[{"author":[{"orcid":"0000-0003-2724-4614","last_name":"Petritsch","id":"406048EC-F248-11E8-B48F-1D18A9856A87","full_name":"Petritsch, Barbara","first_name":"Barbara"}],"file":[{"content_type":"application/pdf","checksum":"7c4544d07efa2c2add8612b489abb4e2","access_level":"open_access","date_updated":"2020-07-14T12:48:11Z","relation":"main_file","date_created":"2019-01-18T13:32:17Z","file_size":7843975,"creator":"dernst","file_id":"5850","file_name":"2017_VOEB_Petritsch.pdf"}],"oa":1,"issue":"2","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"VÖB","oa_version":"Published Version","intvolume":"        70","has_accepted_license":"1","abstract":[{"text":"What data is needed about data? Describing the process to answer this question for the institutional data repository IST DataRep.","lang":"eng"}],"department":[{"_id":"E-Lib"}],"scopus_import":1,"citation":{"short":"B. Petritsch, Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen &#38; Bibliothekare 70 (2017) 200–207.","chicago":"Petritsch, Barbara. “Metadata for Research Data in Practice.” <i>Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen &#38; Bibliothekare</i>. VÖB, 2017. <a href=\"https://doi.org/10.31263/voebm.v70i2.1678\">https://doi.org/10.31263/voebm.v70i2.1678</a>.","apa":"Petritsch, B. (2017). Metadata for research data in practice. <i>Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen &#38; Bibliothekare</i>. VÖB. <a href=\"https://doi.org/10.31263/voebm.v70i2.1678\">https://doi.org/10.31263/voebm.v70i2.1678</a>","ama":"Petritsch B. Metadata for research data in practice. <i>Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen &#38; Bibliothekare</i>. 2017;70(2):200-207. doi:<a href=\"https://doi.org/10.31263/voebm.v70i2.1678\">10.31263/voebm.v70i2.1678</a>","ista":"Petritsch B. 2017. Metadata for research data in practice. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen &#38; Bibliothekare. 70(2), 200–207.","ieee":"B. Petritsch, “Metadata for research data in practice,” <i>Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen &#38; Bibliothekare</i>, vol. 70, no. 2. VÖB, pp. 200–207, 2017.","mla":"Petritsch, Barbara. “Metadata for Research Data in Practice.” <i>Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen &#38; Bibliothekare</i>, vol. 70, no. 2, VÖB, 2017, pp. 200–07, doi:<a href=\"https://doi.org/10.31263/voebm.v70i2.1678\">10.31263/voebm.v70i2.1678</a>."},"publist_id":"6823","month":"08","status":"public","day":"01","volume":70,"title":"Metadata for research data in practice","file_date_updated":"2020-07-14T12:48:11Z","_id":"825","license":"https://creativecommons.org/licenses/by/4.0/","year":"2017","publication":"Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare","doi":"10.31263/voebm.v70i2.1678","language":[{"iso":"eng"}],"date_published":"2017-08-01T00:00:00Z","page":"200 - 207","date_updated":"2021-01-12T08:17:44Z","date_created":"2018-12-11T11:48:42Z","publication_status":"published","publication_identifier":{"issn":["10222588"]},"ddc":["020"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"}},{"conference":{"location":"Ystad, Sweden","end_date":"2017-08-24","start_date":"2017-08-22","name":"CAIP: Computer Analysis of Images and Patterns"},"doi":"10.1007/978-3-319-64689-3_32","year":"2017","_id":"833","title":"Streaming algorithm for Euler characteristic curves of multidimensional images","day":"28","volume":10424,"main_file_link":[{"url":"https://arxiv.org/abs/1705.02045","open_access":"1"}],"status":"public","month":"07","publication_identifier":{"issn":["03029743"]},"publication_status":"published","isi":1,"article_processing_charge":"No","date_created":"2018-12-11T11:48:45Z","date_updated":"2023-09-26T16:10:03Z","page":"397 - 409","date_published":"2017-07-28T00:00:00Z","language":[{"iso":"eng"}],"quality_controlled":"1","editor":[{"first_name":"Michael","full_name":"Felsberg, Michael","last_name":"Felsberg"},{"last_name":"Heyden","first_name":"Anders","full_name":"Heyden, Anders"},{"last_name":"Krüger","full_name":"Krüger, Norbert","first_name":"Norbert"}],"oa_version":"Submitted Version","publisher":"Springer","alternative_title":["LNCS"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","type":"conference","oa":1,"author":[{"last_name":"Heiss","id":"4879BB4E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1780-2689","first_name":"Teresa","full_name":"Heiss, Teresa"},{"id":"379CA8B8-F248-11E8-B48F-1D18A9856A87","last_name":"Wagner","full_name":"Wagner, Hubert","first_name":"Hubert"}],"publist_id":"6815","citation":{"mla":"Heiss, Teresa, and Hubert Wagner. <i>Streaming Algorithm for Euler Characteristic Curves of Multidimensional Images</i>. Edited by Michael Felsberg et al., vol. 10424, Springer, 2017, pp. 397–409, doi:<a href=\"https://doi.org/10.1007/978-3-319-64689-3_32\">10.1007/978-3-319-64689-3_32</a>.","ieee":"T. Heiss and H. Wagner, “Streaming algorithm for Euler characteristic curves of multidimensional images,” presented at the CAIP: Computer Analysis of Images and Patterns, Ystad, Sweden, 2017, vol. 10424, pp. 397–409.","ista":"Heiss T, Wagner H. 2017. Streaming algorithm for Euler characteristic curves of multidimensional images. CAIP: Computer Analysis of Images and Patterns, LNCS, vol. 10424, 397–409.","apa":"Heiss, T., &#38; Wagner, H. (2017). Streaming algorithm for Euler characteristic curves of multidimensional images. In M. Felsberg, A. Heyden, &#38; N. Krüger (Eds.) (Vol. 10424, pp. 397–409). Presented at the CAIP: Computer Analysis of Images and Patterns, Ystad, Sweden: Springer. <a href=\"https://doi.org/10.1007/978-3-319-64689-3_32\">https://doi.org/10.1007/978-3-319-64689-3_32</a>","ama":"Heiss T, Wagner H. Streaming algorithm for Euler characteristic curves of multidimensional images. In: Felsberg M, Heyden A, Krüger N, eds. Vol 10424. Springer; 2017:397-409. doi:<a href=\"https://doi.org/10.1007/978-3-319-64689-3_32\">10.1007/978-3-319-64689-3_32</a>","chicago":"Heiss, Teresa, and Hubert Wagner. “Streaming Algorithm for Euler Characteristic Curves of Multidimensional Images.” edited by Michael Felsberg, Anders Heyden, and Norbert Krüger, 10424:397–409. Springer, 2017. <a href=\"https://doi.org/10.1007/978-3-319-64689-3_32\">https://doi.org/10.1007/978-3-319-64689-3_32</a>.","short":"T. Heiss, H. Wagner, in:, M. Felsberg, A. Heyden, N. Krüger (Eds.), Springer, 2017, pp. 397–409."},"scopus_import":"1","external_id":{"isi":["000432085900032"]},"department":[{"_id":"HeEd"}],"abstract":[{"text":"We present an efficient algorithm to compute Euler characteristic curves of gray scale images of arbitrary dimension. In various applications the Euler characteristic curve is used as a descriptor of an image. Our algorithm is the first streaming algorithm for Euler characteristic curves. The usage of streaming removes the necessity to store the entire image in RAM. Experiments show that our implementation handles terabyte scale images on commodity hardware. Due to lock-free parallelism, it scales well with the number of processor cores. Additionally, we put the concept of the Euler characteristic curve in the wider context of computational topology. In particular, we explain the connection with persistence diagrams.","lang":"eng"}],"intvolume":"     10424"},{"author":[{"first_name":"Maksym","full_name":"Serbyn, Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","last_name":"Serbyn"},{"full_name":"Zlatko, Papic","first_name":"Papic","last_name":"Zlatko"},{"last_name":"Abanin","first_name":"Dmitry","full_name":"Abanin, Dmitry"}],"publisher":"American Physical Society","issue":"10","oa":1,"type":"journal_article","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Submitted Version","intvolume":"        96","abstract":[{"lang":"eng","text":"Thermal and many-body localized phases are separated by a dynamical phase transition of a new kind. We analyze the distribution of off-diagonal matrix elements of local operators across this transition in two different models of disordered spin chains. We show that the behavior of matrix elements can be used to characterize the breakdown of thermalization and to extract the many-body Thouless energy. We find that upon increasing the disorder strength the system enters a critical region around the many-body localization transition. The properties of the system in this region are: (i) the Thouless energy becomes smaller than the level spacing, (ii) the matrix elements show critical dependence on the energy difference, and (iii) the matrix elements, viewed as amplitudes of a fictitious wave function, exhibit strong multifractality. This critical region decreases with the system size, which we interpret as evidence for a diverging correlation length at the many-body localization transition. Our findings show that the correlation length becomes larger than the accessible system sizes in a broad range of disorder strength values and shed light on the critical behavior near the many-body localization transition."}],"department":[{"_id":"MaSe"}],"external_id":{"isi":["000409429300004"]},"scopus_import":"1","acknowledgement":"We   acknowledge   useful   discussions with V. Kravtsov, T. Grover, and R. Vasseur.  M.S. was supported by Gordon and Betty Moore Foundation’s EPiQS Initiative through Grant GBMF4307.  M.S. and D.A.  acknowledge  hospitality  of  KITP,  where  parts  of this work were completed (supported in part by the National Science Foundation under Grant No. NSF PHY11-25915)","citation":{"short":"M. Serbyn, P. Zlatko, D. Abanin, Physical Review B - Condensed Matter and Materials Physics 96 (2017).","chicago":"Serbyn, Maksym, Papic Zlatko, and Dmitry Abanin. “Thouless Energy and Multifractality across the Many-Body Localization Transition.” <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society, 2017. <a href=\"https://doi.org/10.1103/PhysRevB.96.104201\">https://doi.org/10.1103/PhysRevB.96.104201</a>.","apa":"Serbyn, M., Zlatko, P., &#38; Abanin, D. (2017). Thouless energy and multifractality across the many-body localization transition. <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.96.104201\">https://doi.org/10.1103/PhysRevB.96.104201</a>","ama":"Serbyn M, Zlatko P, Abanin D. Thouless energy and multifractality across the many-body localization transition. <i>Physical Review B - Condensed Matter and Materials Physics</i>. 2017;96(10). doi:<a href=\"https://doi.org/10.1103/PhysRevB.96.104201\">10.1103/PhysRevB.96.104201</a>","ista":"Serbyn M, Zlatko P, Abanin D. 2017. Thouless energy and multifractality across the many-body localization transition. Physical Review B - Condensed Matter and Materials Physics. 96(10), 104201.","mla":"Serbyn, Maksym, et al. “Thouless Energy and Multifractality across the Many-Body Localization Transition.” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 96, no. 10, 104201, American Physical Society, 2017, doi:<a href=\"https://doi.org/10.1103/PhysRevB.96.104201\">10.1103/PhysRevB.96.104201</a>.","ieee":"M. Serbyn, P. Zlatko, and D. Abanin, “Thouless energy and multifractality across the many-body localization transition,” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 96, no. 10. American Physical Society, 2017."},"publist_id":"6814","month":"09","day":"06","volume":96,"status":"public","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1610.02389"}],"year":"2017","_id":"834","publication":"Physical Review B - Condensed Matter and Materials Physics","title":"Thouless energy and multifractality across the many-body localization transition","doi":"10.1103/PhysRevB.96.104201","language":[{"iso":"eng"}],"quality_controlled":"1","date_created":"2018-12-11T11:48:45Z","date_updated":"2023-09-26T15:51:54Z","date_published":"2017-09-06T00:00:00Z","isi":1,"article_number":"104201","publication_status":"published","article_processing_charge":"No","publication_identifier":{"issn":["24699950"]}},{"external_id":{"isi":["000434088200008"]},"department":[{"_id":"HeEd"}],"abstract":[{"text":"Recent research has examined how to study the topological features of a continuous self-map by means of the persistence of the eigenspaces, for given eigenvalues, of the endomorphism induced in homology over a field. This raised the question of how to select dynamically significant eigenvalues. The present paper aims to answer this question, giving an algorithm that computes the persistence of eigenspaces for every eigenvalue simultaneously, also expressing said eigenspaces as direct sums of “finite” and “singular” subspaces.","lang":"eng"}],"intvolume":"       198","publist_id":"6812","project":[{"name":"Topological Complex Systems","call_identifier":"FP7","grant_number":"318493","_id":"255D761E-B435-11E9-9278-68D0E5697425"}],"citation":{"ama":"Ethier M, Jablonski G, Mrozek M. Finding eigenvalues of self-maps with the Kronecker canonical form. In: <i>Special Sessions in Applications of Computer Algebra</i>. Vol 198. Springer; 2017:119-136. doi:<a href=\"https://doi.org/10.1007/978-3-319-56932-1_8\">10.1007/978-3-319-56932-1_8</a>","apa":"Ethier, M., Jablonski, G., &#38; Mrozek, M. (2017). Finding eigenvalues of self-maps with the Kronecker canonical form. In <i>Special Sessions in Applications of Computer Algebra</i> (Vol. 198, pp. 119–136). Kalamata, Greece: Springer. <a href=\"https://doi.org/10.1007/978-3-319-56932-1_8\">https://doi.org/10.1007/978-3-319-56932-1_8</a>","chicago":"Ethier, Marc, Grzegorz Jablonski, and Marian Mrozek. “Finding Eigenvalues of Self-Maps with the Kronecker Canonical Form.” In <i>Special Sessions in Applications of Computer Algebra</i>, 198:119–36. Springer, 2017. <a href=\"https://doi.org/10.1007/978-3-319-56932-1_8\">https://doi.org/10.1007/978-3-319-56932-1_8</a>.","short":"M. Ethier, G. Jablonski, M. Mrozek, in:, Special Sessions in Applications of Computer Algebra, Springer, 2017, pp. 119–136.","mla":"Ethier, Marc, et al. “Finding Eigenvalues of Self-Maps with the Kronecker Canonical Form.” <i>Special Sessions in Applications of Computer Algebra</i>, vol. 198, Springer, 2017, pp. 119–36, doi:<a href=\"https://doi.org/10.1007/978-3-319-56932-1_8\">10.1007/978-3-319-56932-1_8</a>.","ieee":"M. Ethier, G. Jablonski, and M. Mrozek, “Finding eigenvalues of self-maps with the Kronecker canonical form,” in <i>Special Sessions in Applications of Computer Algebra</i>, Kalamata, Greece, 2017, vol. 198, pp. 119–136.","ista":"Ethier M, Jablonski G, Mrozek M. 2017. Finding eigenvalues of self-maps with the Kronecker canonical form. Special Sessions in Applications of Computer Algebra. ACA: Applications of Computer Algebra, PROMS, vol. 198, 119–136."},"scopus_import":"1","ec_funded":1,"author":[{"full_name":"Ethier, Marc","first_name":"Marc","last_name":"Ethier"},{"orcid":"0000-0002-3536-9866","id":"4483EF78-F248-11E8-B48F-1D18A9856A87","last_name":"Jablonski","first_name":"Grzegorz","full_name":"Jablonski, Grzegorz"},{"full_name":"Mrozek, Marian","first_name":"Marian","last_name":"Mrozek"}],"oa_version":"None","publisher":"Springer","alternative_title":["PROMS"],"type":"conference","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2018-12-11T11:48:46Z","date_updated":"2023-09-26T15:50:52Z","page":"119 - 136","date_published":"2017-07-27T00:00:00Z","language":[{"iso":"eng"}],"quality_controlled":"1","publication_identifier":{"isbn":["978-331956930-7"]},"publication_status":"published","isi":1,"article_processing_charge":"No","volume":198,"day":"27","status":"public","month":"07","conference":{"location":"Kalamata, Greece","start_date":"2015-07-20","name":"ACA: Applications of Computer Algebra","end_date":"2015-07-23"},"doi":"10.1007/978-3-319-56932-1_8","publication":"Special Sessions in Applications of Computer Algebra","year":"2017","_id":"836","title":"Finding eigenvalues of self-maps with the Kronecker canonical form"},{"status":"public","day":"23","month":"08","doi":"10.15479/AT:ISTA:th_858","title":"Reactivation of the hippocampal cognitive map in goal-directed spatial tasks","degree_awarded":"PhD","file_date_updated":"2020-07-14T12:48:12Z","year":"2017","_id":"837","date_published":"2017-08-23T00:00:00Z","page":"93","date_created":"2018-12-11T11:48:46Z","date_updated":"2023-09-07T12:06:38Z","supervisor":[{"full_name":"Csicsvari, Jozsef L","first_name":"Jozsef L","orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"pubrep_id":"858","ddc":["571"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"No","publication_status":"published","file":[{"file_id":"6213","file_name":"2017_Xu_Haibing_Thesis_Source.docx","checksum":"f11925fbbce31e495124b6bc4f10573c","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2020-07-14T12:48:12Z","relation":"source_file","access_level":"closed","date_created":"2019-04-05T08:59:51Z","file_size":3589490,"creator":"dernst"},{"file_id":"6214","file_name":"2017_Xu_Thesis_IST.pdf","file_size":11668613,"access_level":"open_access","relation":"main_file","date_created":"2019-04-05T08:59:51Z","date_updated":"2020-07-14T12:48:12Z","content_type":"application/pdf","checksum":"ffb10749a537d615fab1ef0937ccb157","creator":"dernst"}],"author":[{"full_name":"Xu, Haibing","first_name":"Haibing","last_name":"Xu","id":"310349D0-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Published Version","oa":1,"type":"dissertation","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"JoCs"}],"abstract":[{"lang":"eng","text":"The hippocampus is a key brain region for memory and notably for spatial memory, and is needed for both spatial working and reference memories. Hippocampal place cells selectively discharge in specific locations of the environment to form mnemonic represen tations of space. Several behavioral protocols have been designed to test spatial memory which requires the experimental subject to utilize working memory and reference memory. However, less is known about how these memory traces are presented in the hippo campus, especially considering tasks that require both spatial working and long -term reference memory demand. The aim of my thesis was to elucidate how spatial working memory, reference memory, and the combination of both are represented in the hippocampus. In this thesis, using a radial eight -arm maze, I examined how the combined demand on these memories influenced place cell assemblies while reference memories were partially updated by changing some of the reward- arms. This was contrasted with task varian ts requiring working or reference memories only. Reference memory update led to gradual place field shifts towards the rewards on the switched arms. Cells developed enhanced firing in passes between newly -rewarded arms as compared to those containing an unchanged reward. The working memory task did not show such gradual changes. Place assemblies on occasions replayed trajectories of the maze; at decision points the next arm choice was preferentially replayed in tasks needing reference memory while in the pure working memory task the previously visited arm was replayed. Hence trajectory replay only reflected the decision of the animal in tasks needing reference memory update. At the reward locations, in all three tasks outbound trajectories of the current arm were preferentially replayed, showing the animals’ next path to the center. At reward locations trajectories were replayed preferentially in reverse temporal order. Moreover, in the center reverse replay was seen in the working memory task but in the other tasks forward replay was seen. Hence, the direction of reactivation was determined by the goal locations so that part of the trajectory which was closer to the goal was reactivated later in an HSE while places further away from the goal were reactivated earlier. Altogether my work demonstrated that reference memory update triggers several levels of reorganization of the hippocampal cognitive map which are not seen in simpler working memory demand s. Moreover, hippocampus is likely to be involved in spatial decisions through reactivating planned trajectories when reference memory recall is required for such a decision. "}],"has_accepted_license":"1","publist_id":"6811","related_material":{"record":[{"relation":"part_of_dissertation","id":"5828","status":"public"}]},"citation":{"apa":"Xu, H. (2017). <i>Reactivation of the hippocampal cognitive map in goal-directed spatial tasks</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_858\">https://doi.org/10.15479/AT:ISTA:th_858</a>","ama":"Xu H. Reactivation of the hippocampal cognitive map in goal-directed spatial tasks. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_858\">10.15479/AT:ISTA:th_858</a>","chicago":"Xu, Haibing. “Reactivation of the Hippocampal Cognitive Map in Goal-Directed Spatial Tasks.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:th_858\">https://doi.org/10.15479/AT:ISTA:th_858</a>.","short":"H. Xu, Reactivation of the Hippocampal Cognitive Map in Goal-Directed Spatial Tasks, Institute of Science and Technology Austria, 2017.","mla":"Xu, Haibing. <i>Reactivation of the Hippocampal Cognitive Map in Goal-Directed Spatial Tasks</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_858\">10.15479/AT:ISTA:th_858</a>.","ieee":"H. Xu, “Reactivation of the hippocampal cognitive map in goal-directed spatial tasks,” Institute of Science and Technology Austria, 2017.","ista":"Xu H. 2017. Reactivation of the hippocampal cognitive map in goal-directed spatial tasks. Institute of Science and Technology Austria."},"acknowledgement":"I am very grateful for the opportunity I have had as a graduate student to explore and incredibly interesting branch of neuroscience, and for the people who made it possible. Firstly, I would like to offer my thanks to my supervisor Professor Jozsef Csicsvari for his great support, guidance and patience offered over the years. The door to his office was always open whenever I had questions. I have learned a lot from him about carefully designing experiments, asking interesting questions and how to integrate results into a broader picture. I also express my gratitude to the remarkable post- doc , Dr. Joseph O’Neill. He is a gre at scientific role model who is always willing to teach , and advice and talk through problems with his full attention. Many thanks to my wonderful “office mates” over the years and their support and encouragement, Alice Avernhe, Philipp Schönenberger, Desiree Dickerson, Karel Blahna, Charlotte Boccara, Igor Gridchyn, Peter Baracskay, Krisztián Kovács, Dámaris Rangel, Karola Käfer and Federico Stella. They were the ones in the lab for the many useful discussions about science and for making the laboratory such a nice and friendly place to work in. A special thank goes to Michael LoBianco and Jago Wallenschus for wonderful technical support. I would also like to thank Professor Peter Jonas and Professor David M Bannerman for being my qualifying exam and thesi s committee members despite their busy schedule. I am also very thankful to IST Austria for their support all throughout my PhD. "},{"author":[{"full_name":"Rybar, Michal","first_name":"Michal","last_name":"Rybar","id":"2B3E3DE8-F248-11E8-B48F-1D18A9856A87"}],"file":[{"file_name":"IST-2017-828-v1+3_2017_Rybar_thesis.pdf","file_id":"4799","creator":"system","file_size":847400,"date_updated":"2020-07-14T12:48:12Z","relation":"main_file","date_created":"2018-12-12T10:10:13Z","access_level":"open_access","content_type":"application/pdf","checksum":"ff8639ec4bded6186f44c7bd3ee26804"},{"file_id":"6202","file_name":"2017_Thesis_Rybar_source.zip","checksum":"3462101745ce8ad199c2d0f75dae4a7e","content_type":"application/zip","file_size":26054879,"date_updated":"2020-07-14T12:48:12Z","date_created":"2019-04-05T08:24:11Z","relation":"source_file","access_level":"closed","creator":"dernst"}],"type":"dissertation","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"In this thesis we discuss the exact security of message authentications codes HMAC , NMAC , and PMAC . NMAC is a mode of operation which turns a fixed input-length keyed hash function f into a variable input-length function. A practical single-key variant of NMAC called HMAC is a very popular and widely deployed message authentication code (MAC). PMAC is a block-cipher based mode of operation, which also happens to be the most famous fully parallel MAC. NMAC was introduced by Bellare, Canetti and Krawczyk Crypto’96, who proved it to be a secure pseudorandom function (PRF), and thus also a MAC, under two assumptions. Unfortunately, for many instantiations of HMAC one of them has been found to be wrong. To restore the provable guarantees for NMAC , Bellare [Crypto’06] showed its security without this assumption. PMAC was introduced by Black and Rogaway at Eurocrypt 2002. If instantiated with a pseudorandom permutation over n -bit strings, PMAC constitutes a provably secure variable input-length PRF. For adversaries making q queries, each of length at most ` (in n -bit blocks), and of total length σ ≤ q` , the original paper proves an upper bound on the distinguishing advantage of O ( σ 2 / 2 n ), while the currently best bound is O ( qσ/ 2 n ). In this work we show that this bound is tight by giving an attack with advantage Ω( q 2 `/ 2 n ). In the PMAC construction one initially XORs a mask to every message block, where the mask for the i th block is computed as τ i := γ i · L , where L is a (secret) random value, and γ i is the i -th codeword of the Gray code. Our attack applies more generally to any sequence of γ i ’s which contains a large coset of a subgroup of GF (2 n ). As for NMAC , our first contribution is a simpler and uniform proof: If f is an ε -secure PRF (against q queries) and a δ - non-adaptively secure PRF (against q queries), then NMAC f is an ( ε + `qδ )-secure PRF against q queries of length at most ` blocks each. We also show that this ε + `qδ bound is basically tight by constructing an f for which an attack with advantage `qδ exists. Moreover, we analyze the PRF-security of a modification of NMAC called NI by An and Bellare that avoids the constant rekeying on multi-block messages in NMAC and allows for an information-theoretic analysis. We carry out such an analysis, obtaining a tight `q 2 / 2 c bound for this step, improving over the trivial bound of ` 2 q 2 / 2 c . Finally, we investigate, if the security of PMAC can be further improved by using τ i ’s that are k -wise independent, for k &gt; 1 (the original has k = 1). We observe that the security of PMAC will not increase in general if k = 2, and then prove that the security increases to O ( q 2 / 2 n ), if the k = 4. Due to simple extension attacks, this is the best bound one can hope for, using any distribution on the masks. Whether k = 3 is already sufficient to get this level of security is left as an open problem. Keywords: Message authentication codes, Pseudorandom functions, HMAC, PMAC. "}],"has_accepted_license":"1","department":[{"_id":"KrPi"}],"citation":{"chicago":"Rybar, Michal. “(The Exact Security of) Message Authentication Codes.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:th_828\">https://doi.org/10.15479/AT:ISTA:th_828</a>.","short":"M. Rybar, (The Exact Security of) Message Authentication Codes, Institute of Science and Technology Austria, 2017.","ama":"Rybar M. (The exact security of) Message authentication codes. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_828\">10.15479/AT:ISTA:th_828</a>","apa":"Rybar, M. (2017). <i>(The exact security of) Message authentication codes</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_828\">https://doi.org/10.15479/AT:ISTA:th_828</a>","ista":"Rybar M. 2017. (The exact security of) Message authentication codes. Institute of Science and Technology Austria.","ieee":"M. Rybar, “(The exact security of) Message authentication codes,” Institute of Science and Technology Austria, 2017.","mla":"Rybar, Michal. <i>(The Exact Security of) Message Authentication Codes</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_828\">10.15479/AT:ISTA:th_828</a>."},"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"2082"},{"relation":"part_of_dissertation","id":"6196","status":"public"}]},"publist_id":"6810","month":"06","status":"public","day":"26","file_date_updated":"2020-07-14T12:48:12Z","degree_awarded":"PhD","title":"(The exact security of) Message authentication codes","year":"2017","_id":"838","doi":"10.15479/AT:ISTA:th_828","language":[{"iso":"eng"}],"page":"86","date_published":"2017-06-26T00:00:00Z","date_updated":"2023-09-07T12:02:28Z","date_created":"2018-12-11T11:48:46Z","article_processing_charge":"No","publication_status":"published","pubrep_id":"828","publication_identifier":{"issn":["2663-337X"]},"ddc":["000"]},{"supervisor":[{"full_name":"Wojtan, Christopher J","first_name":"Christopher J","orcid":"0000-0001-6646-5546","last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2018-12-11T11:48:47Z","date_updated":"2024-02-21T13:48:02Z","page":"124","date_published":"2017-08-14T00:00:00Z","language":[{"iso":"eng"}],"tmp":{"image":"/images/cc_by_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","short":"CC BY-SA (4.0)","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)"},"ddc":["004","005","006","531","621"],"pubrep_id":"855","publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","article_processing_charge":"No","day":"14","status":"public","month":"08","doi":"10.15479/AT:ISTA:th_855","license":"https://creativecommons.org/licenses/by-sa/4.0/","_id":"839","year":"2017","degree_awarded":"PhD","file_date_updated":"2020-07-14T12:48:13Z","title":"Brittle fracture simulation with boundary elements for computer graphics","department":[{"_id":"ChWo"}],"has_accepted_license":"1","abstract":[{"lang":"eng","text":"This thesis describes a brittle fracture simulation method for visual effects applications. Building upon a symmetric Galerkin boundary element method, we first compute stress intensity factors following the theory of linear elastic fracture mechanics. We then use these stress intensities to simulate the motion of a propagating crack front at a significantly higher resolution than the overall deformation of the breaking object. Allowing for spatial variations of the material's toughness during crack propagation produces visually realistic, highly-detailed fracture surfaces. Furthermore, we introduce approximations for stress intensities and crack opening displacements, resulting in both practical speed-up and theoretically superior runtime complexity compared to previous methods. While we choose a quasi-static approach to fracture mechanics, ignoring dynamic deformations, we also couple our fracture simulation framework to a standard rigid-body dynamics solver, enabling visual effects artists to simulate both large scale motion, as well as fracturing due to collision forces in a combined system. As fractures inside of an object grow, their geometry must be represented both in the coarse boundary element mesh, as well as at the desired fine output resolution. Using a boundary element method, we avoid complicated volumetric meshing operations. Instead we describe a simple set of surface meshing operations that allow us to progressively add cracks to the mesh of an object and still re-use all previously computed entries of the linear boundary element system matrix. On the high resolution level, we opt for an implicit surface representation. We then describe how to capture fracture surfaces during crack propagation, as well as separate the individual fragments resulting from the fracture process, based on this implicit representation. We show results obtained with our method, either solving the full boundary element system in every time step, or alternatively using our fast approximations. These results demonstrate that both of these methods perform well in basic test cases and produce realistic fracture surfaces. Furthermore we show that our fast approximations substantially out-perform the standard approach in more demanding scenarios. Finally, these two methods naturally combine, using the full solution while the problem size is manageably small and switching to the fast approximations later on. The resulting hybrid method gives the user a direct way to choose between speed and accuracy of the simulation. "}],"publist_id":"6809","project":[{"grant_number":"638176","call_identifier":"H2020","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","_id":"2533E772-B435-11E9-9278-68D0E5697425"}],"acknowledgement":"ERC H2020 programme (grant agreement no. 638176)\r\nFirst of all, let me thank my committee members, especially my supervisor, Chris\r\nWojtan, for supporting me throughout my PhD. Obviously, none of this work would\r\nhave been possible without you.\r\nFurthermore, Thank You to all the people who have contributed to this work in various\r\nways, in particular Martin Schanz and his group for providing and supporting the\r\nHyENA boundary element library, as well as Eder Miguel and Morten Bojsen-Hansen\r\nfor (repeatedly) proof reading and providing valuable suggestions during the writing\r\nof this thesis.\r\nI would also like to thank Bernd Bickel, and all the members – past and present – of his\r\nand Chris’ research groups at IST Austria for always providing honest and insightful\r\nfeedback throughout many joint group meetings, as well as Christopher Batty, Eitan\r\nGrinspun, and Fang Da for many insights into boundary element methods during our\r\ncollaboration.\r\nAs only virtual objects have been harmed in the process of creating this work, I would\r\nlike to acknowledge the Stanford scanning repository for providing the “Bunny” and\r\n“Armadillo” models, the AIM@SHAPE repository for “Pierre’s hand, watertight”, and\r\nS. Gainsbourg for the “Column” via Archive3D.net. Sorry for breaking these models\r\nin many different ways.\r\n","citation":{"ista":"Hahn D. 2017. Brittle fracture simulation with boundary elements for computer graphics. Institute of Science and Technology Austria.","ieee":"D. Hahn, “Brittle fracture simulation with boundary elements for computer graphics,” Institute of Science and Technology Austria, 2017.","mla":"Hahn, David. <i>Brittle Fracture Simulation with Boundary Elements for Computer Graphics</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_855\">10.15479/AT:ISTA:th_855</a>.","chicago":"Hahn, David. “Brittle Fracture Simulation with Boundary Elements for Computer Graphics.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:th_855\">https://doi.org/10.15479/AT:ISTA:th_855</a>.","short":"D. Hahn, Brittle Fracture Simulation with Boundary Elements for Computer Graphics, Institute of Science and Technology Austria, 2017.","apa":"Hahn, D. (2017). <i>Brittle fracture simulation with boundary elements for computer graphics</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_855\">https://doi.org/10.15479/AT:ISTA:th_855</a>","ama":"Hahn D. Brittle fracture simulation with boundary elements for computer graphics. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_855\">10.15479/AT:ISTA:th_855</a>"},"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"1362"},{"relation":"part_of_dissertation","id":"1633","status":"public"},{"status":"public","id":"5568","relation":"popular_science"}]},"file":[{"file_name":"IST-2017-855-v1+1_thesis_online_pdfA.pdf","file_id":"5100","creator":"system","checksum":"6c1ae8c90bfaba5e089417fefbc4a272","content_type":"application/pdf","file_size":14596191,"date_updated":"2020-07-14T12:48:13Z","relation":"main_file","date_created":"2018-12-12T10:14:46Z","access_level":"open_access"},{"date_created":"2019-04-05T08:40:30Z","date_updated":"2020-07-14T12:48:13Z","access_level":"closed","relation":"source_file","file_size":15060566,"checksum":"421672f68d563b029869c5cf1713f919","content_type":"application/zip","creator":"dernst","file_id":"6207","file_name":"2017_thesis_Hahn_source.zip"}],"ec_funded":1,"author":[{"id":"357A6A66-F248-11E8-B48F-1D18A9856A87","last_name":"Hahn","first_name":"David","full_name":"Hahn, David"}],"oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"type":"dissertation","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1},{"publist_id":"7970","publication_identifier":{"eisbn":["9781498711425"]},"publication_status":"published","scopus_import":"1","article_processing_charge":"No","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>.","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.","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>","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>","ista":"Edelsbrunner H, Koehl P. 2017.Computational topology for structural molecular biology. In: Handbook of Discrete and Computational Geometry, Third Edition. , 1709–1735.","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.","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>."},"department":[{"_id":"HeEd"}],"date_created":"2018-12-11T11:44:32Z","date_updated":"2023-10-16T11:15:22Z","date_published":"2017-11-09T00:00:00Z","page":"1709 - 1735","language":[{"iso":"eng"}],"quality_controlled":"1","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"}],"editor":[{"last_name":"Toth","first_name":"Csaba","full_name":"Toth, Csaba"},{"last_name":"O'Rourke","first_name":"Joseph","full_name":"O'Rourke, Joseph"},{"last_name":"Goodman","full_name":"Goodman, Jacob","first_name":"Jacob"}],"oa_version":"None","doi":"10.1201/9781315119601","_id":"84","year":"2017","publisher":"Taylor & Francis","publication":"Handbook of Discrete and Computational Geometry, Third Edition","title":"Computational topology for structural molecular biology","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"book_chapter","day":"09","status":"public","series_title":"Handbook of Discrete and Computational Geometry","author":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","first_name":"Herbert","full_name":"Edelsbrunner, Herbert"},{"full_name":"Koehl, Patrice","first_name":"Patrice","last_name":"Koehl"}],"month":"11"},{"publist_id":"6808","project":[{"name":"Towards Spin qubits and Majorana fermions in Germanium selfassembled hut-wires","call_identifier":"FP7","grant_number":"335497","_id":"25517E86-B435-11E9-9278-68D0E5697425"}],"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>.","short":"L. Vukušić, J. Kukucka, H. Watzinger, G. Katsaros, Nano Letters 17 (2017) 5706–5710.","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>","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."},"related_material":{"record":[{"relation":"popular_science","id":"7977"},{"relation":"dissertation_contains","id":"69","status":"public"},{"id":"7996","status":"public","relation":"dissertation_contains"}]},"scopus_import":"1","external_id":{"isi":["000411043500078"]},"department":[{"_id":"GeKa"}],"acknowledged_ssus":[{"_id":"M-Shop"}],"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."}],"has_accepted_license":"1","intvolume":"        17","oa_version":"Published Version","publisher":"American Chemical Society","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","type":"journal_article","issue":"9","oa":1,"file":[{"file_id":"4951","file_name":"IST-2017-865-v1+1_acs.nanolett.7b02627.pdf","checksum":"761371a0129b2aa442424b9561450ece","content_type":"application/pdf","file_size":2449546,"relation":"main_file","date_created":"2018-12-12T10:12:33Z","access_level":"open_access","date_updated":"2020-07-14T12:48:13Z","creator":"system"}],"ec_funded":1,"author":[{"full_name":"Vukusic, Lada","first_name":"Lada","last_name":"Vukusic","orcid":"0000-0003-2424-8636","id":"31E9F056-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kukucka, Josip","first_name":"Josip","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","last_name":"Kukucka"},{"first_name":"Hannes","full_name":"Watzinger, Hannes","last_name":"Watzinger","id":"35DF8E50-F248-11E8-B48F-1D18A9856A87"},{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","last_name":"Katsaros","orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios","first_name":"Georgios"}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["539"],"pubrep_id":"865","publication_identifier":{"issn":["15306984"]},"publication_status":"published","isi":1,"article_processing_charge":"No","date_updated":"2023-09-26T15:50:22Z","date_created":"2018-12-11T11:48:47Z","page":"5706 - 5710","date_published":"2017-08-10T00:00:00Z","language":[{"iso":"eng"}],"quality_controlled":"1","doi":"10.1021/acs.nanolett.7b02627","publication":"Nano Letters","_id":"840","year":"2017","file_date_updated":"2020-07-14T12:48:13Z","title":"Fast hole tunneling times in germanium hut wires probed by single-shot reflectometry","day":"10","volume":17,"status":"public","month":"08"},{"publisher":"Wiley-Blackwell","type":"journal_article","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"2","oa":1,"oa_version":"Preprint","author":[{"first_name":"Abraham","full_name":"Martin Del Campo Sanchez, Abraham","last_name":"Martin Del Campo Sanchez"},{"first_name":"Sarah A","full_name":"Cepeda Humerez, Sarah A","id":"3DEE19A4-F248-11E8-B48F-1D18A9856A87","last_name":"Cepeda Humerez"},{"full_name":"Uhler, Caroline","first_name":"Caroline","last_name":"Uhler","orcid":"0000-0002-7008-0216","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87"}],"citation":{"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.","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>.","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.","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>","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.","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>."},"scopus_import":"1","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"6473"}]},"publist_id":"5060","abstract":[{"lang":"eng","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."}],"intvolume":"        44","external_id":{"isi":["000400985000001"],"arxiv":["1410.1242"]},"department":[{"_id":"GaTk"}],"publication":"Scandinavian Journal of Statistics","_id":"2016","year":"2017","title":"Exact goodness-of-fit testing for the Ising model","doi":"10.1111/sjos.12251","month":"06","day":"01","volume":44,"main_file_link":[{"url":"http://arxiv.org/abs/1410.1242","open_access":"1"}],"status":"public","publication_status":"published","isi":1,"article_processing_charge":"No","publication_identifier":{"issn":["03036898"]},"language":[{"iso":"eng"}],"arxiv":1,"quality_controlled":"1","date_updated":"2023-09-19T15:13:27Z","date_created":"2018-12-11T11:55:13Z","page":"285 - 306","date_published":"2017-06-01T00:00:00Z"},{"oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"type":"dissertation","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"file":[{"creator":"system","date_updated":"2020-07-14T12:45:24Z","relation":"main_file","access_level":"open_access","date_created":"2018-12-12T10:08:48Z","file_size":18569590,"checksum":"33cfb59674e91f82e3738396d3fb3776","content_type":"application/pdf","file_name":"IST-2018-916-v1+3_2017_Pleska_Maros_Thesis.pdf","file_id":"4710"},{"creator":"dernst","access_level":"closed","date_updated":"2020-07-14T12:45:24Z","date_created":"2019-04-05T08:33:14Z","relation":"source_file","file_size":2801649,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"dcc239968decb233e7f98cf1083d8c26","file_name":"2017_Pleska_Maros_Thesis.docx","file_id":"6204"}],"author":[{"orcid":"0000-0001-7460-7479","id":"4569785E-F248-11E8-B48F-1D18A9856A87","last_name":"Pleska","first_name":"Maros","full_name":"Pleska, Maros"}],"publist_id":"7711","project":[{"_id":"251D65D8-B435-11E9-9278-68D0E5697425","name":"Effects of Stochasticity on the Function of Restriction-Modi cation Systems at the Single-Cell Level (DOC Fellowship)","grant_number":"24210"}],"citation":{"short":"M. Pleska, Biology of Restriction-Modification Systems at the Single-Cell and Population Level, Institute of Science and Technology Austria, 2017.","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>.","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>","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>","ista":"Pleska M. 2017. Biology of restriction-modification systems at the single-cell and population level. Institute of Science and Technology Austria.","ieee":"M. Pleska, “Biology of restriction-modification systems at the single-cell and population level,” Institute of Science and Technology Austria, 2017.","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>."},"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","id":"1243","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"561","status":"public"},{"status":"public","id":"457","relation":"part_of_dissertation"}]},"department":[{"_id":"CaGu"}],"has_accepted_license":"1","abstract":[{"lang":"eng","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."}],"doi":"10.15479/AT:ISTA:th_916","year":"2017","_id":"202","file_date_updated":"2020-07-14T12:45:24Z","degree_awarded":"PhD","title":"Biology of restriction-modification systems at the single-cell and population level","day":"01","status":"public","month":"10","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["576","579"],"pubrep_id":"916","publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","article_processing_charge":"No","supervisor":[{"orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","full_name":"Guet, Calin C","first_name":"Calin C"}],"date_created":"2018-12-11T11:45:10Z","date_updated":"2023-09-15T12:04:56Z","page":"126","date_published":"2017-10-01T00:00:00Z","language":[{"iso":"eng"}]},{"month":"04","status":"public","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1703.01714"}],"volume":29,"day":"01","title":"Hydrodynamic turbulence in quasi Keplerian rotating flows","publication":"Physics of Fluids","year":"2017","_id":"662","doi":"10.1063/1.4981525","quality_controlled":"1","language":[{"iso":"eng"}],"date_published":"2017-04-01T00:00:00Z","date_created":"2018-12-11T11:47:47Z","date_updated":"2021-01-12T08:08:15Z","article_number":"044107","publication_status":"published","publication_identifier":{"issn":["10706631"]},"author":[{"last_name":"Shi","first_name":"Liang","full_name":"Shi, Liang"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","last_name":"Hof","first_name":"Björn","full_name":"Hof, Björn"},{"last_name":"Rampp","first_name":"Markus","full_name":"Rampp, Markus"},{"last_name":"Avila","full_name":"Avila, Marc","first_name":"Marc"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","type":"journal_article","issue":"4","oa":1,"publisher":"American Institute of Physics","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"We report a direct-numerical-simulation study of the Taylor-Couette flow in the quasi-Keplerian regime at shear Reynolds numbers up to (105). Quasi-Keplerian rotating flow has been investigated for decades as a simplified model system to study the origin of turbulence in accretion disks that is not fully understood. The flow in this study is axially periodic and thus the experimental end-wall effects on the stability of the flow are avoided. Using optimal linear perturbations as initial conditions, our simulations find no sustained turbulence: the strong initial perturbations distort the velocity profile and trigger turbulence that eventually decays."}],"intvolume":"        29","department":[{"_id":"BjHo"}],"citation":{"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.","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.","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>","apa":"Shi, L., Hof, B., Rampp, M., &#38; Avila, M. (2017). Hydrodynamic turbulence in quasi Keplerian rotating flows. <i>Physics of Fluids</i>. American Institute of Physics. <a href=\"https://doi.org/10.1063/1.4981525\">https://doi.org/10.1063/1.4981525</a>","chicago":"Shi, Liang, Björn Hof, Markus Rampp, and Marc Avila. “Hydrodynamic Turbulence in Quasi Keplerian Rotating Flows.” <i>Physics of Fluids</i>. American Institute of Physics, 2017. <a href=\"https://doi.org/10.1063/1.4981525\">https://doi.org/10.1063/1.4981525</a>.","short":"L. Shi, B. Hof, M. Rampp, M. Avila, Physics of Fluids 29 (2017)."},"scopus_import":1,"project":[{"grant_number":"SFB 963  TP A8","name":"Astrophysical instability of currents and turbulences","_id":"2511D90C-B435-11E9-9278-68D0E5697425"}],"publist_id":"7072"},{"_id":"663","year":"2017","publication":"Proceedings of the 20th International Conference on Hybrid Systems","title":"Safety verification of nonlinear hybrid systems based on invariant clusters","file_date_updated":"2020-07-14T12:47:34Z","conference":{"location":"Pittsburgh, PA, United States","name":"HSCC: Hybrid Systems Computation and Control ","end_date":"2017-04-20","start_date":"2017-04-18"},"doi":"10.1145/3049797.3049814","month":"04","day":"01","status":"public","publication_status":"published","ddc":["000"],"publication_identifier":{"isbn":["978-145034590-3"]},"pubrep_id":"817","language":[{"iso":"eng"}],"quality_controlled":"1","date_created":"2018-12-11T11:47:47Z","date_updated":"2021-01-12T08:08:17Z","date_published":"2017-04-01T00:00:00Z","page":"163 - 172","publisher":"ACM","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","oa_version":"Submitted Version","author":[{"orcid":"0000-0002-3066-6941","id":"3BDE25AA-F248-11E8-B48F-1D18A9856A87","last_name":"Kong","first_name":"Hui","full_name":"Kong, Hui"},{"first_name":"Sergiy","full_name":"Bogomolov, Sergiy","orcid":"0000-0002-0686-0365","last_name":"Bogomolov"},{"first_name":"Christian","full_name":"Schilling, Christian","last_name":"Schilling"},{"last_name":"Jiang","first_name":"Yu","full_name":"Jiang, Yu"},{"last_name":"Henzinger","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","first_name":"Thomas A"}],"file":[{"content_type":"application/pdf","checksum":"b7667434cbf5b5f0ade3bea1dbe5bf63","file_size":1650530,"access_level":"open_access","date_updated":"2020-07-14T12:47:34Z","relation":"main_file","date_created":"2018-12-12T10:11:20Z","creator":"system","file_id":"4873","file_name":"IST-2017-817-v1+1_p163-kong.pdf"}],"scopus_import":1,"citation":{"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>","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>","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>.","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.","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>.","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."},"publist_id":"7067","has_accepted_license":"1","abstract":[{"text":"In this paper, we propose an approach to automatically compute invariant clusters for nonlinear semialgebraic hybrid systems. An invariant cluster for an ordinary differential equation (ODE) is a multivariate polynomial invariant g(u→, x→) = 0, parametric in u→, which can yield an infinite number of concrete invariants by assigning different values to u→ so that every trajectory of the system can be overapproximated precisely by the intersection of a group of concrete invariants. For semialgebraic systems, which involve ODEs with multivariate polynomial right-hand sides, given a template multivariate polynomial g(u→, x→), an invariant cluster can be obtained by first computing the remainder of the Lie derivative of g(u→, x→) divided by g(u→, x→) and then solving the system of polynomial equations obtained from the coefficients of the remainder. Based on invariant clusters and sum-of-squares (SOS) programming, we present a new method for the safety verification of hybrid systems. Experiments on nonlinear benchmark systems from biology and control theory show that our approach is efficient. ","lang":"eng"}],"department":[{"_id":"ToHe"}]},{"date_published":"2017-04-18T00:00:00Z","page":"519 - 520","department":[{"_id":"MiSi"}],"date_updated":"2024-03-25T23:30:05Z","date_created":"2018-12-11T11:47:47Z","intvolume":"        46","quality_controlled":"1","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."}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["10747613"]},"publist_id":"7065","related_material":{"record":[{"id":"6947","status":"public","relation":"dissertation_contains"}]},"scopus_import":1,"citation":{"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>","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>","chicago":"Assen, Frank P, and Michael K Sixt. “The Dynamic Cytokine Niche.” <i>Immunity</i>. Cell Press, 2017. <a href=\"https://doi.org/10.1016/j.immuni.2017.04.006\">https://doi.org/10.1016/j.immuni.2017.04.006</a>.","short":"F.P. Assen, M.K. Sixt, Immunity 46 (2017) 519–520.","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>.","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.","ista":"Assen FP, Sixt MK. 2017. The dynamic cytokine niche. Immunity. 46(4), 519–520."},"publication_status":"published","status":"public","volume":46,"day":"18","author":[{"id":"3A8E7F24-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3470-6119","last_name":"Assen","full_name":"Assen, Frank P","first_name":"Frank P"},{"first_name":"Michael K","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt"}],"month":"04","oa_version":"None","doi":"10.1016/j.immuni.2017.04.006","issue":"4","title":"The dynamic cytokine niche","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","type":"journal_article","_id":"664","year":"2017","publisher":"Cell Press","publication":"Immunity"},{"scopus_import":1,"related_material":{"record":[{"relation":"popular_science","id":"5560","status":"public"}]},"citation":{"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>.","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.","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.","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>","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>","short":"T. Bergmiller, A.M. Andersson, K. Tomasek, E. Balleza, D. Kiviet, R. Hauschild, G. Tkačik, C.C. Guet, Science 356 (2017) 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>."},"project":[{"_id":"254E9036-B435-11E9-9278-68D0E5697425","grant_number":"P28844-B27","call_identifier":"FWF","name":"Biophysics of information processing in gene regulation"}],"publist_id":"7064","intvolume":"       356","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"}],"department":[{"_id":"CaGu"},{"_id":"GaTk"},{"_id":"Bio"}],"issue":"6335","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","publisher":"American Association for the Advancement of Science","oa_version":"None","author":[{"orcid":"0000-0001-5396-4346","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","last_name":"Bergmiller","full_name":"Bergmiller, Tobias","first_name":"Tobias"},{"full_name":"Andersson, Anna M","first_name":"Anna M","id":"2B8A40DA-F248-11E8-B48F-1D18A9856A87","last_name":"Andersson","orcid":"0000-0003-2912-6769"},{"id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","last_name":"Tomasek","orcid":"0000-0003-3768-877X","first_name":"Kathrin","full_name":"Tomasek, Kathrin"},{"first_name":"Enrique","full_name":"Balleza, Enrique","last_name":"Balleza"},{"last_name":"Kiviet","full_name":"Kiviet, Daniel","first_name":"Daniel"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","last_name":"Hauschild","first_name":"Robert","full_name":"Hauschild, Robert"},{"orcid":"0000-0002-6699-1455","last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper","first_name":"Gasper"},{"orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","full_name":"Guet, Calin C","first_name":"Calin C"}],"article_type":"original","article_processing_charge":"No","publication_status":"published","publication_identifier":{"issn":["00368075"]},"quality_controlled":"1","language":[{"iso":"eng"}],"date_published":"2017-04-21T00:00:00Z","page":"311 - 315","date_updated":"2024-02-21T13:49:00Z","date_created":"2018-12-11T11:47:48Z","title":"Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity","year":"2017","_id":"665","publication":"Science","doi":"10.1126/science.aaf4762","month":"04","status":"public","day":"21","volume":356},{"intvolume":"         4","has_accepted_license":"1","abstract":[{"lang":"eng","text":"Antibiotics elicit drastic changes in microbial gene expression, including the induction of stress response genes. While certain stress responses are known to “cross-protect” bacteria from other stressors, it is unclear whether cellular responses to antibiotics have a similar protective role. By measuring the genome-wide transcriptional response dynamics of Escherichia coli to four antibiotics, we found that trimethoprim induces a rapid acid stress response that protects bacteria from subsequent exposure to acid. Combining microfluidics with time-lapse imaging to monitor survival and acid stress response in single cells revealed that the noisy expression of the acid resistance operon gadBC correlates with single-cell survival. Cells with higher gadBC expression following trimethoprim maintain higher intracellular pH and survive the acid stress longer. The seemingly random single-cell survival under acid stress can therefore be predicted from gadBC expression and rationalized in terms of GadB/C molecular function. Overall, we provide a roadmap for identifying the molecular mechanisms of single-cell cross-protection between antibiotics and other stressors."}],"department":[{"_id":"ToBo"},{"_id":"GaTk"}],"scopus_import":1,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"818"}]},"citation":{"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>","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>","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.","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>.","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.","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."},"project":[{"_id":"25E83C2C-B435-11E9-9278-68D0E5697425","name":"Optimality principles in responses to antibiotics","call_identifier":"FP7","grant_number":"303507"},{"_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","name":"Revealing the mechanisms underlying drug interactions","call_identifier":"FWF","grant_number":"P27201-B22"},{"grant_number":"RGP0042/2013","name":"Revealing the fundamental limits of cell growth","_id":"25EB3A80-B435-11E9-9278-68D0E5697425"}],"publist_id":"7061","author":[{"id":"39B66846-F248-11E8-B48F-1D18A9856A87","last_name":"Mitosch","full_name":"Mitosch, Karin","first_name":"Karin"},{"full_name":"Rieckh, Georg","first_name":"Georg","last_name":"Rieckh","id":"34DA8BD6-F248-11E8-B48F-1D18A9856A87"},{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X","last_name":"Bollenbach","first_name":"Tobias","full_name":"Bollenbach, Tobias"}],"ec_funded":1,"file":[{"creator":"system","content_type":"application/pdf","checksum":"04ff20011c3d9a601c514aa999a5fe1a","file_size":2438660,"date_created":"2018-12-12T10:13:54Z","date_updated":"2020-07-14T12:47:35Z","access_level":"open_access","relation":"main_file","file_name":"IST-2017-901-v1+1_1-s2.0-S2405471217300868-main.pdf","file_id":"5041"}],"oa":1,"issue":"4","type":"journal_article","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Cell Press","oa_version":"Published Version","quality_controlled":"1","language":[{"iso":"eng"}],"date_published":"2017-04-26T00:00:00Z","page":"393 - 403","date_created":"2018-12-11T11:47:48Z","date_updated":"2023-09-07T12:00:25Z","article_processing_charge":"Yes (in subscription journal)","publication_status":"published","publication_identifier":{"issn":["24054712"]},"pubrep_id":"901","ddc":["576","610"],"tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"month":"04","status":"public","day":"26","volume":4,"title":"Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment","file_date_updated":"2020-07-14T12:47:35Z","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","year":"2017","_id":"666","publication":"Cell Systems","doi":"10.1016/j.cels.2017.03.001"},{"oa_version":"None","doi":"10.1126/scitranslmed.aan2786","_id":"667","year":"2017","publisher":"American Association for the Advancement of Science","publication":"Science Translational Medicine","issue":"387","title":"The antisocial side of antibiotics","type":"journal_article","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","volume":9,"day":"26","status":"public","author":[{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","orcid":"0000-0002-7673-7178","first_name":"Gaia","full_name":"Novarino, Gaia"}],"month":"04","publist_id":"7060","publication_identifier":{"issn":["19466234"]},"publication_status":"published","article_number":"2786","scopus_import":1,"citation":{"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>.","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.","short":"G. Novarino, Science Translational Medicine 9 (2017).","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>.","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>","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>"},"date_updated":"2021-01-12T08:08:30Z","date_created":"2018-12-11T11:47:48Z","department":[{"_id":"GaNo"}],"date_published":"2017-04-26T00:00:00Z","language":[{"iso":"eng"}],"quality_controlled":"1","intvolume":"         9","abstract":[{"lang":"eng","text":"Perinatal exposure to penicillin may result in longlasting gut and behavioral changes."}]},{"oa":1,"issue":"17","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"American Society for Biochemistry and Molecular Biology","oa_version":"Published Version","author":[{"last_name":"Horsthemke","full_name":"Horsthemke, Markus","first_name":"Markus"},{"full_name":"Bachg, Anne","first_name":"Anne","last_name":"Bachg"},{"full_name":"Groll, Katharina","first_name":"Katharina","last_name":"Groll"},{"full_name":"Moyzio, Sven","first_name":"Sven","last_name":"Moyzio"},{"last_name":"Müther","full_name":"Müther, Barbara","first_name":"Barbara"},{"last_name":"Hemkemeyer","first_name":"Sandra","full_name":"Hemkemeyer, Sandra"},{"last_name":"Wedlich Söldner","first_name":"Roland","full_name":"Wedlich Söldner, Roland"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","last_name":"Sixt","full_name":"Sixt, Michael K","first_name":"Michael K"},{"first_name":"Sebastian","full_name":"Tacke, Sebastian","last_name":"Tacke"},{"last_name":"Bähler","first_name":"Martin","full_name":"Bähler, Martin"},{"last_name":"Hanley","full_name":"Hanley, Peter","first_name":"Peter"}],"file":[{"creator":"dernst","content_type":"application/pdf","checksum":"d488162874326a4bb056065fa549dc4a","date_updated":"2020-07-14T12:47:37Z","access_level":"open_access","relation":"main_file","date_created":"2019-10-24T15:25:42Z","file_size":5647880,"file_name":"2017_JBC_Horsthemke.pdf","file_id":"6971"}],"article_type":"original","scopus_import":1,"citation":{"apa":"Horsthemke, M., Bachg, A., Groll, K., Moyzio, S., Müther, B., Hemkemeyer, S., … Hanley, P. (2017). Multiple roles of filopodial dynamics in particle capture and phagocytosis and phenotypes of Cdc42 and Myo10 deletion. <i>Journal of Biological Chemistry</i>. American Society for Biochemistry and Molecular Biology. <a href=\"https://doi.org/10.1074/jbc.M116.766923\">https://doi.org/10.1074/jbc.M116.766923</a>","ama":"Horsthemke M, Bachg A, Groll K, et al. Multiple roles of filopodial dynamics in particle capture and phagocytosis and phenotypes of Cdc42 and Myo10 deletion. <i>Journal of Biological Chemistry</i>. 2017;292(17):7258-7273. doi:<a href=\"https://doi.org/10.1074/jbc.M116.766923\">10.1074/jbc.M116.766923</a>","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>.","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.","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.","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>.","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."},"publist_id":"7059","intvolume":"       292","has_accepted_license":"1","abstract":[{"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.","lang":"eng"}],"department":[{"_id":"MiSi"}],"title":"Multiple roles of filopodial dynamics in particle capture and phagocytosis and phenotypes of Cdc42 and Myo10 deletion","file_date_updated":"2020-07-14T12:47:37Z","year":"2017","_id":"668","publication":"Journal of Biological Chemistry","doi":"10.1074/jbc.M116.766923","month":"04","status":"public","volume":292,"day":"28","publication_status":"published","publication_identifier":{"issn":["00219258"]},"ddc":["570"],"quality_controlled":"1","language":[{"iso":"eng"}],"date_published":"2017-04-28T00:00:00Z","page":"7258 - 7273","date_updated":"2021-01-12T08:08:34Z","date_created":"2018-12-11T11:47:49Z"},{"publication_identifier":{"issn":["00320889"]},"ddc":["580"],"article_processing_charge":"No","publication_status":"published","page":"223 - 240","date_published":"2017-05-01T00:00:00Z","date_created":"2018-12-11T11:47:49Z","date_updated":"2021-01-12T08:08:35Z","quality_controlled":"1","language":[{"iso":"eng"}],"doi":"10.1104/pp.16.01282","pmid":1,"file_date_updated":"2020-07-14T12:47:37Z","title":"EXO70C2 is a key regulatory factor for optimal tip growth of pollen","publication":"Plant Physiology","_id":"669","year":"2017","status":"public","day":"01","volume":174,"month":"05","publist_id":"7058","citation":{"short":"L. Synek, N. Vukašinović, I. Kulich, M. Hála, K. Aldorfová, M. Fendrych, V. Žárský, Plant Physiology 174 (2017) 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>.","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>","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>","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.","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.","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>."},"scopus_import":1,"external_id":{"pmid":["28356503"]},"department":[{"_id":"JiFr"}],"has_accepted_license":"1","abstract":[{"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. ","lang":"eng"}],"intvolume":"       174","oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","oa":1,"issue":"1","publisher":"American Society of Plant Biologists","article_type":"original","file":[{"content_type":"application/pdf","checksum":"97155acc6aa5f0d0a78e0589a932fe02","date_created":"2019-11-18T16:16:18Z","relation":"main_file","access_level":"open_access","date_updated":"2020-07-14T12:47:37Z","file_size":2176903,"creator":"dernst","file_id":"7041","file_name":"2017_PlantPhysio_Synek.pdf"}],"author":[{"full_name":"Synek, Lukáš","first_name":"Lukáš","last_name":"Synek"},{"first_name":"Nemanja","full_name":"Vukašinović, Nemanja","last_name":"Vukašinović"},{"last_name":"Kulich","full_name":"Kulich, Ivan","first_name":"Ivan"},{"first_name":"Michal","full_name":"Hála, Michal","last_name":"Hála"},{"full_name":"Aldorfová, Klára","first_name":"Klára","last_name":"Aldorfová"},{"first_name":"Matyas","full_name":"Fendrych, Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87","last_name":"Fendrych","orcid":"0000-0002-9767-8699"},{"last_name":"Žárský","full_name":"Žárský, Viktor","first_name":"Viktor"}]},{"month":"05","status":"public","main_file_link":[{"open_access":"1","url":"https://hal.inria.fr/hal-01647113/file/eg_2017_schreck_paper_tearing.pdf"}],"day":"01","volume":36,"title":"Interactive paper tearing","year":"2017","_id":"670","publication":"Computer Graphics Forum","doi":"10.1111/cgf.13110","quality_controlled":"1","language":[{"iso":"eng"}],"date_published":"2017-05-01T00:00:00Z","page":"95 - 106","date_updated":"2021-01-12T08:08:37Z","date_created":"2018-12-11T11:47:49Z","article_processing_charge":"No","publication_status":"published","publication_identifier":{"issn":["01677055"]},"ddc":["000"],"author":[{"id":"2B14B676-F248-11E8-B48F-1D18A9856A87","last_name":"Schreck","full_name":"Schreck, Camille","first_name":"Camille"},{"first_name":"Damien","full_name":"Rohmer, Damien","last_name":"Rohmer"},{"last_name":"Hahmann","full_name":"Hahmann, Stefanie","first_name":"Stefanie"}],"article_type":"original","oa":1,"issue":"2","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Wiley","oa_version":"Published Version","intvolume":"        36","abstract":[{"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.","lang":"eng"}],"department":[{"_id":"ChWo"}],"scopus_import":1,"citation":{"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.","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>.","ista":"Schreck C, Rohmer D, Hahmann S. 2017. Interactive paper tearing. Computer Graphics Forum. 36(2), 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>","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>","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>.","short":"C. Schreck, D. Rohmer, S. Hahmann, Computer Graphics Forum 36 (2017) 95–106."},"project":[{"call_identifier":"FWF","grant_number":"P 24352-N23","name":"Deep Pictures: Creating Visual and Haptic Vector Images","_id":"25357BD2-B435-11E9-9278-68D0E5697425"}],"publist_id":"7056"}]