Csaba","full_name":"Toth, Csaba"},{"first_name":"Joseph","last_name":"O'Rourke","full_name":"O'Rourke, Joseph"},{"full_name":"Goodman, Jacob","first_name":"Jacob","last_name":"Goodman"}],"citation":{"chicago":"Edelsbrunner, Herbert, and Patrice Koehl. “Computational Topology for Structural Molecular Biology.” In <i>Handbook of Discrete and Computational Geometry, Third Edition</i>, edited by Csaba Toth, Joseph O’Rourke, and Jacob Goodman, 1709–35. Handbook of Discrete and Computational Geometry. Taylor &#38; Francis, 2017. <a href=\"https://doi.org/10.1201/9781315119601\">https://doi.org/10.1201/9781315119601</a>.","mla":"Edelsbrunner, Herbert, and Patrice Koehl. “Computational Topology for Structural Molecular Biology.” <i>Handbook of Discrete and Computational Geometry, Third Edition</i>, edited by Csaba Toth et al., Taylor &#38; Francis, 2017, pp. 1709–35, doi:<a href=\"https://doi.org/10.1201/9781315119601\">10.1201/9781315119601</a>.","ista":"Edelsbrunner H, Koehl P. 2017.Computational topology for structural molecular biology. In: Handbook of Discrete and Computational Geometry, Third Edition. , 1709–1735.","apa":"Edelsbrunner, H., &#38; Koehl, P. (2017). Computational topology for structural molecular biology. In C. Toth, J. O’Rourke, &#38; J. Goodman (Eds.), <i>Handbook of Discrete and Computational Geometry, Third Edition</i> (pp. 1709–1735). Taylor &#38; Francis. <a href=\"https://doi.org/10.1201/9781315119601\">https://doi.org/10.1201/9781315119601</a>","ama":"Edelsbrunner H, Koehl P. Computational topology for structural molecular biology. In: Toth C, O’Rourke J, Goodman J, eds. <i>Handbook of Discrete and Computational Geometry, Third Edition</i>. Handbook of Discrete and Computational Geometry. Taylor &#38; Francis; 2017:1709-1735. doi:<a href=\"https://doi.org/10.1201/9781315119601\">10.1201/9781315119601</a>","ieee":"H. Edelsbrunner and P. Koehl, “Computational topology for structural molecular biology,” in <i>Handbook of Discrete and Computational Geometry, Third Edition</i>, C. Toth, J. O’Rourke, and J. Goodman, Eds. Taylor &#38; Francis, 2017, pp. 1709–1735.","short":"H. Edelsbrunner, P. Koehl, in:, C. Toth, J. O’Rourke, J. Goodman (Eds.), Handbook of Discrete and Computational Geometry, Third Edition, Taylor &#38; Francis, 2017, pp. 1709–1735."},"article_processing_charge":"No","scopus_import":"1","publist_id":"7970","oa_version":"None","type":"book_chapter","department":[{"_id":"HeEd"}],"date_published":"2017-11-09T00:00:00Z","language":[{"iso":"eng"}],"doi":"10.1201/9781315119601","publication_status":"published","publication":"Handbook of Discrete and Computational Geometry, Third Edition","date_created":"2018-12-11T11:44:32Z","page":"1709 - 1735","month":"11","series_title":"Handbook of Discrete and Computational Geometry","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publisher":"Taylor & Francis","publication_identifier":{"eisbn":["9781498711425"]},"title":"Computational topology for structural molecular biology","author":[{"full_name":"Edelsbrunner, Herbert","first_name":"Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Koehl, Patrice","first_name":"Patrice","last_name":"Koehl"}],"_id":"84","abstract":[{"text":"The advent of high-throughput technologies and the concurrent advances in information sciences have led to a data revolution in biology. This revolution is most significant in molecular biology, with an increase in the number and scale of the “omics” projects over the last decade. Genomics projects, for example, have produced impressive advances in our knowledge of the information concealed into genomes, from the many genes that encode for the proteins that are responsible for most if not all cellular functions, to the noncoding regions that are now known to provide regulatory functions. Proteomics initiatives help to decipher the role of post-translation modifications on the protein structures and provide maps of protein-protein interactions, while functional genomics is the field that attempts to make use of the data produced by these projects to understand protein functions. The biggest challenge today is to assimilate the wealth of information provided by these initiatives into a conceptual framework that will help us decipher life. For example, the current views of the relationship between protein structure and function remain fragmented. We know of their sequences, more and more about their structures, we have information on their biological activities, but we have difficulties connecting this dotted line into an informed whole. We lack the experimental and computational tools for directly studying protein structure, function, and dynamics at the molecular and supra-molecular levels. In this chapter, we review some of the current developments in building the computational tools that are needed, focusing on the role that geometry and topology play in these efforts. One of our goals is to raise the general awareness about the importance of geometric methods in elucidating the mysterious foundations of our very existence. Another goal is the broadening of what we consider a geometric algorithm. There is plenty of valuable no-man’s-land between combinatorial and numerical algorithms, and it seems opportune to explore this land with a computational-geometric frame of mind.","lang":"eng"}],"date_updated":"2023-10-16T11:15:22Z","year":"2017","day":"09"},{"language":[{"iso":"eng"}],"department":[{"_id":"GeKa"}],"type":"journal_article","page":"5706 - 5710","date_created":"2018-12-11T11:48:47Z","publication":"Nano Letters","has_accepted_license":"1","related_material":{"record":[{"id":"7977","relation":"popular_science"},{"id":"69","status":"public","relation":"dissertation_contains"},{"id":"7996","status":"public","relation":"dissertation_contains"}]},"external_id":{"isi":["000411043500078"]},"volume":17,"quality_controlled":"1","publist_id":"6808","pubrep_id":"865","article_processing_charge":"No","file":[{"date_updated":"2020-07-14T12:48:13Z","file_name":"IST-2017-865-v1+1_acs.nanolett.7b02627.pdf","date_created":"2018-12-12T10:12:33Z","checksum":"761371a0129b2aa442424b9561450ece","creator":"system","file_id":"4951","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_size":2449546}],"project":[{"name":"Towards Spin qubits and Majorana fermions in Germanium selfassembled hut-wires","call_identifier":"FP7","_id":"25517E86-B435-11E9-9278-68D0E5697425","grant_number":"335497"}],"author":[{"last_name":"Vukusic","id":"31E9F056-F248-11E8-B48F-1D18A9856A87","first_name":"Lada","orcid":"0000-0003-2424-8636","full_name":"Vukusic, Lada"},{"full_name":"Kukucka, Josip","first_name":"Josip","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","last_name":"Kukucka"},{"first_name":"Hannes","last_name":"Watzinger","id":"35DF8E50-F248-11E8-B48F-1D18A9856A87","full_name":"Watzinger, Hannes"},{"full_name":"Katsaros, Georgios","last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8342-202X","first_name":"Georgios"}],"isi":1,"day":"10","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"license":"https://creativecommons.org/licenses/by/4.0/","title":"Fast hole tunneling times in germanium hut wires probed by single-shot reflectometry","publisher":"American Chemical Society","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_published":"2017-08-10T00:00:00Z","oa_version":"Published Version","publication_status":"published","doi":"10.1021/acs.nanolett.7b02627","intvolume":"        17","citation":{"chicago":"Vukušić, Lada, Josip Kukucka, Hannes Watzinger, and Georgios Katsaros. “Fast Hole Tunneling Times in Germanium Hut Wires Probed by Single-Shot Reflectometry.” <i>Nano Letters</i>. American Chemical Society, 2017. <a href=\"https://doi.org/10.1021/acs.nanolett.7b02627\">https://doi.org/10.1021/acs.nanolett.7b02627</a>.","apa":"Vukušić, L., Kukucka, J., Watzinger, H., &#38; Katsaros, G. (2017). Fast hole tunneling times in germanium hut wires probed by single-shot reflectometry. <i>Nano Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.nanolett.7b02627\">https://doi.org/10.1021/acs.nanolett.7b02627</a>","ista":"Vukušić L, Kukucka J, Watzinger H, Katsaros G. 2017. Fast hole tunneling times in germanium hut wires probed by single-shot reflectometry. Nano Letters. 17(9), 5706–5710.","mla":"Vukušić, Lada, et al. “Fast Hole Tunneling Times in Germanium Hut Wires Probed by Single-Shot Reflectometry.” <i>Nano Letters</i>, vol. 17, no. 9, American Chemical Society, 2017, pp. 5706–10, doi:<a href=\"https://doi.org/10.1021/acs.nanolett.7b02627\">10.1021/acs.nanolett.7b02627</a>.","ieee":"L. Vukušić, J. Kukucka, H. Watzinger, and G. Katsaros, “Fast hole tunneling times in germanium hut wires probed by single-shot reflectometry,” <i>Nano Letters</i>, vol. 17, no. 9. American Chemical Society, pp. 5706–5710, 2017.","ama":"Vukušić L, Kukucka J, Watzinger H, Katsaros G. Fast hole tunneling times in germanium hut wires probed by single-shot reflectometry. <i>Nano Letters</i>. 2017;17(9):5706-5710. doi:<a href=\"https://doi.org/10.1021/acs.nanolett.7b02627\">10.1021/acs.nanolett.7b02627</a>","short":"L. Vukušić, J. Kukucka, H. Watzinger, G. Katsaros, Nano Letters 17 (2017) 5706–5710."},"ddc":["539"],"file_date_updated":"2020-07-14T12:48:13Z","scopus_import":"1","_id":"840","acknowledged_ssus":[{"_id":"M-Shop"}],"year":"2017","date_updated":"2023-09-26T15:50:22Z","abstract":[{"lang":"eng","text":"Heavy holes confined in quantum dots are predicted to be promising candidates for the realization of spin qubits with long coherence times. Here we focus on such heavy-hole states confined in germanium hut wires. By tuning the growth density of the latter we can realize a T-like structure between two neighboring wires. Such a structure allows the realization of a charge sensor, which is electrostatically and tunnel coupled to a quantum dot, with charge-transfer signals as high as 0.3 e. By integrating the T-like structure into a radiofrequency reflectometry setup, single-shot measurements allowing the extraction of hole tunneling times are performed. The extracted tunneling times of less than 10 μs are attributed to the small effective mass of Ge heavy-hole states and pave the way toward projective spin readout measurements."}],"issue":"9","ec_funded":1,"month":"08","publication_identifier":{"issn":["15306984"]},"oa":1,"status":"public"},{"publist_id":"5060","article_processing_charge":"No","related_material":{"record":[{"id":"6473","status":"public","relation":"part_of_dissertation"}]},"external_id":{"isi":["000400985000001"],"arxiv":["1410.1242"]},"quality_controlled":"1","volume":44,"date_created":"2018-12-11T11:55:13Z","page":"285 - 306","publication":"Scandinavian Journal of Statistics","language":[{"iso":"eng"}],"department":[{"_id":"GaTk"}],"type":"journal_article","title":"Exact goodness-of-fit testing for the Ising model","publisher":"Wiley-Blackwell","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"01","author":[{"full_name":"Martin Del Campo Sanchez, Abraham","first_name":"Abraham","last_name":"Martin Del Campo Sanchez"},{"last_name":"Cepeda Humerez","id":"3DEE19A4-F248-11E8-B48F-1D18A9856A87","first_name":"Sarah A","full_name":"Cepeda Humerez, Sarah A"},{"first_name":"Caroline","orcid":"0000-0002-7008-0216","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","last_name":"Uhler","full_name":"Uhler, Caroline"}],"isi":1,"scopus_import":"1","main_file_link":[{"url":"http://arxiv.org/abs/1410.1242","open_access":"1"}],"intvolume":"        44","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>.","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.","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>.","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>","short":"A. Martin Del Campo Sanchez, S.A. Cepeda Humerez, C. Uhler, Scandinavian Journal of Statistics 44 (2017) 285–306.","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.","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>"},"publication_status":"published","doi":"10.1111/sjos.12251","date_published":"2017-06-01T00:00:00Z","oa_version":"Preprint","oa":1,"publication_identifier":{"issn":["03036898"]},"status":"public","month":"06","year":"2017","date_updated":"2023-09-19T15:13:27Z","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"}],"arxiv":1,"issue":"2","_id":"2016"},{"supervisor":[{"full_name":"Guet, Calin C","first_name":"Calin C","orcid":"0000-0001-6220-2052","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"}],"alternative_title":["ISTA Thesis"],"degree_awarded":"PhD","title":"Biology of restriction-modification systems at the single-cell and population level","publisher":"Institute of Science and Technology Austria","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"file_size":18569590,"relation":"main_file","content_type":"application/pdf","access_level":"open_access","checksum":"33cfb59674e91f82e3738396d3fb3776","creator":"system","file_id":"4710","date_created":"2018-12-12T10:08:48Z","file_name":"IST-2018-916-v1+3_2017_Pleska_Maros_Thesis.pdf","date_updated":"2020-07-14T12:45:24Z"},{"file_size":2801649,"relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","file_id":"6204","creator":"dernst","checksum":"dcc239968decb233e7f98cf1083d8c26","date_created":"2019-04-05T08:33:14Z","date_updated":"2020-07-14T12:45:24Z","file_name":"2017_Pleska_Maros_Thesis.docx"}],"project":[{"_id":"251D65D8-B435-11E9-9278-68D0E5697425","grant_number":"24210","name":"Effects of Stochasticity on the Function of Restriction-Modi cation Systems at the Single-Cell Level (DOC Fellowship)"}],"author":[{"last_name":"Pleska","id":"4569785E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7460-7479","first_name":"Maros","full_name":"Pleska, Maros"}],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"01","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","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"1243"},{"status":"public","relation":"part_of_dissertation","id":"561"},{"id":"457","status":"public","relation":"part_of_dissertation"}]},"publist_id":"7711","pubrep_id":"916","article_processing_charge":"No","language":[{"iso":"eng"}],"department":[{"_id":"CaGu"}],"type":"dissertation","date_created":"2018-12-11T11:45:10Z","page":"126","has_accepted_license":"1","month":"10","publication_identifier":{"issn":["2663-337X"]},"oa":1,"status":"public","_id":"202","year":"2017","date_updated":"2023-09-15T12:04:56Z","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"}],"citation":{"short":"M. Pleska, Biology of Restriction-Modification Systems at the Single-Cell and Population Level, Institute of Science and Technology Austria, 2017.","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>","ieee":"M. Pleska, “Biology of restriction-modification systems at the single-cell and population level,” Institute of Science and Technology Austria, 2017.","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>","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>.","ista":"Pleska M. 2017. Biology of restriction-modification systems at the single-cell and population level. Institute of Science and Technology Austria.","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>."},"ddc":["576","579"],"file_date_updated":"2020-07-14T12:45:24Z","date_published":"2017-10-01T00:00:00Z","oa_version":"Published Version","publication_status":"published","doi":"10.15479/AT:ISTA:th_916"},{"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publisher":"American Institute of Physics","title":"Hydrodynamic turbulence in quasi Keplerian rotating flows","day":"01","author":[{"first_name":"Liang","last_name":"Shi","full_name":"Shi, Liang"},{"full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","first_name":"Björn","orcid":"0000-0003-2057-2754"},{"full_name":"Rampp, Markus","last_name":"Rampp","first_name":"Markus"},{"last_name":"Avila","first_name":"Marc","full_name":"Avila, Marc"}],"project":[{"name":"Astrophysical instability of currents and turbulences","_id":"2511D90C-B435-11E9-9278-68D0E5697425","grant_number":"SFB 963  TP A8"}],"publist_id":"7072","quality_controlled":"1","volume":29,"publication":"Physics of Fluids","date_created":"2018-12-11T11:47:47Z","type":"journal_article","department":[{"_id":"BjHo"}],"language":[{"iso":"eng"}],"status":"public","oa":1,"publication_identifier":{"issn":["10706631"]},"month":"04","issue":"4","abstract":[{"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.","lang":"eng"}],"date_updated":"2021-01-12T08:08:15Z","year":"2017","article_number":"044107","_id":"662","main_file_link":[{"url":"https://arxiv.org/abs/1703.01714","open_access":"1"}],"scopus_import":1,"citation":{"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>","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>.","ista":"Shi L, Hof B, Rampp M, Avila M. 2017. Hydrodynamic turbulence in quasi Keplerian rotating flows. Physics of Fluids. 29(4), 044107.","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>.","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>","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.","short":"L. Shi, B. Hof, M. Rampp, M. Avila, Physics of Fluids 29 (2017)."},"intvolume":"        29","doi":"10.1063/1.4981525","publication_status":"published","oa_version":"Submitted Version","date_published":"2017-04-01T00:00:00Z"},{"_id":"663","year":"2017","date_updated":"2021-01-12T08:08:17Z","abstract":[{"lang":"eng","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. "}],"month":"04","oa":1,"publication_identifier":{"isbn":["978-145034590-3"]},"status":"public","date_published":"2017-04-01T00:00:00Z","oa_version":"Submitted Version","conference":{"location":"Pittsburgh, PA, United States","end_date":"2017-04-20","name":"HSCC: Hybrid Systems Computation and Control ","start_date":"2017-04-18"},"publication_status":"published","doi":"10.1145/3049797.3049814","citation":{"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>","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.","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>","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."},"ddc":["000"],"scopus_import":1,"file_date_updated":"2020-07-14T12:47:34Z","file":[{"date_created":"2018-12-12T10:11:20Z","file_name":"IST-2017-817-v1+1_p163-kong.pdf","date_updated":"2020-07-14T12:47:34Z","access_level":"open_access","file_id":"4873","creator":"system","checksum":"b7667434cbf5b5f0ade3bea1dbe5bf63","file_size":1650530,"content_type":"application/pdf","relation":"main_file"}],"author":[{"full_name":"Kong, Hui","orcid":"0000-0002-3066-6941","first_name":"Hui","id":"3BDE25AA-F248-11E8-B48F-1D18A9856A87","last_name":"Kong"},{"last_name":"Bogomolov","orcid":"0000-0002-0686-0365","first_name":"Sergiy","full_name":"Bogomolov, Sergiy"},{"full_name":"Schilling, Christian","last_name":"Schilling","first_name":"Christian"},{"full_name":"Jiang, Yu","first_name":"Yu","last_name":"Jiang"},{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A"}],"day":"01","title":"Safety verification of nonlinear hybrid systems based on invariant clusters","publisher":"ACM","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"department":[{"_id":"ToHe"}],"type":"conference","date_created":"2018-12-11T11:47:47Z","page":"163 - 172","publication":"Proceedings of the 20th International Conference on Hybrid Systems","has_accepted_license":"1","quality_controlled":"1","publist_id":"7067","pubrep_id":"817"},{"year":"2017","day":"18","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."}],"issue":"4","date_updated":"2024-03-25T23:30:05Z","_id":"664","author":[{"last_name":"Assen","id":"3A8E7F24-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3470-6119","first_name":"Frank P","full_name":"Assen, Frank P"},{"full_name":"Sixt, Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","orcid":"0000-0002-6620-9179"}],"publication_identifier":{"issn":["10747613"]},"title":"The dynamic cytokine niche","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publisher":"Cell Press","status":"public","month":"04","publication":"Immunity","page":"519 - 520","date_created":"2018-12-11T11:47:47Z","doi":"10.1016/j.immuni.2017.04.006","publication_status":"published","department":[{"_id":"MiSi"}],"date_published":"2017-04-18T00:00:00Z","language":[{"iso":"eng"}],"oa_version":"None","type":"journal_article","publist_id":"7065","scopus_import":1,"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"6947"}]},"quality_controlled":"1","citation":{"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.","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>","short":"F.P. Assen, M.K. Sixt, Immunity 46 (2017) 519–520.","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>.","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>.","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>","ista":"Assen FP, Sixt MK. 2017. The dynamic cytokine niche. Immunity. 46(4), 519–520."},"intvolume":"        46","volume":46},{"_id":"665","year":"2017","issue":"6335","abstract":[{"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.","lang":"eng"}],"date_updated":"2024-02-21T13:49:00Z","month":"04","publication_identifier":{"issn":["00368075"]},"status":"public","date_published":"2017-04-21T00:00:00Z","oa_version":"None","doi":"10.1126/science.aaf4762","publication_status":"published","intvolume":"       356","citation":{"short":"T. Bergmiller, A.M. Andersson, K. Tomasek, E. Balleza, D. Kiviet, R. Hauschild, G. Tkačik, C.C. Guet, Science 356 (2017) 311–315.","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.","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>","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>","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>.","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.","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>."},"scopus_import":1,"author":[{"id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","last_name":"Bergmiller","first_name":"Tobias","orcid":"0000-0001-5396-4346","full_name":"Bergmiller, Tobias"},{"full_name":"Andersson, Anna M","first_name":"Anna M","orcid":"0000-0003-2912-6769","last_name":"Andersson","id":"2B8A40DA-F248-11E8-B48F-1D18A9856A87"},{"id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","last_name":"Tomasek","first_name":"Kathrin","orcid":"0000-0003-3768-877X","full_name":"Tomasek, Kathrin"},{"last_name":"Balleza","first_name":"Enrique","full_name":"Balleza, Enrique"},{"full_name":"Kiviet, Daniel","first_name":"Daniel","last_name":"Kiviet"},{"full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","first_name":"Robert","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","first_name":"Gasper","orcid":"0000-0002-6699-1455"},{"full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","first_name":"Calin C","orcid":"0000-0001-6220-2052"}],"project":[{"call_identifier":"FWF","name":"Biophysics of information processing in gene regulation","_id":"254E9036-B435-11E9-9278-68D0E5697425","grant_number":"P28844-B27"}],"day":"21","title":"Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"American Association for the Advancement of Science","department":[{"_id":"CaGu"},{"_id":"GaTk"},{"_id":"Bio"}],"language":[{"iso":"eng"}],"type":"journal_article","publication":"Science","date_created":"2018-12-11T11:47:48Z","page":"311 - 315","related_material":{"record":[{"id":"5560","relation":"popular_science","status":"public"}]},"volume":356,"quality_controlled":"1","article_processing_charge":"No","article_type":"original","publist_id":"7064"},{"citation":{"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>.","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.","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>","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>.","short":"K. Mitosch, G. Rieckh, M.T. Bollenbach, Cell Systems 4 (2017) 393–403.","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>"},"intvolume":"         4","ddc":["576","610"],"scopus_import":1,"file_date_updated":"2020-07-14T12:47:35Z","date_published":"2017-04-26T00:00:00Z","oa_version":"Published Version","doi":"10.1016/j.cels.2017.03.001","publication_status":"published","ec_funded":1,"month":"04","publication_identifier":{"issn":["24054712"]},"oa":1,"status":"public","_id":"666","year":"2017","issue":"4","abstract":[{"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.","lang":"eng"}],"date_updated":"2023-09-07T12:00:25Z","related_material":{"record":[{"id":"818","status":"public","relation":"dissertation_contains"}]},"quality_controlled":"1","volume":4,"pubrep_id":"901","article_processing_charge":"Yes (in subscription journal)","publist_id":"7061","department":[{"_id":"ToBo"},{"_id":"GaTk"}],"language":[{"iso":"eng"}],"type":"journal_article","publication":"Cell Systems","page":"393 - 403","date_created":"2018-12-11T11:47:48Z","has_accepted_license":"1","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","title":"Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Cell Press","file":[{"checksum":"04ff20011c3d9a601c514aa999a5fe1a","file_id":"5041","creator":"system","access_level":"open_access","file_name":"IST-2017-901-v1+1_1-s2.0-S2405471217300868-main.pdf","date_updated":"2020-07-14T12:47:35Z","date_created":"2018-12-12T10:13:54Z","content_type":"application/pdf","relation":"main_file","file_size":2438660}],"author":[{"full_name":"Mitosch, Karin","first_name":"Karin","last_name":"Mitosch","id":"39B66846-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Rieckh","id":"34DA8BD6-F248-11E8-B48F-1D18A9856A87","first_name":"Georg","full_name":"Rieckh, Georg"},{"full_name":"Bollenbach, Tobias","last_name":"Bollenbach","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias","orcid":"0000-0003-4398-476X"}],"project":[{"name":"Optimality principles in responses to antibiotics","call_identifier":"FP7","grant_number":"303507","_id":"25E83C2C-B435-11E9-9278-68D0E5697425"},{"name":"Revealing the mechanisms underlying drug interactions","call_identifier":"FWF","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","grant_number":"P27201-B22"},{"name":"Revealing the fundamental limits of cell growth","grant_number":"RGP0042/2013","_id":"25EB3A80-B435-11E9-9278-68D0E5697425"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"day":"26"},{"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","status":"public","publisher":"American Association for the Advancement of Science","publication_identifier":{"issn":["19466234"]},"title":"The antisocial side of antibiotics","month":"04","abstract":[{"text":"Perinatal exposure to penicillin may result in longlasting gut and behavioral changes.","lang":"eng"}],"issue":"387","date_updated":"2021-01-12T08:08:30Z","year":"2017","day":"26","author":[{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","first_name":"Gaia","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia"}],"article_number":"2786","_id":"667","scopus_import":1,"publist_id":"7060","volume":9,"citation":{"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.","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>","short":"G. Novarino, Science Translational Medicine 9 (2017).","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>","ista":"Novarino G. 2017. The antisocial side of antibiotics. Science Translational Medicine. 9(387), 2786.","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>."},"intvolume":"         9","quality_controlled":"1","doi":"10.1126/scitranslmed.aan2786","publication_status":"published","publication":"Science Translational Medicine","date_created":"2018-12-11T11:47:48Z","type":"journal_article","oa_version":"None","date_published":"2017-04-26T00:00:00Z","department":[{"_id":"GaNo"}],"language":[{"iso":"eng"}]},{"citation":{"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.","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>","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>","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.","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>."},"intvolume":"       292","file_date_updated":"2020-07-14T12:47:37Z","scopus_import":1,"ddc":["570"],"oa_version":"Published Version","date_published":"2017-04-28T00:00:00Z","doi":"10.1074/jbc.M116.766923","publication_status":"published","month":"04","status":"public","publication_identifier":{"issn":["00219258"]},"oa":1,"_id":"668","issue":"17","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."}],"date_updated":"2021-01-12T08:08:34Z","year":"2017","volume":292,"quality_controlled":"1","article_type":"original","publist_id":"7059","type":"journal_article","department":[{"_id":"MiSi"}],"language":[{"iso":"eng"}],"has_accepted_license":"1","publication":"Journal of Biological Chemistry","page":"7258 - 7273","date_created":"2018-12-11T11:47:49Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"American Society for Biochemistry and Molecular Biology","title":"Multiple roles of filopodial dynamics in particle capture and phagocytosis and phenotypes of Cdc42 and Myo10 deletion","author":[{"first_name":"Markus","last_name":"Horsthemke","full_name":"Horsthemke, Markus"},{"first_name":"Anne","last_name":"Bachg","full_name":"Bachg, Anne"},{"first_name":"Katharina","last_name":"Groll","full_name":"Groll, Katharina"},{"first_name":"Sven","last_name":"Moyzio","full_name":"Moyzio, Sven"},{"full_name":"Müther, Barbara","last_name":"Müther","first_name":"Barbara"},{"full_name":"Hemkemeyer, Sandra","last_name":"Hemkemeyer","first_name":"Sandra"},{"full_name":"Wedlich Söldner, Roland","last_name":"Wedlich Söldner","first_name":"Roland"},{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","orcid":"0000-0002-6620-9179","first_name":"Michael K"},{"first_name":"Sebastian","last_name":"Tacke","full_name":"Tacke, Sebastian"},{"full_name":"Bähler, Martin","last_name":"Bähler","first_name":"Martin"},{"full_name":"Hanley, Peter","last_name":"Hanley","first_name":"Peter"}],"file":[{"relation":"main_file","content_type":"application/pdf","file_size":5647880,"date_updated":"2020-07-14T12:47:37Z","file_name":"2017_JBC_Horsthemke.pdf","date_created":"2019-10-24T15:25:42Z","file_id":"6971","creator":"dernst","checksum":"d488162874326a4bb056065fa549dc4a","access_level":"open_access"}],"day":"28"},{"quality_controlled":"1","volume":174,"external_id":{"pmid":["28356503"]},"article_processing_charge":"No","article_type":"original","publist_id":"7058","type":"journal_article","department":[{"_id":"JiFr"}],"language":[{"iso":"eng"}],"has_accepted_license":"1","publication":"Plant Physiology","date_created":"2018-12-11T11:47:49Z","page":"223 - 240","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"American Society of Plant Biologists","title":"EXO70C2 is a key regulatory factor for optimal tip growth of pollen","author":[{"full_name":"Synek, Lukáš","last_name":"Synek","first_name":"Lukáš"},{"last_name":"Vukašinović","first_name":"Nemanja","full_name":"Vukašinović, Nemanja"},{"full_name":"Kulich, Ivan","last_name":"Kulich","first_name":"Ivan"},{"last_name":"Hála","first_name":"Michal","full_name":"Hála, Michal"},{"full_name":"Aldorfová, Klára","first_name":"Klára","last_name":"Aldorfová"},{"full_name":"Fendrych, Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87","last_name":"Fendrych","orcid":"0000-0002-9767-8699","first_name":"Matyas"},{"last_name":"Žárský","first_name":"Viktor","full_name":"Žárský, Viktor"}],"file":[{"file_size":2176903,"relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_id":"7041","creator":"dernst","checksum":"97155acc6aa5f0d0a78e0589a932fe02","date_created":"2019-11-18T16:16:18Z","file_name":"2017_PlantPhysio_Synek.pdf","date_updated":"2020-07-14T12:47:37Z"}],"pmid":1,"day":"01","intvolume":"       174","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>.","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>","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.","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>","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.","short":"L. Synek, N. Vukašinović, I. Kulich, M. Hála, K. Aldorfová, M. Fendrych, V. Žárský, Plant Physiology 174 (2017) 223–240."},"scopus_import":1,"file_date_updated":"2020-07-14T12:47:37Z","ddc":["580"],"oa_version":"Submitted Version","date_published":"2017-05-01T00:00:00Z","doi":"10.1104/pp.16.01282","publication_status":"published","month":"05","status":"public","publication_identifier":{"issn":["00320889"]},"oa":1,"_id":"669","issue":"1","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. "}],"date_updated":"2021-01-12T08:08:35Z","year":"2017"},{"ddc":["000"],"scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://hal.inria.fr/hal-01647113/file/eg_2017_schreck_paper_tearing.pdf"}],"citation":{"short":"C. Schreck, D. Rohmer, S. Hahmann, Computer Graphics Forum 36 (2017) 95–106.","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>","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.","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>.","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>.","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>","ista":"Schreck C, Rohmer D, Hahmann S. 2017. Interactive paper tearing. Computer Graphics Forum. 36(2), 95–106."},"intvolume":"        36","doi":"10.1111/cgf.13110","publication_status":"published","date_published":"2017-05-01T00:00:00Z","oa_version":"Published Version","publication_identifier":{"issn":["01677055"]},"oa":1,"status":"public","month":"05","year":"2017","issue":"2","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."}],"date_updated":"2021-01-12T08:08:37Z","_id":"670","article_type":"original","article_processing_charge":"No","publist_id":"7056","quality_controlled":"1","volume":36,"publication":"Computer Graphics Forum","page":"95 - 106","date_created":"2018-12-11T11:47:49Z","department":[{"_id":"ChWo"}],"language":[{"iso":"eng"}],"type":"journal_article","title":"Interactive paper tearing","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Wiley","day":"01","author":[{"full_name":"Schreck, Camille","id":"2B14B676-F248-11E8-B48F-1D18A9856A87","last_name":"Schreck","first_name":"Camille"},{"first_name":"Damien","last_name":"Rohmer","full_name":"Rohmer, Damien"},{"first_name":"Stefanie","last_name":"Hahmann","full_name":"Hahmann, Stefanie"}],"project":[{"_id":"25357BD2-B435-11E9-9278-68D0E5697425","grant_number":"P 24352-N23","name":"Deep Pictures: Creating Visual and Haptic Vector Images","call_identifier":"FWF"}]},{"author":[{"id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","last_name":"Hilbe","orcid":"0000-0001-5116-955X","first_name":"Christian","full_name":"Hilbe, Christian"},{"full_name":"Martinez, Vaquero","first_name":"Vaquero","last_name":"Martinez"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"full_name":"Nowak, Martin","first_name":"Martin","last_name":"Nowak"}],"project":[{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Game Theory"}],"pmid":1,"day":"02","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"National Academy of Sciences","title":"Memory-n strategies of direct reciprocity","type":"journal_article","department":[{"_id":"KrCh"}],"language":[{"iso":"eng"}],"publication":"PNAS","page":"4715 - 4720","date_created":"2018-12-11T11:47:50Z","quality_controlled":"1","volume":114,"external_id":{"pmid":["28420786"]},"article_processing_charge":"Yes (in subscription journal)","publist_id":"7053","_id":"671","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."}],"issue":"18","date_updated":"2021-01-12T08:08:37Z","year":"2017","month":"05","ec_funded":1,"status":"public","publication_identifier":{"issn":["00278424"]},"oa":1,"oa_version":"Published Version","date_published":"2017-05-02T00:00:00Z","doi":"10.1073/pnas.1621239114","publication_status":"published","citation":{"short":"C. Hilbe, V. Martinez, K. Chatterjee, M. Nowak, PNAS 114 (2017) 4715–4720.","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.","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>","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.","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>.","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>"},"intvolume":"       114","scopus_import":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5422766/","open_access":"1"}]},{"title":"Locally triggered release of the chemokine CCL21 promotes dendritic cell transmigration across lymphatic endothelia","publisher":"Cell Press","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","file":[{"date_updated":"2020-07-14T12:47:38Z","file_name":"IST-2017-900-v1+1_1-s2.0-S2211124717305211-main.pdf","date_created":"2018-12-12T10:14:54Z","creator":"system","file_id":"5109","checksum":"8fdddaab1f1d76a6ec9ca94dcb6b07a2","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_size":2248814}],"project":[{"call_identifier":"FP7","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)","_id":"25A603A2-B435-11E9-9278-68D0E5697425","grant_number":"281556"},{"_id":"25A8E5EA-B435-11E9-9278-68D0E5697425","grant_number":"Y 564-B12","name":"Cytoskeletal force generation and transduction of leukocytes (FWF)","call_identifier":"FWF"}],"author":[{"last_name":"Vaahtomeri","id":"368EE576-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7829-3518","first_name":"Kari","full_name":"Vaahtomeri, Kari"},{"full_name":"Brown, Markus","last_name":"Brown","id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87","first_name":"Markus"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","orcid":"0000-0001-9843-3522","first_name":"Robert","full_name":"Hauschild, Robert"},{"last_name":"De Vries","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","first_name":"Ingrid","full_name":"De Vries, Ingrid"},{"full_name":"Leithner, Alexander F","last_name":"Leithner","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander F"},{"full_name":"Mehling, Matthias","last_name":"Mehling","id":"3C23B994-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias","orcid":"0000-0001-8599-1226"},{"last_name":"Kaufmann","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9735-5315","first_name":"Walter","full_name":"Kaufmann, Walter"},{"full_name":"Sixt, Michael K","first_name":"Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"day":"02","volume":19,"quality_controlled":"1","publist_id":"7052","pubrep_id":"900","article_processing_charge":"Yes","language":[{"iso":"eng"}],"department":[{"_id":"MiSi"},{"_id":"Bio"},{"_id":"EM-Fac"}],"type":"journal_article","page":"902 - 909","date_created":"2018-12-11T11:47:50Z","publication":"Cell Reports","has_accepted_license":"1","ec_funded":1,"month":"05","oa":1,"publication_identifier":{"issn":["22111247"]},"status":"public","_id":"672","year":"2017","date_updated":"2023-02-23T12:50:09Z","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","citation":{"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>","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.","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>.","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>.","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.","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>","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."},"intvolume":"        19","ddc":["570"],"file_date_updated":"2020-07-14T12:47:38Z","scopus_import":1,"date_published":"2017-05-02T00:00:00Z","oa_version":"Published Version","publication_status":"published","doi":"10.1016/j.celrep.2017.04.027"},{"title":"Wave propagation reversal for wavy vortices in wide gap counter rotating cylindrical Couette flow","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"American Physical Society","author":[{"full_name":"Altmeyer, Sebastian","orcid":"0000-0001-5964-0203","first_name":"Sebastian","id":"2EE67FDC-F248-11E8-B48F-1D18A9856A87","last_name":"Altmeyer"},{"full_name":"Lueptow, Richard","last_name":"Lueptow","first_name":"Richard"}],"day":"10","volume":95,"article_processing_charge":"No","publist_id":"7049","department":[{"_id":"BjHo"}],"language":[{"iso":"eng"}],"type":"journal_article","publication":"Physical Review E","date_created":"2018-12-11T11:47:50Z","month":"05","publication_identifier":{"issn":["2470-0045"]},"oa":1,"status":"public","_id":"673","article_number":"053103","year":"2017","abstract":[{"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.","lang":"eng"}],"issue":"5","date_updated":"2023-10-10T13:30:03Z","intvolume":"        95","citation":{"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>.","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>","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.","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>.","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.","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)."},"main_file_link":[{"url":"https://arxiv.org/pdf/physics/0505164.pdf","open_access":"1"}],"scopus_import":"1","date_published":"2017-05-10T00:00:00Z","oa_version":"Submitted Version","doi":"10.1103/PhysRevE.95.053103","publication_status":"published"},{"date_published":"2017-05-09T00:00:00Z","oa_version":"None","publication_status":"published","doi":"10.1016/j.cub.2017.04.004","citation":{"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.","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.","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.","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>","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>.","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>."},"intvolume":"        27","scopus_import":1,"_id":"674","year":"2017","date_updated":"2023-02-23T12:50:44Z","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"}],"ec_funded":1,"month":"05","publication_identifier":{"issn":["09609822"]},"status":"public","language":[{"iso":"eng"}],"department":[{"_id":"MiSi"},{"_id":"Bio"},{"_id":"NanoFab"}],"type":"journal_article","date_created":"2018-12-11T11:47:51Z","page":"1314 - 1325","publication":"Current Biology","quality_controlled":"1","volume":27,"publist_id":"7050","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"},{"grant_number":"Y 564-B12","_id":"25A8E5EA-B435-11E9-9278-68D0E5697425","name":"Cytoskeletal force generation and transduction of leukocytes (FWF)","call_identifier":"FWF"}],"author":[{"last_name":"Schwarz","id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","full_name":"Schwarz, Jan"},{"first_name":"Veronika","id":"3FD04378-F248-11E8-B48F-1D18A9856A87","last_name":"Bierbaum","full_name":"Bierbaum, Veronika"},{"full_name":"Vaahtomeri, Kari","last_name":"Vaahtomeri","id":"368EE576-F248-11E8-B48F-1D18A9856A87","first_name":"Kari","orcid":"0000-0001-7829-3518"},{"orcid":"0000-0001-9843-3522","first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","full_name":"Hauschild, Robert"},{"full_name":"Brown, Markus","id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87","last_name":"Brown","first_name":"Markus"},{"first_name":"Ingrid","last_name":"De Vries","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","full_name":"De Vries, Ingrid"},{"full_name":"Leithner, Alexander F","last_name":"Leithner","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander F"},{"full_name":"Reversat, Anne","orcid":"0000-0003-0666-8928","first_name":"Anne","last_name":"Reversat","id":"35B76592-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Merrin, Jack","last_name":"Merrin","id":"4515C308-F248-11E8-B48F-1D18A9856A87","first_name":"Jack","orcid":"0000-0001-5145-4609"},{"full_name":"Tarrant, Teresa","last_name":"Tarrant","first_name":"Teresa"},{"full_name":"Bollenbach, Tobias","orcid":"0000-0003-4398-476X","first_name":"Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","orcid":"0000-0002-6620-9179","first_name":"Michael K","full_name":"Sixt, Michael K"}],"day":"09","title":"Dendritic cells interpret haptotactic chemokine gradients in a manner governed by signal to noise ratio and dependent on GRK6","publisher":"Cell Press","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87"},{"pmid":1,"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"15","author":[{"last_name":"Krens","id":"2B819732-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4761-5996","first_name":"Gabriel","full_name":"Krens, Gabriel"},{"full_name":"Veldhuis, Jim","last_name":"Veldhuis","first_name":"Jim"},{"orcid":"0000-0003-2676-3367","first_name":"Vanessa","id":"419EECCC-F248-11E8-B48F-1D18A9856A87","last_name":"Barone","full_name":"Barone, Vanessa"},{"full_name":"Capek, Daniel","last_name":"Capek","id":"31C42484-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel","orcid":"0000-0001-5199-9940"},{"full_name":"Maître, Jean-Léon","id":"48F1E0D8-F248-11E8-B48F-1D18A9856A87","last_name":"Maître","orcid":"0000-0002-3688-1474","first_name":"Jean-Léon"},{"last_name":"Brodland","first_name":"Wayne","full_name":"Brodland, Wayne"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J"}],"file":[{"content_type":"application/pdf","relation":"main_file","file_size":8194516,"creator":"dernst","file_id":"6905","checksum":"bc25125fb664706cdf180e061429f91d","access_level":"open_access","date_updated":"2020-07-14T12:47:39Z","file_name":"2017_Development_Krens.pdf","date_created":"2019-09-24T06:56:22Z"}],"publisher":"Company of Biologists","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Interstitial fluid osmolarity modulates the action of differential tissue surface tension in progenitor cell segregation during gastrulation","has_accepted_license":"1","page":"1798 - 1806","date_created":"2018-12-11T11:47:52Z","publication":"Development","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"Bio"},{"_id":"CaHe"}],"publist_id":"7047","article_type":"original","article_processing_charge":"No","external_id":{"pmid":["28512197"]},"quality_controlled":"1","volume":144,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"961"},{"relation":"dissertation_contains","status":"public","id":"50"}]},"date_updated":"2024-03-25T23:30:13Z","abstract":[{"lang":"eng","text":"The segregation of different cell types into distinct tissues is a fundamental process in metazoan development. Differences in cell adhesion and cortex tension are commonly thought to drive cell sorting by regulating tissue surface tension (TST). However, the role that differential TST plays in cell segregation within the developing embryo is as yet unclear. Here, we have analyzed the role of differential TST for germ layer progenitor cell segregation during zebrafish gastrulation. Contrary to previous observations that differential TST drives germ layer progenitor cell segregation in vitro, we show that germ layers display indistinguishable TST within the gastrulating embryo, arguing against differential TST driving germ layer progenitor cell segregation in vivo. We further show that the osmolarity of the interstitial fluid (IF) is an important factor that influences germ layer TST in vivo, and that lower osmolarity of the IF compared with standard cell culture medium can explain why germ layers display differential TST in culture but not in vivo. Finally, we show that directed migration of mesendoderm progenitors is required for germ layer progenitor cell segregation and germ layer formation."}],"issue":"10","year":"2017","_id":"676","status":"public","oa":1,"publication_identifier":{"issn":["09501991"]},"month":"05","publication_status":"published","doi":"10.1242/dev.144964","oa_version":"Published Version","date_published":"2017-05-15T00:00:00Z","scopus_import":1,"file_date_updated":"2020-07-14T12:47:39Z","ddc":["570"],"intvolume":"       144","citation":{"chicago":"Krens, Gabriel, Jim Veldhuis, Vanessa Barone, Daniel Capek, Jean-Léon Maître, Wayne Brodland, and Carl-Philipp J Heisenberg. “Interstitial Fluid Osmolarity Modulates the Action of Differential Tissue Surface Tension in Progenitor Cell Segregation during Gastrulation.” <i>Development</i>. Company of Biologists, 2017. <a href=\"https://doi.org/10.1242/dev.144964\">https://doi.org/10.1242/dev.144964</a>.","mla":"Krens, Gabriel, et al. “Interstitial Fluid Osmolarity Modulates the Action of Differential Tissue Surface Tension in Progenitor Cell Segregation during Gastrulation.” <i>Development</i>, vol. 144, no. 10, Company of Biologists, 2017, pp. 1798–806, doi:<a href=\"https://doi.org/10.1242/dev.144964\">10.1242/dev.144964</a>.","ista":"Krens G, Veldhuis J, Barone V, Capek D, Maître J-L, Brodland W, Heisenberg C-PJ. 2017. Interstitial fluid osmolarity modulates the action of differential tissue surface tension in progenitor cell segregation during gastrulation. Development. 144(10), 1798–1806.","apa":"Krens, G., Veldhuis, J., Barone, V., Capek, D., Maître, J.-L., Brodland, W., &#38; Heisenberg, C.-P. J. (2017). Interstitial fluid osmolarity modulates the action of differential tissue surface tension in progenitor cell segregation during gastrulation. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/dev.144964\">https://doi.org/10.1242/dev.144964</a>","ieee":"G. Krens <i>et al.</i>, “Interstitial fluid osmolarity modulates the action of differential tissue surface tension in progenitor cell segregation during gastrulation,” <i>Development</i>, vol. 144, no. 10. Company of Biologists, pp. 1798–1806, 2017.","ama":"Krens G, Veldhuis J, Barone V, et al. Interstitial fluid osmolarity modulates the action of differential tissue surface tension in progenitor cell segregation during gastrulation. <i>Development</i>. 2017;144(10):1798-1806. doi:<a href=\"https://doi.org/10.1242/dev.144964\">10.1242/dev.144964</a>","short":"G. Krens, J. Veldhuis, V. Barone, D. Capek, J.-L. Maître, W. Brodland, C.-P.J. Heisenberg, Development 144 (2017) 1798–1806."}},{"date_published":"2017-05-16T00:00:00Z","oa_version":"Published Version","publication_status":"published","doi":"10.1016/j.celrep.2017.04.051","intvolume":"        19","citation":{"apa":"Lademann, C., Renkawitz, J., Pfander, B., &#38; Jentsch, S. (2017). The INO80 complex removes H2A.Z to promote presynaptic filament formation during homologous recombination. <i>Cell Reports</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.celrep.2017.04.051\">https://doi.org/10.1016/j.celrep.2017.04.051</a>","mla":"Lademann, Claudio, et al. “The INO80 Complex Removes H2A.Z to Promote Presynaptic Filament Formation during Homologous Recombination.” <i>Cell Reports</i>, vol. 19, no. 7, Cell Press, 2017, pp. 1294–303, doi:<a href=\"https://doi.org/10.1016/j.celrep.2017.04.051\">10.1016/j.celrep.2017.04.051</a>.","ista":"Lademann C, Renkawitz J, Pfander B, Jentsch S. 2017. The INO80 complex removes H2A.Z to promote presynaptic filament formation during homologous recombination. Cell Reports. 19(7), 1294–1303.","chicago":"Lademann, Claudio, Jörg Renkawitz, Boris Pfander, and Stefan Jentsch. “The INO80 Complex Removes H2A.Z to Promote Presynaptic Filament Formation during Homologous Recombination.” <i>Cell Reports</i>. Cell Press, 2017. <a href=\"https://doi.org/10.1016/j.celrep.2017.04.051\">https://doi.org/10.1016/j.celrep.2017.04.051</a>.","short":"C. Lademann, J. Renkawitz, B. Pfander, S. Jentsch, Cell Reports 19 (2017) 1294–1303.","ama":"Lademann C, Renkawitz J, Pfander B, Jentsch S. The INO80 complex removes H2A.Z to promote presynaptic filament formation during homologous recombination. <i>Cell Reports</i>. 2017;19(7):1294-1303. doi:<a href=\"https://doi.org/10.1016/j.celrep.2017.04.051\">10.1016/j.celrep.2017.04.051</a>","ieee":"C. Lademann, J. Renkawitz, B. Pfander, and S. Jentsch, “The INO80 complex removes H2A.Z to promote presynaptic filament formation during homologous recombination,” <i>Cell Reports</i>, vol. 19, no. 7. Cell Press, pp. 1294–1303, 2017."},"ddc":["570"],"file_date_updated":"2020-07-14T12:47:40Z","scopus_import":1,"_id":"677","year":"2017","date_updated":"2021-01-12T08:08:57Z","abstract":[{"lang":"eng","text":"The INO80 complex (INO80-C) is an evolutionarily conserved nucleosome remodeler that acts in transcription, replication, and genome stability. It is required for resistance against genotoxic agents and is involved in the repair of DNA double-strand breaks (DSBs) by homologous recombination (HR). However, the causes of the HR defect in INO80-C mutant cells are controversial. Here, we unite previous findings using a system to study HR with high spatial resolution in budding yeast. We find that INO80-C has at least two distinct functions during HR—DNA end resection and presynaptic filament formation. Importantly, the second function is linked to the histone variant H2A.Z. In the absence of H2A.Z, presynaptic filament formation and HR are restored in INO80-C-deficient mutants, suggesting that presynaptic filament formation is the crucial INO80-C function during HR."}],"issue":"7","month":"05","publication_identifier":{"issn":["22111247"]},"oa":1,"status":"public","language":[{"iso":"eng"}],"department":[{"_id":"MiSi"}],"type":"journal_article","page":"1294 - 1303","date_created":"2018-12-11T11:47:52Z","publication":"Cell Reports","has_accepted_license":"1","quality_controlled":"1","volume":19,"publist_id":"7046","pubrep_id":"899","file":[{"date_created":"2018-12-12T10:15:48Z","file_name":"IST-2017-899-v1+1_1-s2.0-S2211124717305454-main.pdf","date_updated":"2020-07-14T12:47:40Z","access_level":"open_access","creator":"system","checksum":"efc7287d9c6354983cb151880e9ad72a","file_id":"5171","file_size":3005610,"relation":"main_file","content_type":"application/pdf"}],"author":[{"full_name":"Lademann, Claudio","first_name":"Claudio","last_name":"Lademann"},{"first_name":"Jörg","orcid":"0000-0003-2856-3369","last_name":"Renkawitz","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","full_name":"Renkawitz, Jörg"},{"full_name":"Pfander, Boris","last_name":"Pfander","first_name":"Boris"},{"first_name":"Stefan","last_name":"Jentsch","full_name":"Jentsch, Stefan"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"day":"16","title":"The INO80 complex removes H2A.Z to promote presynaptic filament formation during homologous recombination","publisher":"Cell Press","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"_id":"678","project":[{"name":"The generation and function of anisotropic tissue tension in zebrafish epiboly (EMBO Fellowship)","_id":"25236028-B435-11E9-9278-68D0E5697425","grant_number":"ALTF534-2016"}],"author":[{"last_name":"Petridou","id":"2A003F6C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8451-1195","first_name":"Nicoletta","full_name":"Petridou, Nicoletta"},{"full_name":"Spiro, Zoltan P","last_name":"Spiro","id":"426AD026-F248-11E8-B48F-1D18A9856A87","first_name":"Zoltan P"},{"full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566"}],"day":"31","year":"2017","date_updated":"2021-01-12T08:08:59Z","abstract":[{"lang":"eng","text":"The seminal observation that mechanical signals can elicit changes in biochemical signalling within cells, a process commonly termed mechanosensation and mechanotransduction, has revolutionized our understanding of the role of cell mechanics in various fundamental biological processes, such as cell motility, adhesion, proliferation and differentiation. In this Review, we will discuss how the interplay and feedback between mechanical and biochemical signals control tissue morphogenesis and cell fate specification in embryonic development."}],"issue":"6","month":"05","title":"Multiscale force sensing in development","publication_identifier":{"issn":["14657392"]},"status":"public","publisher":"Nature Publishing Group","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"date_published":"2017-05-31T00:00:00Z","department":[{"_id":"CaHe"}],"oa_version":"None","type":"journal_article","date_created":"2018-12-11T11:47:53Z","page":"581 - 588","publication":"Nature Cell Biology","publication_status":"published","doi":"10.1038/ncb3524","volume":19,"citation":{"ieee":"N. Petridou, Z. P. Spiro, and C.-P. J. Heisenberg, “Multiscale force sensing in development,” <i>Nature Cell Biology</i>, vol. 19, no. 6. Nature Publishing Group, pp. 581–588, 2017.","ama":"Petridou N, Spiro ZP, Heisenberg C-PJ. Multiscale force sensing in development. <i>Nature Cell Biology</i>. 2017;19(6):581-588. doi:<a href=\"https://doi.org/10.1038/ncb3524\">10.1038/ncb3524</a>","short":"N. Petridou, Z.P. Spiro, C.-P.J. Heisenberg, Nature Cell Biology 19 (2017) 581–588.","chicago":"Petridou, Nicoletta, Zoltan P Spiro, and Carl-Philipp J Heisenberg. “Multiscale Force Sensing in Development.” <i>Nature Cell Biology</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/ncb3524\">https://doi.org/10.1038/ncb3524</a>.","mla":"Petridou, Nicoletta, et al. “Multiscale Force Sensing in Development.” <i>Nature Cell Biology</i>, vol. 19, no. 6, Nature Publishing Group, 2017, pp. 581–88, doi:<a href=\"https://doi.org/10.1038/ncb3524\">10.1038/ncb3524</a>.","apa":"Petridou, N., Spiro, Z. P., &#38; Heisenberg, C.-P. J. (2017). Multiscale force sensing in development. <i>Nature Cell Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncb3524\">https://doi.org/10.1038/ncb3524</a>","ista":"Petridou N, Spiro ZP, Heisenberg C-PJ. 2017. Multiscale force sensing in development. Nature Cell Biology. 19(6), 581–588."},"quality_controlled":"1","intvolume":"        19","scopus_import":1,"publist_id":"7040"}]