[{"volume":9206,"date_created":"2018-12-11T11:52:58Z","date_updated":"2024-02-21T13:52:07Z","related_material":{"record":[{"id":"5549","status":"public","relation":"research_paper"}]},"author":[{"last_name":"Brázdil","first_name":"Tomáš","full_name":"Brázdil, Tomáš"},{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"full_name":"Chmelik, Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Chmelik"},{"full_name":"Fellner, Andreas","first_name":"Andreas","last_name":"Fellner","id":"42BABFB4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jan","last_name":"Kretinsky","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8122-2881","full_name":"Kretinsky, Jan"}],"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publisher":"Springer","publication_status":"published","acknowledgement":"This research was funded in part by Austrian Science Fund (FWF) Grant No P 23499-N23, FWF NFN Grant No S11407-N23 (RiSE) and Z211-N23 (Wittgenstein Award), European Research Council (ERC) Grant No 279307 (Graph Games), ERC Grant No 267989 (QUAREM), the Czech Science Foundation Grant No P202/12/G061, and People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007–2013) REA Grant No 291734.","year":"2015","ec_funded":1,"publist_id":"5564","language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-21690-4_10","conference":{"end_date":"2015-07-24","start_date":"2015-07-18","location":"San Francisco, CA, United States","name":"CAV: Computer Aided Verification"},"project":[{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"},{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1502.02834"}],"oa":1,"publication_identifier":{"eisbn":["978-3-319-21690-4"]},"month":"07","oa_version":"Preprint","intvolume":" 9206","title":"Counterexample explanation by learning small strategies in Markov decision processes","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1603","abstract":[{"text":"For deterministic systems, a counterexample to a property can simply be an error trace, whereas counterexamples in probabilistic systems are necessarily more complex. For instance, a set of erroneous traces with a sufficient cumulative probability mass can be used. Since these are too large objects to understand and manipulate, compact representations such as subchains have been considered. In the case of probabilistic systems with non-determinism, the situation is even more complex. While a subchain for a given strategy (or scheduler, resolving non-determinism) is a straightforward choice, we take a different approach. Instead, we focus on the strategy itself, and extract the most important decisions it makes, and present its succinct representation.\r\nThe key tools we employ to achieve this are (1) introducing a concept of importance of a state w.r.t. the strategy, and (2) learning using decision trees. There are three main consequent advantages of our approach. Firstly, it exploits the quantitative information on states, stressing the more important decisions. Secondly, it leads to a greater variability and degree of freedom in representing the strategies. Thirdly, the representation uses a self-explanatory data structure. In summary, our approach produces more succinct and more explainable strategies, as opposed to e.g. binary decision diagrams. Finally, our experimental results show that we can extract several rules describing the strategy even for very large systems that do not fit in memory, and based on the rules explain the erroneous behaviour.","lang":"eng"}],"alternative_title":["LNCS"],"type":"conference","date_published":"2015-07-16T00:00:00Z","page":"158 - 177","citation":{"ieee":"T. Brázdil, K. Chatterjee, M. Chmelik, A. Fellner, and J. Kretinsky, “Counterexample explanation by learning small strategies in Markov decision processes,” presented at the CAV: Computer Aided Verification, San Francisco, CA, United States, 2015, vol. 9206, pp. 158–177.","apa":"Brázdil, T., Chatterjee, K., Chmelik, M., Fellner, A., & Kretinsky, J. (2015). Counterexample explanation by learning small strategies in Markov decision processes (Vol. 9206, pp. 158–177). Presented at the CAV: Computer Aided Verification, San Francisco, CA, United States: Springer. https://doi.org/10.1007/978-3-319-21690-4_10","ista":"Brázdil T, Chatterjee K, Chmelik M, Fellner A, Kretinsky J. 2015. Counterexample explanation by learning small strategies in Markov decision processes. CAV: Computer Aided Verification, LNCS, vol. 9206, 158–177.","ama":"Brázdil T, Chatterjee K, Chmelik M, Fellner A, Kretinsky J. Counterexample explanation by learning small strategies in Markov decision processes. In: Vol 9206. Springer; 2015:158-177. doi:10.1007/978-3-319-21690-4_10","chicago":"Brázdil, Tomáš, Krishnendu Chatterjee, Martin Chmelik, Andreas Fellner, and Jan Kretinsky. “Counterexample Explanation by Learning Small Strategies in Markov Decision Processes,” 9206:158–77. Springer, 2015. https://doi.org/10.1007/978-3-319-21690-4_10.","short":"T. Brázdil, K. Chatterjee, M. Chmelik, A. Fellner, J. Kretinsky, in:, Springer, 2015, pp. 158–177.","mla":"Brázdil, Tomáš, et al. Counterexample Explanation by Learning Small Strategies in Markov Decision Processes. Vol. 9206, Springer, 2015, pp. 158–77, doi:10.1007/978-3-319-21690-4_10."},"day":"16","scopus_import":1},{"oa":1,"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"project":[{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"}],"doi":"10.15479/AT:ISTA:28","month":"08","year":"2015","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publisher":"Institute of Science and Technology Austria","related_material":{"record":[{"id":"1603","status":"public","relation":"popular_science"}]},"contributor":[{"first_name":"Jan","last_name":"Kretinsky","id":"44CEF464-F248-11E8-B48F-1D18A9856A87"}],"author":[{"last_name":"Fellner","first_name":"Andreas","id":"42BABFB4-F248-11E8-B48F-1D18A9856A87","full_name":"Fellner, Andreas"}],"date_created":"2018-12-12T12:31:29Z","date_updated":"2024-02-21T13:52:07Z","publist_id":"5564","ec_funded":1,"file_date_updated":"2020-07-14T12:47:00Z","license":"https://creativecommons.org/publicdomain/zero/1.0/","citation":{"chicago":"Fellner, Andreas. “Experimental Part of CAV 2015 Publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes.” Institute of Science and Technology Austria, 2015. https://doi.org/10.15479/AT:ISTA:28.","short":"A. Fellner, (2015).","mla":"Fellner, Andreas. Experimental Part of CAV 2015 Publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes. Institute of Science and Technology Austria, 2015, doi:10.15479/AT:ISTA:28.","apa":"Fellner, A. (2015). Experimental part of CAV 2015 publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:28","ieee":"A. Fellner, “Experimental part of CAV 2015 publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes.” Institute of Science and Technology Austria, 2015.","ista":"Fellner A. 2015. Experimental part of CAV 2015 publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes, Institute of Science and Technology Austria, 10.15479/AT:ISTA:28.","ama":"Fellner A. Experimental part of CAV 2015 publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes. 2015. doi:10.15479/AT:ISTA:28"},"date_published":"2015-08-13T00:00:00Z","keyword":["Markov Decision Process","Decision Tree","Probabilistic Verification","Counterexample Explanation"],"article_processing_charge":"No","has_accepted_license":"1","day":"13","_id":"5549","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Experimental part of CAV 2015 publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes","status":"public","ddc":["004"],"oa_version":"Published Version","file":[{"creator":"system","file_size":49557109,"content_type":"application/zip","file_name":"IST-2015-28-v1+2_Fellner_DataRep.zip","access_level":"open_access","date_created":"2018-12-12T13:02:31Z","date_updated":"2020-07-14T12:47:00Z","checksum":"b8bcb43c0893023cda66c1b69c16ac62","file_id":"5597","relation":"main_file"}],"type":"research_data","datarep_id":"28","abstract":[{"text":"This repository contains the experimental part of the CAV 2015 publication Counterexample Explanation by Learning Small Strategies in Markov Decision Processes.\r\nWe extended the probabilistic model checker PRISM to represent strategies of Markov Decision Processes as Decision Trees.\r\nThe archive contains a java executable version of the extended tool (prism_dectree.jar) together with a few examples of the PRISM benchmark library.\r\nTo execute the program, please have a look at the README.txt, which provides instructions and further information on the archive.\r\nThe archive contains scripts that (if run often enough) reproduces the data presented in the publication.","lang":"eng"}]},{"pubrep_id":"501","oa_version":"Submitted Version","file":[{"file_name":"IST-2016-501-v1+1_46.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":633712,"file_id":"4794","relation":"main_file","date_updated":"2020-07-14T12:45:00Z","date_created":"2018-12-12T10:10:09Z","checksum":"e6881df44d87fe0c2529c9f7b2724614"}],"_id":"1512","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Bounding Helly numbers via Betti numbers","status":"public","ddc":["510"],"intvolume":" 34","abstract":[{"text":"We show that very weak topological assumptions are enough to ensure the existence of a Helly-type theorem. More precisely, we show that for any non-negative integers b and d there exists an integer h(b,d) such that the following holds. If F is a finite family of subsets of R^d such that the ith reduced Betti number (with Z_2 coefficients in singular homology) of the intersection of any proper subfamily G of F is at most b for every non-negative integer i less or equal to (d-1)/2, then F has Helly number at most h(b,d). These topological conditions are sharp: not controlling any of these first Betti numbers allow for families with unbounded Helly number. Our proofs combine homological non-embeddability results with a Ramsey-based approach to build, given an arbitrary simplicial complex K, some well-behaved chain map from C_*(K) to C_*(R^d). Both techniques are of independent interest.","lang":"eng"}],"type":"conference","alternative_title":["LIPIcs"],"date_published":"2015-01-01T00:00:00Z","citation":{"chicago":"Goaoc, Xavier, Pavel Paták, Zuzana Patakova, Martin Tancer, and Uli Wagner. “Bounding Helly Numbers via Betti Numbers,” 34:507–21. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015. https://doi.org/10.4230/LIPIcs.SOCG.2015.507.","short":"X. Goaoc, P. Paták, Z. Patakova, M. Tancer, U. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 507–521.","mla":"Goaoc, Xavier, et al. Bounding Helly Numbers via Betti Numbers. Vol. 34, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 507–21, doi:10.4230/LIPIcs.SOCG.2015.507.","ieee":"X. Goaoc, P. Paták, Z. Patakova, M. Tancer, and U. Wagner, “Bounding Helly numbers via Betti numbers,” presented at the SoCG: Symposium on Computational Geometry, Eindhoven, Netherlands, 2015, vol. 34, pp. 507–521.","apa":"Goaoc, X., Paták, P., Patakova, Z., Tancer, M., & Wagner, U. (2015). Bounding Helly numbers via Betti numbers (Vol. 34, pp. 507–521). Presented at the SoCG: Symposium on Computational Geometry, Eindhoven, Netherlands: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SOCG.2015.507","ista":"Goaoc X, Paták P, Patakova Z, Tancer M, Wagner U. 2015. Bounding Helly numbers via Betti numbers. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 34, 507–521.","ama":"Goaoc X, Paták P, Patakova Z, Tancer M, Wagner U. Bounding Helly numbers via Betti numbers. In: Vol 34. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2015:507-521. doi:10.4230/LIPIcs.SOCG.2015.507"},"page":"507 - 521","day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","author":[{"last_name":"Goaoc","first_name":"Xavier","full_name":"Goaoc, Xavier"},{"full_name":"Paták, Pavel","first_name":"Pavel","last_name":"Paták"},{"first_name":"Zuzana","last_name":"Patakova","orcid":"0000-0002-3975-1683","full_name":"Patakova, Zuzana"},{"full_name":"Tancer, Martin","orcid":"0000-0002-1191-6714","first_name":"Martin","last_name":"Tancer"},{"full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","last_name":"Wagner","first_name":"Uli"}],"related_material":{"record":[{"id":"424","status":"public","relation":"later_version"}]},"date_updated":"2024-02-28T12:59:37Z","date_created":"2018-12-11T11:52:27Z","volume":34,"acknowledgement":"PP, ZP and MT were partially supported by the Charles University Grant GAUK 421511. ZP was\r\npartially supported by the Charles University Grant SVV-2014-260103. ZP and MT were partially\r\nsupported by the ERC Advanced Grant No. 267165 and by the project CE-ITI (GACR P202/12/G061)\r\nof the Czech Science Foundation. UW was partially supported by the Swiss National Science Foundation\r\n(grants SNSF-200020-138230 and SNSF-PP00P2-138948). Part of this work was done when XG was affiliated with INRIA Nancy Grand-Est and when MT was affiliated with Institutionen för matematik, Kungliga Tekniska Högskolan, then IST Austria.","year":"2015","publication_status":"published","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"UlWa"}],"file_date_updated":"2020-07-14T12:45:00Z","publist_id":"5665","conference":{"end_date":"2015-06-25","start_date":"2015-06-22","location":"Eindhoven, Netherlands","name":"SoCG: Symposium on Computational Geometry"},"doi":"10.4230/LIPIcs.SOCG.2015.507","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","month":"01"},{"publist_id":"7631","extern":"1","year":"2015","acknowledgement":"While working on this paper the authors were supported by the Leverhulme Trust and ERC grant 306457.","publication_status":"submitted","publisher":"Walter de Gruyter","author":[{"full_name":"Browning, Timothy D","orcid":"0000-0002-8314-0177","id":"35827D50-F248-11E8-B48F-1D18A9856A87","last_name":"Browning","first_name":"Timothy D"},{"last_name":"Prendiville","first_name":"Sean","full_name":"Prendiville, Sean"}],"related_material":{"record":[{"status":"public","relation":"later_version","id":"256"}]},"date_created":"2018-12-11T11:45:32Z","date_updated":"2024-03-05T12:09:22Z","volume":2017,"month":"02","publication_identifier":{"issn":["0075-4102"]},"external_id":{"arxiv":["1402.4489"]},"main_file_link":[{"url":"https://arxiv.org/abs/1402.4489","open_access":"1"}],"oa":1,"quality_controlled":"1","doi":"10.1515/crelle-2014-0122","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"lang":"eng","text":"We show that a non-singular integral form of degree d is soluble non-trivially over the integers if and only if it is soluble non-trivially over the reals and the p-adic numbers, provided that the form has at least (d-\\sqrt{d}/2)2^d variables. This improves on a longstanding result of Birch."}],"issue":"731","_id":"271","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Improvements in Birch's theorem on forms in many variables","intvolume":" 2017","oa_version":"Preprint","day":"20","article_processing_charge":"No","publication":"Journal fur die Reine und Angewandte Mathematik","citation":{"ama":"Browning TD, Prendiville S. Improvements in Birch’s theorem on forms in many variables. Journal fur die Reine und Angewandte Mathematik. 2017(731):203-234. doi:10.1515/crelle-2014-0122","apa":"Browning, T. D., & Prendiville, S. (n.d.). Improvements in Birch’s theorem on forms in many variables. Journal Fur Die Reine Und Angewandte Mathematik. Walter de Gruyter. https://doi.org/10.1515/crelle-2014-0122","ieee":"T. D. Browning and S. Prendiville, “Improvements in Birch’s theorem on forms in many variables,” Journal fur die Reine und Angewandte Mathematik, vol. 2017, no. 731. Walter de Gruyter, pp. 203–234.","ista":"Browning TD, Prendiville S. Improvements in Birch’s theorem on forms in many variables. Journal fur die Reine und Angewandte Mathematik. 2017(731), 203–234.","short":"T.D. Browning, S. Prendiville, Journal Fur Die Reine Und Angewandte Mathematik 2017 (n.d.) 203–234.","mla":"Browning, Timothy D., and Sean Prendiville. “Improvements in Birch’s Theorem on Forms in Many Variables.” Journal Fur Die Reine Und Angewandte Mathematik, vol. 2017, no. 731, Walter de Gruyter, pp. 203–34, doi:10.1515/crelle-2014-0122.","chicago":"Browning, Timothy D, and Sean Prendiville. “Improvements in Birch’s Theorem on Forms in Many Variables.” Journal Fur Die Reine Und Angewandte Mathematik. Walter de Gruyter, n.d. https://doi.org/10.1515/crelle-2014-0122."},"article_type":"original","page":"203 - 234","date_published":"2015-02-20T00:00:00Z"},{"date_published":"2015-08-01T00:00:00Z","citation":{"apa":"Dziembowski, S., Faust, S., Kolmogorov, V., & Pietrzak, K. Z. (2015). Proofs of space. In 35th Annual Cryptology Conference (Vol. 9216, pp. 585–605). Santa Barbara, CA, United States: Springer. https://doi.org/10.1007/978-3-662-48000-7_29","ieee":"S. Dziembowski, S. Faust, V. Kolmogorov, and K. Z. Pietrzak, “Proofs of space,” in 35th Annual Cryptology Conference, Santa Barbara, CA, United States, 2015, vol. 9216, pp. 585–605.","ista":"Dziembowski S, Faust S, Kolmogorov V, Pietrzak KZ. 2015. Proofs of space. 35th Annual Cryptology Conference. CRYPTO: International Cryptology Conference, LNCS, vol. 9216, 585–605.","ama":"Dziembowski S, Faust S, Kolmogorov V, Pietrzak KZ. Proofs of space. In: 35th Annual Cryptology Conference. Vol 9216. Springer; 2015:585-605. doi:10.1007/978-3-662-48000-7_29","chicago":"Dziembowski, Stefan, Sebastian Faust, Vladimir Kolmogorov, and Krzysztof Z Pietrzak. “Proofs of Space.” In 35th Annual Cryptology Conference, 9216:585–605. Springer, 2015. https://doi.org/10.1007/978-3-662-48000-7_29.","short":"S. Dziembowski, S. Faust, V. Kolmogorov, K.Z. Pietrzak, in:, 35th Annual Cryptology Conference, Springer, 2015, pp. 585–605.","mla":"Dziembowski, Stefan, et al. “Proofs of Space.” 35th Annual Cryptology Conference, vol. 9216, Springer, 2015, pp. 585–605, doi:10.1007/978-3-662-48000-7_29."},"publication":"35th Annual Cryptology Conference","page":"585 - 605","article_processing_charge":"No","day":"01","scopus_import":"1","pubrep_id":"671","oa_version":"Preprint","_id":"1675","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 9216","status":"public","title":"Proofs of space","abstract":[{"text":"Proofs of work (PoW) have been suggested by Dwork and Naor (Crypto’92) as protection to a shared resource. The basic idea is to ask the service requestor to dedicate some non-trivial amount of computational work to every request. The original applications included prevention of spam and protection against denial of service attacks. More recently, PoWs have been used to prevent double spending in the Bitcoin digital currency system. In this work, we put forward an alternative concept for PoWs - so-called proofs of space (PoS), where a service requestor must dedicate a significant amount of disk space as opposed to computation. We construct secure PoS schemes in the random oracle model (with one additional mild assumption required for the proof to go through), using graphs with high “pebbling complexity” and Merkle hash-trees. We discuss some applications, including follow-up work where a decentralized digital currency scheme called Spacecoin is constructed that uses PoS (instead of wasteful PoW like in Bitcoin) to prevent double spending. The main technical contribution of this work is the construction of (directed, loop-free) graphs on N vertices with in-degree O(log logN) such that even if one places Θ(N) pebbles on the nodes of the graph, there’s a constant fraction of nodes that needs Θ(N) steps to be pebbled (where in every step one can put a pebble on a node if all its parents have a pebble).","lang":"eng"}],"type":"conference","alternative_title":["LNCS"],"doi":"10.1007/978-3-662-48000-7_29","conference":{"name":"CRYPTO: International Cryptology Conference","end_date":"2015-08-20","start_date":"2015-08-16","location":"Santa Barbara, CA, United States"},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://eprint.iacr.org/2013/796.pdf","open_access":"1"}],"oa":1,"project":[{"_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160","call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice"},{"_id":"258C570E-B435-11E9-9278-68D0E5697425","grant_number":"259668","call_identifier":"FP7","name":"Provable Security for Physical Cryptography"}],"quality_controlled":"1","publication_identifier":{"isbn":["9783662479995"],"issn":["0302-9743"]},"month":"08","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"2274"}]},"author":[{"first_name":"Stefan","last_name":"Dziembowski","full_name":"Dziembowski, Stefan"},{"full_name":"Faust, Sebastian","last_name":"Faust","first_name":"Sebastian"},{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov","first_name":"Vladimir","full_name":"Kolmogorov, Vladimir"},{"full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak","first_name":"Krzysztof Z"}],"volume":9216,"date_created":"2018-12-11T11:53:24Z","date_updated":"2024-03-20T08:31:49Z","year":"2015","publisher":"Springer","department":[{"_id":"VlKo"},{"_id":"KrPi"}],"publication_status":"published","publist_id":"5474","ec_funded":1},{"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.molcel.2015.03.031"}],"language":[{"iso":"eng"}],"doi":"10.1016/j.molcel.2015.03.031","publication_identifier":{"issn":["1097-2765"]},"month":"06","publisher":"Elsevier","publication_status":"published","year":"2015","volume":58,"date_created":"2024-03-21T07:58:08Z","date_updated":"2024-03-25T11:52:26Z","author":[{"full_name":"Michael, Alicia Kathleen","id":"6437c950-2a03-11ee-914d-d6476dd7b75c","first_name":"Alicia Kathleen","last_name":"Michael"},{"full_name":"Harvey, Stacy L.","first_name":"Stacy L.","last_name":"Harvey"},{"full_name":"Sammons, Patrick J.","last_name":"Sammons","first_name":"Patrick J."},{"full_name":"Anderson, Amanda P.","last_name":"Anderson","first_name":"Amanda P."},{"last_name":"Kopalle","first_name":"Hema M.","full_name":"Kopalle, Hema M."},{"last_name":"Banham","first_name":"Alison H.","full_name":"Banham, Alison H."},{"full_name":"Partch, Carrie L.","last_name":"Partch","first_name":"Carrie L."}],"extern":"1","page":"743-754","article_type":"original","citation":{"ama":"Michael AK, Harvey SL, Sammons PJ, et al. Cancer/Testis antigen PASD1 silences the circadian clock. Molecular Cell. 2015;58(5):743-754. doi:10.1016/j.molcel.2015.03.031","ista":"Michael AK, Harvey SL, Sammons PJ, Anderson AP, Kopalle HM, Banham AH, Partch CL. 2015. Cancer/Testis antigen PASD1 silences the circadian clock. Molecular Cell. 58(5), 743–754.","ieee":"A. K. Michael et al., “Cancer/Testis antigen PASD1 silences the circadian clock,” Molecular Cell, vol. 58, no. 5. Elsevier, pp. 743–754, 2015.","apa":"Michael, A. K., Harvey, S. L., Sammons, P. J., Anderson, A. P., Kopalle, H. M., Banham, A. H., & Partch, C. L. (2015). Cancer/Testis antigen PASD1 silences the circadian clock. Molecular Cell. Elsevier. https://doi.org/10.1016/j.molcel.2015.03.031","mla":"Michael, Alicia K., et al. “Cancer/Testis Antigen PASD1 Silences the Circadian Clock.” Molecular Cell, vol. 58, no. 5, Elsevier, 2015, pp. 743–54, doi:10.1016/j.molcel.2015.03.031.","short":"A.K. Michael, S.L. Harvey, P.J. Sammons, A.P. Anderson, H.M. Kopalle, A.H. Banham, C.L. Partch, Molecular Cell 58 (2015) 743–754.","chicago":"Michael, Alicia K., Stacy L. Harvey, Patrick J. Sammons, Amanda P. Anderson, Hema M. Kopalle, Alison H. Banham, and Carrie L. Partch. “Cancer/Testis Antigen PASD1 Silences the Circadian Clock.” Molecular Cell. Elsevier, 2015. https://doi.org/10.1016/j.molcel.2015.03.031."},"publication":"Molecular Cell","date_published":"2015-06-04T00:00:00Z","keyword":["Cell Biology","Molecular Biology"],"scopus_import":"1","article_processing_charge":"No","day":"04","intvolume":" 58","title":"Cancer/Testis antigen PASD1 silences the circadian clock","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15160","oa_version":"Published Version","type":"journal_article","issue":"5","abstract":[{"lang":"eng","text":"The circadian clock orchestrates global changes in transcriptional regulation on a daily basis via the bHLH-PAS transcription factor CLOCK:BMAL1. Pathways driven by other bHLH-PAS transcription factors have a homologous repressor that modulates activity on a tissue-specific basis, but none have been identified for CLOCK:BMAL1. We show here that the cancer/testis antigen PASD1 fulfills this role to suppress circadian rhythms. PASD1 is evolutionarily related to CLOCK and interacts with the CLOCK:BMAL1 complex to repress transcriptional activation. Expression of PASD1 is restricted to germline tissues in healthy individuals but can be induced in cells of somatic origin upon oncogenic transformation. Reducing PASD1 in human cancer cells significantly increases the amplitude of transcriptional oscillations to generate more robust circadian rhythms. Our results describe a function for a germline-specific protein in regulation of the circadian clock and provide a molecular link from oncogenic transformation to suppression of circadian rhythms."}]},{"publication_identifier":{"issn":["0968-0004"]},"month":"09","doi":"10.1016/j.tibs.2015.07.006","language":[{"iso":"eng"}],"quality_controlled":"1","extern":"1","author":[{"full_name":"Michael, Alicia Kathleen","id":"6437c950-2a03-11ee-914d-d6476dd7b75c","first_name":"Alicia Kathleen","last_name":"Michael"},{"full_name":"Asimgil, Hande","first_name":"Hande","last_name":"Asimgil"},{"full_name":"Partch, Carrie L.","first_name":"Carrie L.","last_name":"Partch"}],"volume":40,"date_updated":"2024-03-25T11:53:58Z","date_created":"2024-03-21T07:57:44Z","year":"2015","publisher":"Elsevier","publication_status":"published","article_processing_charge":"No","day":"01","scopus_import":"1","keyword":["Molecular Biology","Biochemistry"],"date_published":"2015-09-01T00:00:00Z","citation":{"ista":"Michael AK, Asimgil H, Partch CL. 2015. Cytosolic BMAL1 moonlights as a translation factor. Trends in Biochemical Sciences. 40(9), 489–490.","apa":"Michael, A. K., Asimgil, H., & Partch, C. L. (2015). Cytosolic BMAL1 moonlights as a translation factor. Trends in Biochemical Sciences. Elsevier. https://doi.org/10.1016/j.tibs.2015.07.006","ieee":"A. K. Michael, H. Asimgil, and C. L. Partch, “Cytosolic BMAL1 moonlights as a translation factor,” Trends in Biochemical Sciences, vol. 40, no. 9. Elsevier, pp. 489–490, 2015.","ama":"Michael AK, Asimgil H, Partch CL. Cytosolic BMAL1 moonlights as a translation factor. Trends in Biochemical Sciences. 2015;40(9):489-490. doi:10.1016/j.tibs.2015.07.006","chicago":"Michael, Alicia K., Hande Asimgil, and Carrie L. Partch. “Cytosolic BMAL1 Moonlights as a Translation Factor.” Trends in Biochemical Sciences. Elsevier, 2015. https://doi.org/10.1016/j.tibs.2015.07.006.","mla":"Michael, Alicia K., et al. “Cytosolic BMAL1 Moonlights as a Translation Factor.” Trends in Biochemical Sciences, vol. 40, no. 9, Elsevier, 2015, pp. 489–90, doi:10.1016/j.tibs.2015.07.006.","short":"A.K. Michael, H. Asimgil, C.L. Partch, Trends in Biochemical Sciences 40 (2015) 489–490."},"publication":"Trends in Biochemical Sciences","page":"489-490","article_type":"original","issue":"9","abstract":[{"lang":"eng","text":"It is widely recognized that BMAL1 is an essential subunit of the primary transcription factor that drives rhythmic circadian transcription in the nucleus. In a surprising turn, Lipton et al. now show that BMAL1 rhythmically interacts with translational machinery in the cytosol to stimulate protein synthesis in response to mTOR signaling."}],"type":"journal_article","oa_version":"None","_id":"15159","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 40","title":"Cytosolic BMAL1 moonlights as a translation factor","status":"public"},{"scopus_import":1,"has_accepted_license":"1","day":"18","citation":{"chicago":"Chevereau, Guillaume, Marta Lukacisinova, Tugce Batur, Aysegul Guvenek, Dilay Ayhan, Erdal Toprak, and Mark Tobias Bollenbach. “Quantifying the Determinants of Evolutionary Dynamics Leading to Drug Resistance.” PLoS Biology. Public Library of Science, 2015. https://doi.org/10.1371/journal.pbio.1002299.","mla":"Chevereau, Guillaume, et al. “Quantifying the Determinants of Evolutionary Dynamics Leading to Drug Resistance.” PLoS Biology, vol. 13, no. 11, e1002299, Public Library of Science, 2015, doi:10.1371/journal.pbio.1002299.","short":"G. Chevereau, M. Lukacisinova, T. Batur, A. Guvenek, D. Ayhan, E. Toprak, M.T. Bollenbach, PLoS Biology 13 (2015).","ista":"Chevereau G, Lukacisinova M, Batur T, Guvenek A, Ayhan D, Toprak E, Bollenbach MT. 2015. Quantifying the determinants of evolutionary dynamics leading to drug resistance. PLoS Biology. 13(11), e1002299.","apa":"Chevereau, G., Lukacisinova, M., Batur, T., Guvenek, A., Ayhan, D., Toprak, E., & Bollenbach, M. T. (2015). Quantifying the determinants of evolutionary dynamics leading to drug resistance. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.1002299","ieee":"G. Chevereau et al., “Quantifying the determinants of evolutionary dynamics leading to drug resistance,” PLoS Biology, vol. 13, no. 11. Public Library of Science, 2015.","ama":"Chevereau G, Lukacisinova M, Batur T, et al. Quantifying the determinants of evolutionary dynamics leading to drug resistance. PLoS Biology. 2015;13(11). doi:10.1371/journal.pbio.1002299"},"publication":"PLoS Biology","date_published":"2015-11-18T00:00:00Z","type":"journal_article","issue":"11","abstract":[{"lang":"eng","text":"The emergence of drug resistant pathogens is a serious public health problem. It is a long-standing goal to predict rates of resistance evolution and design optimal treatment strategies accordingly. To this end, it is crucial to reveal the underlying causes of drug-specific differences in the evolutionary dynamics leading to resistance. However, it remains largely unknown why the rates of resistance evolution via spontaneous mutations and the diversity of mutational paths vary substantially between drugs. Here we comprehensively quantify the distribution of fitness effects (DFE) of mutations, a key determinant of evolutionary dynamics, in the presence of eight antibiotics representing the main modes of action. Using precise high-throughput fitness measurements for genome-wide Escherichia coli gene deletion strains, we find that the width of the DFE varies dramatically between antibiotics and, contrary to conventional wisdom, for some drugs the DFE width is lower than in the absence of stress. We show that this previously underappreciated divergence in DFE width among antibiotics is largely caused by their distinct drug-specific dose-response characteristics. Unlike the DFE, the magnitude of the changes in tolerated drug concentration resulting from genome-wide mutations is similar for most drugs but exceptionally small for the antibiotic nitrofurantoin, i.e., mutations generally have considerably smaller resistance effects for nitrofurantoin than for other drugs. A population genetics model predicts that resistance evolution for drugs with this property is severely limited and confined to reproducible mutational paths. We tested this prediction in laboratory evolution experiments using the “morbidostat”, a device for evolving bacteria in well-controlled drug environments. Nitrofurantoin resistance indeed evolved extremely slowly via reproducible mutations—an almost paradoxical behavior since this drug causes DNA damage and increases the mutation rate. Overall, we identified novel quantitative characteristics of the evolutionary landscape that provide the conceptual foundation for predicting the dynamics of drug resistance evolution."}],"intvolume":" 13","ddc":["570"],"status":"public","title":"Quantifying the determinants of evolutionary dynamics leading to drug resistance","_id":"1619","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"file_name":"IST-2016-468-v1+1_journal.pbio.1002299.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1387760,"creator":"system","relation":"main_file","file_id":"4723","date_created":"2018-12-12T10:09:00Z","date_updated":"2020-07-14T12:45:07Z","checksum":"0e82e3279f50b15c6c170c042627802b"}],"pubrep_id":"468","month":"11","project":[{"name":"Revealing the fundamental limits of cell growth","_id":"25EB3A80-B435-11E9-9278-68D0E5697425","grant_number":"RGP0042/2013"},{"name":"Revealing the mechanisms underlying drug interactions","call_identifier":"FWF","grant_number":"P27201-B22","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425"},{"grant_number":"303507","_id":"25E83C2C-B435-11E9-9278-68D0E5697425","name":"Optimality principles in responses to antibiotics","call_identifier":"FP7"}],"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"doi":"10.1371/journal.pbio.1002299","article_number":"e1002299","publist_id":"5547","ec_funded":1,"file_date_updated":"2020-07-14T12:45:07Z","department":[{"_id":"ToBo"}],"publisher":"Public Library of Science","publication_status":"published","year":"2015","volume":13,"date_updated":"2024-03-28T23:30:28Z","date_created":"2018-12-11T11:53:04Z","related_material":{"record":[{"relation":"research_data","status":"public","id":"9711"},{"status":"public","relation":"research_data","id":"9765"},{"relation":"dissertation_contains","status":"public","id":"6263"}]},"author":[{"full_name":"Chevereau, Guillaume","first_name":"Guillaume","last_name":"Chevereau","id":"424D78A0-F248-11E8-B48F-1D18A9856A87"},{"id":"4342E402-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2519-8004","first_name":"Marta","last_name":"Dravecka","full_name":"Dravecka, Marta"},{"last_name":"Batur","first_name":"Tugce","full_name":"Batur, Tugce"},{"full_name":"Guvenek, Aysegul","last_name":"Guvenek","first_name":"Aysegul"},{"last_name":"Ayhan","first_name":"Dilay","full_name":"Ayhan, Dilay"},{"full_name":"Toprak, Erdal","last_name":"Toprak","first_name":"Erdal"},{"orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach","first_name":"Mark Tobias","full_name":"Bollenbach, Mark Tobias"}]},{"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"month":"12","quality_controlled":"1","main_file_link":[{"url":"https://www.pnas.org/content/111/50/17869","open_access":"1"}],"oa":1,"external_id":{"pmid":["25453085"],"arxiv":["1412.0897"]},"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1410159111","extern":"1","publisher":"National Academy of Sciences","publication_status":"published","pmid":1,"acknowledgement":"We thank Michele Vendruscolo, Iskra Staneva, and William M. Jacobs, for helpful discussions. A.Š. acknowledges support from the Human Frontier Science Program and Emmanuel College. Y.C.C. and D.F. are supported by Engineering and Physical Sciences Research Council Programme Grant EP/I001352/1. T.P.J.K. acknowledges the Frances and Augustus Newman Foundation, the European Research Council, and the Biotechnology and Biological Sciences Research Council. D.F. acknowledges European Research Council Advanced Grant 227758.","year":"2014","volume":111,"date_created":"2021-11-29T13:09:53Z","date_updated":"2021-11-29T13:29:05Z","author":[{"full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","first_name":"Anđela","last_name":"Šarić"},{"first_name":"Yassmine C.","last_name":"Chebaro","full_name":"Chebaro, Yassmine C."},{"full_name":"Knowles, Tuomas P. J.","first_name":"Tuomas P. J.","last_name":"Knowles"},{"full_name":"Frenkel, Daan","last_name":"Frenkel","first_name":"Daan"}],"keyword":["multidisciplinary"],"scopus_import":"1","article_processing_charge":"No","day":"01","page":"17869-17874","article_type":"original","citation":{"chicago":"Šarić, Anđela, Yassmine C. Chebaro, Tuomas P. J. Knowles, and Daan Frenkel. “Crucial Role of Nonspecific Interactions in Amyloid Nucleation.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1410159111.","mla":"Šarić, Anđela, et al. “Crucial Role of Nonspecific Interactions in Amyloid Nucleation.” Proceedings of the National Academy of Sciences, vol. 111, no. 50, National Academy of Sciences, 2014, pp. 17869–74, doi:10.1073/pnas.1410159111.","short":"A. Šarić, Y.C. Chebaro, T.P.J. Knowles, D. Frenkel, Proceedings of the National Academy of Sciences 111 (2014) 17869–17874.","ista":"Šarić A, Chebaro YC, Knowles TPJ, Frenkel D. 2014. Crucial role of nonspecific interactions in amyloid nucleation. Proceedings of the National Academy of Sciences. 111(50), 17869–17874.","ieee":"A. Šarić, Y. C. Chebaro, T. P. J. Knowles, and D. Frenkel, “Crucial role of nonspecific interactions in amyloid nucleation,” Proceedings of the National Academy of Sciences, vol. 111, no. 50. National Academy of Sciences, pp. 17869–17874, 2014.","apa":"Šarić, A., Chebaro, Y. C., Knowles, T. P. J., & Frenkel, D. (2014). Crucial role of nonspecific interactions in amyloid nucleation. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1410159111","ama":"Šarić A, Chebaro YC, Knowles TPJ, Frenkel D. Crucial role of nonspecific interactions in amyloid nucleation. Proceedings of the National Academy of Sciences. 2014;111(50):17869-17874. doi:10.1073/pnas.1410159111"},"publication":"Proceedings of the National Academy of Sciences","date_published":"2014-12-01T00:00:00Z","type":"journal_article","issue":"50","abstract":[{"text":"Protein oligomers have been implicated as toxic agents in a wide range of amyloid-related diseases. However, it has remained unsolved whether the oligomers are a necessary step in the formation of amyloid fibrils or just a dangerous byproduct. Analogously, it has not been resolved if the amyloid nucleation process is a classical one-step nucleation process or a two-step process involving prenucleation clusters. We use coarse-grained computer simulations to study the effect of nonspecific attractions between peptides on the primary nucleation process underlying amyloid fibrillization. We find that, for peptides that do not attract, the classical one-step nucleation mechanism is possible but only at nonphysiologically high peptide concentrations. At low peptide concentrations, which mimic the physiologically relevant regime, attractive interpeptide interactions are essential for fibril formation. Nucleation then inevitably takes place through a two-step mechanism involving prefibrillar oligomers. We show that oligomers not only help peptides meet each other but also, create an environment that facilitates the conversion of monomers into the β-sheet–rich form characteristic of fibrils. Nucleation typically does not proceed through the most prevalent oligomers but through an oligomer size that is only observed in rare fluctuations, which is why such aggregates might be hard to capture experimentally. Finally, we find that the nucleation of amyloid fibrils cannot be described by classical nucleation theory: in the two-step mechanism, the critical nucleus size increases with increases in both concentration and interpeptide interactions, which is in direct contrast with predictions from classical nucleation theory.","lang":"eng"}],"intvolume":" 111","status":"public","title":"Crucial role of nonspecific interactions in amyloid nucleation","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"10382","oa_version":"Published Version"},{"scopus_import":"1","article_processing_charge":"No","day":"06","article_type":"original","citation":{"apa":"Mallory, S. A., Šarić, A., Valeriani, C., & Cacciuto, A. (2014). Anomalous thermomechanical properties of a self-propelled colloidal fluid. Physical Review E. American Physical Society. https://doi.org/10.1103/physreve.89.052303","ieee":"S. A. Mallory, A. Šarić, C. Valeriani, and A. Cacciuto, “Anomalous thermomechanical properties of a self-propelled colloidal fluid,” Physical Review E, vol. 89, no. 5. American Physical Society, 2014.","ista":"Mallory SA, Šarić A, Valeriani C, Cacciuto A. 2014. Anomalous thermomechanical properties of a self-propelled colloidal fluid. Physical Review E. 89(5), 052303.","ama":"Mallory SA, Šarić A, Valeriani C, Cacciuto A. Anomalous thermomechanical properties of a self-propelled colloidal fluid. Physical Review E. 2014;89(5). doi:10.1103/physreve.89.052303","chicago":"Mallory, S. A., Anđela Šarić, C. Valeriani, and A. Cacciuto. “Anomalous Thermomechanical Properties of a Self-Propelled Colloidal Fluid.” Physical Review E. American Physical Society, 2014. https://doi.org/10.1103/physreve.89.052303.","short":"S.A. Mallory, A. Šarić, C. Valeriani, A. Cacciuto, Physical Review E 89 (2014).","mla":"Mallory, S. A., et al. “Anomalous Thermomechanical Properties of a Self-Propelled Colloidal Fluid.” Physical Review E, vol. 89, no. 5, 052303, American Physical Society, 2014, doi:10.1103/physreve.89.052303."},"publication":"Physical Review E","date_published":"2014-05-06T00:00:00Z","type":"journal_article","issue":"5","abstract":[{"lang":"eng","text":"We use numerical simulations to compute the equation of state of a suspension of spherical self-propelled nanoparticles in two and three dimensions. We study in detail the effect of excluded volume interactions and confinement as a function of the system's temperature, concentration, and strength of the propulsion. We find a striking nonmonotonic dependence of the pressure on the temperature and provide simple scaling arguments to predict and explain the occurrence of such anomalous behavior. We explicitly show how our results have important implications for the effective forces on passive components suspended in a bath of active particles."}],"intvolume":" 89","title":"Anomalous thermomechanical properties of a self-propelled colloidal fluid","status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"10383","oa_version":"Preprint","publication_identifier":{"issn":["1539-3755"],"eissn":["1550-2376"]},"month":"05","quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1310.0826"}],"external_id":{"arxiv":["1310.0826"],"pmid":["25353796"]},"language":[{"iso":"eng"}],"doi":"10.1103/physreve.89.052303","article_number":"052303","extern":"1","publisher":"American Physical Society","publication_status":"published","pmid":1,"year":"2014","volume":89,"date_updated":"2021-11-29T13:29:01Z","date_created":"2021-11-29T13:10:33Z","author":[{"first_name":"S. A.","last_name":"Mallory","full_name":"Mallory, S. A."},{"first_name":"Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela"},{"full_name":"Valeriani, C.","first_name":"C.","last_name":"Valeriani"},{"full_name":"Cacciuto, A.","first_name":"A.","last_name":"Cacciuto"}]},{"status":"public","title":"Coordinate-targeted and coordinate-stochastic super-resolution microscopy with the reversibly switchable fluorescent protein dreiklang","publication_status":"published","intvolume":" 15","publisher":"Wiley-Blackwell","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1058","year":"2014","date_updated":"2021-01-12T06:47:58Z","date_created":"2018-12-11T11:49:55Z","volume":15,"oa_version":"None","author":[{"full_name":"Jensen, Nickels","first_name":"Nickels","last_name":"Jensen"},{"first_name":"Johann G","last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G"},{"first_name":"Katrin","last_name":"Willig","full_name":"Willig, Katrin"},{"full_name":"Lavoie Cardinal, Flavie","last_name":"Lavoie Cardinal","first_name":"Flavie"},{"first_name":"Tanja","last_name":"Brakemann","full_name":"Brakemann, Tanja"},{"full_name":"Hell, Stefan","last_name":"Hell","first_name":"Stefan"},{"first_name":"Stefan","last_name":"Jakobs","full_name":"Jakobs, Stefan"}],"type":"journal_article","extern":"1","abstract":[{"text":"Diffraction-unlimited far-field super-resolution fluorescence (nanoscopy) methods typically rely on transiently transferring fluorophores between two states, whereby this transfer is usually laid out as a switch. However, depending on whether this is induced in a spatially controlled manner using a pattern of light (coordinate-targeted) or stochastically on a single-molecule basis, specific requirements on the fluorophores are imposed. Therefore, the fluorophores are usually utilized just for one class of methods only. In this study we demonstrate that the reversibly switchable fluorescent protein Dreiklang enables live-cell recordings in both spatially controlled and stochastic modes. We show that the Dreiklang chromophore entails three different light-induced switching mechanisms, namely a reversible photochemical one, off-switching by stimulated emission, and a reversible transfer to a long-lived dark state from the S1 state, all of which can be utilized to overcome the diffraction barrier. We also find that for the single-molecule- based stochastic GSDIM approach (ground-state depletion followed by individual molecule return), Dreiklang provides a larger number of on-off localization events as compared to its progenitor Citrine. Altogether, Dreiklang is a versatile probe for essentially all popular forms of live-cell fluorescence nanoscopy.","lang":"eng"}],"publist_id":"6332","issue":"4","page":"756 - 762","publication":"ChemPhysChem","citation":{"chicago":"Jensen, Nickels, Johann G Danzl, Katrin Willig, Flavie Lavoie Cardinal, Tanja Brakemann, Stefan Hell, and Stefan Jakobs. “Coordinate-Targeted and Coordinate-Stochastic Super-Resolution Microscopy with the Reversibly Switchable Fluorescent Protein Dreiklang.” ChemPhysChem. Wiley-Blackwell, 2014. https://doi.org/10.1002/cphc.201301034.","short":"N. Jensen, J.G. Danzl, K. Willig, F. Lavoie Cardinal, T. Brakemann, S. Hell, S. Jakobs, ChemPhysChem 15 (2014) 756–762.","mla":"Jensen, Nickels, et al. “Coordinate-Targeted and Coordinate-Stochastic Super-Resolution Microscopy with the Reversibly Switchable Fluorescent Protein Dreiklang.” ChemPhysChem, vol. 15, no. 4, Wiley-Blackwell, 2014, pp. 756–62, doi:10.1002/cphc.201301034.","ieee":"N. Jensen et al., “Coordinate-targeted and coordinate-stochastic super-resolution microscopy with the reversibly switchable fluorescent protein dreiklang,” ChemPhysChem, vol. 15, no. 4. Wiley-Blackwell, pp. 756–762, 2014.","apa":"Jensen, N., Danzl, J. G., Willig, K., Lavoie Cardinal, F., Brakemann, T., Hell, S., & Jakobs, S. (2014). Coordinate-targeted and coordinate-stochastic super-resolution microscopy with the reversibly switchable fluorescent protein dreiklang. ChemPhysChem. Wiley-Blackwell. https://doi.org/10.1002/cphc.201301034","ista":"Jensen N, Danzl JG, Willig K, Lavoie Cardinal F, Brakemann T, Hell S, Jakobs S. 2014. Coordinate-targeted and coordinate-stochastic super-resolution microscopy with the reversibly switchable fluorescent protein dreiklang. ChemPhysChem. 15(4), 756–762.","ama":"Jensen N, Danzl JG, Willig K, et al. Coordinate-targeted and coordinate-stochastic super-resolution microscopy with the reversibly switchable fluorescent protein dreiklang. ChemPhysChem. 2014;15(4):756-762. doi:10.1002/cphc.201301034"},"language":[{"iso":"eng"}],"doi":"10.1002/cphc.201301034","date_published":"2014-03-17T00:00:00Z","day":"17","month":"03","article_processing_charge":"No"},{"day":"01","article_processing_charge":"No","scopus_import":"1","keyword":["Developmental Biology","Embryology","General Medicine","Pediatrics","Perinatology","and Child Health"],"date_published":"2014-02-01T00:00:00Z","publication":"Congenital Anomalies","citation":{"ista":"Hashimoto M, Morita H, Ueno N. 2014. Molecular and cellular mechanisms of development underlying congenital diseases. Congenital Anomalies. 54(1), 1–7.","apa":"Hashimoto, M., Morita, H., & Ueno, N. (2014). Molecular and cellular mechanisms of development underlying congenital diseases. Congenital Anomalies. Wiley. https://doi.org/10.1111/cga.12039","ieee":"M. Hashimoto, H. Morita, and N. Ueno, “Molecular and cellular mechanisms of development underlying congenital diseases,” Congenital Anomalies, vol. 54, no. 1. Wiley, pp. 1–7, 2014.","ama":"Hashimoto M, Morita H, Ueno N. Molecular and cellular mechanisms of development underlying congenital diseases. Congenital Anomalies. 2014;54(1):1-7. doi:10.1111/cga.12039","chicago":"Hashimoto, Masakazu, Hitoshi Morita, and Naoto Ueno. “Molecular and Cellular Mechanisms of Development Underlying Congenital Diseases.” Congenital Anomalies. Wiley, 2014. https://doi.org/10.1111/cga.12039.","mla":"Hashimoto, Masakazu, et al. “Molecular and Cellular Mechanisms of Development Underlying Congenital Diseases.” Congenital Anomalies, vol. 54, no. 1, Wiley, 2014, pp. 1–7, doi:10.1111/cga.12039.","short":"M. Hashimoto, H. Morita, N. Ueno, Congenital Anomalies 54 (2014) 1–7."},"article_type":"original","page":"1-7","abstract":[{"lang":"eng","text":"In the last several decades, developmental biology has clarified the molecular mechanisms of embryogenesis and organogenesis. In particular, it has demonstrated that the “tool-kit genes” essential for regulating developmental processes are not only highly conserved among species, but are also used as systems at various times and places in an organism to control distinct developmental events. Therefore, mutations in many of these tool-kit genes may cause congenital diseases involving morphological abnormalities. This link between genes and abnormal morphological phenotypes underscores the importance of understanding how cells behave and contribute to morphogenesis as a result of gene function. Recent improvements in live imaging and in quantitative analyses of cellular dynamics will advance our understanding of the cellular pathogenesis of congenital diseases associated with aberrant morphologies. In these studies, it is critical to select an appropriate model organism for the particular phenomenon of interest."}],"issue":"1","type":"journal_article","oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"10815","title":"Molecular and cellular mechanisms of development underlying congenital diseases","status":"public","intvolume":" 54","month":"02","publication_identifier":{"issn":["0914-3505"]},"doi":"10.1111/cga.12039","language":[{"iso":"eng"}],"oa":1,"external_id":{"pmid":["24666178"]},"main_file_link":[{"url":"https://doi.org/10.1111/cga.12039","open_access":"1"}],"quality_controlled":"1","author":[{"full_name":"Hashimoto, Masakazu","first_name":"Masakazu","last_name":"Hashimoto"},{"id":"4C6E54C6-F248-11E8-B48F-1D18A9856A87","first_name":"Hitoshi","last_name":"Morita","full_name":"Morita, Hitoshi"},{"full_name":"Ueno, Naoto","first_name":"Naoto","last_name":"Ueno"}],"date_created":"2022-03-04T08:17:25Z","date_updated":"2022-03-04T08:26:05Z","volume":54,"year":"2014","acknowledgement":"The authors thank all the members of the Division of Morphogenesis, National Institute for Basic Biology, for their contributions to the research, their encouragement, and helpful discussions, particularly Dr M. Suzuki for his critical reading of the manuscript. We also thank the Model Animal Research and Spectrography and Bioimaging Facilities, NIBB Core Research Facilities, for technical support. M.H. was supported by a research fellowship from the Japan Society for the Promotion of Science (JSPS). Our work introduced in this review was supported by a Grant-in-Aid for Scientific Research on Innovative Areas from the Ministry of Education, Culture, Sports, Science, and Technology (MEXT), Japan, to N.U.","pmid":1,"publication_status":"published","publisher":"Wiley","department":[{"_id":"CaHe"}]},{"scopus_import":"1","article_processing_charge":"No","publication_identifier":{"isbn":["9783709115251"],"eisbn":["9783709115268"]},"month":"04","day":"01","citation":{"chicago":"Zažímalová, Eva, Jan Petrášek, and Eva Benková, eds. Auxin and Its Role in Plant Development. 1st ed. Vienna: Springer Nature, 2014. https://doi.org/10.1007/978-3-7091-1526-8.","short":"E. Zažímalová, J. Petrášek, E. Benková, eds., Auxin and Its Role in Plant Development, 1st ed., Springer Nature, Vienna, 2014.","mla":"Zažímalová, Eva, et al., editors. Auxin and Its Role in Plant Development. 1st ed., Springer Nature, 2014, doi:10.1007/978-3-7091-1526-8.","apa":"Zažímalová, E., Petrášek, J., & Benková, E. (Eds.). (2014). Auxin and Its Role in Plant Development (1st ed.). Vienna: Springer Nature. https://doi.org/10.1007/978-3-7091-1526-8","ieee":"E. Zažímalová, J. Petrášek, and E. Benková, Eds., Auxin and Its Role in Plant Development, 1st ed. Vienna: Springer Nature, 2014.","ista":"Zažímalová E, Petrášek J, Benková E eds. 2014. Auxin and Its Role in Plant Development 1st ed., Vienna: Springer Nature, 444p.","ama":"Zažímalová E, Petrášek J, Benková E, eds. Auxin and Its Role in Plant Development. 1st ed. Vienna: Springer Nature; 2014. doi:10.1007/978-3-7091-1526-8"},"page":"444","quality_controlled":"1","date_published":"2014-04-01T00:00:00Z","doi":"10.1007/978-3-7091-1526-8","language":[{"iso":"eng"}],"type":"book_editor","place":"Vienna","abstract":[{"text":"Auxin is an important signaling compound in plants and vital for plant development and growth. The present book, Auxin and its Role in Plant Development, provides the reader with detailed and comprehensive insight into the functioning of the molecule on the whole and specifically in plant development. In the first part, the functioning, metabolism and signaling pathways of auxin in plants are explained, the second part depicts the specific role of auxin in plant development and the third part describes the interaction and functioning of the signaling compound upon stimuli of the environment. Each chapter is written by international experts in the respective field and designed for scientists and researchers in plant biology, plant development and cell biology to summarize the recent progress in understanding the role of auxin and suggest future perspectives for auxin research.","lang":"eng"}],"_id":"10811","year":"2014","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer Nature","department":[{"_id":"EvBe"}],"editor":[{"full_name":"Zažímalová, Eva","first_name":"Eva","last_name":"Zažímalová"},{"last_name":"Petrášek","first_name":"Jan","full_name":"Petrášek, Jan"},{"full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","first_name":"Eva"}],"publication_status":"published","status":"public","title":"Auxin and Its Role in Plant Development","edition":"1","oa_version":"None","date_created":"2022-03-03T11:52:44Z","date_updated":"2022-03-04T07:38:15Z"},{"citation":{"ama":"Aminof B, Jacobs S, Khalimov A, Rubin S. Parameterized model checking of token-passing systems. In: Verification, Model Checking, and Abstract Interpretation. Vol 8318. Springer Nature; 2014:262-281. doi:10.1007/978-3-642-54013-4_15","ista":"Aminof B, Jacobs S, Khalimov A, Rubin S. 2014. Parameterized model checking of token-passing systems. Verification, Model Checking, and Abstract Interpretation. VMCAI: Verifcation, Model Checking, and Abstract Interpretation, LNCS, vol. 8318, 262–281.","ieee":"B. Aminof, S. Jacobs, A. Khalimov, and S. Rubin, “Parameterized model checking of token-passing systems,” in Verification, Model Checking, and Abstract Interpretation, San Diego, CA, United States, 2014, vol. 8318, pp. 262–281.","apa":"Aminof, B., Jacobs, S., Khalimov, A., & Rubin, S. (2014). Parameterized model checking of token-passing systems. In Verification, Model Checking, and Abstract Interpretation (Vol. 8318, pp. 262–281). San Diego, CA, United States: Springer Nature. https://doi.org/10.1007/978-3-642-54013-4_15","mla":"Aminof, Benjamin, et al. “Parameterized Model Checking of Token-Passing Systems.” Verification, Model Checking, and Abstract Interpretation, vol. 8318, Springer Nature, 2014, pp. 262–81, doi:10.1007/978-3-642-54013-4_15.","short":"B. Aminof, S. Jacobs, A. Khalimov, S. Rubin, in:, Verification, Model Checking, and Abstract Interpretation, Springer Nature, 2014, pp. 262–281.","chicago":"Aminof, Benjamin, Swen Jacobs, Ayrat Khalimov, and Sasha Rubin. “Parameterized Model Checking of Token-Passing Systems.” In Verification, Model Checking, and Abstract Interpretation, 8318:262–81. Springer Nature, 2014. https://doi.org/10.1007/978-3-642-54013-4_15."},"publication":"Verification, Model Checking, and Abstract Interpretation","page":"262-281","date_published":"2014-01-30T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"30","_id":"10884","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 8318","status":"public","title":"Parameterized model checking of token-passing systems","oa_version":"Preprint","type":"conference","alternative_title":["LNCS"],"abstract":[{"text":"We revisit the parameterized model checking problem for token-passing systems and specifications in indexed CTL ∗ \\X. Emerson and Namjoshi (1995, 2003) have shown that parameterized model checking of indexed CTL ∗ \\X in uni-directional token rings can be reduced to checking rings up to some cutoff size. Clarke et al. (2004) have shown a similar result for general topologies and indexed LTL \\X, provided processes cannot choose the directions for sending or receiving the token.\r\nWe unify and substantially extend these results by systematically exploring fragments of indexed CTL ∗ \\X with respect to general topologies. For each fragment we establish whether a cutoff exists, and for some concrete topologies, such as rings, cliques and stars, we infer small cutoffs. Finally, we show that the problem becomes undecidable, and thus no cutoffs exist, if processes are allowed to choose the directions in which they send or from which they receive the token.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.1311.4425"}],"oa":1,"external_id":{"arxiv":["1311.4425"]},"project":[{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"name":"Game Theory","call_identifier":"FWF","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"}],"quality_controlled":"1","doi":"10.1007/978-3-642-54013-4_15","conference":{"name":"VMCAI: Verifcation, Model Checking, and Abstract Interpretation","end_date":"2014-01-21","start_date":"2014-01-19","location":"San Diego, CA, United States"},"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0302-9743"],"eisbn":["9783642540134"],"eissn":["1611-3349"],"isbn":["9783642540127"]},"month":"01","acknowledgement":"This work was supported by the Austrian Science Fund through grant P23499-N23\r\nand through the RiSE network (S11403, S11405, S11406, S11407-N23); ERC Starting Grant (279307: Graph Games); Vienna Science and Technology Fund (WWTF)\r\ngrants PROSEED, ICT12-059, and VRG11-005.","year":"2014","publisher":"Springer Nature","department":[{"_id":"KrCh"}],"publication_status":"published","author":[{"id":"4A55BD00-F248-11E8-B48F-1D18A9856A87","first_name":"Benjamin","last_name":"Aminof","full_name":"Aminof, Benjamin"},{"last_name":"Jacobs","first_name":"Swen","full_name":"Jacobs, Swen"},{"last_name":"Khalimov","first_name":"Ayrat","full_name":"Khalimov, Ayrat"},{"full_name":"Rubin, Sasha","last_name":"Rubin","first_name":"Sasha","id":"2EC51194-F248-11E8-B48F-1D18A9856A87"}],"volume":8318,"date_created":"2022-03-18T13:01:22Z","date_updated":"2022-05-17T08:36:01Z","ec_funded":1},{"abstract":[{"lang":"eng","text":"Saddle periodic orbits are an essential and stable part of the topological skeleton of a 3D vector field. Nevertheless, there is currently no efficient algorithm to robustly extract these features. In this chapter, we present a novel technique to extract saddle periodic orbits. Exploiting the analytic properties of such an orbit, we propose a scalar measure based on the finite-time Lyapunov exponent (FTLE) that indicates its presence. Using persistent homology, we can then extract the robust cycles of this field. These cycles thereby represent the saddle periodic orbits of the given vector field. We discuss the different existing FTLE approximation schemes regarding their applicability to this specific problem and propose an adapted version of FTLE called Normalized Velocity Separation. Finally, we evaluate our method using simple analytic vector field data."}],"type":"book_chapter","oa_version":"None","title":"Toward the extraction of saddle periodic orbits","status":"public","intvolume":" 1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"10893","day":"19","article_processing_charge":"No","series_title":"Mathematics and Visualization","scopus_import":"1","date_published":"2014-03-19T00:00:00Z","page":"55-69","publication":"Topological Methods in Data Analysis and Visualization III ","citation":{"chicago":"Kasten, Jens, Jan Reininghaus, Wieland Reich, and Gerik Scheuermann. “Toward the Extraction of Saddle Periodic Orbits.” In Topological Methods in Data Analysis and Visualization III , edited by Peer-Timo Bremer, Ingrid Hotz, Valerio Pascucci, and Ronald Peikert, 1:55–69. Mathematics and Visualization. Cham: Springer, 2014. https://doi.org/10.1007/978-3-319-04099-8_4.","mla":"Kasten, Jens, et al. “Toward the Extraction of Saddle Periodic Orbits.” Topological Methods in Data Analysis and Visualization III , edited by Peer-Timo Bremer et al., vol. 1, Springer, 2014, pp. 55–69, doi:10.1007/978-3-319-04099-8_4.","short":"J. Kasten, J. Reininghaus, W. Reich, G. Scheuermann, in:, P.-T. Bremer, I. Hotz, V. Pascucci, R. Peikert (Eds.), Topological Methods in Data Analysis and Visualization III , Springer, Cham, 2014, pp. 55–69.","ista":"Kasten J, Reininghaus J, Reich W, Scheuermann G. 2014.Toward the extraction of saddle periodic orbits. In: Topological Methods in Data Analysis and Visualization III . vol. 1, 55–69.","apa":"Kasten, J., Reininghaus, J., Reich, W., & Scheuermann, G. (2014). Toward the extraction of saddle periodic orbits. In P.-T. Bremer, I. Hotz, V. Pascucci, & R. Peikert (Eds.), Topological Methods in Data Analysis and Visualization III (Vol. 1, pp. 55–69). Cham: Springer. https://doi.org/10.1007/978-3-319-04099-8_4","ieee":"J. Kasten, J. Reininghaus, W. Reich, and G. Scheuermann, “Toward the extraction of saddle periodic orbits,” in Topological Methods in Data Analysis and Visualization III , vol. 1, P.-T. Bremer, I. Hotz, V. Pascucci, and R. Peikert, Eds. Cham: Springer, 2014, pp. 55–69.","ama":"Kasten J, Reininghaus J, Reich W, Scheuermann G. Toward the extraction of saddle periodic orbits. In: Bremer P-T, Hotz I, Pascucci V, Peikert R, eds. Topological Methods in Data Analysis and Visualization III . Vol 1. Mathematics and Visualization. Cham: Springer; 2014:55-69. doi:10.1007/978-3-319-04099-8_4"},"ec_funded":1,"place":"Cham","date_updated":"2022-06-21T12:01:47Z","date_created":"2022-03-21T07:11:23Z","volume":1,"author":[{"full_name":"Kasten, Jens","last_name":"Kasten","first_name":"Jens"},{"last_name":"Reininghaus","first_name":"Jan","id":"4505473A-F248-11E8-B48F-1D18A9856A87","full_name":"Reininghaus, Jan"},{"full_name":"Reich, Wieland","first_name":"Wieland","last_name":"Reich"},{"full_name":"Scheuermann, Gerik","last_name":"Scheuermann","first_name":"Gerik"}],"publication_status":"published","publisher":"Springer","editor":[{"full_name":"Bremer, Peer-Timo","first_name":"Peer-Timo","last_name":"Bremer"},{"last_name":"Hotz","first_name":"Ingrid","full_name":"Hotz, Ingrid"},{"last_name":"Pascucci","first_name":"Valerio","full_name":"Pascucci, Valerio"},{"full_name":"Peikert, Ronald","last_name":"Peikert","first_name":"Ronald"}],"department":[{"_id":"HeEd"}],"year":"2014","acknowledgement":"First, we thank the reviewers of this paper for their ideas and critical comments. In addition, we thank Ronny Peikert and Filip Sadlo for a fruitful discussions. This research is supported by the European Commission under the TOPOSYS project FP7-ICT-318493-STREP, the European Social Fund (ESF App. No. 100098251), and the European Science Foundation under the ACAT Research Network Program.","month":"03","publication_identifier":{"eisbn":["9783319040998"],"issn":["1612-3786"],"isbn":["9783319040981"],"eissn":["2197-666X"]},"language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-04099-8_4","quality_controlled":"1","project":[{"name":"Topological Complex Systems","call_identifier":"FP7","grant_number":"318493","_id":"255D761E-B435-11E9-9278-68D0E5697425"}]},{"month":"02","publication_identifier":{"issn":["0092-8674"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.cell.2014.02.004","quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://doi.org/10.1016/j.cell.2014.02.004","open_access":"1"}],"external_id":{"pmid":["24581486"]},"extern":"1","date_updated":"2022-07-18T08:44:33Z","date_created":"2022-04-07T07:50:04Z","volume":156,"author":[{"full_name":"Buchwalter, Abigail","first_name":"Abigail","last_name":"Buchwalter"},{"full_name":"HETZER, Martin W","orcid":"0000-0002-2111-992X","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","last_name":"HETZER","first_name":"Martin W"}],"publication_status":"published","publisher":"Elsevier","year":"2014","pmid":1,"day":"27","article_processing_charge":"No","keyword":["General Biochemistry","Genetics and Molecular Biology"],"scopus_import":"1","date_published":"2014-02-27T00:00:00Z","article_type":"original","page":"868-869","publication":"Cell","citation":{"ama":"Buchwalter A, Hetzer M. Nuclear pores set the speed limit for mitosis. Cell. 2014;156(5):868-869. doi:10.1016/j.cell.2014.02.004","ista":"Buchwalter A, Hetzer M. 2014. Nuclear pores set the speed limit for mitosis. Cell. 156(5), 868–869.","ieee":"A. Buchwalter and M. Hetzer, “Nuclear pores set the speed limit for mitosis,” Cell, vol. 156, no. 5. Elsevier, pp. 868–869, 2014.","apa":"Buchwalter, A., & Hetzer, M. (2014). Nuclear pores set the speed limit for mitosis. Cell. Elsevier. https://doi.org/10.1016/j.cell.2014.02.004","mla":"Buchwalter, Abigail, and Martin Hetzer. “Nuclear Pores Set the Speed Limit for Mitosis.” Cell, vol. 156, no. 5, Elsevier, 2014, pp. 868–69, doi:10.1016/j.cell.2014.02.004.","short":"A. Buchwalter, M. Hetzer, Cell 156 (2014) 868–869.","chicago":"Buchwalter, Abigail, and Martin Hetzer. “Nuclear Pores Set the Speed Limit for Mitosis.” Cell. Elsevier, 2014. https://doi.org/10.1016/j.cell.2014.02.004."},"abstract":[{"lang":"eng","text":"The spindle assembly checkpoint prevents separation of sister chromatids until each kinetochore is attached to the mitotic spindle. Rodriguez-Bravo et al. report that the nuclear pore complex scaffolds spindle assembly checkpoint signaling in interphase, providing a store of inhibitory signals that limits the speed of the subsequent mitosis."}],"issue":"5","type":"journal_article","oa_version":"Published Version","status":"public","title":"Nuclear pores set the speed limit for mitosis","intvolume":" 156","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","_id":"11080"},{"scopus_import":"1","keyword":["Cell Biology","Molecular Biology"],"article_processing_charge":"No","day":"15","citation":{"chicago":"Buchwalter, Abigail L., Yun Liang, and Martin Hetzer. “Nup50 Is Required for Cell Differentiation and Exhibits Transcription-Dependent Dynamics.” Molecular Biology of the Cell. American Society for Cell Biology, 2014. https://doi.org/10.1091/mbc.e14-04-0865.","mla":"Buchwalter, Abigail L., et al. “Nup50 Is Required for Cell Differentiation and Exhibits Transcription-Dependent Dynamics.” Molecular Biology of the Cell, vol. 25, no. 16, American Society for Cell Biology, 2014, pp. 2472–84, doi:10.1091/mbc.e14-04-0865.","short":"A.L. Buchwalter, Y. Liang, M. Hetzer, Molecular Biology of the Cell 25 (2014) 2472–2484.","ista":"Buchwalter AL, Liang Y, Hetzer M. 2014. Nup50 is required for cell differentiation and exhibits transcription-dependent dynamics. Molecular Biology of the Cell. 25(16), 2472–2484.","ieee":"A. L. Buchwalter, Y. Liang, and M. Hetzer, “Nup50 is required for cell differentiation and exhibits transcription-dependent dynamics,” Molecular Biology of the Cell, vol. 25, no. 16. American Society for Cell Biology, pp. 2472–2484, 2014.","apa":"Buchwalter, A. L., Liang, Y., & Hetzer, M. (2014). Nup50 is required for cell differentiation and exhibits transcription-dependent dynamics. Molecular Biology of the Cell. American Society for Cell Biology. https://doi.org/10.1091/mbc.e14-04-0865","ama":"Buchwalter AL, Liang Y, Hetzer M. Nup50 is required for cell differentiation and exhibits transcription-dependent dynamics. Molecular Biology of the Cell. 2014;25(16):2472-2484. doi:10.1091/mbc.e14-04-0865"},"publication":"Molecular Biology of the Cell","page":"2472-2484","article_type":"original","date_published":"2014-08-15T00:00:00Z","type":"journal_article","issue":"16","abstract":[{"text":"The nuclear pore complex (NPC) plays a critical role in gene expression by mediating import of transcription regulators into the nucleus and export of RNA transcripts to the cytoplasm. Emerging evidence suggests that in addition to mediating transport, a subset of nucleoporins (Nups) engage in transcriptional activation and elongation at genomic loci that are not associated with NPCs. The underlying mechanism and regulation of Nup mobility on and off nuclear pores remain unclear. Here we show that Nup50 is a mobile Nup with a pronounced presence both at the NPC and in the nucleoplasm that can move between these different localizations. Strikingly, the dynamic behavior of Nup50 in both locations is dependent on active transcription by RNA polymerase II and requires the N-terminal half of the protein, which contains importin α– and Nup153-binding domains. However, Nup50 dynamics are independent of importin α, Nup153, and Nup98, even though the latter two proteins also exhibit transcription-dependent mobility. Of interest, depletion of Nup50 from C2C12 myoblasts does not affect cell proliferation but inhibits differentiation into myotubes. Taken together, our results suggest a transport-independent role for Nup50 in chromatin biology that occurs away from the NPC.","lang":"eng"}],"user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","_id":"11082","intvolume":" 25","status":"public","title":"Nup50 is required for cell differentiation and exhibits transcription-dependent dynamics","oa_version":"Published Version","publication_identifier":{"issn":["1059-1524","1939-4586"]},"month":"08","oa":1,"main_file_link":[{"url":"https://doi.org/10.1091/mbc.e14-04-0865","open_access":"1"}],"quality_controlled":"1","doi":"10.1091/mbc.e14-04-0865","language":[{"iso":"eng"}],"extern":"1","year":"2014","publisher":"American Society for Cell Biology","publication_status":"published","author":[{"full_name":"Buchwalter, Abigail L.","first_name":"Abigail L.","last_name":"Buchwalter"},{"full_name":"Liang, Yun","last_name":"Liang","first_name":"Yun"},{"full_name":"HETZER, Martin W","orcid":"0000-0002-2111-992X","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","last_name":"HETZER","first_name":"Martin W"}],"volume":25,"date_created":"2022-04-07T07:50:24Z","date_updated":"2022-07-18T08:45:20Z"},{"author":[{"full_name":"Hatch, Emily","last_name":"Hatch","first_name":"Emily"},{"full_name":"HETZER, Martin W","last_name":"HETZER","first_name":"Martin W","orcid":"0000-0002-2111-992X","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed"}],"volume":205,"date_updated":"2022-07-18T08:45:09Z","date_created":"2022-04-07T07:50:13Z","pmid":1,"year":"2014","publisher":"Rockefeller University Press","publication_status":"published","extern":"1","doi":"10.1083/jcb.201402003","language":[{"iso":"eng"}],"external_id":{"pmid":["24751535"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.1083/jcb.201402003","open_access":"1"}],"quality_controlled":"1","publication_identifier":{"issn":["1540-8140","0021-9525"]},"month":"04","oa_version":"Published Version","_id":"11081","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","intvolume":" 205","status":"public","title":"Breaching the nuclear envelope in development and disease","issue":"2","abstract":[{"lang":"eng","text":"In eukaryotic cells the nuclear genome is enclosed by the nuclear envelope (NE). In metazoans, the NE breaks down in mitosis and it has been assumed that the physical barrier separating nucleoplasm and cytoplasm remains intact during the rest of the cell cycle and cell differentiation. However, recent studies suggest that nonmitotic NE remodeling plays a critical role in development, virus infection, laminopathies, and cancer. Although the mechanisms underlying these NE restructuring events are currently being defined, one common theme is activation of protein kinase C family members in the interphase nucleus to disrupt the nuclear lamina, demonstrating the importance of the lamina in maintaining nuclear integrity."}],"type":"journal_article","date_published":"2014-04-21T00:00:00Z","citation":{"ama":"Hatch E, Hetzer M. Breaching the nuclear envelope in development and disease. Journal of Cell Biology. 2014;205(2):133-141. doi:10.1083/jcb.201402003","ista":"Hatch E, Hetzer M. 2014. Breaching the nuclear envelope in development and disease. Journal of Cell Biology. 205(2), 133–141.","ieee":"E. Hatch and M. Hetzer, “Breaching the nuclear envelope in development and disease,” Journal of Cell Biology, vol. 205, no. 2. Rockefeller University Press, pp. 133–141, 2014.","apa":"Hatch, E., & Hetzer, M. (2014). Breaching the nuclear envelope in development and disease. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.201402003","mla":"Hatch, Emily, and Martin Hetzer. “Breaching the Nuclear Envelope in Development and Disease.” Journal of Cell Biology, vol. 205, no. 2, Rockefeller University Press, 2014, pp. 133–41, doi:10.1083/jcb.201402003.","short":"E. Hatch, M. Hetzer, Journal of Cell Biology 205 (2014) 133–141.","chicago":"Hatch, Emily, and Martin Hetzer. “Breaching the Nuclear Envelope in Development and Disease.” Journal of Cell Biology. Rockefeller University Press, 2014. https://doi.org/10.1083/jcb.201402003."},"publication":"Journal of Cell Biology","page":"133-141","article_type":"review","article_processing_charge":"No","day":"21","scopus_import":"1","keyword":["Cell Biology"]},{"article_processing_charge":"No","day":"21","scopus_import":"1","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: evolution","galaxies: high-redshift","cosmology: observations","dark ages","reionization","first stars"],"date_published":"2014-05-21T00:00:00Z","citation":{"short":"J.J. Matthee, D. Sobral, A.M. Swinbank, I. Smail, P.N. Best, J.-W. Kim, M. Franx, B. Milvang-Jensen, J. Fynbo, Monthly Notices of the Royal Astronomical Society 440 (2014) 2375–2387.","mla":"Matthee, Jorryt J., et al. “A 10 Deg2 Lyman α Survey at Z=8.8 with Spectroscopic Follow-up: Strong Constraints on the Luminosity Function and Implications for Other Surveys.” Monthly Notices of the Royal Astronomical Society, vol. 440, no. 3, Oxford University Press, 2014, pp. 2375–87, doi:10.1093/mnras/stu392.","chicago":"Matthee, Jorryt J, David Sobral, A. M. Swinbank, Ian Smail, P. N. Best, Jae-Woo Kim, Marijn Franx, Bo Milvang-Jensen, and Johan Fynbo. “A 10 Deg2 Lyman α Survey at Z=8.8 with Spectroscopic Follow-up: Strong Constraints on the Luminosity Function and Implications for Other Surveys.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2014. https://doi.org/10.1093/mnras/stu392.","ama":"Matthee JJ, Sobral D, Swinbank AM, et al. A 10 deg2 Lyman α survey at z=8.8 with spectroscopic follow-up: Strong constraints on the luminosity function and implications for other surveys. Monthly Notices of the Royal Astronomical Society. 2014;440(3):2375-2387. doi:10.1093/mnras/stu392","ieee":"J. J. Matthee et al., “A 10 deg2 Lyman α survey at z=8.8 with spectroscopic follow-up: Strong constraints on the luminosity function and implications for other surveys,” Monthly Notices of the Royal Astronomical Society, vol. 440, no. 3. Oxford University Press, pp. 2375–2387, 2014.","apa":"Matthee, J. J., Sobral, D., Swinbank, A. M., Smail, I., Best, P. N., Kim, J.-W., … Fynbo, J. (2014). A 10 deg2 Lyman α survey at z=8.8 with spectroscopic follow-up: Strong constraints on the luminosity function and implications for other surveys. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stu392","ista":"Matthee JJ, Sobral D, Swinbank AM, Smail I, Best PN, Kim J-W, Franx M, Milvang-Jensen B, Fynbo J. 2014. A 10 deg2 Lyman α survey at z=8.8 with spectroscopic follow-up: Strong constraints on the luminosity function and implications for other surveys. Monthly Notices of the Royal Astronomical Society. 440(3), 2375–2387."},"publication":"Monthly Notices of the Royal Astronomical Society","page":"2375-2387","article_type":"original","issue":"3","abstract":[{"lang":"eng","text":"Candidate galaxies at redshifts of z ∼ 10 are now being found in extremely deep surveys, probing very small areas. As a consequence, candidates are very faint, making spectroscopic confirmation practically impossible. In order to overcome such limitations, we have undertaken the CF-HiZELS survey, which is a large-area, medium-depth near-infrared narrow-band survey targeted at z = 8.8 Lyman α (Lyα) emitters (LAEs) and covering 10 deg2 in part of the SSA22 field with the Canada–France–Hawaii Telescope (CFHT). We surveyed a comoving volume of 4.7 × 106 Mpc3 to a Lyα luminosity limit of 6.3 × 1043舁erg舁s−1. We look for Lyα candidates by applying the following criteria: (i) clear emission-line source, (ii) no optical detections (ugriz from CFHTLS), (iii) no visible detection in the optical stack (ugriz > 27), (iv) visually checked reliable NBJ and J detections and (v) J − K ≤ 0. We compute photometric redshifts and remove a significant amount of dusty lower redshift line-emitters at z ∼ 1.4 or 2.2. A total of 13 Lyα candidates were found, of which two are marked as strong candidates, but the majority have very weak constraints on their spectral energy distributions. Using follow-up observations with SINFONI/VLT, we are able to exclude the most robust candidates as LAEs. We put a strong constraint on the Lyα luminosity function at z ∼ 9 and make realistic predictions for ongoing and future surveys. Our results show that surveys for the highest redshift LAEs are susceptible of multiple contaminations and that spectroscopic follow-up is absolutely necessary."}],"type":"journal_article","oa_version":"Preprint","_id":"11583","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 440","status":"public","title":"A 10 deg2 Lyman α survey at z=8.8 with spectroscopic follow-up: Strong constraints on the luminosity function and implications for other surveys","publication_identifier":{"issn":["0035-8711"],"eissn":["1365-2966"]},"month":"05","doi":"10.1093/mnras/stu392","language":[{"iso":"eng"}],"external_id":{"arxiv":["1402.6697"]},"main_file_link":[{"url":"https://arxiv.org/abs/1402.6697","open_access":"1"}],"oa":1,"quality_controlled":"1","extern":"1","author":[{"last_name":"Matthee","first_name":"Jorryt J","orcid":"0000-0003-2871-127X","id":"7439a258-f3c0-11ec-9501-9df22fe06720","full_name":"Matthee, Jorryt J"},{"last_name":"Sobral","first_name":"David","full_name":"Sobral, David"},{"first_name":"A. M.","last_name":"Swinbank","full_name":"Swinbank, A. M."},{"full_name":"Smail, Ian","last_name":"Smail","first_name":"Ian"},{"full_name":"Best, P. N.","last_name":"Best","first_name":"P. N."},{"last_name":"Kim","first_name":"Jae-Woo","full_name":"Kim, Jae-Woo"},{"full_name":"Franx, Marijn","last_name":"Franx","first_name":"Marijn"},{"last_name":"Milvang-Jensen","first_name":"Bo","full_name":"Milvang-Jensen, Bo"},{"full_name":"Fynbo, Johan","last_name":"Fynbo","first_name":"Johan"}],"volume":440,"date_created":"2022-07-14T12:33:24Z","date_updated":"2022-08-19T08:30:30Z","year":"2014","acknowledgement":"We thank the anonymous referee for the comments and suggestions which improved both the quality and clarity of this work. DS acknowledges financial support from the Netherlands Organisation for Scientific Research (NWO) through a Veni fellowship. IRS acknowledges support from STFC (ST/I001573/1), a Leverhulme Fellowship, the ERC Advanced Investigator programme DUSTYGAL 321334 and a Royal Society/Wolfson Merit Award. PNB acknowledges support from the Leverhulme Trust. JWK acknowledges the support from the Creative Research Initiative Program, no. 2008- 0060544, of the National Research Foundation of Korea (NRF) funded by the Korean government (MSIP). JPUF and BMJ acknowledge support from the ERC-StG grant EGGS-278202. The Dark Cosmology Centre is funded by the Danish National Research Foundation. This work is based in part on data obtained as part of the UKIRT Infrared Deep Sky Survey. Based on observations obtained with MegaPrime/MegaCam, a joint project of CFHT and CEA/IRFU, at the Canada–France–Hawaii Telescope (CFHT) which is operated by the National Research Council (NRC) of Canada, the Institut National des Science de l’Univers of the Centre National de la Recherche Scientifique (CNRS) of France and the University of Hawaii. This work is based in part on data products produced at Terapix available at the Canadian Astronomy Data Centre as part of the Canada-France-Hawaii Telescope Legacy Survey, a collaborative project of NRC and CNRS. This work was only possible due to OPTICON/FP7 and the access that it granted to the CFHT telescope. The authors also wish to acknowledge the CFHTLS and UKIDSS surveys for their excellent legacy and complementary value – without such high-quality data sets, this research would not have been possible.","publisher":"Oxford University Press","publication_status":"published"},{"citation":{"short":"J.P. Stott, D. Sobral, A.M. Swinbank, I. Smail, R. Bower, P.N. Best, R.M. Sharples, J.E. Geach, J.J. Matthee, Monthly Notices of the Royal Astronomical Society 443 (2014) 2695–2704.","mla":"Stott, John P., et al. “A Relationship between Specific Star Formation Rate and Metallicity Gradient within z ∼ 1 Galaxies from KMOS-HiZELS.” Monthly Notices of the Royal Astronomical Society, vol. 443, no. 3, Oxford University Press, 2014, pp. 2695–704, doi:10.1093/mnras/stu1343.","chicago":"Stott, John P., David Sobral, A. M. Swinbank, Ian Smail, Richard Bower, Philip N. Best, Ray M. Sharples, James E. Geach, and Jorryt J Matthee. “A Relationship between Specific Star Formation Rate and Metallicity Gradient within z ∼ 1 Galaxies from KMOS-HiZELS.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2014. https://doi.org/10.1093/mnras/stu1343.","ama":"Stott JP, Sobral D, Swinbank AM, et al. A relationship between specific star formation rate and metallicity gradient within z ∼ 1 galaxies from KMOS-HiZELS. Monthly Notices of the Royal Astronomical Society. 2014;443(3):2695-2704. doi:10.1093/mnras/stu1343","apa":"Stott, J. P., Sobral, D., Swinbank, A. M., Smail, I., Bower, R., Best, P. N., … Matthee, J. J. (2014). A relationship between specific star formation rate and metallicity gradient within z ∼ 1 galaxies from KMOS-HiZELS. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stu1343","ieee":"J. P. Stott et al., “A relationship between specific star formation rate and metallicity gradient within z ∼ 1 galaxies from KMOS-HiZELS,” Monthly Notices of the Royal Astronomical Society, vol. 443, no. 3. Oxford University Press, pp. 2695–2704, 2014.","ista":"Stott JP, Sobral D, Swinbank AM, Smail I, Bower R, Best PN, Sharples RM, Geach JE, Matthee JJ. 2014. A relationship between specific star formation rate and metallicity gradient within z ∼ 1 galaxies from KMOS-HiZELS. Monthly Notices of the Royal Astronomical Society. 443(3), 2695–2704."},"publication":"Monthly Notices of the Royal Astronomical Society","page":"2695-2704","article_type":"original","date_published":"2014-09-21T00:00:00Z","scopus_import":"1","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: abundances","galaxies: evolution","galaxies: kinematics and dynamics"],"article_processing_charge":"No","day":"21","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11582","intvolume":" 443","status":"public","title":"A relationship between specific star formation rate and metallicity gradient within z ∼ 1 galaxies from KMOS-HiZELS","oa_version":"Preprint","type":"journal_article","issue":"3","abstract":[{"lang":"eng","text":"We have observed a sample of typical z ∼ 1 star-forming galaxies, selected from the HiZELS survey, with the new K-band Multi-Object Spectrograph (KMOS) near-infrared, multi-integral field unit instrument on the Very Large Telescope (VLT), in order to obtain their dynamics and metallicity gradients. The majority of our galaxies have a metallicity gradient consistent with being flat or negative (i.e. higher metallicity cores than outskirts). Intriguingly, we find a trend between metallicity gradient and specific star formation rate (sSFR), such that galaxies with a high sSFR tend to have relatively metal poor centres, a result which is strengthened when combined with data sets from the literature. This result appears to explain the discrepancies reported between different high-redshift studies and varying claims for evolution. From a galaxy evolution perspective, the trend we see would mean that a galaxy's sSFR is governed by the amount of metal-poor gas that can be funnelled into its core, triggered either by merging or through efficient accretion. In fact, merging may play a significant role as it is the starburst galaxies at all epochs, which have the more positive metallicity gradients. Our results may help to explain the origin of the fundamental metallicity relation, in which galaxies at a fixed mass are observed to have lower metallicities at higher star formation rates, especially if the metallicity is measured in an aperture encompassing only the central regions of the galaxy. Finally, we note that this study demonstrates the power of KMOS as an efficient instrument for large-scale resolved galaxy surveys."}],"external_id":{"arxiv":["1407.1047"]},"main_file_link":[{"url":"https://arxiv.org/abs/1407.1047","open_access":"1"}],"oa":1,"quality_controlled":"1","doi":"10.1093/mnras/stu1343","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1365-2966"],"issn":["0035-8711"]},"month":"09","acknowledgement":"First, we acknowledge the referee for their comments, which have improved the clarity of this paper. JPS and IRS acknowledge support from STFC (ST/I001573/1). IRS also acknowledges support from the ERC Advanced Investigator programme DUSTYGAL and a Royal Society/Wolfson Merit Award. DS acknowledges financial support from NWO through a Veni fellowship and from FCT through the award of an FCT-IF starting grant. PNB acknowledges STFC for financial support.","year":"2014","publisher":"Oxford University Press","publication_status":"published","author":[{"full_name":"Stott, John P.","last_name":"Stott","first_name":"John P."},{"full_name":"Sobral, David","last_name":"Sobral","first_name":"David"},{"first_name":"A. M.","last_name":"Swinbank","full_name":"Swinbank, A. M."},{"full_name":"Smail, Ian","first_name":"Ian","last_name":"Smail"},{"first_name":"Richard","last_name":"Bower","full_name":"Bower, Richard"},{"first_name":"Philip N.","last_name":"Best","full_name":"Best, Philip N."},{"full_name":"Sharples, Ray M.","first_name":"Ray M.","last_name":"Sharples"},{"full_name":"Geach, James E.","first_name":"James E.","last_name":"Geach"},{"orcid":"0000-0003-2871-127X","id":"7439a258-f3c0-11ec-9501-9df22fe06720","last_name":"Matthee","first_name":"Jorryt J","full_name":"Matthee, Jorryt J"}],"volume":443,"date_created":"2022-07-14T12:16:10Z","date_updated":"2022-08-19T08:27:25Z","extern":"1"}]