[{"publisher":"EMBO","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"X10 expansion microscopy enables 25‐nm resolution on conventional microscopes","author":[{"last_name":"Truckenbrodt","id":"45812BD4-F248-11E8-B48F-1D18A9856A87","first_name":"Sven M","full_name":"Truckenbrodt, Sven M"},{"last_name":"Maidorn","first_name":"Manuel","full_name":"Maidorn, Manuel"},{"first_name":"Dagmar","last_name":"Crzan","full_name":"Crzan, Dagmar"},{"last_name":"Wildhagen","first_name":"Hanna","full_name":"Wildhagen, Hanna"},{"full_name":"Kabatas, Selda","last_name":"Kabatas","first_name":"Selda"},{"first_name":"Silvio O","last_name":"Rizzoli","full_name":"Rizzoli, Silvio O"}],"isi":1,"file":[{"date_created":"2019-05-28T13:17:19Z","file_name":"2018_embo_Truckenbrodt.pdf","date_updated":"2020-07-14T12:47:32Z","access_level":"open_access","file_id":"6500","creator":"kschuh","checksum":"6ec90abc637f09cca3a7b6424d7e7a26","file_size":2005572,"relation":"main_file","content_type":"application/pdf"}],"day":"01","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"external_id":{"isi":["000443682200009"]},"quality_controlled":"1","volume":19,"article_processing_charge":"No","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"JoDa"}],"has_accepted_license":"1","date_created":"2019-05-28T13:16:08Z","publication":"EMBO reports","month":"09","status":"public","oa":1,"publication_identifier":{"eissn":["1469-3178"],"issn":["1469-221X"]},"article_number":"e45836","_id":"6499","date_updated":"2023-09-19T14:52:32Z","abstract":[{"lang":"eng","text":"Expansion microscopy is a recently introduced imaging technique that achieves super‐resolution through physically expanding the specimen by ~4×, after embedding into a swellable gel. The resolution attained is, correspondingly, approximately fourfold better than the diffraction limit, or ~70 nm. This is a major improvement over conventional microscopy, but still lags behind modern STED or STORM setups, whose resolution can reach 20–30 nm. We addressed this issue here by introducing an improved gel recipe that enables an expansion factor of ~10× in each dimension, which corresponds to an expansion of the sample volume by more than 1,000‐fold. Our protocol, which we termed X10 microscopy, achieves a resolution of 25–30 nm on conventional epifluorescence microscopes. X10 provides multi‐color images similar or even superior to those produced with more challenging methods, such as STED, STORM, and iterative expansion microscopy (iExM). X10 is therefore the cheapest and easiest option for high‐quality super‐resolution imaging currently available. X10 should be usable in any laboratory, irrespective of the machinery owned or of the technical knowledge."}],"issue":"9","year":"2018","intvolume":"        19","citation":{"chicago":"Truckenbrodt, Sven M, Manuel Maidorn, Dagmar Crzan, Hanna Wildhagen, Selda Kabatas, and Silvio O Rizzoli. “X10 Expansion Microscopy Enables 25‐nm Resolution on Conventional Microscopes.” <i>EMBO Reports</i>. EMBO, 2018. <a href=\"https://doi.org/10.15252/embr.201845836\">https://doi.org/10.15252/embr.201845836</a>.","mla":"Truckenbrodt, Sven M., et al. “X10 Expansion Microscopy Enables 25‐nm Resolution on Conventional Microscopes.” <i>EMBO Reports</i>, vol. 19, no. 9, e45836, EMBO, 2018, doi:<a href=\"https://doi.org/10.15252/embr.201845836\">10.15252/embr.201845836</a>.","apa":"Truckenbrodt, S. M., Maidorn, M., Crzan, D., Wildhagen, H., Kabatas, S., &#38; Rizzoli, S. O. (2018). X10 expansion microscopy enables 25‐nm resolution on conventional microscopes. <i>EMBO Reports</i>. EMBO. <a href=\"https://doi.org/10.15252/embr.201845836\">https://doi.org/10.15252/embr.201845836</a>","ista":"Truckenbrodt SM, Maidorn M, Crzan D, Wildhagen H, Kabatas S, Rizzoli SO. 2018. X10 expansion microscopy enables 25‐nm resolution on conventional microscopes. EMBO reports. 19(9), e45836.","short":"S.M. Truckenbrodt, M. Maidorn, D. Crzan, H. Wildhagen, S. Kabatas, S.O. Rizzoli, EMBO Reports 19 (2018).","ieee":"S. M. Truckenbrodt, M. Maidorn, D. Crzan, H. Wildhagen, S. Kabatas, and S. O. Rizzoli, “X10 expansion microscopy enables 25‐nm resolution on conventional microscopes,” <i>EMBO reports</i>, vol. 19, no. 9. EMBO, 2018.","ama":"Truckenbrodt SM, Maidorn M, Crzan D, Wildhagen H, Kabatas S, Rizzoli SO. X10 expansion microscopy enables 25‐nm resolution on conventional microscopes. <i>EMBO reports</i>. 2018;19(9). doi:<a href=\"https://doi.org/10.15252/embr.201845836\">10.15252/embr.201845836</a>"},"scopus_import":"1","file_date_updated":"2020-07-14T12:47:32Z","ddc":["580"],"oa_version":"Published Version","date_published":"2018-09-01T00:00:00Z","publication_status":"published","doi":"10.15252/embr.201845836"},{"citation":{"chicago":"Hausel, Tamás, Anton Mellit, and Du Pei. “Mirror Symmetry with Branes by Equivariant Verlinde Formulas.” In <i>Geometry and Physics: Volume I</i>, 189–218. Oxford University Press, 2018. <a href=\"https://doi.org/10.1093/oso/9780198802013.003.0009\">https://doi.org/10.1093/oso/9780198802013.003.0009</a>.","ista":"Hausel T, Mellit A, Pei D. 2018.Mirror symmetry with branes by equivariant verlinde formulas. In: Geometry and Physics: Volume I. , 189–218.","apa":"Hausel, T., Mellit, A., &#38; Pei, D. (2018). Mirror symmetry with branes by equivariant verlinde formulas. In <i>Geometry and Physics: Volume I</i> (pp. 189–218). Oxford University Press. <a href=\"https://doi.org/10.1093/oso/9780198802013.003.0009\">https://doi.org/10.1093/oso/9780198802013.003.0009</a>","mla":"Hausel, Tamás, et al. “Mirror Symmetry with Branes by Equivariant Verlinde Formulas.” <i>Geometry and Physics: Volume I</i>, Oxford University Press, 2018, pp. 189–218, doi:<a href=\"https://doi.org/10.1093/oso/9780198802013.003.0009\">10.1093/oso/9780198802013.003.0009</a>.","short":"T. Hausel, A. Mellit, D. Pei, in:, Geometry and Physics: Volume I, Oxford University Press, 2018, pp. 189–218.","ieee":"T. Hausel, A. Mellit, and D. Pei, “Mirror symmetry with branes by equivariant verlinde formulas,” in <i>Geometry and Physics: Volume I</i>, Oxford University Press, 2018, pp. 189–218.","ama":"Hausel T, Mellit A, Pei D. Mirror symmetry with branes by equivariant verlinde formulas. In: <i>Geometry and Physics: Volume I</i>. Oxford University Press; 2018:189-218. doi:<a href=\"https://doi.org/10.1093/oso/9780198802013.003.0009\">10.1093/oso/9780198802013.003.0009</a>"},"quality_controlled":"1","scopus_import":1,"oa_version":"None","type":"book_chapter","department":[{"_id":"TaHa"}],"date_published":"2018-01-01T00:00:00Z","language":[{"iso":"eng"}],"doi":"10.1093/oso/9780198802013.003.0009","publication_status":"published","publication":"Geometry and Physics: Volume I","date_created":"2019-06-06T12:42:01Z","page":"189-218","month":"01","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","publisher":"Oxford University Press","publication_identifier":{"isbn":["9780198802013","9780191840500"]},"title":"Mirror symmetry with branes by equivariant verlinde formulas","author":[{"full_name":"Hausel, Tamás","first_name":"Tamás","id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","last_name":"Hausel"},{"first_name":"Anton","last_name":"Mellit","id":"388D3134-F248-11E8-B48F-1D18A9856A87","full_name":"Mellit, Anton"},{"full_name":"Pei, Du","first_name":"Du","last_name":"Pei"}],"_id":"6525","abstract":[{"lang":"eng","text":"This chapter finds an agreement of equivariant indices of semi-classical homomorphisms between pairwise mirror branes in the GL2 Higgs moduli space on a Riemann surface. On one side of the agreement, components of the Lagrangian brane of U(1,1) Higgs bundles, whose mirror was proposed by Hitchin to be certain even exterior powers of the hyperholomorphic Dirac bundle on the SL2 Higgs moduli space, are present. The agreement arises from a mysterious functional equation. This gives strong computational evidence for Hitchin’s proposal."}],"date_updated":"2021-01-12T08:07:52Z","year":"2018","day":"01"},{"external_id":{"isi":["000461823304061"],"arxiv":["1803.08917"]},"volume":2018,"quality_controlled":"1","article_processing_charge":"No","language":[{"iso":"eng"}],"department":[{"_id":"DaAl"}],"type":"conference","page":"4613-4623","date_created":"2019-06-13T08:22:37Z","publication":"Advances in Neural Information Processing Systems","title":"Byzantine stochastic gradient descent","publisher":"Neural Information Processing Systems Foundation","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","isi":1,"author":[{"last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian"},{"full_name":"Allen-Zhu, Zeyuan","last_name":"Allen-Zhu","first_name":"Zeyuan"},{"first_name":"Jerry","last_name":"Li","full_name":"Li, Jerry"}],"day":"01","citation":{"chicago":"Alistarh, Dan-Adrian, Zeyuan Allen-Zhu, and Jerry Li. “Byzantine Stochastic Gradient Descent.” In <i>Advances in Neural Information Processing Systems</i>, 2018:4613–23. Neural Information Processing Systems Foundation, 2018.","ista":"Alistarh D-A, Allen-Zhu Z, Li J. 2018. Byzantine stochastic gradient descent. Advances in Neural Information Processing Systems. NeurIPS: Conference on Neural Information Processing Systems vol. 2018, 4613–4623.","apa":"Alistarh, D.-A., Allen-Zhu, Z., &#38; Li, J. (2018). Byzantine stochastic gradient descent. In <i>Advances in Neural Information Processing Systems</i> (Vol. 2018, pp. 4613–4623). Montreal, Canada: Neural Information Processing Systems Foundation.","mla":"Alistarh, Dan-Adrian, et al. “Byzantine Stochastic Gradient Descent.” <i>Advances in Neural Information Processing Systems</i>, vol. 2018, Neural Information Processing Systems Foundation, 2018, pp. 4613–23.","ieee":"D.-A. Alistarh, Z. Allen-Zhu, and J. Li, “Byzantine stochastic gradient descent,” in <i>Advances in Neural Information Processing Systems</i>, Montreal, Canada, 2018, vol. 2018, pp. 4613–4623.","ama":"Alistarh D-A, Allen-Zhu Z, Li J. Byzantine stochastic gradient descent. In: <i>Advances in Neural Information Processing Systems</i>. Vol 2018. Neural Information Processing Systems Foundation; 2018:4613-4623.","short":"D.-A. Alistarh, Z. Allen-Zhu, J. Li, in:, Advances in Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2018, pp. 4613–4623."},"intvolume":"      2018","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1803.08917","open_access":"1"}],"date_published":"2018-12-01T00:00:00Z","oa_version":"Published Version","publication_status":"published","conference":{"location":"Montreal, Canada","end_date":"2018-12-08","name":"NeurIPS: Conference on Neural Information Processing Systems","start_date":"2018-12-02"},"month":"12","oa":1,"status":"public","_id":"6558","year":"2018","date_updated":"2023-09-19T15:12:45Z","arxiv":1,"abstract":[{"text":"This paper studies the problem of distributed stochastic optimization in an adversarial setting where, out of m machines which allegedly compute stochastic gradients every iteration, an α-fraction are Byzantine, and may behave adversarially. Our main result is a variant of stochastic gradient descent (SGD) which finds ε-approximate minimizers of convex functions in T=O~(1/ε²m+α²/ε²) iterations. In contrast, traditional mini-batch SGD needs T=O(1/ε²m) iterations, but cannot tolerate Byzantine failures. Further, we provide a lower bound showing that, up to logarithmic factors, our algorithm is information-theoretically optimal both in terms of sample complexity and time complexity.","lang":"eng"}]},{"main_file_link":[{"url":"https://arxiv.org/abs/1809.10505","open_access":"1"}],"scopus_import":"1","citation":{"short":"D.-A. Alistarh, T. Hoefler, M. Johansson, N.H. Konstantinov, S. Khirirat, C. Renggli, in:, Advances in Neural Information Processing Systems 31, Neural Information Processing Systems Foundation, 2018, pp. 5973–5983.","ieee":"D.-A. Alistarh, T. Hoefler, M. Johansson, N. H. Konstantinov, S. Khirirat, and C. Renggli, “The convergence of sparsified gradient methods,” in <i>Advances in Neural Information Processing Systems 31</i>, Montreal, Canada, 2018, vol. Volume 2018, pp. 5973–5983.","ama":"Alistarh D-A, Hoefler T, Johansson M, Konstantinov NH, Khirirat S, Renggli C. The convergence of sparsified gradient methods. In: <i>Advances in Neural Information Processing Systems 31</i>. Vol Volume 2018. Neural Information Processing Systems Foundation; 2018:5973-5983.","apa":"Alistarh, D.-A., Hoefler, T., Johansson, M., Konstantinov, N. H., Khirirat, S., &#38; Renggli, C. (2018). The convergence of sparsified gradient methods. In <i>Advances in Neural Information Processing Systems 31</i> (Vol. Volume 2018, pp. 5973–5983). Montreal, Canada: Neural Information Processing Systems Foundation.","ista":"Alistarh D-A, Hoefler T, Johansson M, Konstantinov NH, Khirirat S, Renggli C. 2018. The convergence of sparsified gradient methods. Advances in Neural Information Processing Systems 31. NeurIPS: Conference on Neural Information Processing Systems vol. Volume 2018, 5973–5983.","mla":"Alistarh, Dan-Adrian, et al. “The Convergence of Sparsified Gradient Methods.” <i>Advances in Neural Information Processing Systems 31</i>, vol. Volume 2018, Neural Information Processing Systems Foundation, 2018, pp. 5973–83.","chicago":"Alistarh, Dan-Adrian, Torsten Hoefler, Mikael Johansson, Nikola H Konstantinov, Sarit Khirirat, and Cedric Renggli. “The Convergence of Sparsified Gradient Methods.” In <i>Advances in Neural Information Processing Systems 31</i>, Volume 2018:5973–83. Neural Information Processing Systems Foundation, 2018."},"publication_status":"published","conference":{"end_date":"2018-12-08","location":"Montreal, Canada","start_date":"2018-12-02","name":"NeurIPS: Conference on Neural Information Processing Systems"},"date_published":"2018-12-01T00:00:00Z","oa_version":"Preprint","oa":1,"status":"public","ec_funded":1,"month":"12","year":"2018","date_updated":"2023-10-17T11:47:20Z","abstract":[{"text":"Distributed training of massive machine learning models, in particular deep neural networks, via Stochastic Gradient Descent (SGD) is becoming commonplace. Several families of communication-reduction methods, such as quantization, large-batch methods, and gradient sparsification, have been proposed. To date, gradient sparsification methods--where each node sorts gradients by magnitude, and only communicates a subset of the components, accumulating the rest locally--are known to yield some of the largest practical gains. Such methods can reduce the amount of communication per step by up to \\emph{three orders of magnitude}, while preserving model accuracy. Yet, this family of methods currently has no theoretical justification. This is the question we address in this paper. We prove that, under analytic assumptions, sparsifying gradients by magnitude with local error correction provides convergence guarantees, for both convex and non-convex smooth objectives, for data-parallel SGD. The main insight is that sparsification methods implicitly maintain bounds on the maximum impact of stale updates, thanks to selection by magnitude. Our analysis and empirical validation also reveal that these methods do require analytical conditions to converge well, justifying existing heuristics.","lang":"eng"}],"arxiv":1,"_id":"6589","article_processing_charge":"No","external_id":{"arxiv":["1809.10505"],"isi":["000461852000047"]},"quality_controlled":"1","volume":"Volume 2018","date_created":"2019-06-27T09:32:55Z","page":"5973-5983","publication":"Advances in Neural Information Processing Systems 31","language":[{"iso":"eng"}],"department":[{"_id":"DaAl"},{"_id":"ChLa"}],"type":"conference","title":"The convergence of sparsified gradient methods","publisher":"Neural Information Processing Systems Foundation","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"}],"isi":1,"author":[{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Torsten","last_name":"Hoefler","full_name":"Hoefler, Torsten"},{"last_name":"Johansson","first_name":"Mikael","full_name":"Johansson, Mikael"},{"full_name":"Konstantinov, Nikola H","first_name":"Nikola H","id":"4B9D76E4-F248-11E8-B48F-1D18A9856A87","last_name":"Konstantinov"},{"full_name":"Khirirat, Sarit","first_name":"Sarit","last_name":"Khirirat"},{"last_name":"Renggli","first_name":"Cedric","full_name":"Renggli, Cedric"}]},{"publication_identifier":{"isbn":["978-3-95977-087-3"]},"oa":1,"status":"public","ec_funded":1,"month":"09","year":"2018","date_updated":"2025-06-02T08:53:46Z","arxiv":1,"abstract":[{"lang":"eng","text":"Crypto-currencies are digital assets designed to work as a medium of exchange, e.g., Bitcoin, but they are susceptible to attacks (dishonest behavior of participants). A framework for the analysis of attacks in crypto-currencies requires (a) modeling of game-theoretic aspects to analyze incentives for deviation from honest behavior; (b) concurrent interactions between participants; and (c) analysis of long-term monetary gains. Traditional game-theoretic approaches for the analysis of security protocols consider either qualitative temporal properties such as safety and termination, or the very special class of one-shot (stateless) games. However, to analyze general attacks on protocols for crypto-currencies, both stateful analysis and quantitative objectives are necessary. In this work our main contributions are as follows: (a) we show how a class of concurrent mean-payo games, namely ergodic games, can model various attacks that arise naturally in crypto-currencies; (b) we present the first practical implementation of algorithms for ergodic games that scales to model realistic problems for crypto-currencies; and (c) we present experimental results showing that our framework can handle games with thousands of states and millions of transitions."}],"_id":"66","article_number":"11","ddc":["000"],"file_date_updated":"2020-07-14T12:47:34Z","scopus_import":"1","citation":{"chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, Rasmus Ibsen-Jensen, and Yaron Velner. “Ergodic Mean-Payoff Games for the Analysis of Attacks in Crypto-Currencies,” Vol. 118. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. <a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2018.11\">https://doi.org/10.4230/LIPIcs.CONCUR.2018.11</a>.","ista":"Chatterjee K, Goharshady AK, Ibsen-Jensen R, Velner Y. 2018. Ergodic mean-payoff games for the analysis of attacks in crypto-currencies. CONCUR: Conference on Concurrency Theory, LIPIcs, vol. 118, 11.","mla":"Chatterjee, Krishnendu, et al. <i>Ergodic Mean-Payoff Games for the Analysis of Attacks in Crypto-Currencies</i>. Vol. 118, 11, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:<a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2018.11\">10.4230/LIPIcs.CONCUR.2018.11</a>.","apa":"Chatterjee, K., Goharshady, A. K., Ibsen-Jensen, R., &#38; Velner, Y. (2018). Ergodic mean-payoff games for the analysis of attacks in crypto-currencies (Vol. 118). Presented at the CONCUR: Conference on Concurrency Theory, Beijing, China: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2018.11\">https://doi.org/10.4230/LIPIcs.CONCUR.2018.11</a>","ieee":"K. Chatterjee, A. K. Goharshady, R. Ibsen-Jensen, and Y. Velner, “Ergodic mean-payoff games for the analysis of attacks in crypto-currencies,” presented at the CONCUR: Conference on Concurrency Theory, Beijing, China, 2018, vol. 118.","ama":"Chatterjee K, Goharshady AK, Ibsen-Jensen R, Velner Y. Ergodic mean-payoff games for the analysis of attacks in crypto-currencies. In: Vol 118. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:<a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2018.11\">10.4230/LIPIcs.CONCUR.2018.11</a>","short":"K. Chatterjee, A.K. Goharshady, R. Ibsen-Jensen, Y. Velner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018."},"intvolume":"       118","conference":{"end_date":"2018-09-07","location":"Beijing, China","start_date":"2018-09-04","name":"CONCUR: Conference on Concurrency Theory"},"publication_status":"published","doi":"10.4230/LIPIcs.CONCUR.2018.11","date_published":"2018-09-01T00:00:00Z","oa_version":"Published Version","title":"Ergodic mean-payoff games for the analysis of attacks in crypto-currencies","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","alternative_title":["LIPIcs"],"day":"01","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_size":1078309,"content_type":"application/pdf","relation":"main_file","date_created":"2018-12-17T12:08:00Z","date_updated":"2020-07-14T12:47:34Z","file_name":"2018_CONCUR_Chatterjee.pdf","access_level":"open_access","checksum":"68a055b1aaa241cc38375083cf832a7d","file_id":"5696","creator":"dernst"}],"project":[{"grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"_id":"266EEEC0-B435-11E9-9278-68D0E5697425","name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts"}],"author":[{"last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"first_name":"Amir","orcid":"0000-0003-1702-6584","id":"391365CE-F248-11E8-B48F-1D18A9856A87","last_name":"Goharshady","full_name":"Goharshady, Amir"},{"full_name":"Ibsen-Jensen, Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87","last_name":"Ibsen-Jensen","orcid":"0000-0003-4783-0389","first_name":"Rasmus"},{"first_name":"Yaron","last_name":"Velner","full_name":"Velner, Yaron"}],"publist_id":"7988","article_processing_charge":"No","related_material":{"record":[{"id":"8934","relation":"dissertation_contains","status":"public"}]},"external_id":{"arxiv":["1806.03108"]},"quality_controlled":"1","volume":118,"date_created":"2018-12-11T11:44:27Z","has_accepted_license":"1","language":[{"iso":"eng"}],"department":[{"_id":"KrCh"}],"type":"conference"},{"month":"04","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","oa":1,"title":"Competitive training of mixtures of independent deep generative models","author":[{"last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco"},{"full_name":"Vincent, Damien","first_name":"Damien","last_name":"Vincent"},{"first_name":"Ilya","last_name":"Tolstikhin","full_name":"Tolstikhin, Ilya"},{"full_name":"Rätsch, Gunnar","last_name":"Rätsch","first_name":"Gunnar"},{"last_name":"Gelly","first_name":"Sylvain","full_name":"Gelly, Sylvain"},{"last_name":"Schölkopf","first_name":"Bernhard","full_name":"Schölkopf, Bernhard"}],"article_number":"1804.11130","_id":"14327","abstract":[{"text":"A common assumption in causal modeling posits that the data is generated by a\r\nset of independent mechanisms, and algorithms should aim to recover this\r\nstructure. Standard unsupervised learning, however, is often concerned with\r\ntraining a single model to capture the overall distribution or aspects thereof.\r\nInspired by clustering approaches, we consider mixtures of implicit generative\r\nmodels that ``disentangle'' the independent generative mechanisms underlying\r\nthe data. Relying on an additional set of discriminators, we propose a\r\ncompetitive training procedure in which the models only need to capture the\r\nportion of the data distribution from which they can produce realistic samples.\r\nAs a by-product, each model is simpler and faster to train. We empirically show\r\nthat our approach splits the training distribution in a sensible way and\r\nincreases the quality of the generated samples.","lang":"eng"}],"arxiv":1,"date_updated":"2023-09-13T12:23:03Z","extern":"1","year":"2018","day":"30","citation":{"short":"F. Locatello, D. Vincent, I. Tolstikhin, G. Rätsch, S. Gelly, B. Schölkopf, ArXiv (n.d.).","ieee":"F. Locatello, D. Vincent, I. Tolstikhin, G. Rätsch, S. Gelly, and B. Schölkopf, “Competitive training of mixtures of independent deep generative models,” <i>arXiv</i>. .","ama":"Locatello F, Vincent D, Tolstikhin I, Rätsch G, Gelly S, Schölkopf B. Competitive training of mixtures of independent deep generative models. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.1804.11130\">10.48550/arXiv.1804.11130</a>","ista":"Locatello F, Vincent D, Tolstikhin I, Rätsch G, Gelly S, Schölkopf B. Competitive training of mixtures of independent deep generative models. arXiv, 1804.11130.","mla":"Locatello, Francesco, et al. “Competitive Training of Mixtures of Independent Deep Generative Models.” <i>ArXiv</i>, 1804.11130, doi:<a href=\"https://doi.org/10.48550/arXiv.1804.11130\">10.48550/arXiv.1804.11130</a>.","apa":"Locatello, F., Vincent, D., Tolstikhin, I., Rätsch, G., Gelly, S., &#38; Schölkopf, B. (n.d.). Competitive training of mixtures of independent deep generative models. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.1804.11130\">https://doi.org/10.48550/arXiv.1804.11130</a>","chicago":"Locatello, Francesco, Damien Vincent, Ilya Tolstikhin, Gunnar Rätsch, Sylvain Gelly, and Bernhard Schölkopf. “Competitive Training of Mixtures of Independent Deep Generative Models.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.1804.11130\">https://doi.org/10.48550/arXiv.1804.11130</a>."},"external_id":{"arxiv":["1804.11130"]},"article_processing_charge":"No","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1804.11130","open_access":"1"}],"oa_version":"Preprint","type":"preprint","date_published":"2018-04-30T00:00:00Z","department":[{"_id":"FrLo"}],"language":[{"iso":"eng"}],"doi":"10.48550/arXiv.1804.11130","publication_status":"submitted","publication":"arXiv","date_created":"2023-09-13T12:20:49Z"},{"title":"A theory of register monitors","publisher":"IEEE","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","month":"07","alternative_title":["ACM/IEEE Symposium on Logic in Computer Science"],"day":"09","year":"2018","date_updated":"2023-09-08T11:49:13Z","abstract":[{"lang":"eng","text":"The task of a monitor is to watch, at run-time, the execution of a reactive system, and signal the occurrence of a safety violation in the observed sequence of events. While finite-state monitors have been studied extensively, in practice, monitoring software also makes use of unbounded memory. We define a model of automata equipped with integer-valued registers which can execute only a bounded number of instructions between consecutive events, and thus can form the theoretical basis for the study of infinite-state monitors. We classify these register monitors according to the number k of available registers, and the type of register instructions. In stark contrast to the theory of computability for register machines, we prove that for every k 1, monitors with k + 1 counters (with instruction set 〈+1, =〉) are strictly more expressive than monitors with k counters. We also show that adder monitors (with instruction set 〈1, +, =〉) are strictly more expressive than counter monitors, but are complete for monitoring all computable safety -languages for k = 6. Real-time monitors are further required to signal the occurrence of a safety violation as soon as it occurs. The expressiveness hierarchy for counter monitors carries over to real-time monitors. We then show that 2 adders cannot simulate 3 counters in real-time. Finally, we show that real-time adder monitors with inequalities are as expressive as real-time Turing machines."}],"_id":"144","author":[{"orcid":"0000-0001-5199-3143","first_name":"Thomas","last_name":"Ferrere","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","full_name":"Ferrere, Thomas"},{"full_name":"Henzinger, Thomas A","first_name":"Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger"},{"first_name":"Ege","last_name":"Saraç","full_name":"Saraç, Ege"}],"isi":1,"publist_id":"7779","scopus_import":"1","article_processing_charge":"No","external_id":{"isi":["000545262800041"]},"citation":{"chicago":"Ferrere, Thomas, Thomas A Henzinger, and Ege Saraç. “A Theory of Register Monitors,” Part F138033:394–403. IEEE, 2018. <a href=\"https://doi.org/10.1145/3209108.3209194\">https://doi.org/10.1145/3209108.3209194</a>.","mla":"Ferrere, Thomas, et al. <i>A Theory of Register Monitors</i>. Vol. Part F138033, IEEE, 2018, pp. 394–403, doi:<a href=\"https://doi.org/10.1145/3209108.3209194\">10.1145/3209108.3209194</a>.","ista":"Ferrere T, Henzinger TA, Saraç E. 2018. A theory of register monitors. LICS: Logic in Computer Science, ACM/IEEE Symposium on Logic in Computer Science, vol. Part F138033, 394–403.","apa":"Ferrere, T., Henzinger, T. A., &#38; Saraç, E. (2018). A theory of register monitors (Vol. Part F138033, pp. 394–403). Presented at the LICS: Logic in Computer Science, Oxford, UK: IEEE. <a href=\"https://doi.org/10.1145/3209108.3209194\">https://doi.org/10.1145/3209108.3209194</a>","ama":"Ferrere T, Henzinger TA, Saraç E. A theory of register monitors. In: Vol Part F138033. IEEE; 2018:394-403. doi:<a href=\"https://doi.org/10.1145/3209108.3209194\">10.1145/3209108.3209194</a>","ieee":"T. Ferrere, T. A. Henzinger, and E. Saraç, “A theory of register monitors,” presented at the LICS: Logic in Computer Science, Oxford, UK, 2018, vol. Part F138033, pp. 394–403.","short":"T. Ferrere, T.A. Henzinger, E. Saraç, in:, IEEE, 2018, pp. 394–403."},"quality_controlled":"1","volume":"Part F138033","page":"394 - 403","date_created":"2018-12-11T11:44:52Z","conference":{"end_date":"2018-07-12","location":"Oxford, UK","start_date":"2018-07-09","name":"LICS: Logic in Computer Science"},"publication_status":"published","doi":"10.1145/3209108.3209194","language":[{"iso":"eng"}],"date_published":"2018-07-09T00:00:00Z","department":[{"_id":"ToHe"}],"type":"conference","oa_version":"None"},{"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"01","acknowledgement":"We thank Reinhard Jahn for providing a plasmid for YFP-SNAP25. We thank Erwin Neher for help with the development of the mathematical model of the synaptic vesicle life cycle. We thank Martin Meschkat, Andreas Höbartner, Annedore Punge, and Peer Hoopmann for help with the experiments. We thank Burkhard Rammner for providing the illustrations of synaptic vesicle and protein dynamics. We thank Manuel Maidorn, Martin Helm, and Katharina N. Richter for critically reading the manuscript. S.T. was supported by an Excellence Stipend of the Göttingen Graduate School for Neurosciences, Biophysics, and Molecular Biosciences (GGNB). E.F.F. is a recipient of long-term fellowships from the European Molecular Biology Organization (ALTF_797-2012) and from the Human Frontier Science Program (HFSP_LT000830/2013). The work was supported by grants to S.O.R. from the European Research Council (ERC-2013-CoG NeuroMolAnatomy) and from the Deutsche Forschungsgemeinschaft (Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, SFB1190/P09, SFB889/A05, and SFB1286/A03, and DFG RI 1967 7/1). The nanoSIMS instrument was funded by the German Federal Ministry of Education and Research (03F0626A).","pmid":1,"file":[{"date_created":"2018-12-17T14:17:29Z","date_updated":"2020-07-14T12:44:56Z","file_name":"2018_EMBO_Truckenbrodt.pdf","access_level":"open_access","file_id":"5710","creator":"dernst","checksum":"a540feb6c9af6aefc78de531461a8835","file_size":2846470,"content_type":"application/pdf","relation":"main_file"}],"author":[{"full_name":"Truckenbrodt, Sven M","last_name":"Truckenbrodt","id":"45812BD4-F248-11E8-B48F-1D18A9856A87","first_name":"Sven M"},{"first_name":"Abhiyan","last_name":"Viplav","full_name":"Viplav, Abhiyan"},{"first_name":"Sebsatian","last_name":"Jähne","full_name":"Jähne, Sebsatian"},{"full_name":"Vogts, Angela","last_name":"Vogts","first_name":"Angela"},{"full_name":"Denker, Annette","last_name":"Denker","first_name":"Annette"},{"full_name":"Wildhagen, Hanna","first_name":"Hanna","last_name":"Wildhagen"},{"last_name":"Fornasiero","first_name":"Eugenio","full_name":"Fornasiero, Eugenio"},{"full_name":"Rizzoli, Silvio","first_name":"Silvio","last_name":"Rizzoli"}],"isi":1,"title":"Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission","publisher":"Wiley","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2018-12-11T11:44:52Z","publication":"The EMBO Journal","has_accepted_license":"1","language":[{"iso":"eng"}],"department":[{"_id":"JoDa"}],"type":"journal_article","publist_id":"7778","article_processing_charge":"No","article_type":"original","external_id":{"pmid":["29950309"],"isi":["000440416900005"]},"quality_controlled":"1","volume":37,"year":"2018","date_updated":"2023-09-13T09:02:48Z","abstract":[{"text":"Aged proteins can become hazardous to cellular function, by accumulating molecular damage. This implies that cells should preferentially rely on newly produced ones. We tested this hypothesis in cultured hippocampal neurons, focusing on synaptic transmission. We found that newly synthesized vesicle proteins were incorporated in the actively recycling pool of vesicles responsible for all neurotransmitter release during physiological activity. We observed this for the calcium sensor Synaptotagmin 1, for the neurotransmitter transporter VGAT, and for the fusion protein VAMP2 (Synaptobrevin 2). Metabolic labeling of proteins and visualization by secondary ion mass spectrometry enabled us to query the entire protein makeup of the actively recycling vesicles, which we found to be younger than that of non-recycling vesicles. The young vesicle proteins remained in use for up to ~ 24 h, during which they participated in recycling a few hundred times. They were afterward reluctant to release and were degraded after an additional ~ 24–48 h. We suggest that the recycling pool of synaptic vesicles relies on newly synthesized proteins, while the inactive reserve pool contains older proteins.","lang":"eng"}],"issue":"15","_id":"145","article_number":"e98044","oa":1,"publication_identifier":{"issn":["0261-4189"]},"status":"public","month":"08","publication_status":"published","doi":"10.15252/embj.201798044","date_published":"2018-08-01T00:00:00Z","oa_version":"Published Version","ddc":["570"],"scopus_import":"1","file_date_updated":"2020-07-14T12:44:56Z","intvolume":"        37","citation":{"ieee":"S. M. Truckenbrodt <i>et al.</i>, “Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission,” <i>The EMBO Journal</i>, vol. 37, no. 15. Wiley, 2018.","ama":"Truckenbrodt SM, Viplav A, Jähne S, et al. Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission. <i>The EMBO Journal</i>. 2018;37(15). doi:<a href=\"https://doi.org/10.15252/embj.201798044\">10.15252/embj.201798044</a>","short":"S.M. Truckenbrodt, A. Viplav, S. Jähne, A. Vogts, A. Denker, H. Wildhagen, E. Fornasiero, S. Rizzoli, The EMBO Journal 37 (2018).","chicago":"Truckenbrodt, Sven M, Abhiyan Viplav, Sebsatian Jähne, Angela Vogts, Annette Denker, Hanna Wildhagen, Eugenio Fornasiero, and Silvio Rizzoli. “Newly Produced Synaptic Vesicle Proteins Are Preferentially Used in Synaptic Transmission.” <i>The EMBO Journal</i>. Wiley, 2018. <a href=\"https://doi.org/10.15252/embj.201798044\">https://doi.org/10.15252/embj.201798044</a>.","ista":"Truckenbrodt SM, Viplav A, Jähne S, Vogts A, Denker A, Wildhagen H, Fornasiero E, Rizzoli S. 2018. Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission. The EMBO Journal. 37(15), e98044.","apa":"Truckenbrodt, S. M., Viplav, A., Jähne, S., Vogts, A., Denker, A., Wildhagen, H., … Rizzoli, S. (2018). Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission. <i>The EMBO Journal</i>. Wiley. <a href=\"https://doi.org/10.15252/embj.201798044\">https://doi.org/10.15252/embj.201798044</a>","mla":"Truckenbrodt, Sven M., et al. “Newly Produced Synaptic Vesicle Proteins Are Preferentially Used in Synaptic Transmission.” <i>The EMBO Journal</i>, vol. 37, no. 15, e98044, Wiley, 2018, doi:<a href=\"https://doi.org/10.15252/embj.201798044\">10.15252/embj.201798044</a>."}},{"publisher":"Nature Publishing Group","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling","pmid":1,"day":"30","isi":1,"author":[{"full_name":"Shi, Chun Lin","first_name":"Chun Lin","last_name":"Shi"},{"full_name":"Von Wangenheim, Daniel","id":"49E91952-F248-11E8-B48F-1D18A9856A87","last_name":"Von Wangenheim","orcid":"0000-0002-6862-1247","first_name":"Daniel"},{"last_name":"Herrmann","first_name":"Ullrich","full_name":"Herrmann, Ullrich"},{"full_name":"Wildhagen, Mari","first_name":"Mari","last_name":"Wildhagen"},{"last_name":"Kulik","id":"F0AB3FCE-02D1-11E9-BD0E-99399A5D3DEB","first_name":"Ivan","full_name":"Kulik, Ivan"},{"first_name":"Andreas","last_name":"Kopf","full_name":"Kopf, Andreas"},{"full_name":"Ishida, Takashi","last_name":"Ishida","first_name":"Takashi"},{"full_name":"Olsson, Vilde","first_name":"Vilde","last_name":"Olsson"},{"full_name":"Anker, Mari Kristine","first_name":"Mari Kristine","last_name":"Anker"},{"first_name":"Markus","last_name":"Albert","full_name":"Albert, Markus"},{"full_name":"Butenko, Melinka A","last_name":"Butenko","first_name":"Melinka A"},{"full_name":"Felix, Georg","first_name":"Georg","last_name":"Felix"},{"last_name":"Sawa","first_name":"Shinichiro","full_name":"Sawa, Shinichiro"},{"full_name":"Claassen, Manfred","first_name":"Manfred","last_name":"Claassen"},{"full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jirí"},{"first_name":"Reidunn B","last_name":"Aalen","full_name":"Aalen, Reidunn B"}],"file":[{"date_updated":"2020-07-14T12:44:56Z","file_name":"2018_NaturePlants_Shi.pdf","date_created":"2019-11-18T16:24:07Z","file_id":"7043","creator":"dernst","checksum":"da33101c76ee1b2dc5ab28fd2ccba9d0","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_size":226829}],"publist_id":"7777","article_type":"original","article_processing_charge":"No","external_id":{"pmid":["30061750"],"isi":["000443861300016"]},"quality_controlled":"1","volume":4,"related_material":{"link":[{"url":"https://ist.ac.at/en/news/new-process-in-root-development-discovered/","relation":"press_release","description":"News on IST Homepage"}]},"has_accepted_license":"1","date_created":"2018-12-11T11:44:52Z","page":"596 - 604","publication":"Nature Plants","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"JiFr"}],"status":"public","oa":1,"month":"07","date_updated":"2023-09-19T10:08:45Z","abstract":[{"lang":"eng","text":"The root cap protects the stem cell niche of angiosperm roots from damage. In Arabidopsis, lateral root cap (LRC) cells covering the meristematic zone are regularly lost through programmed cell death, while the outermost layer of the root cap covering the tip is repeatedly sloughed. Efficient coordination with stem cells producing new layers is needed to maintain a constant size of the cap. We present a signalling pair, the peptide IDA-LIKE1 (IDL1) and its receptor HAESA-LIKE2 (HSL2), mediating such communication. Live imaging over several days characterized this process from initial fractures in LRC cell files to full separation of a layer. Enhanced expression of IDL1 in the separating root cap layers resulted in increased frequency of sloughing, balanced with generation of new layers in a HSL2-dependent manner. Transcriptome analyses linked IDL1-HSL2 signalling to the transcription factors BEARSKIN1/2 and genes associated with programmed cell death. Mutations in either IDL1 or HSL2 slowed down cell division, maturation and separation. Thus, IDL1-HSL2 signalling potentiates dynamic regulation of the homeostatic balance between stem cell division and sloughing activity."}],"issue":"8","year":"2018","_id":"146","scopus_import":"1","file_date_updated":"2020-07-14T12:44:56Z","ddc":["580"],"intvolume":"         4","citation":{"apa":"Shi, C. L., von Wangenheim, D., Herrmann, U., Wildhagen, M., Kulik, I., Kopf, A., … Aalen, R. B. (2018). The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling. <i>Nature Plants</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41477-018-0212-z\">https://doi.org/10.1038/s41477-018-0212-z</a>","ista":"Shi CL, von Wangenheim D, Herrmann U, Wildhagen M, Kulik I, Kopf A, Ishida T, Olsson V, Anker MK, Albert M, Butenko MA, Felix G, Sawa S, Claassen M, Friml J, Aalen RB. 2018. The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling. Nature Plants. 4(8), 596–604.","mla":"Shi, Chun Lin, et al. “The Dynamics of Root Cap Sloughing in Arabidopsis Is Regulated by Peptide Signalling.” <i>Nature Plants</i>, vol. 4, no. 8, Nature Publishing Group, 2018, pp. 596–604, doi:<a href=\"https://doi.org/10.1038/s41477-018-0212-z\">10.1038/s41477-018-0212-z</a>.","chicago":"Shi, Chun Lin, Daniel von Wangenheim, Ullrich Herrmann, Mari Wildhagen, Ivan Kulik, Andreas Kopf, Takashi Ishida, et al. “The Dynamics of Root Cap Sloughing in Arabidopsis Is Regulated by Peptide Signalling.” <i>Nature Plants</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41477-018-0212-z\">https://doi.org/10.1038/s41477-018-0212-z</a>.","ama":"Shi CL, von Wangenheim D, Herrmann U, et al. The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling. <i>Nature Plants</i>. 2018;4(8):596-604. doi:<a href=\"https://doi.org/10.1038/s41477-018-0212-z\">10.1038/s41477-018-0212-z</a>","ieee":"C. L. Shi <i>et al.</i>, “The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling,” <i>Nature Plants</i>, vol. 4, no. 8. Nature Publishing Group, pp. 596–604, 2018.","short":"C.L. Shi, D. von Wangenheim, U. Herrmann, M. Wildhagen, I. Kulik, A. Kopf, T. Ishida, V. Olsson, M.K. Anker, M. Albert, M.A. Butenko, G. Felix, S. Sawa, M. Claassen, J. Friml, R.B. Aalen, Nature Plants 4 (2018) 596–604."},"publication_status":"published","doi":"10.1038/s41477-018-0212-z","oa_version":"Submitted Version","date_published":"2018-07-30T00:00:00Z"},{"issue":"10","abstract":[{"lang":"eng","text":"The trafficking of subcellular cargos in eukaryotic cells crucially depends on vesicle budding, a process mediated by ARF-GEFs (ADP-ribosylation factor guanine nucleotide exchange factors). In plants, ARF-GEFs play essential roles in endocytosis, vacuolar trafficking, recycling, secretion, and polar trafficking. Moreover, they are important for plant development, mainly through controlling the polar subcellular localization of PIN-FORMED (PIN) transporters of the plant hormone auxin. Here, using a chemical genetics screen in Arabidopsis thaliana, we identified Endosidin 4 (ES4), an inhibitor of eukaryotic ARF-GEFs. ES4 acts similarly to and synergistically with the established ARF-GEF inhibitor Brefeldin A and has broad effects on intracellular trafficking, including endocytosis, exocytosis, and vacuolar targeting. Additionally, Arabidopsis and yeast (Sacharomyces cerevisiae) mutants defective in ARF-GEF show altered sensitivity to ES4. ES4 interferes with the activation-based membrane association of the ARF1 GTPases, but not of their mutant variants that are activated independently of ARF-GEF activity. Biochemical approaches and docking simulations confirmed that ES4 specifically targets the SEC7 domain-containing ARF-GEFs. These observations collectively identify ES4 as a chemical tool enabling the study of ARF-GEF-mediated processes, including ARF-GEF-mediated plant development."}],"date_updated":"2025-05-07T11:12:30Z","year":"2018","_id":"147","status":"public","publication_identifier":{"issn":["1040-4651"]},"oa":1,"month":"11","ec_funded":1,"doi":"10.1105/tpc.18.00127","publication_status":"published","oa_version":"Published Version","date_published":"2018-11-12T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1105/tpc.18.00127"}],"scopus_import":"1","intvolume":"        30","citation":{"chicago":"Kania, Urszula, Tomasz Nodzyński, Qing Lu, Glenn R Hicks, Wim Nerinckx, Kiril Mishev, Francois Peurois, et al. “The Inhibitor Endosidin 4 Targets SEC7 Domain-Type ARF GTPase Exchange Factors and Interferes with Sub Cellular Trafficking in Eukaryotes.” <i>The Plant Cell</i>. Oxford University Press, 2018. <a href=\"https://doi.org/10.1105/tpc.18.00127\">https://doi.org/10.1105/tpc.18.00127</a>.","mla":"Kania, Urszula, et al. “The Inhibitor Endosidin 4 Targets SEC7 Domain-Type ARF GTPase Exchange Factors and Interferes with Sub Cellular Trafficking in Eukaryotes.” <i>The Plant Cell</i>, vol. 30, no. 10, Oxford University Press, 2018, pp. 2553–72, doi:<a href=\"https://doi.org/10.1105/tpc.18.00127\">10.1105/tpc.18.00127</a>.","ista":"Kania U, Nodzyński T, Lu Q, Hicks GR, Nerinckx W, Mishev K, Peurois F, Cherfils J, De RRM, Grones P, Robert S, Russinova E, Friml J. 2018. The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes. The Plant Cell. 30(10), 2553–2572.","apa":"Kania, U., Nodzyński, T., Lu, Q., Hicks, G. R., Nerinckx, W., Mishev, K., … Friml, J. (2018). The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes. <i>The Plant Cell</i>. Oxford University Press. <a href=\"https://doi.org/10.1105/tpc.18.00127\">https://doi.org/10.1105/tpc.18.00127</a>","ieee":"U. Kania <i>et al.</i>, “The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes,” <i>The Plant Cell</i>, vol. 30, no. 10. Oxford University Press, pp. 2553–2572, 2018.","ama":"Kania U, Nodzyński T, Lu Q, et al. The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes. <i>The Plant Cell</i>. 2018;30(10):2553-2572. doi:<a href=\"https://doi.org/10.1105/tpc.18.00127\">10.1105/tpc.18.00127</a>","short":"U. Kania, T. Nodzyński, Q. Lu, G.R. Hicks, W. Nerinckx, K. Mishev, F. Peurois, J. Cherfils, R.R.M. De, P. Grones, S. Robert, E. Russinova, J. Friml, The Plant Cell 30 (2018) 2553–2572."},"pmid":1,"acknowledgement":"We thank Gerd Jürgens, Sandra Richter, and Sheng Yang He for providing antibodies; Maciek Adamowski, Fernando Aniento, Sebastian Bednarek, Nico Callewaert, Matyás Fendrych, Elena Feraru, and Mugurel I. Feraru for helpful suggestions; Siamsa Doyle for critical reading of the manuscript and helpful comments and suggestions; and Stephanie Smith and Martine De Cock for help in editing and language corrections. We acknowledge the core facility Cellular Imaging of CEITEC supported by the Czech-BioImaging large RI project (LM2015062 funded by MEYS CR) for their support with obtaining scientific data presented in this article. Plant Sciences Core Facility of CEITEC Masaryk University is gratefully acknowledged for obtaining part of the scientific data presented in this article. We acknowledge support from the Fondation pour la Recherche Médicale and from the Institut National du Cancer (J.C.). The research leading to these results was funded by the European Research Council under the European Union's 7th Framework Program (FP7/2007-2013)/ERC grant agreement numbers 282300 and 742985 and the Czech Science Foundation GAČR (GA18-26981S; J.F.); Ministry of Education, Youth, and Sports/MEYS of the Czech Republic under the Project CEITEC 2020 (LQ1601; T.N.); the China Science Council for a predoctoral fellowship (Q.L.); a joint research project within the framework of cooperation between the Research Foundation-Flanders and the Bulgarian Academy of Sciences (VS.025.13N; K.M. and E.R.); Vetenskapsrådet and Vinnova (Verket för Innovationssystem; S.R.), Knut och Alice Wallenbergs Stiftelse via “Shapesystem” Grant 2012.0050 (S.R.), Kempe stiftelserna (P.G.), Tryggers CTS410 (P.G.).","day":"12","author":[{"last_name":"Kania","id":"4AE5C486-F248-11E8-B48F-1D18A9856A87","first_name":"Urszula","full_name":"Kania, Urszula"},{"full_name":"Nodzyński, Tomasz","first_name":"Tomasz","last_name":"Nodzyński"},{"last_name":"Lu","first_name":"Qing","full_name":"Lu, Qing"},{"last_name":"Hicks","first_name":"Glenn R","full_name":"Hicks, Glenn R"},{"full_name":"Nerinckx, Wim","last_name":"Nerinckx","first_name":"Wim"},{"first_name":"Kiril","last_name":"Mishev","full_name":"Mishev, Kiril"},{"last_name":"Peurois","first_name":"Francois","full_name":"Peurois, Francois"},{"full_name":"Cherfils, Jacqueline","last_name":"Cherfils","first_name":"Jacqueline"},{"first_name":"Rycke Riet Maria","last_name":"De","full_name":"De, Rycke Riet Maria"},{"id":"399876EC-F248-11E8-B48F-1D18A9856A87","last_name":"Grones","first_name":"Peter","full_name":"Grones, Peter"},{"last_name":"Robert","first_name":"Stéphanie","full_name":"Robert, Stéphanie"},{"last_name":"Russinova","first_name":"Eugenia","full_name":"Russinova, Eugenia"},{"full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596"}],"isi":1,"project":[{"grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants"},{"call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Oxford University Press","title":"The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes","publication":"The Plant Cell","date_created":"2018-12-11T11:44:52Z","page":"2553 - 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Marc","last_name":"Delaux"},{"full_name":"Quint, Marcel","first_name":"Marcel","last_name":"Quint"},{"full_name":"Theissen, Gunter","last_name":"Theissen","first_name":"Gunter"},{"full_name":"Hagemann, Martin","first_name":"Martin","last_name":"Hagemann"},{"last_name":"Harholt","first_name":"Jesper","full_name":"Harholt, Jesper"},{"first_name":"Christophe","last_name":"Dunand","full_name":"Dunand, Christophe"},{"first_name":"Sabine","last_name":"Zachgo","full_name":"Zachgo, Sabine"},{"last_name":"Langdale","first_name":"Jane","full_name":"Langdale, Jane"},{"full_name":"Maumus, Florian","first_name":"Florian","last_name":"Maumus"},{"full_name":"Van Der Straeten, Dominique","last_name":"Van Der Straeten","first_name":"Dominique"},{"full_name":"Gould, Sven B","first_name":"Sven B","last_name":"Gould"},{"full_name":"Rensing, Stefan","last_name":"Rensing","first_name":"Stefan"}],"isi":1,"project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"}],"scopus_import":"1","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30007417","open_access":"1"}],"citation":{"ieee":"T. Nishiyama <i>et al.</i>, “The Chara genome: Secondary complexity and implications for plant terrestrialization,” <i>Cell</i>, vol. 174, no. 2. Cell Press, p. 448–464.e24, 2018.","ama":"Nishiyama T, Sakayama H, De Vries J, et al. The Chara genome: Secondary complexity and implications for plant terrestrialization. <i>Cell</i>. 2018;174(2):448-464.e24. doi:<a href=\"https://doi.org/10.1016/j.cell.2018.06.033\">10.1016/j.cell.2018.06.033</a>","short":"T. Nishiyama, H. Sakayama, J. De Vries, H. Buschmann, D. Saint Marcoux, K. Ullrich, F. Haas, L. Vanderstraeten, D. Becker, D. Lang, S. Vosolsobě, S. Rombauts, P. Wilhelmsson, P. Janitza, R. Kern, A. Heyl, F. Rümpler, L. Calderón Villalobos, J. Clay, R. Skokan, A. Toyoda, Y. Suzuki, H. Kagoshima, E. Schijlen, N. Tajeshwar, B. Catarino, A. Hetherington, A. Saltykova, C. Bonnot, H. Breuninger, A. Symeonidi, G. Radhakrishnan, F. Van Nieuwerburgh, D. Deforce, C. Chang, K. Karol, R. Hedrich, P. Ulvskov, G. Glöckner, C. Delwiche, J. Petrášek, Y. Van De Peer, J. Friml, M. Beilby, L. Dolan, Y. Kohara, S. Sugano, A. Fujiyama, P.M. Delaux, M. Quint, G. Theissen, M. Hagemann, J. Harholt, C. Dunand, S. Zachgo, J. Langdale, F. Maumus, D. Van Der Straeten, S.B. Gould, S. Rensing, Cell 174 (2018) 448–464.e24.","mla":"Nishiyama, Tomoaki, et al. “The Chara Genome: Secondary Complexity and Implications for Plant Terrestrialization.” <i>Cell</i>, vol. 174, no. 2, Cell Press, 2018, p. 448–464.e24, doi:<a href=\"https://doi.org/10.1016/j.cell.2018.06.033\">10.1016/j.cell.2018.06.033</a>.","apa":"Nishiyama, T., Sakayama, H., De Vries, J., Buschmann, H., Saint Marcoux, D., Ullrich, K., … Rensing, S. (2018). The Chara genome: Secondary complexity and implications for plant terrestrialization. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2018.06.033\">https://doi.org/10.1016/j.cell.2018.06.033</a>","ista":"Nishiyama T, Sakayama H, De Vries J, Buschmann H, Saint Marcoux D, Ullrich K, Haas F, Vanderstraeten L, Becker D, Lang D, Vosolsobě S, Rombauts S, Wilhelmsson P, Janitza P, Kern R, Heyl A, Rümpler F, Calderón Villalobos L, Clay J, Skokan R, Toyoda A, Suzuki Y, Kagoshima H, Schijlen E, Tajeshwar N, Catarino B, Hetherington A, Saltykova A, Bonnot C, Breuninger H, Symeonidi A, Radhakrishnan G, Van Nieuwerburgh F, Deforce D, Chang C, Karol K, Hedrich R, Ulvskov P, Glöckner G, Delwiche C, Petrášek J, Van De Peer Y, Friml J, Beilby M, Dolan L, Kohara Y, Sugano S, Fujiyama A, Delaux PM, Quint M, Theissen G, Hagemann M, Harholt J, Dunand C, Zachgo S, Langdale J, Maumus F, Van Der Straeten D, Gould SB, Rensing S. 2018. The Chara genome: Secondary complexity and implications for plant terrestrialization. Cell. 174(2), 448–464.e24.","chicago":"Nishiyama, Tomoaki, Hidetoshi Sakayama, Jan De Vries, Henrik Buschmann, Denis Saint Marcoux, Kristian Ullrich, Fabian Haas, et al. “The Chara Genome: Secondary Complexity and Implications for Plant Terrestrialization.” <i>Cell</i>. Cell Press, 2018. <a href=\"https://doi.org/10.1016/j.cell.2018.06.033\">https://doi.org/10.1016/j.cell.2018.06.033</a>."},"intvolume":"       174","doi":"10.1016/j.cell.2018.06.033","publication_status":"published","oa_version":"Published Version","date_published":"2018-07-12T00:00:00Z","status":"public","oa":1,"month":"07","ec_funded":1,"issue":"2","abstract":[{"text":"Land plants evolved from charophytic algae, among which Charophyceae possess the most complex body plans. We present the genome of Chara braunii; comparison of the genome to those of land plants identified evolutionary novelties for plant terrestrialization and land plant heritage genes. C. braunii employs unique xylan synthases for cell wall biosynthesis, a phragmoplast (cell separation) mechanism similar to that of land plants, and many phytohormones. C. braunii plastids are controlled via land-plant-like retrograde signaling, and transcriptional regulation is more elaborate than in other algae. The morphological complexity of this organism may result from expanded gene families, with three cases of particular note: genes effecting tolerance to reactive oxygen species (ROS), LysM receptor-like kinases, and transcription factors (TFs). Transcriptomic analysis of sexual reproductive structures reveals intricate control by TFs, activity of the ROS gene network, and the ancestral use of plant-like storage and stress protection proteins in the zygote.","lang":"eng"}],"date_updated":"2023-09-19T10:02:47Z","year":"2018","_id":"148"},{"date_published":"2018-07-12T00:00:00Z","oa_version":"Published Version","publication_status":"published","doi":"10.15479/AT:ISTA:TH_1040","citation":{"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>.","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>","ista":"Alt J. 2018. Dyson equation and eigenvalue statistics of random matrices. Institute of Science and Technology Austria.","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>.","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>","ieee":"J. Alt, “Dyson equation and eigenvalue statistics of random matrices,” Institute of Science and Technology Austria, 2018.","short":"J. Alt, Dyson Equation and Eigenvalue Statistics of Random Matrices, Institute of Science and Technology Austria, 2018."},"ddc":["515","519"],"file_date_updated":"2020-07-14T12:44:57Z","_id":"149","year":"2018","date_updated":"2024-02-22T14:34:33Z","abstract":[{"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.","lang":"eng"}],"ec_funded":1,"month":"07","oa":1,"publication_identifier":{"issn":["2663-337X"]},"status":"public","language":[{"iso":"eng"}],"department":[{"_id":"LaEr"}],"type":"dissertation","page":"456","date_created":"2018-12-11T11:44:53Z","has_accepted_license":"1","related_material":{"record":[{"id":"1677","status":"public","relation":"part_of_dissertation"},{"id":"550","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"6183"},{"relation":"part_of_dissertation","status":"public","id":"566"},{"status":"public","relation":"part_of_dissertation","id":"1010"},{"id":"6240","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"6184"}]},"publist_id":"7772","article_processing_charge":"No","pubrep_id":"1040","file":[{"content_type":"application/pdf","relation":"main_file","file_size":5801709,"checksum":"d4dad55a7513f345706aaaba90cb1bb8","file_id":"6241","creator":"dernst","access_level":"open_access","file_name":"2018_thesis_Alt.pdf","date_updated":"2020-07-14T12:44:57Z","date_created":"2019-04-08T13:55:20Z"},{"file_size":3802059,"relation":"source_file","content_type":"application/zip","access_level":"closed","checksum":"d73fcf46300dce74c403f2b491148ab4","file_id":"6242","creator":"dernst","date_created":"2019-04-08T13:55:20Z","date_updated":"2020-07-14T12:44:57Z","file_name":"2018_thesis_Alt_source.zip"}],"project":[{"name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804"}],"author":[{"full_name":"Alt, Johannes","id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87","last_name":"Alt","first_name":"Johannes"}],"day":"12","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"supervisor":[{"full_name":"Erdös, László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","orcid":"0000-0001-5366-9603","first_name":"László"}],"alternative_title":["ISTA Thesis"],"degree_awarded":"PhD","title":"Dyson equation and eigenvalue statistics of random matrices","publisher":"Institute of Science and Technology Austria","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"publication_status":"published","doi":"10.1038/s41590-018-0109-z","date_published":"2018-05-18T00:00:00Z","oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/29777221"}],"scopus_import":"1","citation":{"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>.","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.","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>.","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>","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.","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."},"intvolume":"        19","year":"2018","date_updated":"2024-03-25T23:30:22Z","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"}],"issue":"6","_id":"15","acknowledged_ssus":[{"_id":"SSU"}],"oa":1,"status":"public","ec_funded":1,"month":"05","page":"606 - 616","date_created":"2018-12-11T11:44:10Z","publication":"Nature Immunology","language":[{"iso":"eng"}],"department":[{"_id":"MiSi"},{"_id":"Bio"}],"type":"journal_article","publist_id":"8040","article_processing_charge":"No","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"6891"}]},"external_id":{"pmid":["29777221"],"isi":["000433041500026"]},"volume":19,"quality_controlled":"1","day":"18","pmid":1,"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).","project":[{"grant_number":"724373","_id":"25FE9508-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Cellular navigation along spatial gradients"},{"name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells","call_identifier":"H2020","grant_number":"747687","_id":"260AA4E2-B435-11E9-9278-68D0E5697425"},{"name":"Molecular and system level view of immune cell migration","grant_number":"ALTF 1396-2014","_id":"25A48D24-B435-11E9-9278-68D0E5697425"},{"_id":"25A603A2-B435-11E9-9278-68D0E5697425","grant_number":"281556","call_identifier":"FP7","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)"}],"isi":1,"author":[{"orcid":"0000-0002-6625-3348","first_name":"Miroslav","id":"4167FE56-F248-11E8-B48F-1D18A9856A87","last_name":"Hons","full_name":"Hons, Miroslav"},{"full_name":"Kopf, Aglaja","first_name":"Aglaja","orcid":"0000-0002-2187-6656","id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87","last_name":"Kopf"},{"full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","first_name":"Robert","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Leithner, Alexander F","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","last_name":"Leithner","orcid":"0000-0002-1073-744X","first_name":"Alexander F"},{"full_name":"Gärtner, Florian R","id":"397A88EE-F248-11E8-B48F-1D18A9856A87","last_name":"Gärtner","orcid":"0000-0001-6120-3723","first_name":"Florian R"},{"full_name":"Abe, Jun","first_name":"Jun","last_name":"Abe"},{"full_name":"Renkawitz, Jörg","first_name":"Jörg","orcid":"0000-0003-2856-3369","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","last_name":"Renkawitz"},{"full_name":"Stein, Jens","first_name":"Jens","last_name":"Stein"},{"orcid":"0000-0002-6620-9179","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","full_name":"Sixt, Michael K"}],"title":"Chemokines and integrins independently tune actin flow and substrate friction during intranodal migration of T cells","publisher":"Nature Publishing Group","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"publication":"Nature","date_created":"2018-12-11T11:44:53Z","page":"509–512","department":[{"_id":"FlSc"}],"language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","article_processing_charge":"No","related_material":{"link":[{"url":"https://doi.org/10.1038/s41586-018-0505-4","relation":"erratum"}]},"volume":560,"quality_controlled":"1","external_id":{"pmid":["30158708"],"isi":["000442483400046"]},"day":"29","pmid":1,"author":[{"full_name":"Dick, Robert","first_name":"Robert","last_name":"Dick"},{"full_name":"Zadrozny, Kaneil K","last_name":"Zadrozny","first_name":"Kaneil K"},{"first_name":"Chaoyi","last_name":"Xu","full_name":"Xu, Chaoyi"},{"first_name":"Florian","orcid":"0000-0003-4790-8078","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian"},{"last_name":"Lyddon","first_name":"Terri D","full_name":"Lyddon, Terri D"},{"full_name":"Ricana, Clifton L","first_name":"Clifton L","last_name":"Ricana"},{"first_name":"Jonathan M","last_name":"Wagner","full_name":"Wagner, Jonathan M"},{"last_name":"Perilla","first_name":"Juan R","full_name":"Perilla, Juan R"},{"full_name":"Ganser, Pornillos Barbie K","first_name":"Pornillos Barbie K","last_name":"Ganser"},{"last_name":"Johnson","first_name":"Marc C","full_name":"Johnson, Marc C"},{"first_name":"Owen","last_name":"Pornillos","full_name":"Pornillos, Owen"},{"last_name":"Vogt","first_name":"Volker","full_name":"Vogt, Volker"}],"isi":1,"title":"Inositol phosphates are assembly co-factors for HIV-1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Nature Publishing Group","doi":"10.1038/s41586-018-0396-4","publication_status":"published","date_published":"2018-08-29T00:00:00Z","oa_version":"Submitted Version","scopus_import":"1","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6242333/","open_access":"1"}],"citation":{"ieee":"R. Dick <i>et al.</i>, “Inositol phosphates are assembly co-factors for HIV-1,” <i>Nature</i>, vol. 560, no. 7719. Nature Publishing Group, pp. 509–512, 2018.","ama":"Dick R, Zadrozny KK, Xu C, et al. Inositol phosphates are assembly co-factors for HIV-1. <i>Nature</i>. 2018;560(7719):509–512. doi:<a href=\"https://doi.org/10.1038/s41586-018-0396-4\">10.1038/s41586-018-0396-4</a>","short":"R. Dick, K.K. Zadrozny, C. Xu, F.K. Schur, T.D. Lyddon, C.L. Ricana, J.M. Wagner, J.R. Perilla, P.B.K. Ganser, M.C. Johnson, O. Pornillos, V. Vogt, Nature 560 (2018) 509–512.","ista":"Dick R, Zadrozny KK, Xu C, Schur FK, Lyddon TD, Ricana CL, Wagner JM, Perilla JR, Ganser PBK, Johnson MC, Pornillos O, Vogt V. 2018. Inositol phosphates are assembly co-factors for HIV-1. Nature. 560(7719), 509–512.","mla":"Dick, Robert, et al. “Inositol Phosphates Are Assembly Co-Factors for HIV-1.” <i>Nature</i>, vol. 560, no. 7719, Nature Publishing Group, 2018, pp. 509–512, doi:<a href=\"https://doi.org/10.1038/s41586-018-0396-4\">10.1038/s41586-018-0396-4</a>.","apa":"Dick, R., Zadrozny, K. K., Xu, C., Schur, F. K., Lyddon, T. D., Ricana, C. L., … Vogt, V. (2018). Inositol phosphates are assembly co-factors for HIV-1. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41586-018-0396-4\">https://doi.org/10.1038/s41586-018-0396-4</a>","chicago":"Dick, Robert, Kaneil K Zadrozny, Chaoyi Xu, Florian KM Schur, Terri D Lyddon, Clifton L Ricana, Jonathan M Wagner, et al. “Inositol Phosphates Are Assembly Co-Factors for HIV-1.” <i>Nature</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41586-018-0396-4\">https://doi.org/10.1038/s41586-018-0396-4</a>."},"intvolume":"       560","year":"2018","abstract":[{"lang":"eng","text":"A short, 14-amino-acid segment called SP1, located in the Gag structural protein1, has a critical role during the formation of the HIV-1 virus particle. During virus assembly, the SP1 peptide and seven preceding residues fold into a six-helix bundle, which holds together the Gag hexamer and facilitates the formation of a curved immature hexagonal lattice underneath the viral membrane2,3. Upon completion of assembly and budding, proteolytic cleavage of Gag leads to virus maturation, in which the immature lattice is broken down; the liberated CA domain of Gag then re-assembles into the mature conical capsid that encloses the viral genome and associated enzymes. Folding and proteolysis of the six-helix bundle are crucial rate-limiting steps of both Gag assembly and disassembly, and the six-helix bundle is an established target of HIV-1 inhibitors4,5. Here, using a combination of structural and functional analyses, we show that inositol hexakisphosphate (InsP6, also known as IP6) facilitates the formation of the six-helix bundle and assembly of the immature HIV-1 Gag lattice. IP6 makes ionic contacts with two rings of lysine residues at the centre of the Gag hexamer. Proteolytic cleavage then unmasks an alternative binding site, where IP6 interaction promotes the assembly of the mature capsid lattice. These studies identify IP6 as a naturally occurring small molecule that promotes both assembly and maturation of HIV-1."}],"issue":"7719","date_updated":"2023-09-12T07:44:37Z","_id":"150","publication_identifier":{"eissn":["1476-4687"]},"oa":1,"status":"public","month":"08"},{"date_published":"2018-07-26T00:00:00Z","oa_version":"Submitted Version","publication_status":"published","doi":"10.1016/j.tcb.2018.06.006","intvolume":"        28","citation":{"short":"K. Fiedorczuk, L.A. Sazanov, Trends in Cell Biology 28 (2018) 835–867.","ama":"Fiedorczuk K, Sazanov LA. Mammalian mitochondrial complex I structure and disease causing mutations. <i>Trends in Cell Biology</i>. 2018;28(10):835-867. doi:<a href=\"https://doi.org/10.1016/j.tcb.2018.06.006\">10.1016/j.tcb.2018.06.006</a>","ieee":"K. Fiedorczuk and L. A. Sazanov, “Mammalian mitochondrial complex I structure and disease causing mutations,” <i>Trends in Cell Biology</i>, vol. 28, no. 10. Elsevier, pp. 835–867, 2018.","apa":"Fiedorczuk, K., &#38; Sazanov, L. A. (2018). Mammalian mitochondrial complex I structure and disease causing mutations. <i>Trends in Cell Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tcb.2018.06.006\">https://doi.org/10.1016/j.tcb.2018.06.006</a>","ista":"Fiedorczuk K, Sazanov LA. 2018. Mammalian mitochondrial complex I structure and disease causing mutations. Trends in Cell Biology. 28(10), 835–867.","mla":"Fiedorczuk, Karol, and Leonid A. Sazanov. “Mammalian Mitochondrial Complex I Structure and Disease Causing Mutations.” <i>Trends in Cell Biology</i>, vol. 28, no. 10, Elsevier, 2018, pp. 835–67, doi:<a href=\"https://doi.org/10.1016/j.tcb.2018.06.006\">10.1016/j.tcb.2018.06.006</a>.","chicago":"Fiedorczuk, Karol, and Leonid A Sazanov. “Mammalian Mitochondrial Complex I Structure and Disease Causing Mutations.” <i>Trends in Cell Biology</i>. Elsevier, 2018. <a href=\"https://doi.org/10.1016/j.tcb.2018.06.006\">https://doi.org/10.1016/j.tcb.2018.06.006</a>."},"ddc":["572"],"scopus_import":"1","file_date_updated":"2020-07-14T12:45:00Z","_id":"152","year":"2018","date_updated":"2023-09-13T08:51:56Z","abstract":[{"lang":"eng","text":"Complex I has an essential role in ATP production by coupling electron transfer from NADH to quinone with translocation of protons across the inner mitochondrial membrane. Isolated complex I deficiency is a frequent cause of mitochondrial inherited diseases. Complex I has also been implicated in cancer, ageing, and neurodegenerative conditions. Until recently, the understanding of complex I deficiency on the molecular level was limited due to the lack of high-resolution structures of the enzyme. However, due to developments in single particle cryo-electron microscopy (cryo-EM), recent studies have reported nearly atomic resolution maps and models of mitochondrial complex I. These structures significantly add to our understanding of complex I mechanism and assembly. The disease-causing mutations are discussed here in their structural context."}],"issue":"10","month":"07","oa":1,"status":"public","language":[{"iso":"eng"}],"department":[{"_id":"LeSa"}],"type":"journal_article","page":"835 - 867","date_created":"2018-12-11T11:44:54Z","publication":"Trends in Cell Biology","has_accepted_license":"1","external_id":{"isi":["000445118200007"]},"quality_controlled":"1","volume":28,"publist_id":"7769","article_processing_charge":"No","article_type":"original","file":[{"file_size":2185385,"relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_id":"6994","creator":"lsazanov","checksum":"ef6d2b4e1fd63948539639242610bfa6","date_created":"2019-11-07T12:55:20Z","file_name":"SasanovFinalMS+EdComments_LS_allacc_withFigs.pdf","date_updated":"2020-07-14T12:45:00Z"}],"isi":1,"author":[{"last_name":"Fiedorczuk","id":"5BFF67CE-02D1-11E9-B11A-A5A4D7DFFFD0","first_name":"Karol","full_name":"Fiedorczuk, Karol"},{"full_name":"Sazanov, Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov","orcid":"0000-0002-0977-7989","first_name":"Leonid A"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"day":"26","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","title":"Mammalian mitochondrial complex I structure and disease causing mutations","publisher":"Elsevier","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"publication":"Methods in Cell Biology","page":"79 - 91","date_created":"2018-12-11T11:44:54Z","type":"book_chapter","department":[{"_id":"MiSi"},{"_id":"NanoFab"}],"language":[{"iso":"eng"}],"article_processing_charge":"No","publist_id":"7768","quality_controlled":"1","volume":147,"external_id":{"pmid":["30165964"],"isi":["000452412300006"]},"pmid":1,"day":"27","isi":1,"author":[{"full_name":"Renkawitz, Jörg","orcid":"0000-0003-2856-3369","first_name":"Jörg","last_name":"Renkawitz","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Reversat, Anne","first_name":"Anne","orcid":"0000-0003-0666-8928","last_name":"Reversat","id":"35B76592-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Leithner, Alexander F","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","last_name":"Leithner","orcid":"0000-0002-1073-744X","first_name":"Alexander F"},{"first_name":"Jack","orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87","last_name":"Merrin","full_name":"Merrin, Jack"},{"full_name":"Sixt, Michael K","first_name":"Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Academic Press","title":"Micro-engineered “pillar forests” to study cell migration in complex but controlled 3D environments","doi":"10.1016/bs.mcb.2018.07.004","publication_status":"published","oa_version":"None","date_published":"2018-07-27T00:00:00Z","scopus_import":"1","intvolume":"       147","citation":{"mla":"Renkawitz, Jörg, et al. “Micro-Engineered ‘Pillar Forests’ to Study Cell Migration in Complex but Controlled 3D Environments.” <i>Methods in Cell Biology</i>, vol. 147, Academic Press, 2018, pp. 79–91, doi:<a href=\"https://doi.org/10.1016/bs.mcb.2018.07.004\">10.1016/bs.mcb.2018.07.004</a>.","apa":"Renkawitz, J., Reversat, A., Leithner, A. F., Merrin, J., &#38; Sixt, M. K. (2018). Micro-engineered “pillar forests” to study cell migration in complex but controlled 3D environments. In <i>Methods in Cell Biology</i> (Vol. 147, pp. 79–91). Academic Press. <a href=\"https://doi.org/10.1016/bs.mcb.2018.07.004\">https://doi.org/10.1016/bs.mcb.2018.07.004</a>","ista":"Renkawitz J, Reversat A, Leithner AF, Merrin J, Sixt MK. 2018.Micro-engineered “pillar forests” to study cell migration in complex but controlled 3D environments. In: Methods in Cell Biology. vol. 147, 79–91.","chicago":"Renkawitz, Jörg, Anne Reversat, Alexander F Leithner, Jack Merrin, and Michael K Sixt. “Micro-Engineered ‘Pillar Forests’ to Study Cell Migration in Complex but Controlled 3D Environments.” In <i>Methods in Cell Biology</i>, 147:79–91. Academic Press, 2018. <a href=\"https://doi.org/10.1016/bs.mcb.2018.07.004\">https://doi.org/10.1016/bs.mcb.2018.07.004</a>.","ama":"Renkawitz J, Reversat A, Leithner AF, Merrin J, Sixt MK. Micro-engineered “pillar forests” to study cell migration in complex but controlled 3D environments. In: <i>Methods in Cell Biology</i>. Vol 147. Academic Press; 2018:79-91. doi:<a href=\"https://doi.org/10.1016/bs.mcb.2018.07.004\">10.1016/bs.mcb.2018.07.004</a>","ieee":"J. Renkawitz, A. Reversat, A. F. Leithner, J. Merrin, and M. K. Sixt, “Micro-engineered ‘pillar forests’ to study cell migration in complex but controlled 3D environments,” in <i>Methods in Cell Biology</i>, vol. 147, Academic Press, 2018, pp. 79–91.","short":"J. Renkawitz, A. Reversat, A.F. Leithner, J. Merrin, M.K. Sixt, in:, Methods in Cell Biology, Academic Press, 2018, pp. 79–91."},"abstract":[{"lang":"eng","text":"Cells migrating in multicellular organisms steadily traverse complex three-dimensional (3D) environments. To decipher the underlying cell biology, current experimental setups either use simplified 2D, tissue-mimetic 3D (e.g., collagen matrices) or in vivo environments. While only in vivo experiments are truly physiological, they do not allow for precise manipulation of environmental parameters. 2D in vitro experiments do allow mechanical and chemical manipulations, but increasing evidence demonstrates substantial differences of migratory mechanisms in 2D and 3D. Here, we describe simple, robust, and versatile “pillar forests” to investigate cell migration in complex but fully controllable 3D environments. Pillar forests are polydimethylsiloxane-based setups, in which two closely adjacent surfaces are interconnected by arrays of micrometer-sized pillars. Changing the pillar shape, size, height and the inter-pillar distance precisely manipulates microenvironmental parameters (e.g., pore sizes, micro-geometry, micro-topology), while being easily combined with chemotactic cues, surface coatings, diverse cell types and advanced imaging techniques. Thus, pillar forests combine the advantages of 2D cell migration assays with the precise definition of 3D environmental parameters."}],"date_updated":"2023-09-13T08:56:35Z","year":"2018","_id":"153","status":"public","publication_identifier":{"issn":["0091679X"]},"month":"07"},{"_id":"154","article_number":"19","year":"2018","date_updated":"2023-09-19T09:31:15Z","abstract":[{"lang":"eng","text":"We give a lower bound on the ground state energy of a system of two fermions of one species interacting with two fermions of another species via point interactions. We show that there is a critical mass ratio m2 ≈ 0.58 such that the system is stable, i.e., the energy is bounded from below, for m∈[m2,m2−1]. So far it was not known whether this 2 + 2 system exhibits a stable region at all or whether the formation of four-body bound states causes an unbounded spectrum for all mass ratios, similar to the Thomas effect. Our result gives further evidence for the stability of the more general N + M system."}],"issue":"3","ec_funded":1,"month":"09","oa":1,"publication_identifier":{"eissn":["15729656"],"issn":["13850172"]},"status":"public","date_published":"2018-09-01T00:00:00Z","oa_version":"Published Version","publication_status":"published","doi":"10.1007/s11040-018-9275-3","intvolume":"        21","citation":{"short":"T. Moser, R. Seiringer, Mathematical Physics Analysis and Geometry 21 (2018).","ieee":"T. Moser and R. Seiringer, “Stability of the 2+2 fermionic system with point interactions,” <i>Mathematical Physics Analysis and Geometry</i>, vol. 21, no. 3. Springer, 2018.","ama":"Moser T, Seiringer R. Stability of the 2+2 fermionic system with point interactions. <i>Mathematical Physics Analysis and Geometry</i>. 2018;21(3). doi:<a href=\"https://doi.org/10.1007/s11040-018-9275-3\">10.1007/s11040-018-9275-3</a>","chicago":"Moser, Thomas, and Robert Seiringer. “Stability of the 2+2 Fermionic System with Point Interactions.” <i>Mathematical Physics Analysis and Geometry</i>. Springer, 2018. <a href=\"https://doi.org/10.1007/s11040-018-9275-3\">https://doi.org/10.1007/s11040-018-9275-3</a>.","mla":"Moser, Thomas, and Robert Seiringer. “Stability of the 2+2 Fermionic System with Point Interactions.” <i>Mathematical Physics Analysis and Geometry</i>, vol. 21, no. 3, 19, Springer, 2018, doi:<a href=\"https://doi.org/10.1007/s11040-018-9275-3\">10.1007/s11040-018-9275-3</a>.","apa":"Moser, T., &#38; Seiringer, R. (2018). Stability of the 2+2 fermionic system with point interactions. <i>Mathematical Physics Analysis and Geometry</i>. Springer. <a href=\"https://doi.org/10.1007/s11040-018-9275-3\">https://doi.org/10.1007/s11040-018-9275-3</a>","ista":"Moser T, Seiringer R. 2018. Stability of the 2+2 fermionic system with point interactions. Mathematical Physics Analysis and Geometry. 21(3), 19."},"ddc":["530"],"file_date_updated":"2020-07-14T12:45:01Z","scopus_import":"1","file":[{"date_updated":"2020-07-14T12:45:01Z","file_name":"2018_MathPhysics_Moser.pdf","date_created":"2018-12-17T16:49:02Z","file_id":"5729","checksum":"411c4db5700d7297c9cd8ebc5dd29091","creator":"dernst","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_size":496973}],"project":[{"name":"Analysis of quantum many-body systems","call_identifier":"H2020","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"},{"grant_number":"P27533_N27","_id":"25C878CE-B435-11E9-9278-68D0E5697425","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","call_identifier":"FWF"},{"call_identifier":"FWF","name":"FWF Open Access Fund","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1"}],"author":[{"full_name":"Moser, Thomas","first_name":"Thomas","last_name":"Moser","id":"2B5FC9A4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Robert","orcid":"0000-0002-6781-0521","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert"}],"isi":1,"day":"01","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledgement":"Open access funding provided by Austrian Science Fund (FWF).","title":"Stability of the 2+2 fermionic system with point interactions","publisher":"Springer","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"department":[{"_id":"RoSe"}],"type":"journal_article","date_created":"2018-12-11T11:44:55Z","publication":"Mathematical Physics Analysis and Geometry","has_accepted_license":"1","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"52"}]},"external_id":{"isi":["000439639700001"]},"quality_controlled":"1","volume":21,"publist_id":"7767","article_type":"original","article_processing_charge":"No"},{"title":"Routing thermal noise through quantum networks","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"SPIE","alternative_title":["Proceedings of SPIE"],"day":"04","isi":1,"author":[{"last_name":"Xuereb","first_name":"André","full_name":"Xuereb, André"},{"first_name":"Matteo","last_name":"Aquilina","full_name":"Aquilina, Matteo"},{"full_name":"Barzanjeh, Shabir","last_name":"Barzanjeh","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0415-1423","first_name":"Shabir"}],"article_processing_charge":"No","publist_id":"7766","volume":10672,"editor":[{"first_name":"D L","last_name":"Andrews","full_name":"Andrews, D L"},{"last_name":"Ostendorf","first_name":"A","full_name":"Ostendorf, A"},{"full_name":"Bain, A J","first_name":"A J","last_name":"Bain"},{"full_name":"Nunzi, J M","first_name":"J M","last_name":"Nunzi"}],"quality_controlled":"1","external_id":{"arxiv":["1806.01000"],"isi":["000453298500019"]},"date_created":"2018-12-11T11:44:55Z","department":[{"_id":"JoFi"}],"language":[{"iso":"eng"}],"type":"conference","oa":1,"status":"public","month":"05","year":"2018","arxiv":1,"abstract":[{"lang":"eng","text":"There is currently significant interest in operating devices in the quantum regime, where their behaviour cannot be explained through classical mechanics. Quantum states, including entangled states, are fragile and easily disturbed by excessive thermal noise. Here we address the question of whether it is possible to create non-reciprocal devices that encourage the flow of thermal noise towards or away from a particular quantum device in a network. Our work makes use of the cascaded systems formalism to answer this question in the affirmative, showing how a three-port device can be used as an effective thermal transistor, and illustrates how this formalism maps onto an experimentally-realisable optomechanical system. Our results pave the way to more resilient quantum devices and to the use of thermal noise as a resource."}],"date_updated":"2023-09-18T08:12:24Z","_id":"155","article_number":"106721N","main_file_link":[{"url":"https://arxiv.org/abs/1806.01000","open_access":"1"}],"scopus_import":"1","intvolume":"     10672","citation":{"short":"A. Xuereb, M. Aquilina, S. Barzanjeh, in:, D.L. Andrews, A. Ostendorf, A.J. Bain, J.M. Nunzi (Eds.), SPIE, 2018.","ama":"Xuereb A, Aquilina M, Barzanjeh S. Routing thermal noise through quantum networks. In: Andrews DL, Ostendorf A, Bain AJ, Nunzi JM, eds. Vol 10672. SPIE; 2018. doi:<a href=\"https://doi.org/10.1117/12.2309928\">10.1117/12.2309928</a>","ieee":"A. Xuereb, M. Aquilina, and S. Barzanjeh, “Routing thermal noise through quantum networks,” presented at the SPIE: The international society for optical engineering, Strasbourg, France, 2018, vol. 10672.","ista":"Xuereb A, Aquilina M, Barzanjeh S. 2018. Routing thermal noise through quantum networks. SPIE: The international society for optical engineering, Proceedings of SPIE, vol. 10672, 106721N.","apa":"Xuereb, A., Aquilina, M., &#38; Barzanjeh, S. (2018). Routing thermal noise through quantum networks. In D. L. Andrews, A. Ostendorf, A. J. Bain, &#38; J. M. Nunzi (Eds.) (Vol. 10672). Presented at the SPIE: The international society for optical engineering, Strasbourg, France: SPIE. <a href=\"https://doi.org/10.1117/12.2309928\">https://doi.org/10.1117/12.2309928</a>","mla":"Xuereb, André, et al. <i>Routing Thermal Noise through Quantum Networks</i>. Edited by D L Andrews et al., vol. 10672, 106721N, SPIE, 2018, doi:<a href=\"https://doi.org/10.1117/12.2309928\">10.1117/12.2309928</a>.","chicago":"Xuereb, André, Matteo Aquilina, and Shabir Barzanjeh. “Routing Thermal Noise through Quantum Networks.” edited by D L Andrews, A Ostendorf, A J Bain, and J M Nunzi, Vol. 10672. SPIE, 2018. <a href=\"https://doi.org/10.1117/12.2309928\">https://doi.org/10.1117/12.2309928</a>."},"doi":"10.1117/12.2309928","conference":{"location":"Strasbourg, France","end_date":"2018-04-26","name":"SPIE: The international society for optical engineering","start_date":"2018-04-22"},"publication_status":"published","date_published":"2018-05-04T00:00:00Z","oa_version":"Preprint"},{"year":"2018","date_updated":"2023-09-19T10:05:37Z","abstract":[{"lang":"eng","text":"Imprecision in timing can sometimes be beneficial: Metric interval temporal logic (MITL), disabling the expression of punctuality constraints, was shown to translate to timed automata, yielding an elementary decision procedure. We show how this principle extends to other forms of dense-time specification using regular expressions. By providing a clean, automaton-based formal framework for non-punctual languages, we are able to recover and extend several results in timed systems. Metric interval regular expressions (MIRE) are introduced, providing regular expressions with non-singular duration constraints. We obtain that MIRE are expressively complete relative to a class of one-clock timed automata, which can be determinized using additional clocks. Metric interval dynamic logic (MIDL) is then defined using MIRE as temporal modalities. We show that MIDL generalizes known extensions of MITL, while translating to timed automata at comparable cost."}],"_id":"156","oa":1,"status":"public","month":"07","publication_status":"published","conference":{"start_date":"2018-07-15","name":"FM: International Symposium on Formal Methods","end_date":"2018-07-17","location":"Oxford, UK"},"doi":"10.1007/978-3-319-95582-7_9","date_published":"2018-07-12T00:00:00Z","oa_version":"Submitted Version","ddc":["000"],"file_date_updated":"2020-10-09T06:22:41Z","scopus_import":"1","intvolume":"     10951","citation":{"chicago":"Ferrere, Thomas. “The Compound Interest in Relaxing Punctuality,” 10951:147–64. Springer, 2018. <a href=\"https://doi.org/10.1007/978-3-319-95582-7_9\">https://doi.org/10.1007/978-3-319-95582-7_9</a>.","apa":"Ferrere, T. (2018). The compound interest in relaxing punctuality (Vol. 10951, pp. 147–164). Presented at the FM: International Symposium on Formal Methods, Oxford, UK: Springer. <a href=\"https://doi.org/10.1007/978-3-319-95582-7_9\">https://doi.org/10.1007/978-3-319-95582-7_9</a>","ista":"Ferrere T. 2018. The compound interest in relaxing punctuality. FM: International Symposium on Formal Methods, LNCS, vol. 10951, 147–164.","mla":"Ferrere, Thomas. <i>The Compound Interest in Relaxing Punctuality</i>. Vol. 10951, Springer, 2018, pp. 147–64, doi:<a href=\"https://doi.org/10.1007/978-3-319-95582-7_9\">10.1007/978-3-319-95582-7_9</a>.","ieee":"T. Ferrere, “The compound interest in relaxing punctuality,” presented at the FM: International Symposium on Formal Methods, Oxford, UK, 2018, vol. 10951, pp. 147–164.","ama":"Ferrere T. The compound interest in relaxing punctuality. In: Vol 10951. Springer; 2018:147-164. doi:<a href=\"https://doi.org/10.1007/978-3-319-95582-7_9\">10.1007/978-3-319-95582-7_9</a>","short":"T. Ferrere, in:, Springer, 2018, pp. 147–164."},"day":"12","file":[{"file_name":"2018_LNCS_Ferrere.pdf","date_updated":"2020-10-09T06:22:41Z","date_created":"2020-10-09T06:22:41Z","file_id":"8637","checksum":"a045c213c42c445f1889326f8db82a0a","creator":"dernst","access_level":"open_access","content_type":"application/pdf","relation":"main_file","success":1,"file_size":485576}],"project":[{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"author":[{"last_name":"Ferrere","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","orcid":"0000-0001-5199-3143","full_name":"Ferrere, Thomas"}],"isi":1,"title":"The compound interest in relaxing punctuality","publisher":"Springer","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","alternative_title":["LNCS"],"date_created":"2018-12-11T11:44:55Z","page":"147 - 164","has_accepted_license":"1","language":[{"iso":"eng"}],"department":[{"_id":"ToHe"}],"type":"conference","publist_id":"7765","article_processing_charge":"No","external_id":{"isi":["000489765800009"]},"volume":10951,"quality_controlled":"1"},{"_id":"157","year":"2018","date_updated":"2023-09-11T13:43:22Z","issue":"7713","abstract":[{"text":"Social dilemmas occur when incentives for individuals are misaligned with group interests 1-7 . According to the 'tragedy of the commons', these misalignments can lead to overexploitation and collapse of public resources. The resulting behaviours can be analysed with the tools of game theory 8 . The theory of direct reciprocity 9-15 suggests that repeated interactions can alleviate such dilemmas, but previous work has assumed that the public resource remains constant over time. Here we introduce the idea that the public resource is instead changeable and depends on the strategic choices of individuals. An intuitive scenario is that cooperation increases the public resource, whereas defection decreases it. Thus, cooperation allows the possibility of playing a more valuable game with higher payoffs, whereas defection leads to a less valuable game. We analyse this idea using the theory of stochastic games 16-19 and evolutionary game theory. We find that the dependence of the public resource on previous interactions can greatly enhance the propensity for cooperation. For these results, the interaction between reciprocity and payoff feedback is crucial: neither repeated interactions in a constant environment nor single interactions in a changing environment yield similar cooperation rates. Our framework shows which feedbacks between exploitation and environment - either naturally occurring or designed - help to overcome social dilemmas.","lang":"eng"}],"ec_funded":1,"month":"07","oa":1,"status":"public","date_published":"2018-07-04T00:00:00Z","oa_version":"Submitted Version","publication_status":"published","doi":"10.1038/s41586-018-0277-x","intvolume":"       559","citation":{"mla":"Hilbe, Christian, et al. “Evolution of Cooperation in Stochastic Games.” <i>Nature</i>, vol. 559, no. 7713, Nature Publishing Group, 2018, pp. 246–49, doi:<a href=\"https://doi.org/10.1038/s41586-018-0277-x\">10.1038/s41586-018-0277-x</a>.","ista":"Hilbe C, Šimsa Š, Chatterjee K, Nowak M. 2018. Evolution of cooperation in stochastic games. Nature. 559(7713), 246–249.","apa":"Hilbe, C., Šimsa, Š., Chatterjee, K., &#38; Nowak, M. (2018). Evolution of cooperation in stochastic games. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41586-018-0277-x\">https://doi.org/10.1038/s41586-018-0277-x</a>","chicago":"Hilbe, Christian, Štepán Šimsa, Krishnendu Chatterjee, and Martin Nowak. “Evolution of Cooperation in Stochastic Games.” <i>Nature</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41586-018-0277-x\">https://doi.org/10.1038/s41586-018-0277-x</a>.","short":"C. Hilbe, Š. Šimsa, K. Chatterjee, M. Nowak, Nature 559 (2018) 246–249.","ieee":"C. Hilbe, Š. Šimsa, K. Chatterjee, and M. Nowak, “Evolution of cooperation in stochastic games,” <i>Nature</i>, vol. 559, no. 7713. Nature Publishing Group, pp. 246–249, 2018.","ama":"Hilbe C, Šimsa Š, Chatterjee K, Nowak M. Evolution of cooperation in stochastic games. <i>Nature</i>. 2018;559(7713):246-249. doi:<a href=\"https://doi.org/10.1038/s41586-018-0277-x\">10.1038/s41586-018-0277-x</a>"},"ddc":["000"],"scopus_import":"1","file_date_updated":"2020-07-14T12:45:02Z","file":[{"file_size":2834442,"relation":"main_file","content_type":"application/pdf","access_level":"open_access","creator":"dernst","file_id":"7049","checksum":"011ab905cf9a410bc2b96f15174d654d","date_created":"2019-11-19T08:09:57Z","date_updated":"2020-07-14T12:45:02Z","file_name":"2018_Nature_Hilbe.pdf"}],"project":[{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory","call_identifier":"FWF"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"isi":1,"author":[{"full_name":"Hilbe, Christian","orcid":"0000-0001-5116-955X","first_name":"Christian","last_name":"Hilbe","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Šimsa, Štepán","first_name":"Štepán","last_name":"Šimsa"},{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","first_name":"Krishnendu"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"}],"day":"04","acknowledgement":"European Research Council Start Grant 279307, Austrian Science Fund (FWF) grant P23499-N23, \r\nC.H. acknowledges support from the ISTFELLOW programme.","title":"Evolution of cooperation in stochastic games","publisher":"Nature Publishing Group","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"department":[{"_id":"KrCh"}],"type":"journal_article","date_created":"2018-12-11T11:44:56Z","page":"246 - 249","publication":"Nature","has_accepted_license":"1","related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/engineering-cooperation/"}]},"external_id":{"isi":["000438240900054"]},"volume":559,"quality_controlled":"1","publist_id":"7764","article_processing_charge":"No"}]