[{"language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-89960-2_21","conference":{"name":"TACAS 2018: Tools and Algorithms for the Construction and Analysis of Systems","end_date":"2018-04-20","start_date":"2018-04-14","location":"Thessaloniki, Greece"},"project":[{"name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"quality_controlled":"1","isi":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"},"external_id":{"isi":["000546326300021"]},"oa":1,"month":"04","volume":10805,"date_created":"2018-12-11T11:45:41Z","date_updated":"2023-09-19T09:57:08Z","author":[{"last_name":"Brázdil","first_name":"Tomáš","full_name":"Brázdil, Tomáš"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"full_name":"Kretinsky, Jan","first_name":"Jan","last_name":"Kretinsky","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8122-2881"},{"full_name":"Toman, Viktor","first_name":"Viktor","last_name":"Toman","id":"3AF3DA7C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9036-063X"}],"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publisher":"Springer","publication_status":"published","year":"2018","publist_id":"7584","ec_funded":1,"file_date_updated":"2020-07-14T12:45:57Z","date_published":"2018-04-12T00:00:00Z","page":"385 - 407","citation":{"mla":"Brázdil, Tomáš, et al. Strategy Representation by Decision Trees in Reactive Synthesis. Vol. 10805, Springer, 2018, pp. 385–407, doi:10.1007/978-3-319-89960-2_21.","short":"T. Brázdil, K. Chatterjee, J. Kretinsky, V. Toman, in:, Springer, 2018, pp. 385–407.","chicago":"Brázdil, Tomáš, Krishnendu Chatterjee, Jan Kretinsky, and Viktor Toman. “Strategy Representation by Decision Trees in Reactive Synthesis,” 10805:385–407. Springer, 2018. https://doi.org/10.1007/978-3-319-89960-2_21.","ama":"Brázdil T, Chatterjee K, Kretinsky J, Toman V. Strategy representation by decision trees in reactive synthesis. In: Vol 10805. Springer; 2018:385-407. doi:10.1007/978-3-319-89960-2_21","ista":"Brázdil T, Chatterjee K, Kretinsky J, Toman V. 2018. Strategy representation by decision trees in reactive synthesis. TACAS 2018: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 10805, 385–407.","ieee":"T. Brázdil, K. Chatterjee, J. Kretinsky, and V. Toman, “Strategy representation by decision trees in reactive synthesis,” presented at the TACAS 2018: Tools and Algorithms for the Construction and Analysis of Systems, Thessaloniki, Greece, 2018, vol. 10805, pp. 385–407.","apa":"Brázdil, T., Chatterjee, K., Kretinsky, J., & Toman, V. (2018). Strategy representation by decision trees in reactive synthesis (Vol. 10805, pp. 385–407). Presented at the TACAS 2018: Tools and Algorithms for the Construction and Analysis of Systems, Thessaloniki, Greece: Springer. https://doi.org/10.1007/978-3-319-89960-2_21"},"has_accepted_license":"1","article_processing_charge":"No","day":"12","scopus_import":"1","file":[{"creator":"dernst","content_type":"application/pdf","file_size":1829940,"access_level":"open_access","file_name":"2018_LNCS_Brazdil.pdf","checksum":"b13874ffb114932ad9cc2586b7469db4","date_created":"2018-12-17T16:29:08Z","date_updated":"2020-07-14T12:45:57Z","file_id":"5723","relation":"main_file"}],"oa_version":"Published Version","intvolume":" 10805","status":"public","ddc":["000"],"title":"Strategy representation by decision trees in reactive synthesis","_id":"297","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"text":"Graph games played by two players over finite-state graphs are central in many problems in computer science. In particular, graph games with ω -regular winning conditions, specified as parity objectives, which can express properties such as safety, liveness, fairness, are the basic framework for verification and synthesis of reactive systems. The decisions for a player at various states of the graph game are represented as strategies. While the algorithmic problem for solving graph games with parity objectives has been widely studied, the most prominent data-structure for strategy representation in graph games has been binary decision diagrams (BDDs). However, due to the bit-level representation, BDDs do not retain the inherent flavor of the decisions of strategies, and are notoriously hard to minimize to obtain succinct representation. In this work we propose decision trees for strategy representation in graph games. Decision trees retain the flavor of decisions of strategies and allow entropy-based minimization to obtain succinct trees. However, decision trees work in settings (e.g., probabilistic models) where errors are allowed, and overfitting of data is typically avoided. In contrast, for strategies in graph games no error is allowed, and the decision tree must represent the entire strategy. We develop new techniques to extend decision trees to overcome the above obstacles, while retaining the entropy-based techniques to obtain succinct trees. We have implemented our techniques to extend the existing decision tree solvers. We present experimental results for problems in reactive synthesis to show that decision trees provide a much more efficient data-structure for strategy representation as compared to BDDs.","lang":"eng"}],"alternative_title":["LNCS"],"type":"conference"},{"page":"178-197","citation":{"ista":"Chatterjee K, Henzinger MH, Loitzenbauer V, Oraee S, Toman V. 2018. Symbolic algorithms for graphs and Markov decision processes with fairness objectives. CAV: Computer Aided Verification, LNCS, vol. 10982, 178–197.","apa":"Chatterjee, K., Henzinger, M. H., Loitzenbauer, V., Oraee, S., & Toman, V. (2018). Symbolic algorithms for graphs and Markov decision processes with fairness objectives (Vol. 10982, pp. 178–197). Presented at the CAV: Computer Aided Verification, Oxford, United Kingdom: Springer. https://doi.org/10.1007/978-3-319-96142-2_13","ieee":"K. Chatterjee, M. H. Henzinger, V. Loitzenbauer, S. Oraee, and V. Toman, “Symbolic algorithms for graphs and Markov decision processes with fairness objectives,” presented at the CAV: Computer Aided Verification, Oxford, United Kingdom, 2018, vol. 10982, pp. 178–197.","ama":"Chatterjee K, Henzinger MH, Loitzenbauer V, Oraee S, Toman V. Symbolic algorithms for graphs and Markov decision processes with fairness objectives. In: Vol 10982. Springer; 2018:178-197. doi:10.1007/978-3-319-96142-2_13","chicago":"Chatterjee, Krishnendu, Monika H Henzinger, Veronika Loitzenbauer, Simin Oraee, and Viktor Toman. “Symbolic Algorithms for Graphs and Markov Decision Processes with Fairness Objectives,” 10982:178–97. Springer, 2018. https://doi.org/10.1007/978-3-319-96142-2_13.","mla":"Chatterjee, Krishnendu, et al. Symbolic Algorithms for Graphs and Markov Decision Processes with Fairness Objectives. Vol. 10982, Springer, 2018, pp. 178–97, doi:10.1007/978-3-319-96142-2_13.","short":"K. Chatterjee, M.H. Henzinger, V. Loitzenbauer, S. Oraee, V. Toman, in:, Springer, 2018, pp. 178–197."},"date_published":"2018-07-18T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"18","intvolume":" 10982","status":"public","ddc":["000"],"title":"Symbolic algorithms for graphs and Markov decision processes with fairness objectives","_id":"141","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","file":[{"checksum":"1a6ffa4febe8bb8ac28be3adb3eafebc","date_updated":"2020-07-14T12:44:53Z","date_created":"2018-12-18T08:52:38Z","file_id":"5737","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":675606,"access_level":"open_access","file_name":"2018_LNCS_Chatterjee.pdf"}],"alternative_title":["LNCS"],"type":"conference","abstract":[{"text":"Given a model and a specification, the fundamental model-checking problem asks for algorithmic verification of whether the model satisfies the specification. We consider graphs and Markov decision processes (MDPs), which are fundamental models for reactive systems. One of the very basic specifications that arise in verification of reactive systems is the strong fairness (aka Streett) objective. Given different types of requests and corresponding grants, the objective requires that for each type, if the request event happens infinitely often, then the corresponding grant event must also happen infinitely often. All ω -regular objectives can be expressed as Streett objectives and hence they are canonical in verification. To handle the state-space explosion, symbolic algorithms are required that operate on a succinct implicit representation of the system rather than explicitly accessing the system. While explicit algorithms for graphs and MDPs with Streett objectives have been widely studied, there has been no improvement of the basic symbolic algorithms. The worst-case numbers of symbolic steps required for the basic symbolic algorithms are as follows: quadratic for graphs and cubic for MDPs. In this work we present the first sub-quadratic symbolic algorithm for graphs with Streett objectives, and our algorithm is sub-quadratic even for MDPs. Based on our algorithmic insights we present an implementation of the new symbolic approach and show that it improves the existing approach on several academic benchmark examples.","lang":"eng"}],"project":[{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"isi":1,"quality_controlled":"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"},"oa":1,"external_id":{"isi":["000491469700013"]},"language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-96142-2_13","conference":{"name":"CAV: Computer Aided Verification","end_date":"2018-07-17","start_date":"2018-07-14","location":"Oxford, United Kingdom"},"month":"07","publisher":"Springer","department":[{"_id":"KrCh"}],"publication_status":"published","year":"2018","acknowledgement":"Acknowledgements. K. C. and M. H. are partially supported by the Vienna Science and Technology Fund (WWTF) grant ICT15-003. K. C. is partially supported by the Austrian Science Fund (FWF): S11407-N23 (RiSE/SHiNE), and an ERC Start Grant (279307: Graph Games). V. T. is partially supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Sk lodowska-Curie Grant Agreement No. 665385.","volume":10982,"date_created":"2018-12-11T11:44:51Z","date_updated":"2023-09-19T09:59:55Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10199"}]},"author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"full_name":"Henzinger, Monika H","first_name":"Monika H","last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530"},{"last_name":"Loitzenbauer","first_name":"Veronika","full_name":"Loitzenbauer, Veronika"},{"first_name":"Simin","last_name":"Oraee","full_name":"Oraee, Simin"},{"last_name":"Toman","first_name":"Viktor","orcid":"0000-0001-9036-063X","id":"3AF3DA7C-F248-11E8-B48F-1D18A9856A87","full_name":"Toman, Viktor"}],"ec_funded":1,"publist_id":"7782","file_date_updated":"2020-07-14T12:44:53Z"},{"project":[{"grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Teaching Old Crypto New Tricks"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000517098700004"],"arxiv":["1705.05313"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.05313"}],"language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-78375-8_4","conference":{"name":"Eurocrypt 2018: Advances in Cryptology","start_date":"2018-04-29","location":"Tel Aviv, Israel","end_date":"2018-05-03"},"month":"03","department":[{"_id":"KrPi"}],"publisher":"Springer","publication_status":"published","year":"2018","volume":10821,"date_updated":"2023-09-19T09:59:30Z","date_created":"2018-12-11T11:45:41Z","author":[{"full_name":"Alwen, Joel F","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","first_name":"Joel F","last_name":"Alwen"},{"full_name":"Blocki, Jeremiah","first_name":"Jeremiah","last_name":"Blocki"},{"full_name":"Pietrzak, Krzysztof Z","first_name":"Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654"}],"ec_funded":1,"publist_id":"7583","page":"99 - 130","citation":{"chicago":"Alwen, Joel F, Jeremiah Blocki, and Krzysztof Z Pietrzak. “Sustained Space Complexity,” 10821:99–130. Springer, 2018. https://doi.org/10.1007/978-3-319-78375-8_4.","short":"J.F. Alwen, J. Blocki, K.Z. Pietrzak, in:, Springer, 2018, pp. 99–130.","mla":"Alwen, Joel F., et al. Sustained Space Complexity. Vol. 10821, Springer, 2018, pp. 99–130, doi:10.1007/978-3-319-78375-8_4.","apa":"Alwen, J. F., Blocki, J., & Pietrzak, K. Z. (2018). Sustained space complexity (Vol. 10821, pp. 99–130). Presented at the Eurocrypt 2018: Advances in Cryptology, Tel Aviv, Israel: Springer. https://doi.org/10.1007/978-3-319-78375-8_4","ieee":"J. F. Alwen, J. Blocki, and K. Z. Pietrzak, “Sustained space complexity,” presented at the Eurocrypt 2018: Advances in Cryptology, Tel Aviv, Israel, 2018, vol. 10821, pp. 99–130.","ista":"Alwen JF, Blocki J, Pietrzak KZ. 2018. Sustained space complexity. Eurocrypt 2018: Advances in Cryptology, LNCS, vol. 10821, 99–130.","ama":"Alwen JF, Blocki J, Pietrzak KZ. Sustained space complexity. In: Vol 10821. Springer; 2018:99-130. doi:10.1007/978-3-319-78375-8_4"},"date_published":"2018-03-31T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"31","intvolume":" 10821","status":"public","title":"Sustained space complexity","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"298","oa_version":"Preprint","alternative_title":["LNCS"],"type":"conference","abstract":[{"lang":"eng","text":"Memory-hard functions (MHF) are functions whose evaluation cost is dominated by memory cost. MHFs are egalitarian, in the sense that evaluating them on dedicated hardware (like FPGAs or ASICs) is not much cheaper than on off-the-shelf hardware (like x86 CPUs). MHFs have interesting cryptographic applications, most notably to password hashing and securing blockchains.\r\n\r\nAlwen and Serbinenko [STOC’15] define the cumulative memory complexity (cmc) of a function as the sum (over all time-steps) of the amount of memory required to compute the function. They advocate that a good MHF must have high cmc. Unlike previous notions, cmc takes into account that dedicated hardware might exploit amortization and parallelism. Still, cmc has been critizised as insufficient, as it fails to capture possible time-memory trade-offs; as memory cost doesn’t scale linearly, functions with the same cmc could still have very different actual hardware cost.\r\n\r\nIn this work we address this problem, and introduce the notion of sustained-memory complexity, which requires that any algorithm evaluating the function must use a large amount of memory for many steps. We construct functions (in the parallel random oracle model) whose sustained-memory complexity is almost optimal: our function can be evaluated using n steps and O(n/log(n)) memory, in each step making one query to the (fixed-input length) random oracle, while any algorithm that can make arbitrary many parallel queries to the random oracle, still needs Ω(n/log(n)) memory for Ω(n) steps.\r\n\r\nAs has been done for various notions (including cmc) before, we reduce the task of constructing an MHFs with high sustained-memory complexity to proving pebbling lower bounds on DAGs. Our main technical contribution is the construction is a family of DAGs on n nodes with constant indegree with high “sustained-space complexity”, meaning that any parallel black-pebbling strategy requires Ω(n/log(n)) pebbles for at least Ω(n) steps.\r\n\r\nAlong the way we construct a family of maximally “depth-robust” DAGs with maximum indegree O(logn) , improving upon the construction of Mahmoody et al. [ITCS’13] which had maximum indegree O(log2n⋅"}]},{"file_date_updated":"2020-07-14T12:46:13Z","publist_id":"8019","publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Oxford University Press","acknowledgement":"TZ is supported by a grant from the Chinese Scholarship Council.","year":"2018","date_created":"2018-12-11T11:44:17Z","date_updated":"2023-09-19T10:00:46Z","volume":69,"author":[{"full_name":"Vu, Lam","last_name":"Vu","first_name":"Lam"},{"full_name":"Zhu, Tingting","first_name":"Tingting","last_name":"Zhu"},{"full_name":"Verstraeten, Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7241-2328","first_name":"Inge","last_name":"Verstraeten"},{"full_name":"Van De Cotte, Brigitte","last_name":"Van De Cotte","first_name":"Brigitte"},{"last_name":"Gevaert","first_name":"Kris","full_name":"Gevaert, Kris"},{"full_name":"De Smet, Ive","first_name":"Ive","last_name":"De Smet"}],"month":"08","quality_controlled":"1","isi":1,"external_id":{"isi":["000443568700010"]},"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"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1093/jxb/ery204","type":"journal_article","abstract":[{"lang":"eng","text":"Wheat (Triticum ssp.) is one of the most important human food sources. However, this crop is very sensitive to temperature changes. Specifically, processes during wheat leaf, flower, and seed development and photosynthesis, which all contribute to the yield of this crop, are affected by high temperature. While this has to some extent been investigated on physiological, developmental, and molecular levels, very little is known about early signalling events associated with an increase in temperature. Phosphorylation-mediated signalling mechanisms, which are quick and dynamic, are associated with plant growth and development, also under abiotic stress conditions. Therefore, we probed the impact of a short-term and mild increase in temperature on the wheat leaf and spikelet phosphoproteome. In total, 3822 (containing 5178 phosphosites) and 5581 phosphopeptides (containing 7023 phosphosites) were identified in leaf and spikelet samples, respectively. Following statistical analysis, the resulting data set provides the scientific community with a first large-scale plant phosphoproteome under the control of higher ambient temperature. This community resource on the high temperature-mediated wheat phosphoproteome will be valuable for future studies. Our analyses also revealed a core set of common proteins between leaf and spikelet, suggesting some level of conserved regulatory mechanisms. Furthermore, we observed temperature-regulated interconversion of phosphoforms, which probably impacts protein activity."}],"issue":"19","status":"public","title":"Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms","ddc":["581"],"intvolume":" 69","_id":"36","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"creator":"dernst","file_size":3359316,"content_type":"application/pdf","file_name":"2018_JournalExperimBotany_Vu.pdf","access_level":"open_access","date_created":"2018-12-18T09:47:51Z","date_updated":"2020-07-14T12:46:13Z","checksum":"34cb0a1611588b75bd6f4913fb4e30f1","file_id":"5741","relation":"main_file"}],"oa_version":"Published Version","scopus_import":"1","day":"31","has_accepted_license":"1","article_processing_charge":"No","page":"4609 - 4624","publication":"Journal of Experimental Botany","citation":{"chicago":"Vu, Lam, Tingting Zhu, Inge Verstraeten, Brigitte Van De Cotte, Kris Gevaert, and Ive De Smet. “Temperature-Induced Changes in the Wheat Phosphoproteome Reveal Temperature-Regulated Interconversion of Phosphoforms.” Journal of Experimental Botany. Oxford University Press, 2018. https://doi.org/10.1093/jxb/ery204.","mla":"Vu, Lam, et al. “Temperature-Induced Changes in the Wheat Phosphoproteome Reveal Temperature-Regulated Interconversion of Phosphoforms.” Journal of Experimental Botany, vol. 69, no. 19, Oxford University Press, 2018, pp. 4609–24, doi:10.1093/jxb/ery204.","short":"L. Vu, T. Zhu, I. Verstraeten, B. Van De Cotte, K. Gevaert, I. De Smet, Journal of Experimental Botany 69 (2018) 4609–4624.","ista":"Vu L, Zhu T, Verstraeten I, Van De Cotte B, Gevaert K, De Smet I. 2018. Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms. Journal of Experimental Botany. 69(19), 4609–4624.","apa":"Vu, L., Zhu, T., Verstraeten, I., Van De Cotte, B., Gevaert, K., & De Smet, I. (2018). Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/ery204","ieee":"L. Vu, T. Zhu, I. Verstraeten, B. Van De Cotte, K. Gevaert, and I. De Smet, “Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms,” Journal of Experimental Botany, vol. 69, no. 19. Oxford University Press, pp. 4609–4624, 2018.","ama":"Vu L, Zhu T, Verstraeten I, Van De Cotte B, Gevaert K, De Smet I. Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms. Journal of Experimental Botany. 2018;69(19):4609-4624. doi:10.1093/jxb/ery204"},"date_published":"2018-08-31T00:00:00Z"},{"month":"03","external_id":{"isi":["000431496400001"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"quality_controlled":"1","isi":1,"doi":"10.1111/ejn.13901","acknowledged_ssus":[{"_id":"EM-Fac"}],"language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:46:06Z","publist_id":"7539","year":"2018","publication_status":"published","publisher":"Wiley","department":[{"_id":"RySh"}],"author":[{"full_name":"Sawada, Kazuaki","last_name":"Sawada","first_name":"Kazuaki"},{"first_name":"Ryosuke","last_name":"Kawakami","full_name":"Kawakami, Ryosuke"},{"full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444"},{"full_name":"Nemoto, Tomomi","first_name":"Tomomi","last_name":"Nemoto"}],"date_created":"2018-12-11T11:45:50Z","date_updated":"2023-09-19T09:58:40Z","volume":47,"scopus_import":"1","day":"07","has_accepted_license":"1","article_processing_charge":"No","publication":"European Journal of Neuroscience","citation":{"ama":"Sawada K, Kawakami R, Shigemoto R, Nemoto T. Super resolution structural analysis of dendritic spines using three-dimensional structured illumination microscopy in cleared mouse brain slices. European Journal of Neuroscience. 2018;47(9):1033-1042. doi:10.1111/ejn.13901","apa":"Sawada, K., Kawakami, R., Shigemoto, R., & Nemoto, T. (2018). Super resolution structural analysis of dendritic spines using three-dimensional structured illumination microscopy in cleared mouse brain slices. European Journal of Neuroscience. Wiley. https://doi.org/10.1111/ejn.13901","ieee":"K. Sawada, R. Kawakami, R. Shigemoto, and T. Nemoto, “Super resolution structural analysis of dendritic spines using three-dimensional structured illumination microscopy in cleared mouse brain slices,” European Journal of Neuroscience, vol. 47, no. 9. Wiley, pp. 1033–1042, 2018.","ista":"Sawada K, Kawakami R, Shigemoto R, Nemoto T. 2018. Super resolution structural analysis of dendritic spines using three-dimensional structured illumination microscopy in cleared mouse brain slices. European Journal of Neuroscience. 47(9), 1033–1042.","short":"K. Sawada, R. Kawakami, R. Shigemoto, T. Nemoto, European Journal of Neuroscience 47 (2018) 1033–1042.","mla":"Sawada, Kazuaki, et al. “Super Resolution Structural Analysis of Dendritic Spines Using Three-Dimensional Structured Illumination Microscopy in Cleared Mouse Brain Slices.” European Journal of Neuroscience, vol. 47, no. 9, Wiley, 2018, pp. 1033–42, doi:10.1111/ejn.13901.","chicago":"Sawada, Kazuaki, Ryosuke Kawakami, Ryuichi Shigemoto, and Tomomi Nemoto. “Super Resolution Structural Analysis of Dendritic Spines Using Three-Dimensional Structured Illumination Microscopy in Cleared Mouse Brain Slices.” European Journal of Neuroscience. Wiley, 2018. https://doi.org/10.1111/ejn.13901."},"page":"1033 - 1042","date_published":"2018-03-07T00:00:00Z","type":"journal_article","abstract":[{"text":"Three-dimensional (3D) super-resolution microscopy technique structured illumination microscopy (SIM) imaging of dendritic spines along the dendrite has not been previously performed in fixed tissues, mainly due to deterioration of the stripe pattern of the excitation laser induced by light scattering and optical aberrations. To address this issue and solve these optical problems, we applied a novel clearing reagent, LUCID, to fixed brains. In SIM imaging, the penetration depth and the spatial resolution were improved in LUCID-treated slices, and 160-nm spatial resolution was obtained in a large portion of the imaging volume on a single apical dendrite. Furthermore, in a morphological analysis of spine heads of layer V pyramidal neurons (L5PNs) in the medial prefrontal cortex (mPFC) of chronic dexamethasone (Dex)-treated mice, SIM imaging revealed an altered distribution of spine forms that could not be detected by high-NA confocal imaging. Thus, super-resolution SIM imaging represents a promising high-throughput method for revealing spine morphologies in single dendrites.","lang":"eng"}],"issue":"9","_id":"326","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","ddc":["570"],"title":"Super resolution structural analysis of dendritic spines using three-dimensional structured illumination microscopy in cleared mouse brain slices","intvolume":" 47","file":[{"access_level":"open_access","file_name":"2018_EJN_Sawada.pdf","file_size":4850261,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"5721","checksum":"98e901d8229e44aa8f3b51d248dedd09","date_updated":"2020-07-14T12:46:06Z","date_created":"2018-12-17T16:16:50Z"}],"oa_version":"Published Version"},{"type":"journal_article","abstract":[{"text":"Retroviruses assemble and bud from infected cells in an immature form and require proteolytic maturation for infectivity. The CA (capsid) domains of the Gag polyproteins assemble a protein lattice as a truncated sphere in the immature virion. Proteolytic cleavage of Gag induces dramatic structural rearrangements; a subset of cleaved CA subsequently assembles into the mature core, whose architecture varies among retroviruses. Murine leukemia virus (MLV) is the prototypical γ-retrovirus and serves as the basis of retroviral vectors, but the structure of the MLV CA layer is unknown. Here we have combined X-ray crystallography with cryoelectron tomography to determine the structures of immature and mature MLV CA layers within authentic viral particles. This reveals the structural changes associated with maturation, and, by comparison with HIV-1, uncovers conserved and variable features. In contrast to HIV-1, most MLV CA is used for assembly of the mature core, which adopts variable, multilayered morphologies and does not form a closed structure. Unlike in HIV-1, there is similarity between protein–protein interfaces in the immature MLV CA layer and those in the mature CA layer, and structural maturation of MLV could be achieved through domain rotations that largely maintain hexameric interactions. Nevertheless, the dramatic architectural change on maturation indicates that extensive disassembly and reassembly are required for mature core growth. The core morphology suggests that wrapping of the genome in CA sheets may be sufficient to protect the MLV ribonucleoprotein during cell entry.","lang":"eng"}],"issue":"50","_id":"5770","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Structure and architecture of immature and mature murine leukemia virus capsids","status":"public","intvolume":" 115","oa_version":"Submitted Version","scopus_import":"1","day":"11","article_processing_charge":"No","publication":"Proceedings of the National Academy of Sciences","citation":{"chicago":"Qu, Kun, Bärbel Glass, Michal Doležal, Florian KM Schur, Brice Murciano, Alan Rein, Michaela Rumlová, Tomáš Ruml, Hans-Georg Kräusslich, and John A. G. Briggs. “Structure and Architecture of Immature and Mature Murine Leukemia Virus Capsids.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1811580115.","mla":"Qu, Kun, et al. “Structure and Architecture of Immature and Mature Murine Leukemia Virus Capsids.” Proceedings of the National Academy of Sciences, vol. 115, no. 50, Proceedings of the National Academy of Sciences, 2018, pp. E11751–60, doi:10.1073/pnas.1811580115.","short":"K. Qu, B. Glass, M. Doležal, F.K. Schur, B. Murciano, A. Rein, M. Rumlová, T. Ruml, H.-G. Kräusslich, J.A.G. Briggs, Proceedings of the National Academy of Sciences 115 (2018) E11751–E11760.","ista":"Qu K, Glass B, Doležal M, Schur FK, Murciano B, Rein A, Rumlová M, Ruml T, Kräusslich H-G, Briggs JAG. 2018. Structure and architecture of immature and mature murine leukemia virus capsids. Proceedings of the National Academy of Sciences. 115(50), E11751–E11760.","apa":"Qu, K., Glass, B., Doležal, M., Schur, F. K., Murciano, B., Rein, A., … Briggs, J. A. G. (2018). Structure and architecture of immature and mature murine leukemia virus capsids. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1811580115","ieee":"K. Qu et al., “Structure and architecture of immature and mature murine leukemia virus capsids,” Proceedings of the National Academy of Sciences, vol. 115, no. 50. Proceedings of the National Academy of Sciences, pp. E11751–E11760, 2018.","ama":"Qu K, Glass B, Doležal M, et al. Structure and architecture of immature and mature murine leukemia virus capsids. Proceedings of the National Academy of Sciences. 2018;115(50):E11751-E11760. doi:10.1073/pnas.1811580115"},"page":"E11751-E11760","date_published":"2018-12-11T00:00:00Z","year":"2018","pmid":1,"publication_status":"published","publisher":"Proceedings of the National Academy of Sciences","department":[{"_id":"FlSc"}],"author":[{"full_name":"Qu, Kun","first_name":"Kun","last_name":"Qu"},{"last_name":"Glass","first_name":"Bärbel","full_name":"Glass, Bärbel"},{"full_name":"Doležal, Michal","first_name":"Michal","last_name":"Doležal"},{"full_name":"Schur, Florian","first_name":"Florian","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078"},{"full_name":"Murciano, Brice","first_name":"Brice","last_name":"Murciano"},{"last_name":"Rein","first_name":"Alan","full_name":"Rein, Alan"},{"full_name":"Rumlová, Michaela","last_name":"Rumlová","first_name":"Michaela"},{"first_name":"Tomáš","last_name":"Ruml","full_name":"Ruml, Tomáš"},{"full_name":"Kräusslich, Hans-Georg","first_name":"Hans-Georg","last_name":"Kräusslich"},{"full_name":"Briggs, John A. G.","last_name":"Briggs","first_name":"John A. G."}],"date_created":"2018-12-20T21:09:37Z","date_updated":"2023-09-19T09:57:45Z","volume":115,"month":"12","publication_identifier":{"issn":["00278424"]},"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30478053","open_access":"1"}],"oa":1,"external_id":{"pmid":["30478053"],"isi":["000452866000022"]},"isi":1,"quality_controlled":"1","doi":"10.1073/pnas.1811580115","language":[{"iso":"eng"}]},{"page":"50 - 72","article_type":"original","citation":{"ama":"Avni G, Kupferman O. Synthesis from component libraries with costs. Theoretical Computer Science. 2018;712:50-72. doi:10.1016/j.tcs.2017.11.001","ista":"Avni G, Kupferman O. 2018. Synthesis from component libraries with costs. Theoretical Computer Science. 712, 50–72.","apa":"Avni, G., & Kupferman, O. (2018). Synthesis from component libraries with costs. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2017.11.001","ieee":"G. Avni and O. Kupferman, “Synthesis from component libraries with costs,” Theoretical Computer Science, vol. 712. Elsevier, pp. 50–72, 2018.","mla":"Avni, Guy, and Orna Kupferman. “Synthesis from Component Libraries with Costs.” Theoretical Computer Science, vol. 712, Elsevier, 2018, pp. 50–72, doi:10.1016/j.tcs.2017.11.001.","short":"G. Avni, O. Kupferman, Theoretical Computer Science 712 (2018) 50–72.","chicago":"Avni, Guy, and Orna Kupferman. “Synthesis from Component Libraries with Costs.” Theoretical Computer Science. Elsevier, 2018. https://doi.org/10.1016/j.tcs.2017.11.001."},"publication":"Theoretical Computer Science","date_published":"2018-02-15T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"15","intvolume":" 712","status":"public","title":"Synthesis from component libraries with costs","_id":"608","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Synthesis is the automated construction of a system from its specification. In real life, hardware and software systems are rarely constructed from scratch. Rather, a system is typically constructed from a library of components. Lustig and Vardi formalized this intuition and studied LTL synthesis from component libraries. In real life, designers seek optimal systems. In this paper we add optimality considerations to the setting. We distinguish between quality considerations (for example, size - the smaller a system is, the better it is), and pricing (for example, the payment to the company who manufactured the component). We study the problem of designing systems with minimal quality-cost and price. A key point is that while the quality cost is individual - the choices of a designer are independent of choices made by other designers that use the same library, pricing gives rise to a resource-allocation game - designers that use the same component share its price, with the share being proportional to the number of uses (a component can be used several times in a design). We study both closed and open settings, and in both we solve the problem of finding an optimal design. In a setting with multiple designers, we also study the game-theoretic problems of the induced resource-allocation game.","lang":"eng"}],"project":[{"name":"Quantitative Reactive Modeling","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"}],"quality_controlled":"1","isi":1,"main_file_link":[{"url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.636.4529","open_access":"1"}],"external_id":{"isi":["000424959200003"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.tcs.2017.11.001","month":"02","department":[{"_id":"ToHe"}],"publisher":"Elsevier","publication_status":"published","year":"2018","volume":712,"date_created":"2018-12-11T11:47:28Z","date_updated":"2023-09-19T10:00:21Z","author":[{"full_name":"Avni, Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5588-8287","first_name":"Guy","last_name":"Avni"},{"full_name":"Kupferman, Orna","first_name":"Orna","last_name":"Kupferman"}],"ec_funded":1,"publist_id":"7197"},{"publist_id":"6991","author":[{"full_name":"Miklosi, Andras","first_name":"Andras","last_name":"Miklosi"},{"last_name":"Del Favero","first_name":"Giorgia","full_name":"Del Favero, Giorgia"},{"full_name":"Bulat, Tanja","last_name":"Bulat","first_name":"Tanja"},{"full_name":"Höger, Harald","first_name":"Harald","last_name":"Höger"},{"first_name":"Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi"},{"first_name":"Doris","last_name":"Marko","full_name":"Marko, Doris"},{"last_name":"Lubec","first_name":"Gert","full_name":"Lubec, Gert"}],"date_updated":"2023-09-19T09:58:11Z","date_created":"2018-12-11T11:48:02Z","volume":55,"year":"2018","publication_status":"published","department":[{"_id":"RySh"}],"publisher":"Springer","month":"06","doi":"10.1007/s12035-017-0688-y","language":[{"iso":"eng"}],"external_id":{"isi":["000431991500025"]},"isi":1,"quality_controlled":"1","abstract":[{"lang":"eng","text":"Although dopamine receptors D1 and D2 play key roles in hippocampal function, their synaptic localization within the hippocampus has not been fully elucidated. In order to understand precise functions of pre- or postsynaptic dopamine receptors (DRs), the development of protocols to differentiate pre- and postsynaptic DRs is essential. So far, most studies on determination and quantification of DRs did not discriminate between subsynaptic localization. Therefore, the aim of the study was to generate a robust workflow for the localization of DRs. This work provides the basis for future work on hippocampal DRs, in light that DRs may have different functions at pre- or postsynaptic sites. Synaptosomes from rat hippocampi isolated by a sucrose gradient protocol were prepared for super-resolution direct stochastic optical reconstruction microscopy (dSTORM) using Bassoon as a presynaptic zone and Homer1 as postsynaptic density marker. Direct labeling of primary validated antibodies against dopamine receptors D1 (D1R) and D2 (D2R) with Alexa Fluor 594 enabled unequivocal assignment of D1R and D2R to both, pre- and postsynaptic sites. D1R immunoreactivity clusters were observed within the presynaptic active zone as well as at perisynaptic sites at the edge of the presynaptic active zone. The results may be useful for the interpretation of previous studies and the design of future work on DRs in the hippocampus. Moreover, the reduction of the complexity of brain tissue by the use of synaptosomal preparations and dSTORM technology may represent a useful tool for synaptic localization of brain proteins."}],"issue":"6","type":"journal_article","oa_version":"None","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"705","title":"Super resolution microscopical localization of dopamine receptors 1 and 2 in rat hippocampal synaptosomes","status":"public","intvolume":" 55","day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2018-06-01T00:00:00Z","publication":"Molecular Neurobiology","citation":{"ama":"Miklosi A, Del Favero G, Bulat T, et al. Super resolution microscopical localization of dopamine receptors 1 and 2 in rat hippocampal synaptosomes. Molecular Neurobiology. 2018;55(6):4857 – 4869. doi:10.1007/s12035-017-0688-y","ista":"Miklosi A, Del Favero G, Bulat T, Höger H, Shigemoto R, Marko D, Lubec G. 2018. Super resolution microscopical localization of dopamine receptors 1 and 2 in rat hippocampal synaptosomes. Molecular Neurobiology. 55(6), 4857 – 4869.","ieee":"A. Miklosi et al., “Super resolution microscopical localization of dopamine receptors 1 and 2 in rat hippocampal synaptosomes,” Molecular Neurobiology, vol. 55, no. 6. Springer, pp. 4857 – 4869, 2018.","apa":"Miklosi, A., Del Favero, G., Bulat, T., Höger, H., Shigemoto, R., Marko, D., & Lubec, G. (2018). Super resolution microscopical localization of dopamine receptors 1 and 2 in rat hippocampal synaptosomes. Molecular Neurobiology. Springer. https://doi.org/10.1007/s12035-017-0688-y","mla":"Miklosi, Andras, et al. “Super Resolution Microscopical Localization of Dopamine Receptors 1 and 2 in Rat Hippocampal Synaptosomes.” Molecular Neurobiology, vol. 55, no. 6, Springer, 2018, pp. 4857 – 4869, doi:10.1007/s12035-017-0688-y.","short":"A. Miklosi, G. Del Favero, T. Bulat, H. Höger, R. Shigemoto, D. Marko, G. Lubec, Molecular Neurobiology 55 (2018) 4857 – 4869.","chicago":"Miklosi, Andras, Giorgia Del Favero, Tanja Bulat, Harald Höger, Ryuichi Shigemoto, Doris Marko, and Gert Lubec. “Super Resolution Microscopical Localization of Dopamine Receptors 1 and 2 in Rat Hippocampal Synaptosomes.” Molecular Neurobiology. Springer, 2018. https://doi.org/10.1007/s12035-017-0688-y."},"page":"4857 – 4869"},{"oa_version":"Published Version","_id":"148","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 174","title":"The Chara genome: Secondary complexity and implications for plant terrestrialization","status":"public","issue":"2","abstract":[{"lang":"eng","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."}],"type":"journal_article","date_published":"2018-07-12T00:00:00Z","citation":{"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.” Cell. Cell Press, 2018. https://doi.org/10.1016/j.cell.2018.06.033.","mla":"Nishiyama, Tomoaki, et al. “The Chara Genome: Secondary Complexity and Implications for Plant Terrestrialization.” Cell, vol. 174, no. 2, Cell Press, 2018, p. 448–464.e24, doi:10.1016/j.cell.2018.06.033.","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.","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.","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. Cell. Cell Press. https://doi.org/10.1016/j.cell.2018.06.033","ieee":"T. Nishiyama et al., “The Chara genome: Secondary complexity and implications for plant terrestrialization,” Cell, 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. Cell. 2018;174(2):448-464.e24. doi:10.1016/j.cell.2018.06.033"},"publication":"Cell","page":"448 - 464.e24","article_processing_charge":"No","day":"12","scopus_import":"1","author":[{"first_name":"Tomoaki","last_name":"Nishiyama","full_name":"Nishiyama, Tomoaki"},{"full_name":"Sakayama, Hidetoshi","last_name":"Sakayama","first_name":"Hidetoshi"},{"first_name":"Jan","last_name":"De Vries","full_name":"De Vries, Jan"},{"last_name":"Buschmann","first_name":"Henrik","full_name":"Buschmann, Henrik"},{"last_name":"Saint Marcoux","first_name":"Denis","full_name":"Saint Marcoux, Denis"},{"full_name":"Ullrich, Kristian","first_name":"Kristian","last_name":"Ullrich"},{"full_name":"Haas, Fabian","first_name":"Fabian","last_name":"Haas"},{"full_name":"Vanderstraeten, Lisa","first_name":"Lisa","last_name":"Vanderstraeten"},{"last_name":"Becker","first_name":"Dirk","full_name":"Becker, Dirk"},{"full_name":"Lang, Daniel","last_name":"Lang","first_name":"Daniel"},{"first_name":"Stanislav","last_name":"Vosolsobě","full_name":"Vosolsobě, Stanislav"},{"full_name":"Rombauts, Stephane","first_name":"Stephane","last_name":"Rombauts"},{"full_name":"Wilhelmsson, Per","first_name":"Per","last_name":"Wilhelmsson"},{"last_name":"Janitza","first_name":"Philipp","full_name":"Janitza, Philipp"},{"full_name":"Kern, Ramona","last_name":"Kern","first_name":"Ramona"},{"full_name":"Heyl, Alexander","first_name":"Alexander","last_name":"Heyl"},{"last_name":"Rümpler","first_name":"Florian","full_name":"Rümpler, Florian"},{"last_name":"Calderón Villalobos","first_name":"Luz","full_name":"Calderón Villalobos, Luz"},{"full_name":"Clay, John","first_name":"John","last_name":"Clay"},{"last_name":"Skokan","first_name":"Roman","full_name":"Skokan, Roman"},{"full_name":"Toyoda, Atsushi","first_name":"Atsushi","last_name":"Toyoda"},{"last_name":"Suzuki","first_name":"Yutaka","full_name":"Suzuki, Yutaka"},{"last_name":"Kagoshima","first_name":"Hiroshi","full_name":"Kagoshima, Hiroshi"},{"last_name":"Schijlen","first_name":"Elio","full_name":"Schijlen, Elio"},{"full_name":"Tajeshwar, Navindra","last_name":"Tajeshwar","first_name":"Navindra"},{"last_name":"Catarino","first_name":"Bruno","full_name":"Catarino, Bruno"},{"full_name":"Hetherington, Alexander","last_name":"Hetherington","first_name":"Alexander"},{"full_name":"Saltykova, Assia","last_name":"Saltykova","first_name":"Assia"},{"last_name":"Bonnot","first_name":"Clemence","full_name":"Bonnot, Clemence"},{"first_name":"Holger","last_name":"Breuninger","full_name":"Breuninger, Holger"},{"full_name":"Symeonidi, Aikaterini","first_name":"Aikaterini","last_name":"Symeonidi"},{"full_name":"Radhakrishnan, Guru","first_name":"Guru","last_name":"Radhakrishnan"},{"full_name":"Van Nieuwerburgh, Filip","last_name":"Van Nieuwerburgh","first_name":"Filip"},{"first_name":"Dieter","last_name":"Deforce","full_name":"Deforce, Dieter"},{"full_name":"Chang, Caren","first_name":"Caren","last_name":"Chang"},{"first_name":"Kenneth","last_name":"Karol","full_name":"Karol, Kenneth"},{"full_name":"Hedrich, Rainer","last_name":"Hedrich","first_name":"Rainer"},{"full_name":"Ulvskov, Peter","first_name":"Peter","last_name":"Ulvskov"},{"full_name":"Glöckner, Gernot","last_name":"Glöckner","first_name":"Gernot"},{"full_name":"Delwiche, Charles","first_name":"Charles","last_name":"Delwiche"},{"full_name":"Petrášek, Jan","last_name":"Petrášek","first_name":"Jan"},{"full_name":"Van De Peer, Yves","first_name":"Yves","last_name":"Van De Peer"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí"},{"full_name":"Beilby, Mary","first_name":"Mary","last_name":"Beilby"},{"last_name":"Dolan","first_name":"Liam","full_name":"Dolan, Liam"},{"last_name":"Kohara","first_name":"Yuji","full_name":"Kohara, Yuji"},{"full_name":"Sugano, Sumio","last_name":"Sugano","first_name":"Sumio"},{"last_name":"Fujiyama","first_name":"Asao","full_name":"Fujiyama, Asao"},{"first_name":"Pierre Marc","last_name":"Delaux","full_name":"Delaux, Pierre Marc"},{"full_name":"Quint, Marcel","last_name":"Quint","first_name":"Marcel"},{"last_name":"Theissen","first_name":"Gunter","full_name":"Theissen, Gunter"},{"first_name":"Martin","last_name":"Hagemann","full_name":"Hagemann, Martin"},{"last_name":"Harholt","first_name":"Jesper","full_name":"Harholt, Jesper"},{"full_name":"Dunand, Christophe","first_name":"Christophe","last_name":"Dunand"},{"last_name":"Zachgo","first_name":"Sabine","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"},{"first_name":"Sven B","last_name":"Gould","full_name":"Gould, Sven B"},{"full_name":"Rensing, Stefan","last_name":"Rensing","first_name":"Stefan"}],"volume":174,"date_created":"2018-12-11T11:44:53Z","date_updated":"2023-09-19T10:02:47Z","pmid":1,"year":"2018","acknowledgement":"In-Data-Review","department":[{"_id":"JiFr"}],"publisher":"Cell Press","publication_status":"published","ec_funded":1,"publist_id":"7774","doi":"10.1016/j.cell.2018.06.033","language":[{"iso":"eng"}],"external_id":{"pmid":["30007417"],"isi":["000438482800019"]},"oa":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30007417","open_access":"1"}],"project":[{"call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985"}],"isi":1,"quality_controlled":"1","month":"07"},{"citation":{"ieee":"N. Cavallari, C. Nibau, A. Fuchs, D. Dadarou, A. Barta, and J. Doonan, “The cyclin‐dependent kinase G group defines a thermo‐sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU 2AF 65A,” The Plant Journal, vol. 94, no. 6. Wiley, pp. 1010–1022, 2018.","apa":"Cavallari, N., Nibau, C., Fuchs, A., Dadarou, D., Barta, A., & Doonan, J. (2018). The cyclin‐dependent kinase G group defines a thermo‐sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU 2AF 65A. The Plant Journal. Wiley. https://doi.org/10.1111/tpj.13914","ista":"Cavallari N, Nibau C, Fuchs A, Dadarou D, Barta A, Doonan J. 2018. The cyclin‐dependent kinase G group defines a thermo‐sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU 2AF 65A. The Plant Journal. 94(6), 1010–1022.","ama":"Cavallari N, Nibau C, Fuchs A, Dadarou D, Barta A, Doonan J. The cyclin‐dependent kinase G group defines a thermo‐sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU 2AF 65A. The Plant Journal. 2018;94(6):1010-1022. doi:10.1111/tpj.13914","chicago":"Cavallari, Nicola, Candida Nibau, Armin Fuchs, Despoina Dadarou, Andrea Barta, and John Doonan. “The Cyclin‐dependent Kinase G Group Defines a Thermo‐sensitive Alternative Splicing Circuit Modulating the Expression of Arabidopsis ATU 2AF 65A.” The Plant Journal. Wiley, 2018. https://doi.org/10.1111/tpj.13914.","short":"N. Cavallari, C. Nibau, A. Fuchs, D. Dadarou, A. Barta, J. Doonan, The Plant Journal 94 (2018) 1010–1022.","mla":"Cavallari, Nicola, et al. “The Cyclin‐dependent Kinase G Group Defines a Thermo‐sensitive Alternative Splicing Circuit Modulating the Expression of Arabidopsis ATU 2AF 65A.” The Plant Journal, vol. 94, no. 6, Wiley, 2018, pp. 1010–22, doi:10.1111/tpj.13914."},"publication":"The Plant Journal","page":"1010 - 1022","date_published":"2018-06-01T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"01","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"403","intvolume":" 94","title":"The cyclin‐dependent kinase G group defines a thermo‐sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU 2AF 65A","status":"public","ddc":["580"],"file":[{"file_id":"5934","relation":"main_file","checksum":"d9d3ad3215ac0e581731443fca312266","date_updated":"2020-07-14T12:46:22Z","date_created":"2019-02-06T11:40:54Z","access_level":"open_access","file_name":"2018_PlantJourn_Cavallari.pdf","creator":"dernst","file_size":1543354,"content_type":"application/pdf"}],"oa_version":"Published Version","type":"journal_article","issue":"6","abstract":[{"text":"The ability to adapt growth and development to temperature variations is crucial to generate plant varieties resilient to predicted temperature changes. However, the mechanisms underlying plant response to progressive increases in temperature have just started to be elucidated. Here, we report that the Cyclin-dependent Kinase G1 (CDKG1) is a central element in a thermo-sensitive mRNA splicing cascade that transduces changes in ambient temperature into differential expression of the fundamental spliceosome component, ATU2AF65A. CDKG1 is alternatively spliced in a temperature-dependent manner. We found that this process is partly dependent on both the Cyclin-dependent Kinase G2 (CDKG2) and the interacting co-factor CYCLIN L1 resulting in two distinct messenger RNAs. Relative abundance of both CDKG1 transcripts correlates with ambient temperature and possibly with different expression levels of the associated protein isoforms. Both CDKG1 alternative transcripts are necessary to fully complement the expression of ATU2AF65A across the temperature range. Our data support a previously unidentified temperature-dependent mechanism based on the alternative splicing of CDKG1 and regulated by CDKG2 and CYCLIN L1. We propose that changes in ambient temperature affect the relative abundance of CDKG1 transcripts and this in turn translates into differential CDKG1 protein expression coordinating the alternative splicing of ATU2AF65A. This article is protected by copyright. All rights reserved.","lang":"eng"}],"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"},"external_id":{"isi":["000434365500008"]},"oa":1,"quality_controlled":"1","isi":1,"doi":"10.1111/tpj.13914","language":[{"iso":"eng"}],"month":"06","year":"2018","acknowledgement":"CN, DD and JHD were funded by the BBSRC (grant number BB/M009459/1). NC was funded by the VIPS Program of the Austrian Federal Ministry of Science and Research and the City of Vienna. AB and AF were supported by the Austrian Science Fund (FWF) [DK W1207; SFB RNAreg F43-P10]","department":[{"_id":"EvBe"}],"publisher":"Wiley","publication_status":"published","author":[{"last_name":"Cavallari","first_name":"Nicola","id":"457160E6-F248-11E8-B48F-1D18A9856A87","full_name":"Cavallari, Nicola"},{"first_name":"Candida","last_name":"Nibau","full_name":"Nibau, Candida"},{"full_name":"Fuchs, Armin","last_name":"Fuchs","first_name":"Armin"},{"first_name":"Despoina","last_name":"Dadarou","full_name":"Dadarou, Despoina"},{"last_name":"Barta","first_name":"Andrea","full_name":"Barta, Andrea"},{"last_name":"Doonan","first_name":"John","full_name":"Doonan, John"}],"volume":94,"date_updated":"2023-09-19T10:07:08Z","date_created":"2018-12-11T11:46:17Z","publist_id":"7426","file_date_updated":"2020-07-14T12:46:22Z"}]