[{"date_created":"2019-02-14T12:50:50Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1709.06372"}],"year":"2018","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-07-28T14:02:09Z","volume":839,"date_published":"2018-03-25T00:00:00Z","project":[{"_id":"25152F3A-B435-11E9-9278-68D0E5697425","grant_number":"306589","call_identifier":"FP7","name":"Decoding the complexity of turbulence at its origin"}],"doi":"10.1017/jfm.2017.923","ec_funded":1,"abstract":[{"lang":"eng","text":"In pipes, turbulence sets in despite the linear stability of the laminar Hagen–Poiseuille flow. The Reynolds number ( ) for which turbulence first appears in a given experiment – the ‘natural transition point’ – depends on imperfections of the set-up, or, more precisely, on the magnitude of finite amplitude perturbations. At onset, turbulence typically only occupies a certain fraction of the flow, and this fraction equally is found to differ from experiment to experiment. Despite these findings, Reynolds proposed that after sufficiently long times, flows may settle to steady conditions: below a critical velocity, flows should (regardless of initial conditions) always return to laminar, while above this velocity, eddying motion should persist. As will be shown, even in pipes several thousand diameters long, the spatio-temporal intermittent flow patterns observed at the end of the pipe strongly depend on the initial conditions, and there is no indication that different flow patterns would eventually settle to a (statistical) steady state. Exploiting the fact that turbulent puffs do not age (i.e. they are memoryless), we continuously recreate the puff sequence exiting the pipe at the pipe entrance, and in doing so introduce periodic boundary conditions for the puff pattern. This procedure allows us to study the evolution of the flow patterns for arbitrary long times, and we find that after times in excess of advective time units, indeed a statistical steady state is reached. Although the resulting flows remain spatio-temporally intermittent, puff splitting and decay rates eventually reach a balance, so that the turbulent fraction fluctuates around a well-defined level which only depends on . In accordance with Reynolds’ proposition, we find that at lower (here 2020), flows eventually always resume to laminar, while for higher ( ), turbulence persists. The critical point for pipe flow hence falls in the interval of $2020 , which is in very good agreement with the recently proposed value of . The latter estimate was based on single-puff statistics and entirely neglected puff interactions. Unlike in typical contact processes where such interactions strongly affect the percolation threshold, in pipe flow, the critical point is only marginally influenced. Interactions, on the other hand, are responsible for the approach to the statistical steady state. As shown, they strongly affect the resulting flow patterns, where they cause ‘puff clustering’, and these regions of large puff densities are observed to travel across the puff pattern in a wave-like fashion."}],"department":[{"_id":"BjHo"}],"external_id":{"arxiv":["1709.06372"],"isi":["000437858300003"]},"publication_status":"published","intvolume":"       839","publication":"Journal of Fluid Mechanics","publication_identifier":{"eissn":["1469-7645"],"issn":["0022-1120"]},"publisher":"Cambridge University Press","quality_controlled":"1","month":"03","OA_place":"repository","status":"public","page":"76-94","day":"25","type":"journal_article","author":[{"last_name":"Vasudevan","full_name":"Vasudevan, Mukund","id":"3C5A959A-F248-11E8-B48F-1D18A9856A87","first_name":"Mukund"},{"first_name":"Björn","last_name":"Hof","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"oa":1,"_id":"5996","corr_author":"1","article_processing_charge":"No","article_type":"original","isi":1,"OA_type":"green","scopus_import":"1","oa_version":"Preprint","acknowledgement":" We  also  thank  Philipp  Maier  and  the  IST  Austria  workshop  for  their dedicated technical support","acknowledged_ssus":[{"_id":"M-Shop"}],"title":"The critical point of the transition to turbulence in pipe flow","arxiv":1,"citation":{"mla":"Vasudevan, Mukund, and Björn Hof. “The Critical Point of the Transition to Turbulence in Pipe Flow.” <i>Journal of Fluid Mechanics</i>, vol. 839, Cambridge University Press, 2018, pp. 76–94, doi:<a href=\"https://doi.org/10.1017/jfm.2017.923\">10.1017/jfm.2017.923</a>.","chicago":"Vasudevan, Mukund, and Björn Hof. “The Critical Point of the Transition to Turbulence in Pipe Flow.” <i>Journal of Fluid Mechanics</i>. Cambridge University Press, 2018. <a href=\"https://doi.org/10.1017/jfm.2017.923\">https://doi.org/10.1017/jfm.2017.923</a>.","apa":"Vasudevan, M., &#38; Hof, B. (2018). The critical point of the transition to turbulence in pipe flow. <i>Journal of Fluid Mechanics</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/jfm.2017.923\">https://doi.org/10.1017/jfm.2017.923</a>","ista":"Vasudevan M, Hof B. 2018. The critical point of the transition to turbulence in pipe flow. Journal of Fluid Mechanics. 839, 76–94.","ieee":"M. Vasudevan and B. Hof, “The critical point of the transition to turbulence in pipe flow,” <i>Journal of Fluid Mechanics</i>, vol. 839. Cambridge University Press, pp. 76–94, 2018.","ama":"Vasudevan M, Hof B. The critical point of the transition to turbulence in pipe flow. <i>Journal of Fluid Mechanics</i>. 2018;839:76-94. doi:<a href=\"https://doi.org/10.1017/jfm.2017.923\">10.1017/jfm.2017.923</a>","short":"M. Vasudevan, B. Hof, Journal of Fluid Mechanics 839 (2018) 76–94."}},{"article_processing_charge":"No","corr_author":"1","_id":"197","language":[{"iso":"eng"}],"oa":1,"author":[{"first_name":"Alexander","full_name":"Kolesnikov, Alexander","last_name":"Kolesnikov","id":"2D157DB6-F248-11E8-B48F-1D18A9856A87"}],"supervisor":[{"first_name":"Christoph","last_name":"Lampert","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"type":"dissertation","day":"25","page":"113","status":"public","OA_place":"publisher","month":"05","publication_identifier":{"issn":["2663-337X"]},"publisher":"Institute of Science and Technology Austria","citation":{"short":"A. Kolesnikov, Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images, Institute of Science and Technology Austria, 2018.","ieee":"A. Kolesnikov, “Weakly-supervised segmentation and unsupervised modeling of natural images,” Institute of Science and Technology Austria, 2018.","ama":"Kolesnikov A. Weakly-supervised segmentation and unsupervised modeling of natural images. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_1021\">10.15479/AT:ISTA:th_1021</a>","apa":"Kolesnikov, A. (2018). <i>Weakly-supervised segmentation and unsupervised modeling of natural images</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_1021\">https://doi.org/10.15479/AT:ISTA:th_1021</a>","ista":"Kolesnikov A. 2018. Weakly-supervised segmentation and unsupervised modeling of natural images. Institute of Science and Technology Austria.","mla":"Kolesnikov, Alexander. <i>Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_1021\">10.15479/AT:ISTA:th_1021</a>.","chicago":"Kolesnikov, Alexander. “Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:th_1021\">https://doi.org/10.15479/AT:ISTA:th_1021</a>."},"pubrep_id":"1021","has_accepted_license":"1","title":"Weakly-supervised segmentation and unsupervised modeling of natural images","acknowledgement":"I also gratefully acknowledge the support of NVIDIA Corporation with the donation of the GPUs used for this research.","oa_version":"Published Version","ddc":["004"],"project":[{"call_identifier":"FP7","_id":"2532554C-B435-11E9-9278-68D0E5697425","grant_number":"308036","name":"Lifelong Learning of Visual Scene Understanding"}],"date_published":"2018-05-25T00:00:00Z","date_updated":"2026-07-29T13:22:05Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","year":"2018","publist_id":"7718","date_created":"2018-12-11T11:45:09Z","file_date_updated":"2020-07-14T12:45:22Z","file":[{"checksum":"bc678e02468d8ebc39dc7267dfb0a1c4","file_id":"5113","relation":"main_file","date_created":"2018-12-12T10:14:57Z","content_type":"application/pdf","creator":"system","access_level":"open_access","file_name":"IST-2018-1021-v1+1_thesis-unsigned-pdfa.pdf","file_size":12918758,"date_updated":"2020-07-14T12:45:22Z"},{"creator":"dernst","date_updated":"2020-07-14T12:45:22Z","file_name":"2018_Thesis_Kolesnikov_source.zip","file_size":55973760,"access_level":"closed","relation":"source_file","file_id":"6225","checksum":"bc66973b086da5a043f1162dcfb1fde4","content_type":"application/zip","date_created":"2019-04-05T09:34:49Z"}],"publication_status":"published","doi_confirm":"1","department":[{"_id":"ChLa"},{"_id":"GradSch"}],"abstract":[{"lang":"eng","text":"Modern computer vision systems heavily rely on statistical machine learning models, which typically require large amounts of labeled data to be learned reliably. Moreover, very recently computer vision research widely adopted techniques for representation learning, which further increase the demand for labeled data. However, for many important practical problems there is relatively small amount of labeled data available, so it is problematic to leverage full potential of the representation learning methods. One way to overcome this obstacle is to invest substantial resources into producing large labelled datasets. Unfortunately, this can be prohibitively expensive in practice. In this thesis we focus on the alternative way of tackling the aforementioned issue. We concentrate on methods, which make use of weakly-labeled or even unlabeled data. Specifically, the first half of the thesis is dedicated to the semantic image segmentation task. We develop a technique, which achieves competitive segmentation performance and only requires annotations in a form of global image-level labels instead of dense segmentation masks. Subsequently, we present a new methodology, which further improves segmentation performance by leveraging tiny additional feedback from a human annotator. By using our methods practitioners can greatly reduce the amount of data annotation effort, which is required to learn modern image segmentation models. In the second half of the thesis we focus on methods for learning from unlabeled visual data. We study a family of autoregressive models for modeling structure of natural images and discuss potential applications of these models. Moreover, we conduct in-depth study of one of these applications, where we develop the state-of-the-art model for the probabilistic image colorization task."}],"ec_funded":1,"alternative_title":["ISTA Thesis"],"doi":"10.15479/AT:ISTA:th_1021","degree_awarded":"PhD"},{"oa_version":"Published Version","title":"Multiple covers with balls","pubrep_id":"1026","has_accepted_license":"1","citation":{"ista":"Iglesias Ham M. 2018. Multiple covers with balls. Institute of Science and Technology Austria.","apa":"Iglesias Ham, M. (2018). <i>Multiple covers with balls</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_1026\">https://doi.org/10.15479/AT:ISTA:th_1026</a>","ama":"Iglesias Ham M. Multiple covers with balls. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_1026\">10.15479/AT:ISTA:th_1026</a>","ieee":"M. Iglesias Ham, “Multiple covers with balls,” Institute of Science and Technology Austria, 2018.","short":"M. Iglesias Ham, Multiple Covers with Balls, Institute of Science and Technology Austria, 2018.","chicago":"Iglesias Ham, Mabel. “Multiple Covers with Balls.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:th_1026\">https://doi.org/10.15479/AT:ISTA:th_1026</a>.","mla":"Iglesias Ham, Mabel. <i>Multiple Covers with Balls</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_1026\">10.15479/AT:ISTA:th_1026</a>."},"publisher":"Institute of Science and Technology Austria","publication_identifier":{"issn":["2663-337X"]},"month":"06","page":"171","status":"public","OA_place":"publisher","type":"dissertation","day":"11","author":[{"id":"41B58C0C-F248-11E8-B48F-1D18A9856A87","last_name":"Iglesias Ham","full_name":"Iglesias Ham, Mabel","first_name":"Mabel"}],"supervisor":[{"first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert"}],"language":[{"iso":"eng"}],"oa":1,"corr_author":"1","_id":"201","article_processing_charge":"No","alternative_title":["ISTA Thesis"],"degree_awarded":"PhD","doi":"10.15479/AT:ISTA:th_1026","abstract":[{"lang":"eng","text":"We describe arrangements of three-dimensional spheres from a geometrical and topological point of view. Real data (fitting this setup) often consist of soft spheres which show certain degree of deformation while strongly packing against each other. In this context, we answer the following questions: If we model a soft packing of spheres by hard spheres that are allowed to overlap, can we measure the volume in the overlapped areas? Can we be more specific about the overlap volume, i.e. quantify how much volume is there covered exactly twice, three times, or k times? What would be a good optimization criteria that rule the arrangement of soft spheres while making a good use of the available space? Fixing a particular criterion, what would be the optimal sphere configuration? The first result of this thesis are short formulas for the computation of volumes covered by at least k of the balls. The formulas exploit information contained in the order-k Voronoi diagrams and its closely related Level-k complex. The used complexes lead to a natural generalization into poset diagrams, a theoretical formalism that contains the order-k and degree-k diagrams as special cases. In parallel, we define different criteria to determine what could be considered an optimal arrangement from a geometrical point of view. Fixing a criterion, we find optimal soft packing configurations in 2D and 3D where the ball centers lie on a lattice. As a last step, we use tools from computational topology on real physical data, to show the potentials of higher-order diagrams in the description of melting crystals. The results of the experiments leaves us with an open window to apply the theories developed in this thesis in real applications."}],"department":[{"_id":"HeEd"},{"_id":"GradSch"}],"doi_confirm":"1","publication_status":"published","file":[{"file_name":"IST-2018-1025-v2+5_ist-thesis-iglesias-11June2018(1).zip","date_updated":"2020-07-14T12:45:24Z","file_size":11827713,"access_level":"closed","creator":"kschuh","content_type":"application/zip","date_created":"2019-02-05T07:43:31Z","relation":"source_file","file_id":"5918","checksum":"dd699303623e96d1478a6ae07210dd05"},{"date_created":"2019-02-05T07:43:45Z","content_type":"application/pdf","checksum":"ba163849a190d2b41d66fef0e4983294","file_id":"5919","relation":"main_file","access_level":"open_access","file_name":"IST-2018-1025-v2+4_ThesisIglesiasFinal11June2018.pdf","date_updated":"2020-07-14T12:45:24Z","file_size":4783846,"creator":"kschuh"}],"file_date_updated":"2020-07-14T12:45:24Z","date_created":"2018-12-11T11:45:10Z","year":"2018","publist_id":"7712","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2026-07-29T13:24:38Z","ddc":["514","516"],"date_published":"2018-06-11T00:00:00Z"},{"article_processing_charge":"No","corr_author":"1","_id":"68","language":[{"iso":"eng"}],"oa":1,"supervisor":[{"full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph"}],"author":[{"id":"37099E9C-F248-11E8-B48F-1D18A9856A87","last_name":"Zimin","full_name":"Zimin, Alexander","first_name":"Alexander"}],"day":"01","type":"dissertation","OA_place":"publisher","status":"public","page":"92","month":"09","publication_identifier":{"issn":["2663-337X"]},"publisher":"Institute of Science and Technology Austria","citation":{"apa":"Zimin, A. (2018). <i>Learning from dependent data</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:TH1048\">https://doi.org/10.15479/AT:ISTA:TH1048</a>","ista":"Zimin A. 2018. Learning from dependent data. Institute of Science and Technology Austria.","ieee":"A. Zimin, “Learning from dependent data,” Institute of Science and Technology Austria, 2018.","ama":"Zimin A. Learning from dependent data. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:TH1048\">10.15479/AT:ISTA:TH1048</a>","short":"A. Zimin, Learning from Dependent Data, Institute of Science and Technology Austria, 2018.","chicago":"Zimin, Alexander. “Learning from Dependent Data.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:TH1048\">https://doi.org/10.15479/AT:ISTA:TH1048</a>.","mla":"Zimin, Alexander. <i>Learning from Dependent Data</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:TH1048\">10.15479/AT:ISTA:TH1048</a>."},"has_accepted_license":"1","pubrep_id":"1048","title":"Learning from dependent data","oa_version":"Published Version","date_published":"2018-09-01T00:00:00Z","ddc":["004","519"],"project":[{"name":"Lifelong Learning of Visual Scene Understanding","_id":"2532554C-B435-11E9-9278-68D0E5697425","grant_number":"308036","call_identifier":"FP7"}],"date_updated":"2026-07-29T13:31:12Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publist_id":"7986","year":"2018","date_created":"2018-12-11T11:44:27Z","file_date_updated":"2020-07-14T12:47:40Z","file":[{"date_created":"2019-04-09T07:32:47Z","content_type":"application/pdf","file_id":"6253","checksum":"e849dd40a915e4d6c5572b51b517f098","relation":"main_file","access_level":"open_access","file_size":1036137,"file_name":"2018_Thesis_Zimin.pdf","date_updated":"2020-07-14T12:47:40Z","creator":"dernst"},{"checksum":"da092153cec55c97461bd53c45c5d139","file_id":"6254","relation":"source_file","date_created":"2019-04-09T07:32:47Z","content_type":"application/zip","creator":"dernst","access_level":"closed","file_name":"2018_Thesis_Zimin_Source.zip","file_size":637490,"date_updated":"2020-07-14T12:47:40Z"}],"publication_status":"published","doi_confirm":"1","department":[{"_id":"ChLa"},{"_id":"GradSch"}],"abstract":[{"lang":"eng","text":"The most common assumption made in statistical learning theory is the assumption of the independent and identically distributed (i.i.d.) data. While being very convenient mathematically, it is often very clearly violated in practice. This disparity between the machine learning theory and applications underlies a growing demand in the development of algorithms that learn from dependent data and theory that can provide generalization guarantees similar to the independent situations. This thesis is dedicated to two variants of dependencies that can arise in practice. One is a dependence on the level of samples in a single learning task. Another dependency type arises in the multi-task setting when the tasks are dependent on each other even though the data for them can be i.i.d. In both cases we model the data (samples or tasks) as stochastic processes and introduce new algorithms for both settings that take into account and exploit the resulting dependencies. We prove the theoretical guarantees on the performance of the introduced algorithms under different evaluation criteria and, in addition, we compliment the theoretical study by the empirical one, where we evaluate some of the algorithms on two real world datasets to highlight their practical applicability."}],"ec_funded":1,"degree_awarded":"PhD","doi":"10.15479/AT:ISTA:TH1048","alternative_title":["ISTA Thesis"]},{"page":"59","status":"public","OA_place":"publisher","type":"dissertation","day":"05","publisher":"Institute of Science and Technology Austria","publication_identifier":{"issn":["2663-337X"]},"month":"09","_id":"83","corr_author":"1","article_processing_charge":"No","supervisor":[{"first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z"}],"author":[{"id":"40297222-F248-11E8-B48F-1D18A9856A87","full_name":"Abusalah, Hamza M","last_name":"Abusalah","first_name":"Hamza M"}],"language":[{"iso":"eng"}],"oa":1,"title":"Proof systems for sustainable decentralized cryptocurrencies","related_material":{"record":[{"id":"559","status":"public","relation":"part_of_dissertation"},{"id":"1236","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"1235"},{"id":"1229","relation":"part_of_dissertation","status":"public"}]},"oa_version":"Published Version","pubrep_id":"1046","has_accepted_license":"1","citation":{"apa":"Abusalah, H. M. (2018). <i>Proof systems for sustainable decentralized cryptocurrencies</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:TH_1046\">https://doi.org/10.15479/AT:ISTA:TH_1046</a>","ista":"Abusalah HM. 2018. Proof systems for sustainable decentralized cryptocurrencies. Institute of Science and Technology Austria.","short":"H.M. Abusalah, Proof Systems for Sustainable Decentralized Cryptocurrencies, Institute of Science and Technology Austria, 2018.","ieee":"H. M. Abusalah, “Proof systems for sustainable decentralized cryptocurrencies,” Institute of Science and Technology Austria, 2018.","ama":"Abusalah HM. Proof systems for sustainable decentralized cryptocurrencies. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:TH_1046\">10.15479/AT:ISTA:TH_1046</a>","chicago":"Abusalah, Hamza M. “Proof Systems for Sustainable Decentralized Cryptocurrencies.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:TH_1046\">https://doi.org/10.15479/AT:ISTA:TH_1046</a>.","mla":"Abusalah, Hamza M. <i>Proof Systems for Sustainable Decentralized Cryptocurrencies</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:TH_1046\">10.15479/AT:ISTA:TH_1046</a>."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_created":"2018-12-11T11:44:32Z","year":"2018","publist_id":"7971","project":[{"_id":"258C570E-B435-11E9-9278-68D0E5697425","grant_number":"259668","call_identifier":"FP7","name":"Provable Security for Physical Cryptography"},{"call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815","name":"Teaching Old Crypto New Tricks"}],"ddc":["004"],"date_published":"2018-09-05T00:00:00Z","date_updated":"2026-07-29T13:38:08Z","department":[{"_id":"KrPi"},{"_id":"GradSch"}],"publication_status":"published","doi_confirm":"1","alternative_title":["ISTA Thesis"],"degree_awarded":"PhD","doi":"10.15479/AT:ISTA:TH_1046","ec_funded":1,"abstract":[{"text":"A proof system is a protocol between a prover and a verifier over a common input in which an honest prover convinces the verifier of the validity of true statements. Motivated by the success of decentralized cryptocurrencies, exemplified by Bitcoin, the focus of this thesis will be on proof systems which found applications in some sustainable alternatives to Bitcoin, such as the Spacemint and Chia cryptocurrencies. In particular, we focus on proofs of space and proofs of sequential work.\r\nProofs of space (PoSpace) were suggested as more ecological, economical, and egalitarian alternative to the energy-wasteful proof-of-work mining of Bitcoin. However, the state-of-the-art constructions of PoSpace are based on sophisticated graph pebbling lower bounds, and are therefore complex. Moreover, when these PoSpace are used in cryptocurrencies like Spacemint, miners can only start mining after ensuring that a commitment to their space is already added in a special transaction to the blockchain. Proofs of sequential work (PoSW) are proof systems in which a prover, upon receiving a statement x and a time parameter T, computes a proof which convinces the verifier that T time units had passed since x was received. Whereas Spacemint assumes synchrony to retain some interesting Bitcoin dynamics, Chia requires PoSW with unique proofs, i.e., PoSW in which it is hard to come up with more than one accepting proof for any true statement. In this thesis we construct simple and practically-efficient PoSpace and PoSW. When using our PoSpace in cryptocurrencies, miners can start mining on the fly, like in Bitcoin, and unlike current constructions of PoSW, which either achieve efficient verification of sequential work, or faster-than-recomputing verification of correctness of proofs, but not both at the same time, ours achieve the best of these two worlds.","lang":"eng"}],"file_date_updated":"2020-07-14T12:48:11Z","file":[{"checksum":"c4b5f7d111755d1396787f41886fc674","file_id":"6245","relation":"main_file","date_created":"2019-04-09T06:43:41Z","content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2018_Thesis_Abusalah.pdf","file_size":876241,"date_updated":"2020-07-14T12:48:11Z"},{"date_updated":"2020-07-14T12:48:11Z","file_size":2029190,"file_name":"2018_Thesis_Abusalah_source.tar.gz","access_level":"closed","creator":"dernst","content_type":"application/x-gzip","date_created":"2019-04-09T06:43:41Z","relation":"source_file","file_id":"6246","checksum":"0f382ac56b471c48fd907d63eb87dafe"}]},{"author":[{"first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","full_name":"Erdös, László","orcid":"0000-0001-5366-9603","last_name":"Erdös"},{"id":"408ED176-F248-11E8-B48F-1D18A9856A87","last_name":"Schröder","full_name":"Schröder, Dominik J","orcid":"0000-0002-2904-1856","first_name":"Dominik J"}],"language":[{"iso":"eng"}],"oa":1,"_id":"1012","issue":"10","article_processing_charge":"No","publication_identifier":{"issn":["1073-7928"]},"publisher":"Oxford University Press","quality_controlled":"1","month":"05","page":"3255-3298","status":"public","type":"journal_article","day":"18","citation":{"ama":"Erdös L, Schröder DJ. Fluctuations of rectangular young diagrams of interlacing wigner eigenvalues. <i>International Mathematics Research Notices</i>. 2018;2018(10):3255-3298. doi:<a href=\"https://doi.org/10.1093/imrn/rnw330\">10.1093/imrn/rnw330</a>","short":"L. Erdös, D.J. Schröder, International Mathematics Research Notices 2018 (2018) 3255–3298.","ieee":"L. Erdös and D. J. Schröder, “Fluctuations of rectangular young diagrams of interlacing wigner eigenvalues,” <i>International Mathematics Research Notices</i>, vol. 2018, no. 10. Oxford University Press, pp. 3255–3298, 2018.","ista":"Erdös L, Schröder DJ. 2018. Fluctuations of rectangular young diagrams of interlacing wigner eigenvalues. International Mathematics Research Notices. 2018(10), 3255–3298.","apa":"Erdös, L., &#38; Schröder, D. J. (2018). Fluctuations of rectangular young diagrams of interlacing wigner eigenvalues. <i>International Mathematics Research Notices</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/imrn/rnw330\">https://doi.org/10.1093/imrn/rnw330</a>","mla":"Erdös, László, and Dominik J. Schröder. “Fluctuations of Rectangular Young Diagrams of Interlacing Wigner Eigenvalues.” <i>International Mathematics Research Notices</i>, vol. 2018, no. 10, Oxford University Press, 2018, pp. 3255–98, doi:<a href=\"https://doi.org/10.1093/imrn/rnw330\">10.1093/imrn/rnw330</a>.","chicago":"Erdös, László, and Dominik J Schröder. “Fluctuations of Rectangular Young Diagrams of Interlacing Wigner Eigenvalues.” <i>International Mathematics Research Notices</i>. Oxford University Press, 2018. <a href=\"https://doi.org/10.1093/imrn/rnw330\">https://doi.org/10.1093/imrn/rnw330</a>."},"arxiv":1,"isi":1,"scopus_import":"1","oa_version":"Preprint","related_material":{"record":[{"id":"6179","status":"public","relation":"dissertation_contains"}]},"title":"Fluctuations of rectangular young diagrams of interlacing wigner eigenvalues","volume":2018,"date_updated":"2026-07-29T13:46:19Z","project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804","call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems"}],"date_published":"2018-05-18T00:00:00Z","main_file_link":[{"url":"https://arxiv.org/abs/1608.05163","open_access":"1"}],"date_created":"2018-12-11T11:49:41Z","year":"2018","publist_id":"6383","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"      2018","publication":"International Mathematics Research Notices","doi":"10.1093/imrn/rnw330","abstract":[{"text":"We prove a new central limit theorem (CLT) for the difference of linear eigenvalue statistics of a Wigner random matrix H and its minor H and find that the fluctuation is much smaller than the fluctuations of the individual linear statistics, as a consequence of the strong correlation between the eigenvalues of H and H. In particular, our theorem identifies the fluctuation of Kerov's rectangular Young diagrams, defined by the interlacing eigenvalues ofH and H, around their asymptotic shape, the Vershik'Kerov'Logan'Shepp curve. Young diagrams equipped with the Plancherel measure follow the same limiting shape. For this, algebraically motivated, ensemble a CLT has been obtained in Ivanov and Olshanski [20] which is structurally similar to our result but the variance is different, indicating that the analogy between the two models has its limitations. Moreover, our theorem shows that Borodin's result [7] on the convergence of the spectral distribution of Wigner matrices to a Gaussian free field also holds in derivative sense.","lang":"eng"}],"ec_funded":1,"external_id":{"isi":["000441668300009"],"arxiv":["1608.05163"]},"department":[{"_id":"LaEr"}],"publication_status":"published"},{"department":[{"_id":"GeKa"},{"_id":"GradSch"}],"doi_confirm":"1","publication_status":"published","alternative_title":["ISTA Thesis"],"degree_awarded":"PhD","doi":"10.15479/AT:ISTA:th_1033","abstract":[{"text":"Nowadays, quantum computation is receiving more and more attention as an alternative to the classical way of computing. For realizing a quantum computer, different devices are investigated as potential quantum bits. In this thesis, the focus is on Ge hut wires, which turned out to be promising candidates for implementing hole spin quantum bits. The advantages of Ge as a material system are the low hyperfine interaction for holes and the strong spin orbit coupling, as well as the compatibility with the highly developed CMOS processes in industry. In addition, Ge can also be isotopically purified which is expected to boost the spin coherence times. The strong spin orbit interaction for holes in Ge on the one hand enables the full electrical control of the quantum bit and on the other hand should allow short spin manipulation times. Starting with a bare Si wafer, this work covers the entire process reaching from growth over the fabrication and characterization of hut wire devices up to the demonstration of hole spin resonance. From experiments with single quantum dots, a large g-factor anisotropy between the in-plane and the out-of-plane direction was found. A comparison to a theoretical model unveiled the heavy-hole character of the lowest energy states. The second part of the thesis addresses double quantum dot devices, which were realized by adding two gate electrodes to a hut wire. In such devices, Pauli spin blockade was observed, which can serve as a read-out mechanism for spin quantum bits. Applying oscillating electric fields in spin blockade allowed the demonstration of continuous spin rotations and the extraction of a lower bound for the spin dephasing time. Despite the strong spin orbit coupling in Ge, the obtained value for the dephasing time is comparable to what has been recently reported for holes in Si. All in all, the presented results point out the high potential of Ge hut wires as a platform for long-lived, fast and fully electrically tunable hole spin quantum bits.","lang":"eng"}],"file_date_updated":"2020-07-14T12:46:35Z","file":[{"date_created":"2019-04-09T07:13:28Z","content_type":"application/pdf","checksum":"b653b5216251f938ddbeafd1de88667c","file_id":"6249","relation":"main_file","access_level":"open_access","file_name":"2018_Thesis_Watzinger.pdf","date_updated":"2020-07-14T12:46:35Z","file_size":85539748,"creator":"dernst"},{"relation":"source_file","checksum":"39bcf8de7ac5b1bb516b11ce2f966785","file_id":"6250","content_type":"application/zip","date_created":"2019-04-09T07:13:27Z","creator":"dernst","date_updated":"2020-07-14T12:46:35Z","file_size":21830697,"file_name":"2018_Thesis_Watzinger_source.zip","access_level":"closed"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_created":"2018-12-11T11:44:21Z","year":"2018","publist_id":"8005","ddc":["530"],"date_published":"2018-07-30T00:00:00Z","tmp":{"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)","image":"/images/cc_by.png"},"date_updated":"2026-07-31T09:15:25Z","title":"Ge hut wires - from growth to hole spin resonance","oa_version":"Published Version","has_accepted_license":"1","pubrep_id":"1033","citation":{"chicago":"Watzinger, Hannes. “Ge Hut Wires - from Growth to Hole Spin Resonance.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:th_1033\">https://doi.org/10.15479/AT:ISTA:th_1033</a>.","mla":"Watzinger, Hannes. <i>Ge Hut Wires - from Growth to Hole Spin Resonance</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_1033\">10.15479/AT:ISTA:th_1033</a>.","short":"H. Watzinger, Ge Hut Wires - from Growth to Hole Spin Resonance, Institute of Science and Technology Austria, 2018.","ama":"Watzinger H. Ge hut wires - from growth to hole spin resonance. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_1033\">10.15479/AT:ISTA:th_1033</a>","ieee":"H. Watzinger, “Ge hut wires - from growth to hole spin resonance,” Institute of Science and Technology Austria, 2018.","ista":"Watzinger H. 2018. Ge hut wires - from growth to hole spin resonance. Institute of Science and Technology Austria.","apa":"Watzinger, H. (2018). <i>Ge hut wires - from growth to hole spin resonance</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_1033\">https://doi.org/10.15479/AT:ISTA:th_1033</a>"},"status":"public","page":"77","OA_place":"publisher","type":"dissertation","day":"30","publication_identifier":{"issn":["2663-337X"]},"publisher":"Institute of Science and Technology Austria","month":"07","corr_author":"1","_id":"49","article_processing_charge":"No","author":[{"full_name":"Watzinger, Hannes","last_name":"Watzinger","id":"35DF8E50-F248-11E8-B48F-1D18A9856A87","first_name":"Hannes"}],"supervisor":[{"last_name":"Katsaros","orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios"}],"language":[{"iso":"eng"}],"oa":1},{"related_material":{"record":[{"id":"6184","relation":"part_of_dissertation","status":"public"},{"id":"6183","status":"public","relation":"part_of_dissertation"},{"id":"1010","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"550"},{"status":"public","relation":"part_of_dissertation","id":"1677"},{"status":"public","relation":"part_of_dissertation","id":"6240"},{"relation":"part_of_dissertation","status":"public","id":"566"}]},"title":"Dyson equation and eigenvalue statistics of random matrices","oa_version":"Published Version","citation":{"mla":"Alt, Johannes. <i>Dyson Equation and Eigenvalue Statistics of Random Matrices</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:TH_1040\">10.15479/AT:ISTA:TH_1040</a>.","chicago":"Alt, Johannes. “Dyson Equation and Eigenvalue Statistics of Random Matrices.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:TH_1040\">https://doi.org/10.15479/AT:ISTA:TH_1040</a>.","ieee":"J. Alt, “Dyson equation and eigenvalue statistics of random matrices,” Institute of Science and Technology Austria, 2018.","ama":"Alt J. Dyson equation and eigenvalue statistics of random matrices. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:TH_1040\">10.15479/AT:ISTA:TH_1040</a>","short":"J. Alt, Dyson Equation and Eigenvalue Statistics of Random Matrices, Institute of Science and Technology Austria, 2018.","ista":"Alt J. 2018. Dyson equation and eigenvalue statistics of random matrices. Institute of Science and Technology Austria.","apa":"Alt, J. (2018). <i>Dyson equation and eigenvalue statistics of random matrices</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:TH_1040\">https://doi.org/10.15479/AT:ISTA:TH_1040</a>"},"has_accepted_license":"1","pubrep_id":"1040","type":"dissertation","day":"12","page":"456","status":"public","OA_place":"publisher","month":"07","publisher":"Institute of Science and Technology Austria","publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","corr_author":"1","_id":"149","language":[{"iso":"eng"}],"oa":1,"author":[{"first_name":"Johannes","last_name":"Alt","full_name":"Alt, Johannes","id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87"}],"supervisor":[{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","orcid":"0000-0001-5366-9603","full_name":"Erdös, László","first_name":"László"}],"publication_status":"published","department":[{"_id":"LaEr"}],"abstract":[{"lang":"eng","text":"The eigenvalue density of many large random matrices is well approximated by a deterministic measure, the self-consistent density of states. In the present work, we show this behaviour for several classes of random matrices. In fact, we establish that, in each of these classes, the self-consistent density of states approximates the eigenvalue density of the random matrix on all scales slightly above the typical eigenvalue spacing. For large classes of random matrices, the self-consistent density of states exhibits several universal features. We prove that, under suitable assumptions, random Gram matrices and Hermitian random matrices with decaying correlations have a 1/3-Hölder continuous self-consistent density of states ρ on R, which is analytic, where it is positive, and has either a square root edge or a cubic root cusp, where it vanishes. We, thus, extend the validity of the corresponding result for Wigner-type matrices from [4, 5, 7]. We show that ρ is determined as the inverse Stieltjes transform of the normalized trace of the unique solution m(z) to the Dyson equation −m(z) −1 = z − a + S[m(z)] on C N×N with the constraint Im m(z) ≥ 0. Here, z lies in the complex upper half-plane, a is a self-adjoint element of C N×N and S is a positivity-preserving operator on C N×N encoding the first two moments of the random matrix. In order to analyze a possible limit of ρ for N → ∞ and address some applications in free probability theory, we also consider the Dyson equation on infinite dimensional von Neumann algebras. We present two applications to random matrices. We first establish that, under certain assumptions, large random matrices with independent entries have a rotationally symmetric self-consistent density of states which is supported on a centered disk in C. Moreover, it is infinitely often differentiable apart from a jump on the boundary of this disk. Second, we show edge universality at all regular (not necessarily extreme) spectral edges for Hermitian random matrices with decaying correlations."}],"ec_funded":1,"alternative_title":["ISTA Thesis"],"doi":"10.15479/AT:ISTA:TH_1040","degree_awarded":"PhD","file_date_updated":"2020-07-14T12:44:57Z","file":[{"access_level":"open_access","date_updated":"2020-07-14T12:44:57Z","file_name":"2018_thesis_Alt.pdf","file_size":5801709,"creator":"dernst","date_created":"2019-04-08T13:55:20Z","content_type":"application/pdf","file_id":"6241","checksum":"d4dad55a7513f345706aaaba90cb1bb8","relation":"main_file"},{"file_size":3802059,"date_updated":"2020-07-14T12:44:57Z","file_name":"2018_thesis_Alt_source.zip","access_level":"closed","creator":"dernst","content_type":"application/zip","date_created":"2019-04-08T13:55:20Z","relation":"source_file","file_id":"6242","checksum":"d73fcf46300dce74c403f2b491148ab4"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","year":"2018","publist_id":"7772","date_created":"2018-12-11T11:44:53Z","project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804","call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems"}],"ddc":["515","519"],"date_published":"2018-07-12T00:00:00Z","tmp":{"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)","image":"/images/cc_by.png"},"date_updated":"2026-08-05T08:14:16Z"},{"user_id":"9947682f-b9fa-11ee-9c4a-b3ffaafe6614","year":"2018","main_file_link":[{"url":"https://arxiv.org/abs/1612.07776 ","open_access":"1"}],"date_created":"2018-12-11T11:47:13Z","project":[{"name":"Random matrices, universality and disordered quantum systems","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804","call_identifier":"FP7"}],"date_published":"2018-03-03T00:00:00Z","volume":28,"date_updated":"2026-08-05T08:14:17Z","publication_status":"published","external_id":{"isi":["000431721800005"],"arxiv":["1612.07776 "]},"department":[{"_id":"LaEr"}],"abstract":[{"text":"We consider large random matrices X with centered, independent entries which have comparable but not necessarily identical variances. Girko's circular law asserts that the spectrum is supported in a disk and in case of identical variances, the limiting density is uniform. In this special case, the local circular law by Bourgade et. al. [11,12] shows that the empirical density converges even locally on scales slightly above the typical eigenvalue spacing. In the general case, the limiting density is typically inhomogeneous and it is obtained via solving a system of deterministic equations. Our main result is the local inhomogeneous circular law in the bulk spectrum on the optimal scale for a general variance profile of the entries of X. \r\n\r\n","lang":"eng"}],"ec_funded":1,"doi":"10.1214/17-AAP1302","das_tickbox":"1","publication":"Annals of Applied Probability","intvolume":"        28","type":"journal_article","day":"03","status":"public","page":"148-203","month":"03","quality_controlled":"1","publisher":"Institute of Mathematical Statistics","article_processing_charge":"No","article_type":"original","_id":"566","corr_author":"1","issue":"1","language":[{"iso":"eng"}],"oa":1,"author":[{"id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87","last_name":"Alt","full_name":"Alt, Johannes","first_name":"Johannes"},{"last_name":"Erdös","orcid":"0000-0001-5366-9603","full_name":"Erdös, László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László"},{"id":"3020C786-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4821-3297","full_name":"Krüger, Torben H","last_name":"Krüger","first_name":"Torben H"}],"title":"Local inhomogeneous circular law","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"149"}]},"scopus_import":"1","oa_version":"Preprint","isi":1,"citation":{"apa":"Alt, J., Erdös, L., &#38; Krüger, T. H. (2018). Local inhomogeneous circular law. <i>Annals of Applied Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/17-AAP1302\">https://doi.org/10.1214/17-AAP1302</a>","ista":"Alt J, Erdös L, Krüger TH. 2018. Local inhomogeneous circular law. Annals of Applied Probability. 28(1), 148–203.","short":"J. Alt, L. Erdös, T.H. Krüger, Annals of Applied Probability 28 (2018) 148–203.","ieee":"J. Alt, L. Erdös, and T. H. Krüger, “Local inhomogeneous circular law,” <i>Annals of Applied Probability</i>, vol. 28, no. 1. Institute of Mathematical Statistics, pp. 148–203, 2018.","ama":"Alt J, Erdös L, Krüger TH. Local inhomogeneous circular law. <i>Annals of Applied Probability</i>. 2018;28(1):148-203. doi:<a href=\"https://doi.org/10.1214/17-AAP1302\">10.1214/17-AAP1302</a>","mla":"Alt, Johannes, et al. “Local Inhomogeneous Circular Law.” <i>Annals of Applied Probability</i>, vol. 28, no. 1, Institute of Mathematical Statistics, 2018, pp. 148–203, doi:<a href=\"https://doi.org/10.1214/17-AAP1302\">10.1214/17-AAP1302</a>.","chicago":"Alt, Johannes, László Erdös, and Torben H Krüger. “Local Inhomogeneous Circular Law.” <i>Annals of Applied Probability</i>. Institute of Mathematical Statistics, 2018. <a href=\"https://doi.org/10.1214/17-AAP1302\">https://doi.org/10.1214/17-AAP1302</a>."},"arxiv":1},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"8054","year":"2018","date_created":"2018-12-11T11:44:05Z","date_published":"2018-11-19T00:00:00Z","project":[{"_id":"254BA948-B435-11E9-9278-68D0E5697425","grant_number":"401299","name":"Probing development and reversibility of autism spectrum disorders"}],"ddc":["570"],"date_updated":"2026-08-09T22:30:06Z","volume":21,"publication_status":"published","department":[{"_id":"GaNo"},{"_id":"EdHa"}],"external_id":{"isi":["000451324700010"]},"abstract":[{"text":"SETD5 gene mutations have been identified as a frequent cause of idiopathic intellectual disability. Here we show that Setd5-haploinsufficient mice present developmental defects such as abnormal brain-to-body weight ratios and neural crest defect-associated phenotypes. Furthermore, Setd5-mutant mice show impairments in cognitive tasks, enhanced long-term potentiation, delayed ontogenetic profile of ultrasonic vocalization, and behavioral inflexibility. Behavioral issues are accompanied by abnormal expression of postsynaptic density proteins previously associated with cognition. Our data additionally indicate that Setd5 regulates RNA polymerase II dynamics and gene transcription via its interaction with the Hdac3 and Paf1 complexes, findings potentially explaining the gene expression defects observed in Setd5-haploinsufficient mice. Our results emphasize the decisive role of Setd5 in a biological pathway found to be disrupted in humans with intellectual disability and autism spectrum disorder.","lang":"eng"}],"doi":"10.1038/s41593-018-0266-2","file_date_updated":"2020-07-14T12:45:58Z","intvolume":"        21","file":[{"file_size":8167169,"date_updated":"2020-07-14T12:45:58Z","file_name":"2017_NatureNeuroscience_Deliu.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","date_created":"2019-04-09T07:41:57Z","relation":"main_file","checksum":"60abd0f05b7cdc08a6b0ec460884084f","file_id":"6255"}],"publication":"Nature Neuroscience","day":"19","type":"journal_article","page":"1717 - 1727","status":"public","quality_controlled":"1","month":"11","publisher":"Nature Publishing Group","article_processing_charge":"No","article_type":"original","_id":"3","corr_author":"1","issue":"12","language":[{"iso":"eng"}],"oa":1,"author":[{"first_name":"Elena","last_name":"Deliu","orcid":"0000-0002-7370-5293","full_name":"Deliu, Elena","id":"37A40D7E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Arecco, Niccoló","last_name":"Arecco","first_name":"Niccoló"},{"id":"4739D480-F248-11E8-B48F-1D18A9856A87","last_name":"Morandell","full_name":"Morandell, Jasmin","first_name":"Jasmin"},{"first_name":"Christoph","id":"4C66542E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9033-9096","full_name":"Dotter, Christoph","last_name":"Dotter"},{"first_name":"Ximena","full_name":"Contreras, Ximena","last_name":"Contreras","id":"475990FE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Girardot, Charles","last_name":"Girardot","first_name":"Charles"},{"first_name":"Eva","full_name":"Käsper, Eva","last_name":"Käsper"},{"first_name":"Alena","id":"C50A9596-02D0-11E9-976E-E38CFE5CBC1D","full_name":"Kozlova, Alena","last_name":"Kozlova"},{"first_name":"Kasumi","id":"3065DFC4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6060-4795","full_name":"Kishi, Kasumi","last_name":"Kishi"},{"orcid":"0000-0002-9529-4464","full_name":"Chiaradia, Ilaria","last_name":"Chiaradia","id":"B6467F20-02D0-11E9-BDA5-E960C241894A","first_name":"Ilaria"},{"first_name":"Kyung","full_name":"Noh, Kyung","last_name":"Noh"},{"first_name":"Gaia","full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"6074","relation":"popular_science","status":"public"},{"status":"public","relation":"dissertation_contains","id":"12364"}],"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/mutation-that-causes-autism-and-intellectual-disability-makes-brain-less-flexible/"}]},"title":"Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"PreCl"}],"oa_version":"Submitted Version","scopus_import":"1","acknowledgement":"This work was supported by the Simons Foundation Autism Research Initiative (grant 401299) to G.N. and the DFG (SPP1738 grant NO 1249) to K.-M.N.","isi":1,"citation":{"chicago":"Deliu, Elena, Niccoló Arecco, Jasmin Morandell, Christoph Dotter, Ximena Contreras, Charles Girardot, Eva Käsper, et al. “Haploinsufficiency of the Intellectual Disability Gene SETD5 Disturbs Developmental Gene Expression and Cognition.” <i>Nature Neuroscience</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41593-018-0266-2\">https://doi.org/10.1038/s41593-018-0266-2</a>.","mla":"Deliu, Elena, et al. “Haploinsufficiency of the Intellectual Disability Gene SETD5 Disturbs Developmental Gene Expression and Cognition.” <i>Nature Neuroscience</i>, vol. 21, no. 12, Nature Publishing Group, 2018, pp. 1717–27, doi:<a href=\"https://doi.org/10.1038/s41593-018-0266-2\">10.1038/s41593-018-0266-2</a>.","ista":"Deliu E, Arecco N, Morandell J, Dotter C, Contreras X, Girardot C, Käsper E, Kozlova A, Kishi K, Chiaradia I, Noh K, Novarino G. 2018. Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition. Nature Neuroscience. 21(12), 1717–1727.","apa":"Deliu, E., Arecco, N., Morandell, J., Dotter, C., Contreras, X., Girardot, C., … Novarino, G. (2018). Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition. <i>Nature Neuroscience</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41593-018-0266-2\">https://doi.org/10.1038/s41593-018-0266-2</a>","ieee":"E. Deliu <i>et al.</i>, “Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition,” <i>Nature Neuroscience</i>, vol. 21, no. 12. Nature Publishing Group, pp. 1717–1727, 2018.","short":"E. Deliu, N. Arecco, J. Morandell, C. Dotter, X. Contreras, C. Girardot, E. Käsper, A. Kozlova, K. Kishi, I. Chiaradia, K. Noh, G. Novarino, Nature Neuroscience 21 (2018) 1717–1727.","ama":"Deliu E, Arecco N, Morandell J, et al. Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition. <i>Nature Neuroscience</i>. 2018;21(12):1717-1727. doi:<a href=\"https://doi.org/10.1038/s41593-018-0266-2\">10.1038/s41593-018-0266-2</a>"},"has_accepted_license":"1","pubrep_id":"1071"},{"year":"2018","publist_id":"8029","date_created":"2018-12-11T11:44:14Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_updated":"2026-04-08T14:15:35Z","ddc":["576","579"],"date_published":"2018-10-30T00:00:00Z","abstract":[{"lang":"eng","text":"Expression of genes is a fundamental molecular phenotype that is subject to evolution by different types of mutations. Both the rate and the effect of mutations may depend on the DNA sequence context of a particular gene or a particular promoter sequence. In this thesis I investigate the nature of this dependence using simple genetic systems in Escherichia coli. With these systems I explore the evolution of constitutive gene expression from random starting sequences at different loci on the chromosome and at different locations in sequence space. First, I dissect chromosomal neighborhood effects that underlie locus-dependent differences in the potential of a gene under selection to become more highly expressed. Next, I find that the effects of point mutations in promoter sequences are dependent on sequence context, and that an existing energy matrix model performs poorly in predicting relative expression of unrelated sequences. Finally, I show that a substantial fraction of random sequences contain functional promoters and I present an extended thermodynamic model that predicts promoter strength in full sequence space. Taken together, these results provide new insights and guides on how to integrate information on sequence context to improve our qualitative and quantitative understanding of bacterial gene expression, with implications for rapid evolution of drug resistance, de novo evolution of genes, and horizontal gene transfer."}],"alternative_title":["ISTA Thesis"],"degree_awarded":"PhD","doi":"10.15479/AT:ISTA:th1059","publication_status":"published","department":[{"_id":"CaGu"}],"file":[{"creator":"dernst","embargo_to":"open_access","access_level":"closed","file_name":"Thesis_Steinrueck_final.docx","file_size":9190845,"date_updated":"2020-07-14T12:45:43Z","file_id":"5941","checksum":"413cbce1cd1debeae3abe2a25dbc70d1","relation":"source_file","date_created":"2019-02-08T10:51:22Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"},{"access_level":"open_access","file_size":7521973,"date_updated":"2021-02-11T11:17:14Z","file_name":"Thesis_Steinrueck_final.pdf","embargo":"2019-11-02","creator":"dernst","date_created":"2019-02-08T10:51:22Z","content_type":"application/pdf","checksum":"3def8b7854c8b42d643597ce0215efac","file_id":"5942","relation":"main_file"}],"file_date_updated":"2021-02-11T11:17:14Z","month":"10","publisher":"Institute of Science and Technology Austria","publication_identifier":{"issn":["2663-337X"]},"type":"dissertation","day":"30","status":"public","page":"109","OA_place":"publisher","language":[{"iso":"eng"}],"oa":1,"author":[{"id":"2C023F40-F248-11E8-B48F-1D18A9856A87","last_name":"Steinrück","orcid":"0000-0003-1229-9719","full_name":"Steinrück, Magdalena","first_name":"Magdalena"}],"supervisor":[{"last_name":"Guet","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C"}],"article_processing_charge":"No","corr_author":"1","_id":"26","oa_version":"Published Version","title":"The influence of sequence context on the evolution of bacterial gene expression","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"704"}]},"citation":{"short":"M. Steinrück, The Influence of Sequence Context on the Evolution of Bacterial Gene Expression, Institute of Science and Technology Austria, 2018.","ieee":"M. Steinrück, “The influence of sequence context on the evolution of bacterial gene expression,” Institute of Science and Technology Austria, 2018.","ama":"Steinrück M. The influence of sequence context on the evolution of bacterial gene expression. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th1059\">10.15479/AT:ISTA:th1059</a>","ista":"Steinrück M. 2018. The influence of sequence context on the evolution of bacterial gene expression. Institute of Science and Technology Austria.","apa":"Steinrück, M. (2018). <i>The influence of sequence context on the evolution of bacterial gene expression</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th1059\">https://doi.org/10.15479/AT:ISTA:th1059</a>","chicago":"Steinrück, Magdalena. “The Influence of Sequence Context on the Evolution of Bacterial Gene Expression.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:th1059\">https://doi.org/10.15479/AT:ISTA:th1059</a>.","mla":"Steinrück, Magdalena. <i>The Influence of Sequence Context on the Evolution of Bacterial Gene Expression</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th1059\">10.15479/AT:ISTA:th1059</a>."},"has_accepted_license":"1","pubrep_id":"1059"},{"citation":{"chicago":"Contreras, Ximena, and Simon Hippenmeyer. “Incorrect Trafficking Route Leads to Autism.” <i>Brain a Journal of Neurology</i>. Oxford University Press, 2018. <a href=\"https://doi.org/10.1093/brain/awy218\">https://doi.org/10.1093/brain/awy218</a>.","mla":"Contreras, Ximena, and Simon Hippenmeyer. “Incorrect Trafficking Route Leads to Autism.” <i>Brain a Journal of Neurology</i>, vol. 141, no. 9, Oxford University Press, 2018, pp. 2542–44, doi:<a href=\"https://doi.org/10.1093/brain/awy218\">10.1093/brain/awy218</a>.","ieee":"X. Contreras and S. Hippenmeyer, “Incorrect trafficking route leads to autism,” <i>Brain a journal of neurology</i>, vol. 141, no. 9. Oxford University Press, pp. 2542–2544, 2018.","short":"X. Contreras, S. Hippenmeyer, Brain a Journal of Neurology 141 (2018) 2542–2544.","ama":"Contreras X, Hippenmeyer S. Incorrect trafficking route leads to autism. <i>Brain a journal of neurology</i>. 2018;141(9):2542-2544. doi:<a href=\"https://doi.org/10.1093/brain/awy218\">10.1093/brain/awy218</a>","ista":"Contreras X, Hippenmeyer S. 2018. Incorrect trafficking route leads to autism. Brain a journal of neurology. 141(9), 2542–2544.","apa":"Contreras, X., &#38; Hippenmeyer, S. (2018). Incorrect trafficking route leads to autism. <i>Brain a Journal of Neurology</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/brain/awy218\">https://doi.org/10.1093/brain/awy218</a>"},"isi":1,"oa_version":"None","scopus_import":"1","related_material":{"record":[{"id":"7902","relation":"part_of_dissertation","status":"public"}]},"title":"Incorrect trafficking route leads to autism","author":[{"full_name":"Contreras, Ximena","last_name":"Contreras","id":"475990FE-F248-11E8-B48F-1D18A9856A87","first_name":"Ximena"},{"first_name":"Simon","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"issue":"9","_id":"28","article_processing_charge":"No","publisher":"Oxford University Press","month":"09","quality_controlled":"1","status":"public","page":"2542 - 2544","day":"01","type":"journal_article","intvolume":"       141","publication":"Brain a journal of neurology","doi":"10.1093/brain/awy218","abstract":[{"lang":"eng","text":"This scientific commentary refers to ‘NEGR1 and FGFR2 cooperatively regulate cortical development and core behaviours related to autism disorders in mice’ by Szczurkowska et al. "}],"department":[{"_id":"SiHi"}],"external_id":{"isi":["000446548100012"]},"publication_status":"published","date_updated":"2026-08-09T22:30:16Z","volume":141,"date_published":"2018-09-01T00:00:00Z","date_created":"2018-12-11T11:44:14Z","year":"2018","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"month":"07","publisher":"Institute of Science and Technology Austria","publication_identifier":{"issn":["2663-337X"]},"day":"01","type":"dissertation","OA_place":"publisher","page":"96","status":"public","oa":1,"language":[{"iso":"eng"}],"supervisor":[{"id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","full_name":"Siekhaus, Daria E","orcid":"0000-0001-8323-8353","last_name":"Siekhaus","first_name":"Daria E"}],"author":[{"first_name":"Vera","last_name":"Belyaeva","full_name":"Belyaeva, Vera","id":"47F080FE-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","corr_author":"1","_id":"9","oa_version":"Published Version","title":"Transcriptional regulation of macrophage migration in the Drosophila melanogaster embryo ","citation":{"chicago":"Belyaeva, Vera. “Transcriptional Regulation of Macrophage Migration in the Drosophila Melanogaster Embryo .” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:th1064\">https://doi.org/10.15479/AT:ISTA:th1064</a>.","mla":"Belyaeva, Vera. <i>Transcriptional Regulation of Macrophage Migration in the Drosophila Melanogaster Embryo </i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th1064\">10.15479/AT:ISTA:th1064</a>.","ieee":"V. Belyaeva, “Transcriptional regulation of macrophage migration in the Drosophila melanogaster embryo ,” Institute of Science and Technology Austria, 2018.","short":"V. Belyaeva, Transcriptional Regulation of Macrophage Migration in the Drosophila Melanogaster Embryo , Institute of Science and Technology Austria, 2018.","ama":"Belyaeva V. Transcriptional regulation of macrophage migration in the Drosophila melanogaster embryo . 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th1064\">10.15479/AT:ISTA:th1064</a>","apa":"Belyaeva, V. (2018). <i>Transcriptional regulation of macrophage migration in the Drosophila melanogaster embryo </i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th1064\">https://doi.org/10.15479/AT:ISTA:th1064</a>","ista":"Belyaeva V. 2018. Transcriptional regulation of macrophage migration in the Drosophila melanogaster embryo . Institute of Science and Technology Austria."},"pubrep_id":"1064","has_accepted_license":"1","publist_id":"8047","year":"2018","date_created":"2018-12-11T11:44:08Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_updated":"2026-04-08T14:13:03Z","date_published":"2018-07-01T00:00:00Z","ddc":["570"],"abstract":[{"lang":"eng","text":"Immune cells migrating to the sites of infection navigate through diverse tissue architectures and switch their migratory mechanisms upon demand. However, little is known about systemic regulators that could allow the acquisition of these mechanisms. We performed a genetic screen in Drosophila melanogaster to identify regulators of germband invasion by embryonic macrophages into the confined space between the ectoderm and mesoderm. We have found that bZIP circadian transcription factors (TFs) Kayak (dFos) and Vrille (dNFIL3) have opposite effects on macrophage germband infiltration: Kayak facilitated and Vrille inhibited it. These TFs are enriched in the macrophages during migration and genetically interact to control it. Kayak sets a less coordinated mode of migration of the macrophage group and increases the probability and length of Levy walks. Intriguingly, the motility of kayak mutant macrophages was also strongly affected during initial germband invasion but not along another less confined route. Inhibiting Rho1 signaling within the tail ectoderm partially rescued the Kayak mutant phenotype, strongly suggesting that migrating macrophages have to overcome a barrier imposed by the stiffness of the ectoderm. Also, Kayak appeared to be important for the maintenance of the round cell shape and the rear edge translocation of the macrophages invading the germband. Complementary to this, the cortical actin cytoskeleton of Kayak- deficient macrophages was strongly affected. RNA sequencing revealed the filamin Cheerio and tetraspanin TM4SF to be downstream of Kayak. Chromatin immunoprecipitation and immunostaining revealed that the formin Diaphanous is another downstream target of Kayak. Immunostaining revealed that the formin Diaphanous is another downstream target of Kayak. Indeed, Cheerio, TM4SF and Diaphanous are required within macrophages for germband invasion, and expression of constitutively active Diaphanous in macrophages was able to rescue the kayak mutant phenotype. Moreover, Cher and Diaphanous are also reduced in the macrophages overexpressing Vrille. We hypothesize that Kayak, through its targets, increases actin polymerization and cortical tension in macrophages and thus allows extra force generation necessary for macrophage dissemination and migration through confined stiff tissues, while Vrille counterbalances it."}],"doi":"10.15479/AT:ISTA:th1064","degree_awarded":"PhD","alternative_title":["ISTA Thesis"],"publication_status":"published","department":[{"_id":"DaSi"}],"file":[{"creator":"dernst","date_updated":"2020-07-14T12:48:14Z","file_size":102737483,"file_name":"2018_Thesis_Belyaeva_source.docx","embargo_to":"open_access","access_level":"closed","relation":"source_file","file_id":"6243","checksum":"d27b2465cb70d0c9678a0381b9b6ced1","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2019-04-08T14:13:12Z"},{"date_created":"2019-04-08T14:14:08Z","content_type":"application/pdf","file_id":"6244","checksum":"a2939b61bde2de7b8ced77bbae0eaaed","relation":"main_file","access_level":"open_access","file_size":88077843,"file_name":"2018_Thesis_Belyaeva.pdf","date_updated":"2021-02-11T11:17:16Z","embargo":"2019-11-19","creator":"dernst"}],"file_date_updated":"2021-02-11T11:17:16Z"},{"file_date_updated":"2020-07-14T12:46:56Z","intvolume":"         8","publication":"G3: Genes, Genomes, Genetics","file":[{"content_type":"application/pdf","date_created":"2018-12-12T10:11:48Z","relation":"main_file","file_id":"4905","checksum":"7d9d28b915159078a4ca7add568010e8","file_size":2251222,"file_name":"IST-2018-990-v1+1_2018_Gyoergy_Tools_allowing.pdf","date_updated":"2020-07-14T12:46:56Z","access_level":"open_access","creator":"system"}],"publication_status":"published","external_id":{"isi":["000426693300011"]},"department":[{"_id":"DaSi"}],"ec_funded":1,"abstract":[{"text":"Drosophila melanogaster plasmatocytes, the phagocytic cells among hemocytes, are essential for immune responses, but also play key roles from early development to death through their interactions with other cell types. They regulate homeostasis and signaling during development, stem cell proliferation, metabolism, cancer, wound responses and aging, displaying intriguing molecular and functional conservation with vertebrate macrophages. Given the relative ease of genetics in Drosophila compared to vertebrates, tools permitting visualization and genetic manipulation of plasmatocytes and surrounding tissues independently at all stages would greatly aid in fully understanding these processes, but are lacking. Here we describe a comprehensive set of transgenic lines that allow this. These include extremely brightly fluorescing mCherry-based lines that allow GAL4-independent visualization of plasmatocyte nuclei, cytoplasm or actin cytoskeleton from embryonic Stage 8 through adulthood in both live and fixed samples even as heterozygotes, greatly facilitating screening. These lines allow live visualization and tracking of embryonic plasmatocytes, as well as larval plasmatocytes residing at the body wall or flowing with the surrounding hemolymph. With confocal imaging, interactions of plasmatocytes and inner tissues can be seen in live or fixed embryos, larvae and adults. They permit efficient GAL4-independent FACS analysis/sorting of plasmatocytes throughout life. To facilitate genetic analysis of reciprocal signaling, we have also made a plasmatocyte-expressing QF2 line that in combination with extant GAL4 drivers allows independent genetic manipulation of both plasmatocytes and surrounding tissues, and a GAL80 line that blocks GAL4 drivers from affecting plasmatocytes, both of which function from the early embryo to the adult.","lang":"eng"}],"doi":"10.1534/g3.117.300452","project":[{"name":"The role of Drosophila TNF alpha in immune cell invasion","grant_number":"P29638","_id":"253B6E48-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"The role of Drosophila TNF alpha in immune cell invasion","_id":"253B6E48-B435-11E9-9278-68D0E5697425","grant_number":"P29638","call_identifier":"FWF"},{"name":"Investigating the role of the novel major superfamily facilitator transporter family member MFSD1 in metastasis","grant_number":"LSC16-021","_id":"2637E9C0-B435-11E9-9278-68D0E5697425"},{"name":"Investigating the role of transporters in invasive migration through junctions","call_identifier":"FP7","grant_number":"334077","_id":"2536F660-B435-11E9-9278-68D0E5697425"}],"ddc":["570"],"date_published":"2018-03-01T00:00:00Z","volume":8,"tmp":{"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)","image":"/images/cc_by.png"},"date_updated":"2026-08-09T22:30:22Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","year":"2018","publist_id":"7271","date_created":"2018-12-11T11:47:05Z","citation":{"chicago":"György, Attila, Marko Roblek, Aparna Ratheesh, Katarina Valosková, Vera Belyaeva, Stephanie Wachner, Yutaka Matsubayashi, Besaiz Sanchez Sanchez, Brian Stramer, and Daria E Siekhaus. “Tools Allowing Independent Visualization and Genetic Manipulation of Drosophila Melanogaster Macrophages and Surrounding Tissues.” <i>G3: Genes, Genomes, Genetics</i>. Genetics Society of America, 2018. <a href=\"https://doi.org/10.1534/g3.117.300452\">https://doi.org/10.1534/g3.117.300452</a>.","mla":"György, Attila, et al. “Tools Allowing Independent Visualization and Genetic Manipulation of Drosophila Melanogaster Macrophages and Surrounding Tissues.” <i>G3: Genes, Genomes, Genetics</i>, vol. 8, no. 3, Genetics Society of America, 2018, pp. 845–57, doi:<a href=\"https://doi.org/10.1534/g3.117.300452\">10.1534/g3.117.300452</a>.","short":"A. György, M. Roblek, A. Ratheesh, K. Valosková, V. Belyaeva, S. Wachner, Y. Matsubayashi, B. Sanchez Sanchez, B. Stramer, D.E. Siekhaus, G3: Genes, Genomes, Genetics 8 (2018) 845–857.","ieee":"A. György <i>et al.</i>, “Tools allowing independent visualization and genetic manipulation of Drosophila melanogaster macrophages and surrounding tissues,” <i>G3: Genes, Genomes, Genetics</i>, vol. 8, no. 3. Genetics Society of America, pp. 845–857, 2018.","ama":"György A, Roblek M, Ratheesh A, et al. Tools allowing independent visualization and genetic manipulation of Drosophila melanogaster macrophages and surrounding tissues. <i>G3: Genes, Genomes, Genetics</i>. 2018;8(3):845-857. doi:<a href=\"https://doi.org/10.1534/g3.117.300452\">10.1534/g3.117.300452</a>","apa":"György, A., Roblek, M., Ratheesh, A., Valosková, K., Belyaeva, V., Wachner, S., … Siekhaus, D. E. (2018). Tools allowing independent visualization and genetic manipulation of Drosophila melanogaster macrophages and surrounding tissues. <i>G3: Genes, Genomes, Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/g3.117.300452\">https://doi.org/10.1534/g3.117.300452</a>","ista":"György A, Roblek M, Ratheesh A, Valosková K, Belyaeva V, Wachner S, Matsubayashi Y, Sanchez Sanchez B, Stramer B, Siekhaus DE. 2018. Tools allowing independent visualization and genetic manipulation of Drosophila melanogaster macrophages and surrounding tissues. G3: Genes, Genomes, Genetics. 8(3), 845–857."},"has_accepted_license":"1","pubrep_id":"990","title":"Tools allowing independent visualization and genetic manipulation of Drosophila melanogaster macrophages and surrounding tissues","related_material":{"record":[{"id":"6530","relation":"research_paper"},{"id":"6543","relation":"research_paper"},{"id":"11193","relation":"dissertation_contains","status":"public"},{"id":"6546","relation":"dissertation_contains","status":"public"}]},"acknowledged_ssus":[{"_id":"LifeSc"}],"acknowledgement":" A. Ratheesh also by Marie Curie IIF GA-2012-32950BB:DICJI, Marko Roblek by the provincial government of Lower Austria, K. Valoskova and S. Wachner by DOC Fellowships from the Austrian Academy of Sciences, ","oa_version":"Published Version","scopus_import":"1","isi":1,"article_processing_charge":"No","issue":"3","_id":"544","corr_author":"1","language":[{"iso":"eng"}],"oa":1,"author":[{"last_name":"György","full_name":"György, Attila","orcid":"0000-0002-1819-198X","id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87","first_name":"Attila"},{"last_name":"Roblek","orcid":"0000-0001-9588-1389","full_name":"Roblek, Marko","id":"3047D808-F248-11E8-B48F-1D18A9856A87","first_name":"Marko"},{"last_name":"Ratheesh","full_name":"Ratheesh, Aparna","orcid":"0000-0001-7190-0776","id":"2F064CFE-F248-11E8-B48F-1D18A9856A87","first_name":"Aparna"},{"first_name":"Katarina","id":"46F146FC-F248-11E8-B48F-1D18A9856A87","last_name":"Valosková","orcid":"0000-0002-7926-0221","full_name":"Valosková, Katarina"},{"full_name":"Belyaeva, Vera","last_name":"Belyaeva","id":"47F080FE-F248-11E8-B48F-1D18A9856A87","first_name":"Vera"},{"id":"2A95E7B0-F248-11E8-B48F-1D18A9856A87","last_name":"Wachner","full_name":"Wachner, Stephanie","first_name":"Stephanie"},{"last_name":"Matsubayashi","full_name":"Matsubayashi, Yutaka","first_name":"Yutaka"},{"last_name":"Sanchez Sanchez","full_name":"Sanchez Sanchez, Besaiz","first_name":"Besaiz"},{"first_name":"Brian","last_name":"Stramer","full_name":"Stramer, Brian"},{"first_name":"Daria E","last_name":"Siekhaus","full_name":"Siekhaus, Daria E","orcid":"0000-0001-8323-8353","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87"}],"type":"journal_article","day":"01","status":"public","page":"845 - 857","quality_controlled":"1","month":"03","publisher":"Genetics Society of America"},{"intvolume":"        19","publication":"Nature Immunology","doi":"10.1038/s41590-018-0109-z","ec_funded":1,"abstract":[{"text":"Although much is known about the physiological framework of T cell motility, and numerous rate-limiting molecules have been identified through loss-of-function approaches, an integrated functional concept of T cell motility is lacking. Here, we used in vivo precision morphometry together with analysis of cytoskeletal dynamics in vitro to deconstruct the basic mechanisms of T cell migration within lymphatic organs. We show that the contributions of the integrin LFA-1 and the chemokine receptor CCR7 are complementary rather than positioned in a linear pathway, as they are during leukocyte extravasation from the blood vasculature. Our data demonstrate that CCR7 controls cortical actin flows, whereas integrins mediate substrate friction that is sufficient to drive locomotion in the absence of considerable surface adhesions and plasma membrane flux.","lang":"eng"}],"department":[{"_id":"MiSi"},{"_id":"Bio"}],"external_id":{"pmid":["29777221"],"isi":["000433041500026"]},"publication_status":"published","date_updated":"2026-08-09T22:30:21Z","volume":19,"date_published":"2018-05-18T00:00:00Z","project":[{"call_identifier":"H2020","grant_number":"724373","_id":"25FE9508-B435-11E9-9278-68D0E5697425","name":"Cellular Navigation Along Spatial Gradients"},{"name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells","grant_number":"747687","_id":"260AA4E2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Molecular and system level view of immune cell migration","grant_number":"ALTF 1396-2014","_id":"25A48D24-B435-11E9-9278-68D0E5697425"},{"name":"Cytoskeletal force generation and force transduction of migrating leukocytes","call_identifier":"FP7","_id":"25A603A2-B435-11E9-9278-68D0E5697425","grant_number":"281556"}],"ddc":["570"],"date_created":"2018-12-11T11:44:10Z","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/29777221"}],"publist_id":"8040","year":"2018","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Hons, M., Kopf, A., Hauschild, R., Leithner, A. F., Gärtner, F. R., Abe, J., … Sixt, M. K. (2018). Chemokines and integrins independently tune actin flow and substrate friction during intranodal migration of T cells. <i>Nature Immunology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41590-018-0109-z\">https://doi.org/10.1038/s41590-018-0109-z</a>","ista":"Hons M, Kopf A, Hauschild R, Leithner AF, Gärtner FR, Abe J, Renkawitz J, Stein J, Sixt MK. 2018. Chemokines and integrins independently tune actin flow and substrate friction during intranodal migration of T cells. Nature Immunology. 19(6), 606–616.","ama":"Hons M, Kopf A, Hauschild R, et al. Chemokines and integrins independently tune actin flow and substrate friction during intranodal migration of T cells. <i>Nature Immunology</i>. 2018;19(6):606-616. doi:<a href=\"https://doi.org/10.1038/s41590-018-0109-z\">10.1038/s41590-018-0109-z</a>","short":"M. Hons, A. Kopf, R. Hauschild, A.F. Leithner, F.R. Gärtner, J. Abe, J. Renkawitz, J. Stein, M.K. Sixt, Nature Immunology 19 (2018) 606–616.","ieee":"M. Hons <i>et al.</i>, “Chemokines and integrins independently tune actin flow and substrate friction during intranodal migration of T cells,” <i>Nature Immunology</i>, vol. 19, no. 6. Nature Publishing Group, pp. 606–616, 2018.","chicago":"Hons, Miroslav, Aglaja Kopf, Robert Hauschild, Alexander F Leithner, Florian R Gärtner, Jun Abe, Jörg Renkawitz, Jens Stein, and Michael K Sixt. “Chemokines and Integrins Independently Tune Actin Flow and Substrate Friction during Intranodal Migration of T Cells.” <i>Nature Immunology</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41590-018-0109-z\">https://doi.org/10.1038/s41590-018-0109-z</a>.","mla":"Hons, Miroslav, et al. “Chemokines and Integrins Independently Tune Actin Flow and Substrate Friction during Intranodal Migration of T Cells.” <i>Nature Immunology</i>, vol. 19, no. 6, Nature Publishing Group, 2018, pp. 606–16, doi:<a href=\"https://doi.org/10.1038/s41590-018-0109-z\">10.1038/s41590-018-0109-z</a>."},"pmid":1,"isi":1,"scopus_import":"1","oa_version":"Published Version","acknowledgement":"This work was funded by grants from the European Research Council (ERC StG 281556 and CoG 724373) and the Austrian Science Foundation (FWF) to M.S. and by Swiss National Foundation (SNF) project grants 31003A_135649, 31003A_153457 and CR23I3_156234 to J.V.S. F.G. received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 747687, and J.R. was funded by an EMBO long-term fellowship (ALTF 1396-2014).","acknowledged_ssus":[{"_id":"SSU"}],"related_material":{"record":[{"id":"6891","relation":"dissertation_contains","status":"public"}]},"title":"Chemokines and integrins independently tune actin flow and substrate friction during intranodal migration of T cells","author":[{"full_name":"Hons, Miroslav","orcid":"0000-0002-6625-3348","last_name":"Hons","id":"4167FE56-F248-11E8-B48F-1D18A9856A87","first_name":"Miroslav"},{"orcid":"0000-0002-2187-6656","full_name":"Kopf, Aglaja","last_name":"Kopf","id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87","first_name":"Aglaja"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert","last_name":"Hauschild","first_name":"Robert"},{"first_name":"Alexander F","last_name":"Leithner","full_name":"Leithner, Alexander F","orcid":"0000-0002-1073-744X","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87"},{"id":"397A88EE-F248-11E8-B48F-1D18A9856A87","full_name":"Gärtner, Florian R","orcid":"0000-0001-6120-3723","last_name":"Gärtner","first_name":"Florian R"},{"last_name":"Abe","full_name":"Abe, Jun","first_name":"Jun"},{"orcid":"0000-0003-2856-3369","full_name":"Renkawitz, Jörg","last_name":"Renkawitz","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","first_name":"Jörg"},{"last_name":"Stein","full_name":"Stein, Jens","first_name":"Jens"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","first_name":"Michael K"}],"oa":1,"language":[{"iso":"eng"}],"issue":"6","_id":"15","article_processing_charge":"No","publisher":"Nature Publishing Group","quality_controlled":"1","month":"05","status":"public","page":"606 - 616","day":"18","type":"journal_article"},{"ec_funded":1,"abstract":[{"lang":"eng","text":"We show that a rather simple, steady modification of the streamwise velocity profile in a pipe can lead to a complete collapse of turbulence and the flow fully relaminarizes. Two different devices, a stationary obstacle (inset) and a device which injects fluid through an annular gap close to the wall, are used to control the flow. Both devices modify the streamwise velocity profile such that the flow in the center of the pipe is decelerated and the flow in the near wall region is accelerated. We present measurements with stereoscopic particle image velocimetry to investigate and capture the development of the relaminarizing flow downstream these devices and the specific circumstances responsible for relaminarization. We find total relaminarization up to Reynolds numbers of 6000, where the skin friction in the far downstream distance is reduced by a factor of 3.4 due to relaminarization. In a smooth straight pipe the flow remains completely laminar downstream of the control. Furthermore, we show that transient (temporary) relaminarization in a spatially confined region right downstream the devices occurs also at much higher Reynolds numbers, accompanied by a significant local skin friction drag reduction. The underlying physical mechanism of relaminarization is attributed to a weakening of the near-wall turbulence production cycle."}],"doi":"10.1007/s10494-018-9896-4","publication_status":"published","external_id":{"isi":["000433113900004"]},"department":[{"_id":"BjHo"}],"file":[{"date_created":"2018-12-17T15:52:37Z","content_type":"application/pdf","checksum":"d7c0bade150faabca150b0a9986e60ca","file_id":"5717","relation":"main_file","access_level":"open_access","date_updated":"2020-07-14T12:46:25Z","file_name":"2018_FlowTurbulenceCombust_Kuehnen.pdf","file_size":2210020,"creator":"dernst"}],"intvolume":"       100","publication":"Flow Turbulence and Combustion","file_date_updated":"2020-07-14T12:46:25Z","year":"2018","publist_id":"7401","date_created":"2018-12-11T11:46:23Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","tmp":{"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)","image":"/images/cc_by.png"},"volume":100,"date_updated":"2026-08-09T22:30:23Z","project":[{"grant_number":"306589","_id":"25152F3A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Decoding the complexity of turbulence at its origin"}],"ddc":["530"],"date_published":"2018-01-01T00:00:00Z","oa_version":"Published Version","scopus_import":"1","isi":1,"title":"Relaminarization by steady modification of the streamwise velocity profile in a pipe","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"7258"}]},"citation":{"short":"J. Kühnen, D. Scarselli, M. Schaner, B. Hof, Flow Turbulence and Combustion 100 (2018) 919–942.","ama":"Kühnen J, Scarselli D, Schaner M, Hof B. Relaminarization by steady modification of the streamwise velocity profile in a pipe. <i>Flow Turbulence and Combustion</i>. 2018;100(4):919-942. doi:<a href=\"https://doi.org/10.1007/s10494-018-9896-4\">10.1007/s10494-018-9896-4</a>","ieee":"J. Kühnen, D. Scarselli, M. Schaner, and B. Hof, “Relaminarization by steady modification of the streamwise velocity profile in a pipe,” <i>Flow Turbulence and Combustion</i>, vol. 100, no. 4. Springer, pp. 919–942, 2018.","ista":"Kühnen J, Scarselli D, Schaner M, Hof B. 2018. Relaminarization by steady modification of the streamwise velocity profile in a pipe. Flow Turbulence and Combustion. 100(4), 919–942.","apa":"Kühnen, J., Scarselli, D., Schaner, M., &#38; Hof, B. (2018). Relaminarization by steady modification of the streamwise velocity profile in a pipe. <i>Flow Turbulence and Combustion</i>. Springer. <a href=\"https://doi.org/10.1007/s10494-018-9896-4\">https://doi.org/10.1007/s10494-018-9896-4</a>","mla":"Kühnen, Jakob, et al. “Relaminarization by Steady Modification of the Streamwise Velocity Profile in a Pipe.” <i>Flow Turbulence and Combustion</i>, vol. 100, no. 4, Springer, 2018, pp. 919–42, doi:<a href=\"https://doi.org/10.1007/s10494-018-9896-4\">10.1007/s10494-018-9896-4</a>.","chicago":"Kühnen, Jakob, Davide Scarselli, Markus Schaner, and Björn Hof. “Relaminarization by Steady Modification of the Streamwise Velocity Profile in a Pipe.” <i>Flow Turbulence and Combustion</i>. Springer, 2018. <a href=\"https://doi.org/10.1007/s10494-018-9896-4\">https://doi.org/10.1007/s10494-018-9896-4</a>."},"has_accepted_license":"1","month":"01","quality_controlled":"1","publisher":"Springer","type":"journal_article","day":"01","status":"public","page":"919 - 942","language":[{"iso":"eng"}],"oa":1,"author":[{"id":"3A47AE32-F248-11E8-B48F-1D18A9856A87","last_name":"Kühnen","orcid":"0000-0003-4312-0179","full_name":"Kühnen, Jakob","first_name":"Jakob"},{"first_name":"Davide","id":"40315C30-F248-11E8-B48F-1D18A9856A87","full_name":"Scarselli, Davide","orcid":"0000-0001-5227-4271","last_name":"Scarselli"},{"id":"316CE034-F248-11E8-B48F-1D18A9856A87","last_name":"Schaner","full_name":"Schaner, Markus","first_name":"Markus"},{"first_name":"Björn","last_name":"Hof","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"Yes (via OA deal)","corr_author":"1","_id":"422","issue":"4"},{"publication":"Nature Physics","intvolume":"        14","doi":"10.1038/s41567-017-0018-3","ec_funded":1,"abstract":[{"text":"Turbulence is the major cause of friction losses in transport processes and it is responsible for a drastic drag increase in flows over bounding surfaces. While much effort is invested into developing ways to control and reduce turbulence intensities, so far no methods exist to altogether eliminate turbulence if velocities are sufficiently large. We demonstrate for pipe flow that appropriate distortions to the velocity profile lead to a complete collapse of turbulence and subsequently friction losses are reduced by as much as 90%. Counterintuitively, the return to laminar motion is accomplished by initially increasing turbulence intensities or by transiently amplifying wall shear. Since neither the Reynolds number nor the shear stresses decrease (the latter often increase), these measures are not indicative of turbulence collapse. Instead, an amplification mechanism                      measuring the interaction between eddies and the mean shear is found to set a threshold below which turbulence is suppressed beyond recovery.","lang":"eng"}],"department":[{"_id":"BjHo"}],"external_id":{"arxiv":["1711.06543"],"isi":["000429434100020"]},"publication_status":"published","date_updated":"2026-08-09T22:30:23Z","volume":14,"date_published":"2018-01-08T00:00:00Z","project":[{"name":"Decoding the complexity of turbulence at its origin","_id":"25152F3A-B435-11E9-9278-68D0E5697425","grant_number":"306589","call_identifier":"FP7"},{"grant_number":"737549","_id":"25104D44-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Eliminating turbulence in oil pipelines"}],"date_created":"2018-12-11T11:46:36Z","main_file_link":[{"url":"https://arxiv.org/abs/1711.06543","open_access":"1"}],"publist_id":"7360","year":"2018","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","arxiv":1,"citation":{"ama":"Kühnen J, Song B, Scarselli D, et al. Destabilizing turbulence in pipe flow. <i>Nature Physics</i>. 2018;14:386-390. doi:<a href=\"https://doi.org/10.1038/s41567-017-0018-3\">10.1038/s41567-017-0018-3</a>","ieee":"J. Kühnen <i>et al.</i>, “Destabilizing turbulence in pipe flow,” <i>Nature Physics</i>, vol. 14. Nature Publishing Group, pp. 386–390, 2018.","short":"J. Kühnen, B. Song, D. Scarselli, N.B. Budanur, M. Riedl, A. Willis, M. Avila, B. Hof, Nature Physics 14 (2018) 386–390.","ista":"Kühnen J, Song B, Scarselli D, Budanur NB, Riedl M, Willis A, Avila M, Hof B. 2018. Destabilizing turbulence in pipe flow. Nature Physics. 14, 386–390.","apa":"Kühnen, J., Song, B., Scarselli, D., Budanur, N. B., Riedl, M., Willis, A., … Hof, B. (2018). Destabilizing turbulence in pipe flow. <i>Nature Physics</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41567-017-0018-3\">https://doi.org/10.1038/s41567-017-0018-3</a>","mla":"Kühnen, Jakob, et al. “Destabilizing Turbulence in Pipe Flow.” <i>Nature Physics</i>, vol. 14, Nature Publishing Group, 2018, pp. 386–90, doi:<a href=\"https://doi.org/10.1038/s41567-017-0018-3\">10.1038/s41567-017-0018-3</a>.","chicago":"Kühnen, Jakob, Baofang Song, Davide Scarselli, Nazmi B Budanur, Michael Riedl, Ashley Willis, Marc Avila, and Björn Hof. “Destabilizing Turbulence in Pipe Flow.” <i>Nature Physics</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41567-017-0018-3\">https://doi.org/10.1038/s41567-017-0018-3</a>."},"isi":1,"oa_version":"Preprint","acknowledgement":"We acknowledge the European Research Council under the European Union’s Seventh Framework Programme (FP/2007-2013)/ERC Grant Agreement 306589, the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 737549) and the Deutsche Forschungsgemeinschaft (Project No. FOR 1182) for financial support. We thank our technician P. Maier for providing highly valuable ideas and greatly supporting us in all technical aspects. We thank M. Schaner for technical drawings, construction and design. We thank M. Schwegel for a Matlab code to post-process experimental data.","scopus_import":"1","related_material":{"record":[{"id":"12726","relation":"dissertation_contains","status":"public"},{"relation":"dissertation_contains","status":"public","id":"14530"},{"id":"7258","status":"public","relation":"dissertation_contains"}]},"title":"Destabilizing turbulence in pipe flow","author":[{"first_name":"Jakob","id":"3A47AE32-F248-11E8-B48F-1D18A9856A87","last_name":"Kühnen","full_name":"Kühnen, Jakob","orcid":"0000-0003-4312-0179"},{"last_name":"Song","full_name":"Song, Baofang","first_name":"Baofang"},{"id":"40315C30-F248-11E8-B48F-1D18A9856A87","full_name":"Scarselli, Davide","orcid":"0000-0001-5227-4271","last_name":"Scarselli","first_name":"Davide"},{"id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","last_name":"Budanur","full_name":"Budanur, Nazmi B","orcid":"0000-0003-0423-5010","first_name":"Nazmi B"},{"first_name":"Michael","id":"3BE60946-F248-11E8-B48F-1D18A9856A87","last_name":"Riedl","orcid":"0000-0003-4844-6311","full_name":"Riedl, Michael"},{"full_name":"Willis, Ashley","last_name":"Willis","first_name":"Ashley"},{"first_name":"Marc","full_name":"Avila, Marc","last_name":"Avila"},{"first_name":"Björn","last_name":"Hof","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"language":[{"iso":"eng"}],"_id":"461","corr_author":"1","article_processing_charge":"No","publisher":"Nature Publishing Group","quality_controlled":"1","month":"01","status":"public","page":"386-390","day":"08","type":"journal_article"},{"date_created":"2018-12-11T11:47:04Z","year":"2018","publist_id":"7274","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":208,"tmp":{"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)","image":"/images/cc_by.png"},"date_updated":"2026-08-09T22:30:27Z","ddc":["576"],"project":[{"name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","_id":"250BDE62-B435-11E9-9278-68D0E5697425","grant_number":"715257","call_identifier":"H2020"}],"date_published":"2018-01-01T00:00:00Z","doi":"10.1534/genetics.117.300513","ec_funded":1,"abstract":[{"lang":"eng","text":"The t-haplotype, a mouse meiotic driver found on chromosome 17, has been a model for autosomal segregation distortion for close to a century, but several questions remain regarding its biology and evolutionary history. A recently published set of population genomics resources for wild mice includes several individuals heterozygous for the t-haplotype, which we use to characterize this selfish element at the genomic and transcriptomic level. Our results show that large sections of the t-haplotype have been replaced by standard homologous sequences, possibly due to occasional events of recombination, and that this complicates the inference of its history. As expected for a long genomic segment of very low recombination, the t-haplotype carries an excess of fixed nonsynonymous mutations compared to the standard chromosome. This excess is stronger for regions that have not undergone recent recombination, suggesting that occasional gene flow between the t and the standard chromosome may provide a mechanism to regenerate coding sequences that have accumulated deleterious mutations. Finally, we find that t-complex genes with altered expression largely overlap with deleted or amplified regions, and that carrying a t-haplotype alters the testis expression of genes outside of the t-complex, providing new leads into the pathways involved in the biology of this segregation distorter."}],"external_id":{"isi":["000419356300024"]},"department":[{"_id":"BeVi"}],"publication_status":"published","intvolume":"       208","file":[{"date_created":"2018-12-12T10:15:14Z","content_type":"application/pdf","file_id":"5132","checksum":"2123845e7031a0cf043905be160f9e69","relation":"main_file","access_level":"open_access","file_name":"IST-2018-1058-v1+1_365.full__1_.pdf","date_updated":"2020-07-14T12:46:50Z","file_size":1311661,"creator":"system"}],"publication":"Genetics","file_date_updated":"2020-07-14T12:46:50Z","publisher":"Genetics Society of America","month":"01","quality_controlled":"1","status":"public","page":"365 - 375","type":"journal_article","day":"01","author":[{"first_name":"Réka K","id":"48D3F8DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8489-9281","full_name":"Kelemen, Réka K","last_name":"Kelemen"},{"first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz"}],"oa":1,"language":[{"iso":"eng"}],"issue":"1","_id":"542","corr_author":"1","article_processing_charge":"No","article_type":"original","isi":1,"scopus_import":"1","oa_version":"Published Version","related_material":{"record":[{"relation":"popular_science","status":"public","id":"5571"},{"relation":"popular_science","status":"public","id":"5572"},{"relation":"dissertation_contains","status":"public","id":"17119"}]},"title":"Complex history and differentiation patterns of the t-haplotype, a mouse meiotic driver","pubrep_id":"1058","has_accepted_license":"1","citation":{"mla":"Kelemen, Réka K., and Beatriz Vicoso. “Complex History and Differentiation Patterns of the T-Haplotype, a Mouse Meiotic Driver.” <i>Genetics</i>, vol. 208, no. 1, Genetics Society of America, 2018, pp. 365–75, doi:<a href=\"https://doi.org/10.1534/genetics.117.300513\">10.1534/genetics.117.300513</a>.","chicago":"Kelemen, Réka K, and Beatriz Vicoso. “Complex History and Differentiation Patterns of the T-Haplotype, a Mouse Meiotic Driver.” <i>Genetics</i>. Genetics Society of America, 2018. <a href=\"https://doi.org/10.1534/genetics.117.300513\">https://doi.org/10.1534/genetics.117.300513</a>.","ieee":"R. K. Kelemen and B. Vicoso, “Complex history and differentiation patterns of the t-haplotype, a mouse meiotic driver,” <i>Genetics</i>, vol. 208, no. 1. Genetics Society of America, pp. 365–375, 2018.","ama":"Kelemen RK, Vicoso B. Complex history and differentiation patterns of the t-haplotype, a mouse meiotic driver. <i>Genetics</i>. 2018;208(1):365-375. doi:<a href=\"https://doi.org/10.1534/genetics.117.300513\">10.1534/genetics.117.300513</a>","short":"R.K. Kelemen, B. Vicoso, Genetics 208 (2018) 365–375.","ista":"Kelemen RK, Vicoso B. 2018. Complex history and differentiation patterns of the t-haplotype, a mouse meiotic driver. Genetics. 208(1), 365–375.","apa":"Kelemen, R. K., &#38; Vicoso, B. (2018). Complex history and differentiation patterns of the t-haplotype, a mouse meiotic driver. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.117.300513\">https://doi.org/10.1534/genetics.117.300513</a>"}},{"doi":"10.1105/tpc.17.00785","abstract":[{"lang":"eng","text":"Clathrin-mediated endocytosis (CME) is a cellular trafficking process in which cargoes and lipids are internalized from the plasma membrane into vesicles coated with clathrin and adaptor proteins. CME is essential for many developmental and physiological processes in plants, but its underlying mechanism is not well characterised compared to that in yeast and animal systems. Here, we searched for new factors involved in CME in Arabidopsis thaliana by performing Tandem Affinity Purification of proteins that interact with clathrin light chain, a principal component of the clathrin coat. Among the confirmed interactors, we found two putative homologues of the clathrin-coat uncoating factor auxilin previously described in non-plant systems. Overexpression of AUXILIN-LIKE1 and AUXILIN-LIKE2 in A. thaliana caused an arrest of seedling growth and development. This was concomitant with inhibited endocytosis due to blocking of clathrin recruitment after the initial step of adaptor protein binding to the plasma membrane. By contrast, auxilin-like(1/2) loss-of-function lines did not present endocytosis-related developmental or cellular phenotypes under normal growth conditions. This work contributes to the on-going characterization of the endocytotic machinery in plants and provides a robust tool for conditionally and specifically interfering with CME in A. thaliana."}],"ec_funded":1,"department":[{"_id":"JiFr"}],"external_id":{"isi":["000429441400018"],"pmid":["29511054"]},"publication_status":"published","file":[{"content_type":"application/pdf","success":1,"date_created":"2022-05-23T09:12:38Z","relation":"main_file","checksum":"4e165e653b67d3f0684697f21aace5a1","file_id":"11406","file_size":4407538,"file_name":"2018_PlantCell_Adamowski.pdf","date_updated":"2022-05-23T09:12:38Z","access_level":"open_access","creator":"dernst"}],"publication":"The Plant Cell","intvolume":"        30","file_date_updated":"2022-05-23T09:12:38Z","date_created":"2018-12-11T11:46:20Z","publist_id":"7417","year":"2018","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2026-08-09T22:30:34Z","tmp":{"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)","image":"/images/cc_by.png"},"volume":30,"date_published":"2018-04-09T00:00:00Z","ddc":["580"],"project":[{"name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300"}],"isi":1,"oa_version":"Published Version","acknowledgement":"We thank James Matthew Watson, Monika Borowska, and Peggy Stolt-Bergner at ProTech Facility of the Vienna Biocenter Core Facilities for the CRISPR/CAS9 construct; Anna Müller for assistance with molecular cloning; Sebastian Bednarek, Liwen Jiang, and Daniël Van Damme for sharing published material; Matyáš Fendrych, Daniël Van Damme, and Lindy Abas for valuable discussions; and Martine De Cock for help with correcting the manuscript. This work was supported by the European Research Council under the European Union Seventh Framework Programme (FP7/2007-2013)/ERC Grant 282300 and by the Ministry of Education of the Czech Republic/MŠMT project NPUI-LO1417.","scopus_import":"1","title":"A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis","related_material":{"record":[{"id":"6269","relation":"dissertation_contains","status":"public"}]},"has_accepted_license":"1","citation":{"chicago":"Adamowski, Maciek, Madhumitha Narasimhan, Urszula Kania, Matous Glanc, Geert De Jaeger, and Jiří Friml. “A Functional Study of AUXILIN LIKE1 and 2 Two Putative Clathrin Uncoating Factors in Arabidopsis.” <i>The Plant Cell</i>. American Society of Plant Biologists, 2018. <a href=\"https://doi.org/10.1105/tpc.17.00785\">https://doi.org/10.1105/tpc.17.00785</a>.","mla":"Adamowski, Maciek, et al. “A Functional Study of AUXILIN LIKE1 and 2 Two Putative Clathrin Uncoating Factors in Arabidopsis.” <i>The Plant Cell</i>, vol. 30, no. 3, American Society of Plant Biologists, 2018, pp. 700–16, doi:<a href=\"https://doi.org/10.1105/tpc.17.00785\">10.1105/tpc.17.00785</a>.","ama":"Adamowski M, Narasimhan M, Kania U, Glanc M, De Jaeger G, Friml J. A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis. <i>The Plant Cell</i>. 2018;30(3):700-716. doi:<a href=\"https://doi.org/10.1105/tpc.17.00785\">10.1105/tpc.17.00785</a>","short":"M. Adamowski, M. Narasimhan, U. Kania, M. Glanc, G. De Jaeger, J. Friml, The Plant Cell 30 (2018) 700–716.","ieee":"M. Adamowski, M. Narasimhan, U. Kania, M. Glanc, G. De Jaeger, and J. Friml, “A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis,” <i>The Plant Cell</i>, vol. 30, no. 3. American Society of Plant Biologists, pp. 700–716, 2018.","ista":"Adamowski M, Narasimhan M, Kania U, Glanc M, De Jaeger G, Friml J. 2018. A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis. The Plant Cell. 30(3), 700–716.","apa":"Adamowski, M., Narasimhan, M., Kania, U., Glanc, M., De Jaeger, G., &#38; Friml, J. (2018). A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis. <i>The Plant Cell</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1105/tpc.17.00785\">https://doi.org/10.1105/tpc.17.00785</a>"},"pmid":1,"publisher":"American Society of Plant Biologists","publication_identifier":{"eissn":["1532-298X"],"issn":["1040-4651"]},"month":"04","quality_controlled":"1","page":"700 - 716","status":"public","day":"09","type":"journal_article","author":[{"id":"45F536D2-F248-11E8-B48F-1D18A9856A87","full_name":"Adamowski, Maciek","orcid":"0000-0001-6463-5257","last_name":"Adamowski","first_name":"Maciek"},{"first_name":"Madhumitha","orcid":"0000-0002-8600-0671","full_name":"Narasimhan, Madhumitha","last_name":"Narasimhan","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87"},{"id":"4AE5C486-F248-11E8-B48F-1D18A9856A87","last_name":"Kania","full_name":"Kania, Urszula","first_name":"Urszula"},{"first_name":"Matous","last_name":"Glanc","orcid":"0000-0003-0619-7783","full_name":"Glanc, Matous","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2"},{"first_name":"Geert","full_name":"De Jaeger, Geert","last_name":"De Jaeger"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","first_name":"Jirí"}],"oa":1,"language":[{"iso":"eng"}],"_id":"412","issue":"3","corr_author":"1","article_type":"original","article_processing_charge":"No"},{"language":[{"iso":"eng"}],"oa":1,"author":[{"first_name":"Igor","id":"4B60654C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1807-1929","full_name":"Gridchyn, Igor","last_name":"Gridchyn"}],"supervisor":[{"id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari","orcid":"0000-0002-5193-4036","full_name":"Csicsvari, Jozsef L","first_name":"Jozsef L"}],"article_processing_charge":"No","corr_author":"1","_id":"48","month":"08","publisher":"Institute of Science and Technology Austria","publication_identifier":{"issn":["2663-337X"]},"type":"dissertation","day":"27","page":"104","status":"public","OA_place":"publisher","citation":{"chicago":"Gridchyn, Igor. “Reactivation Content Is Important for Consolidation of Spatial Memory.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:th_1042\">https://doi.org/10.15479/AT:ISTA:th_1042</a>.","mla":"Gridchyn, Igor. <i>Reactivation Content Is Important for Consolidation of Spatial Memory</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_1042\">10.15479/AT:ISTA:th_1042</a>.","ama":"Gridchyn I. Reactivation content is important for consolidation of spatial memory. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_1042\">10.15479/AT:ISTA:th_1042</a>","ieee":"I. Gridchyn, “Reactivation content is important for consolidation of spatial memory,” Institute of Science and Technology Austria, 2018.","short":"I. Gridchyn, Reactivation Content Is Important for Consolidation of Spatial Memory, Institute of Science and Technology Austria, 2018.","apa":"Gridchyn, I. (2018). <i>Reactivation content is important for consolidation of spatial memory</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_1042\">https://doi.org/10.15479/AT:ISTA:th_1042</a>","ista":"Gridchyn I. 2018. Reactivation content is important for consolidation of spatial memory. Institute of Science and Technology Austria."},"pubrep_id":"1042","has_accepted_license":"1","oa_version":"Published Version","title":"Reactivation content is important for consolidation of spatial memory","tmp":{"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)","image":"/images/cc_by.png"},"date_updated":"2026-04-08T14:13:15Z","ddc":["573"],"date_published":"2018-08-27T00:00:00Z","year":"2018","publist_id":"8006","date_created":"2018-12-11T11:44:21Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file":[{"file_name":"2018_Thesis_Gridchyn_source.docx","date_updated":"2021-02-11T23:30:22Z","file_size":7666687,"embargo_to":"open_access","access_level":"closed","creator":"dernst","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2019-04-08T13:36:01Z","relation":"source_file","checksum":"7db4415e435590fa33542c7b0a0321d7","file_id":"6236"},{"file_id":"6237","checksum":"f96f3fe8979f7b1e6db6acaca962b10c","relation":"main_file","date_created":"2019-04-08T13:36:01Z","content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2018_Thesis_Gridchyn.pdf","file_size":6034153,"date_updated":"2021-02-11T11:17:18Z","embargo":"2019-08-29"}],"file_date_updated":"2021-02-11T23:30:22Z","abstract":[{"text":"The hippocampus is a key brain region for spatial memory and navigation and is needed at all stages of memory, including encoding, consolidation, and recall. Hippocampal place cells selectively discharge at specific locations of the environment to form a cognitive map of the space. During the rest period and sleep following spatial navigation and/or learning, the waking activity of the place cells is reactivated within high synchrony events. This reactivation is thought to be important for memory consolidation and stabilization of the spatial representations. The aim of my thesis was to directly test whether the reactivation content encoded in firing patterns of place cells is important for consolidation of spatial memories. In particular, I aimed to test whether, in cases when multiple spatial memory traces are acquired during learning, the specific disruption of the reactivation of a subset of these memories leads to the selective disruption of the corresponding memory traces or through memory interference the other learned memories are disrupted as well. In this thesis, using a modified cheeseboard paradigm and a closed-loop recording setup with feedback optogenetic stimulation, I examined how the disruption of the reactivation of specific spiking patterns affects consolidation of the corresponding memory traces. To obtain multiple distinctive memories, animals had to perform a spatial task in two distinct cheeseboard environments and the reactivation of spiking patterns associated with one of the environments (target) was disrupted after learning during four hours rest period using a real-time decoding method. This real-time decoding method was capable of selectively affecting the firing rates and cofiring correlations of the target environment-encoding cells. The selective disruption led to behavioural impairment in the memory tests after the rest periods in the target environment but not in the other undisrupted control environment. In addition, the map of the target environment was less stable in the impaired memory tests compared to the learning session before than the map of the control environment. However, when the animal relearned the task, the same map recurred in the target environment that was present during learning before the disruption. Altogether my work demonstrated that the reactivation content is important: assembly-related disruption of reactivation can lead to a selective memory impairment and deficiency in map stability. These findings indeed suggest that reactivated assembly patterns reflect processes associated with the consolidation of memory traces. ","lang":"eng"}],"alternative_title":["ISTA Thesis"],"doi":"10.15479/AT:ISTA:th_1042","degree_awarded":"PhD","publication_status":"published","department":[{"_id":"JoCs"}]}]