[{"article_processing_charge":"No","external_id":{"isi":["000446394503031"]},"author":[{"first_name":"Maria","full_name":"Pozzi, Maria","last_name":"Pozzi"},{"first_name":"Eder","id":"3FB91342-F248-11E8-B48F-1D18A9856A87","last_name":"Miguel Villalba","full_name":"Miguel Villalba, Eder","orcid":"0000-0001-5665-0430"},{"last_name":"Deimel","full_name":"Deimel, Raphael","first_name":"Raphael"},{"first_name":"Monica","last_name":"Malvezzi","full_name":"Malvezzi, Monica"},{"last_name":"Bickel","full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Brock","full_name":"Brock, Oliver","first_name":"Oliver"},{"first_name":"Domenico","full_name":"Prattichizzo, Domenico","last_name":"Prattichizzo"}],"title":"Efficient FEM-based simulation of soft robots modeled as kinematic chains","department":[{"_id":"BeBi"}],"citation":{"ista":"Pozzi M, Miguel Villalba E, Deimel R, Malvezzi M, Bickel B, Brock O, Prattichizzo D. 2018. Efficient FEM-based simulation of soft robots modeled as kinematic chains. ICRA: International Conference on Robotics and Automation, 8461106.","chicago":"Pozzi, Maria, Eder Miguel Villalba, Raphael Deimel, Monica Malvezzi, Bernd Bickel, Oliver Brock, and Domenico Prattichizzo. “Efficient FEM-Based Simulation of Soft Robots Modeled as Kinematic Chains.” IEEE, 2018. https://doi.org/10.1109/icra.2018.8461106.","apa":"Pozzi, M., Miguel Villalba, E., Deimel, R., Malvezzi, M., Bickel, B., Brock, O., & Prattichizzo, D. (2018). Efficient FEM-based simulation of soft robots modeled as kinematic chains. Presented at the ICRA: International Conference on Robotics and Automation, Brisbane, Australia: IEEE. https://doi.org/10.1109/icra.2018.8461106","ama":"Pozzi M, Miguel Villalba E, Deimel R, et al. Efficient FEM-based simulation of soft robots modeled as kinematic chains. In: IEEE; 2018. doi:10.1109/icra.2018.8461106","short":"M. Pozzi, E. Miguel Villalba, R. Deimel, M. Malvezzi, B. Bickel, O. Brock, D. Prattichizzo, in:, IEEE, 2018.","ieee":"M. Pozzi et al., “Efficient FEM-based simulation of soft robots modeled as kinematic chains,” presented at the ICRA: International Conference on Robotics and Automation, Brisbane, Australia, 2018.","mla":"Pozzi, Maria, et al. Efficient FEM-Based Simulation of Soft Robots Modeled as Kinematic Chains. 8461106, IEEE, 2018, doi:10.1109/icra.2018.8461106."},"date_updated":"2023-09-19T14:49:03Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","conference":{"name":"ICRA: International Conference on Robotics and Automation","start_date":"2018-05-21","location":"Brisbane, Australia","end_date":"2018-05-25"},"type":"conference","status":"public","_id":"6195","article_number":"8461106","date_created":"2019-04-04T09:50:38Z","doi":"10.1109/icra.2018.8461106","date_published":"2018-09-10T00:00:00Z","year":"2018","publication_status":"published","isi":1,"publication_identifier":{"isbn":["9781538630815"]},"language":[{"iso":"eng"}],"day":"10","scopus_import":"1","publisher":"IEEE","quality_controlled":"1","month":"09","abstract":[{"lang":"eng","text":"In the context of robotic manipulation and grasping, the shift from a view that is static (force closure of a single posture) and contact-deprived (only contact for force closure is allowed, everything else is obstacle) towards a view that is dynamic and contact-rich (soft manipulation) has led to an increased interest in soft hands. These hands can easily exploit environmental constraints and object surfaces without risk, and safely interact with humans, but present also some challenges. Designing them is difficult, as well as predicting, modelling, and “programming” their interactions with the objects and the environment. This paper tackles the problem of simulating them in a fast and effective way, leveraging on novel and existing simulation technologies. We present a triple-layered simulation framework where dynamic properties such as stiffness are determined from slow but accurate FEM simulation data once, and then condensed into a lumped parameter model that can be used to fast simulate soft fingers and soft hands. We apply our approach to the simulation of soft pneumatic fingers."}],"oa_version":"None"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Park, Sunoo, Albert Kwon, Georg Fuchsbauer, Peter Gazi, Joel F Alwen, and Krzysztof Z Pietrzak. “SpaceMint: A Cryptocurrency Based on Proofs of Space.” In 22nd International Conference on Financial Cryptography and Data Security, 10957:480–99. Springer Nature, 2018. https://doi.org/10.1007/978-3-662-58387-6_26.","ista":"Park S, Kwon A, Fuchsbauer G, Gazi P, Alwen JF, Pietrzak KZ. 2018. SpaceMint: A cryptocurrency based on proofs of space. 22nd International Conference on Financial Cryptography and Data Security. FC: Financial Cryptography and Data Security, LNCS, vol. 10957, 480–499.","mla":"Park, Sunoo, et al. “SpaceMint: A Cryptocurrency Based on Proofs of Space.” 22nd International Conference on Financial Cryptography and Data Security, vol. 10957, Springer Nature, 2018, pp. 480–99, doi:10.1007/978-3-662-58387-6_26.","apa":"Park, S., Kwon, A., Fuchsbauer, G., Gazi, P., Alwen, J. F., & Pietrzak, K. Z. (2018). SpaceMint: A cryptocurrency based on proofs of space. In 22nd International Conference on Financial Cryptography and Data Security (Vol. 10957, pp. 480–499). Nieuwpoort, Curacao: Springer Nature. https://doi.org/10.1007/978-3-662-58387-6_26","ama":"Park S, Kwon A, Fuchsbauer G, Gazi P, Alwen JF, Pietrzak KZ. SpaceMint: A cryptocurrency based on proofs of space. In: 22nd International Conference on Financial Cryptography and Data Security. Vol 10957. Springer Nature; 2018:480-499. doi:10.1007/978-3-662-58387-6_26","short":"S. Park, A. Kwon, G. Fuchsbauer, P. Gazi, J.F. Alwen, K.Z. Pietrzak, in:, 22nd International Conference on Financial Cryptography and Data Security, Springer Nature, 2018, pp. 480–499.","ieee":"S. Park, A. Kwon, G. Fuchsbauer, P. Gazi, J. F. Alwen, and K. Z. Pietrzak, “SpaceMint: A cryptocurrency based on proofs of space,” in 22nd International Conference on Financial Cryptography and Data Security, Nieuwpoort, Curacao, 2018, vol. 10957, pp. 480–499."},"title":"SpaceMint: A cryptocurrency based on proofs of space","author":[{"last_name":"Park","full_name":"Park, Sunoo","first_name":"Sunoo"},{"last_name":"Kwon","full_name":"Kwon, Albert","first_name":"Albert"},{"first_name":"Georg","id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","full_name":"Fuchsbauer, Georg","last_name":"Fuchsbauer"},{"full_name":"Gazi, Peter","last_name":"Gazi","id":"3E0BFE38-F248-11E8-B48F-1D18A9856A87","first_name":"Peter"},{"full_name":"Alwen, Joel F","last_name":"Alwen","first_name":"Joel F","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak","first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"isi":["000540656400026"]},"project":[{"grant_number":"682815","name":"Teaching Old Crypto New Tricks","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"day":"07","publication":"22nd International Conference on Financial Cryptography and Data Security","isi":1,"year":"2018","doi":"10.1007/978-3-662-58387-6_26","date_published":"2018-12-07T00:00:00Z","date_created":"2019-10-14T06:35:38Z","page":"480-499","quality_controlled":"1","publisher":"Springer Nature","oa":1,"date_updated":"2023-09-19T15:02:13Z","department":[{"_id":"KrPi"}],"_id":"6941","status":"public","type":"conference","conference":{"name":"FC: Financial Cryptography and Data Security","start_date":"2018-02-26","location":"Nieuwpoort, Curacao","end_date":"2018-03-02"},"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9783662583869","9783662583876"],"eissn":["1611-3349"],"issn":["0302-9743"]},"publication_status":"published","volume":10957,"ec_funded":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Bitcoin has become the most successful cryptocurrency ever deployed, and its most distinctive feature is that it is decentralized. Its underlying protocol (Nakamoto consensus) achieves this by using proof of work, which has the drawback that it causes the consumption of vast amounts of energy to maintain the ledger. Moreover, Bitcoin mining dynamics have become less distributed over time.\r\n\r\nTowards addressing these issues, we propose SpaceMint, a cryptocurrency based on proofs of space instead of proofs of work. Miners in SpaceMint dedicate disk space rather than computation. We argue that SpaceMint’s design solves or alleviates several of Bitcoin’s issues: most notably, its large energy consumption. SpaceMint also rewards smaller miners fairly according to their contribution to the network, thus incentivizing more distributed participation.\r\n\r\nThis paper adapts proof of space to enable its use in cryptocurrency, studies the attacks that can arise against a Bitcoin-like blockchain that uses proof of space, and proposes a new blockchain format and transaction types to address these attacks. Our prototype shows that initializing 1 TB for mining takes about a day (a one-off setup cost), and miners spend on average just a fraction of a second per block mined. Finally, we provide a game-theoretic analysis modeling SpaceMint as an extensive game (the canonical game-theoretic notion for games that take place over time) and show that this stylized game satisfies a strong equilibrium notion, thereby arguing for SpaceMint ’s stability and consensus."}],"month":"12","intvolume":" 10957","scopus_import":"1","alternative_title":["LNCS"],"main_file_link":[{"url":"https://eprint.iacr.org/2015/528","open_access":"1"}]},{"file_date_updated":"2020-07-14T12:47:32Z","department":[{"_id":"MiSi"}],"ddc":["570"],"date_updated":"2023-09-19T14:52:08Z","status":"public","type":"journal_article","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"_id":"6497","volume":2015,"issue":"7","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","file":[{"checksum":"86ae5331f9bfced9a6358a790a04bef4","file_id":"6498","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2019-05-28T12:40:05Z","file_name":"2018_rupress_Moalli.pdf","creator":"kschuh","date_updated":"2020-07-14T12:47:32Z","file_size":3841660}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1540-9538"],"issn":["0022-1007"]},"publication_status":"published","month":"06","intvolume":" 2015","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"T cells are actively scanning pMHC-presenting cells in lymphoid organs and nonlymphoid tissues (NLTs) with divergent topologies and confinement. How the T cell actomyosin cytoskeleton facilitates this task in distinct environments is incompletely understood. Here, we show that lack of Myosin IXb (Myo9b), a negative regulator of the small GTPase Rho, led to increased Rho-GTP levels and cell surface stiffness in primary T cells. Nonetheless, intravital imaging revealed robust motility of Myo9b−/− CD8+ T cells in lymphoid tissue and similar expansion and differentiation during immune responses. In contrast, accumulation of Myo9b−/− CD8+ T cells in NLTs was strongly impaired. Specifically, Myo9b was required for T cell crossing of basement membranes, such as those which are present between dermis and epidermis. As consequence, Myo9b−/− CD8+ T cells showed impaired control of skin infections. In sum, we show that Myo9b is critical for the CD8+ T cell adaptation from lymphoid to NLT surveillance and the establishment of protective tissue–resident T cell populations."}],"title":"The Rho regulator Myosin IXb enables nonlymphoid tissue seeding of protective CD8+T cells","author":[{"first_name":"Federica","last_name":"Moalli","full_name":"Moalli, Federica"},{"first_name":"Xenia","full_name":"Ficht, Xenia","last_name":"Ficht"},{"first_name":"Philipp","last_name":"Germann","full_name":"Germann, Philipp"},{"full_name":"Vladymyrov, Mykhailo","last_name":"Vladymyrov","first_name":"Mykhailo"},{"first_name":"Bettina","full_name":"Stolp, Bettina","last_name":"Stolp"},{"full_name":"de Vries, Ingrid","last_name":"de Vries","first_name":"Ingrid","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ruth","full_name":"Lyck, Ruth","last_name":"Lyck"},{"last_name":"Balmer","full_name":"Balmer, Jasmin","first_name":"Jasmin"},{"first_name":"Amleto","full_name":"Fiocchi, Amleto","last_name":"Fiocchi"},{"full_name":"Kreutzfeldt, Mario","last_name":"Kreutzfeldt","first_name":"Mario"},{"full_name":"Merkler, Doron","last_name":"Merkler","first_name":"Doron"},{"last_name":"Iannacone","full_name":"Iannacone, Matteo","first_name":"Matteo"},{"first_name":"Akitaka","last_name":"Ariga","full_name":"Ariga, Akitaka"},{"first_name":"Michael H.","last_name":"Stoffel","full_name":"Stoffel, Michael H."},{"last_name":"Sharpe","full_name":"Sharpe, James","first_name":"James"},{"first_name":"Martin","last_name":"Bähler","full_name":"Bähler, Martin"},{"last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K"},{"first_name":"Alba","full_name":"Diz-Muñoz, Alba","last_name":"Diz-Muñoz"},{"first_name":"Jens V.","last_name":"Stein","full_name":"Stein, Jens V."}],"article_processing_charge":"No","external_id":{"isi":["000440822900011"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Moalli F, Ficht X, Germann P, Vladymyrov M, Stolp B, de Vries I, Lyck R, Balmer J, Fiocchi A, Kreutzfeldt M, Merkler D, Iannacone M, Ariga A, Stoffel MH, Sharpe J, Bähler M, Sixt MK, Diz-Muñoz A, Stein JV. 2018. The Rho regulator Myosin IXb enables nonlymphoid tissue seeding of protective CD8+T cells. The Journal of Experimental Medicine. 2015(7), 1869–1890.","chicago":"Moalli, Federica, Xenia Ficht, Philipp Germann, Mykhailo Vladymyrov, Bettina Stolp, Ingrid de Vries, Ruth Lyck, et al. “The Rho Regulator Myosin IXb Enables Nonlymphoid Tissue Seeding of Protective CD8+T Cells.” The Journal of Experimental Medicine. Rockefeller University Press, 2018. https://doi.org/10.1084/jem.20170896.","apa":"Moalli, F., Ficht, X., Germann, P., Vladymyrov, M., Stolp, B., de Vries, I., … Stein, J. V. (2018). The Rho regulator Myosin IXb enables nonlymphoid tissue seeding of protective CD8+T cells. The Journal of Experimental Medicine. Rockefeller University Press. https://doi.org/10.1084/jem.20170896","ama":"Moalli F, Ficht X, Germann P, et al. The Rho regulator Myosin IXb enables nonlymphoid tissue seeding of protective CD8+T cells. The Journal of Experimental Medicine. 2018;2015(7):1869–1890. doi:10.1084/jem.20170896","ieee":"F. Moalli et al., “The Rho regulator Myosin IXb enables nonlymphoid tissue seeding of protective CD8+T cells,” The Journal of Experimental Medicine, vol. 2015, no. 7. Rockefeller University Press, pp. 1869–1890, 2018.","short":"F. Moalli, X. Ficht, P. Germann, M. Vladymyrov, B. Stolp, I. de Vries, R. Lyck, J. Balmer, A. Fiocchi, M. Kreutzfeldt, D. Merkler, M. Iannacone, A. Ariga, M.H. Stoffel, J. Sharpe, M. Bähler, M.K. Sixt, A. Diz-Muñoz, J.V. Stein, The Journal of Experimental Medicine 2015 (2018) 1869–1890.","mla":"Moalli, Federica, et al. “The Rho Regulator Myosin IXb Enables Nonlymphoid Tissue Seeding of Protective CD8+T Cells.” The Journal of Experimental Medicine, vol. 2015, no. 7, Rockefeller University Press, 2018, pp. 1869–1890, doi:10.1084/jem.20170896."},"date_published":"2018-06-06T00:00:00Z","doi":"10.1084/jem.20170896","date_created":"2019-05-28T12:36:47Z","page":"1869–1890","day":"06","publication":"The Journal of Experimental Medicine","has_accepted_license":"1","isi":1,"year":"2018","publisher":"Rockefeller University Press","quality_controlled":"1","oa":1},{"publisher":"EMBO","quality_controlled":"1","oa":1,"isi":1,"has_accepted_license":"1","year":"2018","day":"01","publication":"EMBO reports","date_published":"2018-09-01T00:00:00Z","doi":"10.15252/embr.201845836","date_created":"2019-05-28T13:16:08Z","article_number":"e45836","citation":{"chicago":"Truckenbrodt, Sven M, Manuel Maidorn, Dagmar Crzan, Hanna Wildhagen, Selda Kabatas, and Silvio O Rizzoli. “X10 Expansion Microscopy Enables 25‐nm Resolution on Conventional Microscopes.” EMBO Reports. EMBO, 2018. https://doi.org/10.15252/embr.201845836.","ista":"Truckenbrodt SM, Maidorn M, Crzan D, Wildhagen H, Kabatas S, Rizzoli SO. 2018. X10 expansion microscopy enables 25‐nm resolution on conventional microscopes. EMBO reports. 19(9), e45836.","mla":"Truckenbrodt, Sven M., et al. “X10 Expansion Microscopy Enables 25‐nm Resolution on Conventional Microscopes.” EMBO Reports, vol. 19, no. 9, e45836, EMBO, 2018, doi:10.15252/embr.201845836.","ieee":"S. M. Truckenbrodt, M. Maidorn, D. Crzan, H. Wildhagen, S. Kabatas, and S. O. Rizzoli, “X10 expansion microscopy enables 25‐nm resolution on conventional microscopes,” EMBO reports, vol. 19, no. 9. EMBO, 2018.","short":"S.M. Truckenbrodt, M. Maidorn, D. Crzan, H. Wildhagen, S. Kabatas, S.O. Rizzoli, EMBO Reports 19 (2018).","apa":"Truckenbrodt, S. M., Maidorn, M., Crzan, D., Wildhagen, H., Kabatas, S., & Rizzoli, S. O. (2018). X10 expansion microscopy enables 25‐nm resolution on conventional microscopes. EMBO Reports. EMBO. https://doi.org/10.15252/embr.201845836","ama":"Truckenbrodt SM, Maidorn M, Crzan D, Wildhagen H, Kabatas S, Rizzoli SO. X10 expansion microscopy enables 25‐nm resolution on conventional microscopes. EMBO reports. 2018;19(9). doi:10.15252/embr.201845836"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"id":"45812BD4-F248-11E8-B48F-1D18A9856A87","first_name":"Sven M","last_name":"Truckenbrodt","full_name":"Truckenbrodt, Sven M"},{"full_name":"Maidorn, Manuel","last_name":"Maidorn","first_name":"Manuel"},{"full_name":"Crzan, Dagmar","last_name":"Crzan","first_name":"Dagmar"},{"first_name":"Hanna","last_name":"Wildhagen","full_name":"Wildhagen, Hanna"},{"last_name":"Kabatas","full_name":"Kabatas, Selda","first_name":"Selda"},{"last_name":"Rizzoli","full_name":"Rizzoli, Silvio O","first_name":"Silvio O"}],"external_id":{"isi":["000443682200009"]},"article_processing_charge":"No","title":"X10 expansion microscopy enables 25‐nm resolution on conventional microscopes","abstract":[{"lang":"eng","text":"Expansion microscopy is a recently introduced imaging technique that achieves super‐resolution through physically expanding the specimen by ~4×, after embedding into a swellable gel. The resolution attained is, correspondingly, approximately fourfold better than the diffraction limit, or ~70 nm. This is a major improvement over conventional microscopy, but still lags behind modern STED or STORM setups, whose resolution can reach 20–30 nm. We addressed this issue here by introducing an improved gel recipe that enables an expansion factor of ~10× in each dimension, which corresponds to an expansion of the sample volume by more than 1,000‐fold. Our protocol, which we termed X10 microscopy, achieves a resolution of 25–30 nm on conventional epifluorescence microscopes. X10 provides multi‐color images similar or even superior to those produced with more challenging methods, such as STED, STORM, and iterative expansion microscopy (iExM). X10 is therefore the cheapest and easiest option for high‐quality super‐resolution imaging currently available. X10 should be usable in any laboratory, irrespective of the machinery owned or of the technical knowledge."}],"oa_version":"Published Version","scopus_import":"1","month":"09","intvolume":" 19","publication_identifier":{"issn":["1469-221X"],"eissn":["1469-3178"]},"publication_status":"published","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"6ec90abc637f09cca3a7b6424d7e7a26","file_id":"6500","creator":"kschuh","file_size":2005572,"date_updated":"2020-07-14T12:47:32Z","file_name":"2018_embo_Truckenbrodt.pdf","date_created":"2019-05-28T13:17:19Z"}],"language":[{"iso":"eng"}],"volume":19,"issue":"9","license":"https://creativecommons.org/licenses/by/4.0/","_id":"6499","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","date_updated":"2023-09-19T14:52:32Z","ddc":["580"],"department":[{"_id":"JoDa"}],"file_date_updated":"2020-07-14T12:47:32Z"},{"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1704.04947","open_access":"1"}],"quality_controlled":"1","publisher":"ACM","month":"01","abstract":[{"text":"Population protocols are a popular model of distributed computing, in which n agents with limited local state interact randomly, and cooperate to collectively compute global predicates. Inspired by recent developments in DNA programming, an extensive series of papers, across different communities, has examined the computability and complexity characteristics of this model. Majority, or consensus, is a central task in this model, in which agents need to collectively reach a decision as to which one of two states A or B had a higher initial count. Two metrics are important: the time that a protocol requires to stabilize to an output decision, and the state space size that each agent requires to do so. It is known that majority requires Ω(log log n) states per agent to allow for fast (poly-logarithmic time) stabilization, and that O(log2 n) states are sufficient. Thus, there is an exponential gap between the space upper and lower bounds for this problem. This paper addresses this question.\r\n\r\nOn the negative side, we provide a new lower bound of Ω(log n) states for any protocol which stabilizes in O(n1–c) expected time, for any constant c > 0. This result is conditional on monotonicity and output assumptions, satisfied by all known protocols. Technically, it represents a departure from previous lower bounds, in that it does not rely on the existence of dense configurations. Instead, we introduce a new generalized surgery technique to prove the existence of incorrect executions for any algorithm which would contradict the lower bound. Subsequently, our lower bound also applies to general initial configurations, including ones with a leader. On the positive side, we give a new algorithm for majority which uses O(log n) states, and stabilizes in O(log2 n) expected time. Central to the algorithm is a new leaderless phase clock technique, which allows agents to synchronize in phases of Θ(n log n) consecutive interactions using O(log n) states per agent, exploiting a new connection between population protocols and power-of-two-choices load balancing mechanisms. We also employ our phase clock to build a leader election algorithm with a state space of size O(log n), which stabilizes in O(log2 n) expected time.","lang":"eng"}],"oa_version":"Preprint","page":"2221-2239","date_created":"2019-11-26T15:10:55Z","date_published":"2018-01-30T00:00:00Z","doi":"10.1137/1.9781611975031.144","year":"2018","publication_status":"published","isi":1,"publication_identifier":{"isbn":["9781611975031"]},"publication":"Proceedings of the 29th Annual ACM-SIAM Symposium on Discrete Algorithms","language":[{"iso":"eng"}],"day":"30","conference":{"end_date":"2018-01-10","location":"New Orleans, LA, United States","start_date":"2018-01-07","name":"SODA: Symposium on Discrete Algorithms"},"type":"conference","status":"public","_id":"7123","article_processing_charge":"No","external_id":{"isi":["000483921200145"],"arxiv":["1704.04947"]},"author":[{"first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian"},{"first_name":"James","full_name":"Aspnes, James","last_name":"Aspnes"},{"first_name":"Rati","last_name":"Gelashvili","full_name":"Gelashvili, Rati"}],"title":"Space-optimal majority in population protocols","department":[{"_id":"DaAl"}],"date_updated":"2023-09-19T15:03:16Z","citation":{"ista":"Alistarh D-A, Aspnes J, Gelashvili R. 2018. Space-optimal majority in population protocols. Proceedings of the 29th Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms, 2221–2239.","chicago":"Alistarh, Dan-Adrian, James Aspnes, and Rati Gelashvili. “Space-Optimal Majority in Population Protocols.” In Proceedings of the 29th Annual ACM-SIAM Symposium on Discrete Algorithms, 2221–39. ACM, 2018. https://doi.org/10.1137/1.9781611975031.144.","short":"D.-A. Alistarh, J. Aspnes, R. Gelashvili, in:, Proceedings of the 29th Annual ACM-SIAM Symposium on Discrete Algorithms, ACM, 2018, pp. 2221–2239.","ieee":"D.-A. Alistarh, J. Aspnes, and R. Gelashvili, “Space-optimal majority in population protocols,” in Proceedings of the 29th Annual ACM-SIAM Symposium on Discrete Algorithms, New Orleans, LA, United States, 2018, pp. 2221–2239.","ama":"Alistarh D-A, Aspnes J, Gelashvili R. Space-optimal majority in population protocols. In: Proceedings of the 29th Annual ACM-SIAM Symposium on Discrete Algorithms. ACM; 2018:2221-2239. doi:10.1137/1.9781611975031.144","apa":"Alistarh, D.-A., Aspnes, J., & Gelashvili, R. (2018). Space-optimal majority in population protocols. In Proceedings of the 29th Annual ACM-SIAM Symposium on Discrete Algorithms (pp. 2221–2239). New Orleans, LA, United States: ACM. https://doi.org/10.1137/1.9781611975031.144","mla":"Alistarh, Dan-Adrian, et al. “Space-Optimal Majority in Population Protocols.” Proceedings of the 29th Annual ACM-SIAM Symposium on Discrete Algorithms, ACM, 2018, pp. 2221–39, doi:10.1137/1.9781611975031.144."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"related_material":{"record":[{"relation":"research_data","id":"9930","status":"public"}]},"issue":"4","volume":2,"publication_identifier":{"issn":["2056-3744"],"eissn":["2056-3744"]},"publication_status":"published","file":[{"file_size":764299,"date_updated":"2021-08-16T07:48:03Z","creator":"asandaue","file_name":"2018_EvolutionLetters_Westram.pdf","date_created":"2021-08-16T07:48:03Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"9918","checksum":"8524e72507d521416be3f8ccfcd5e3f5"}],"language":[{"iso":"eng"}],"month":"08","intvolume":" 2","abstract":[{"text":"Adaptive divergence and speciation may happen despite opposition by gene flow. Identifying the genomic basis underlying divergence with gene flow is a major task in evolutionary genomics. Most approaches (e.g., outlier scans) focus on genomic regions of high differentiation. However, not all genomic architectures potentially underlying divergence are expected to show extreme differentiation. Here, we develop an approach that combines hybrid zone analysis (i.e., focuses on spatial patterns of allele frequency change) with system-specific simulations to identify loci inconsistent with neutral evolution. We apply this to a genome-wide SNP set from an ideally suited study organism, the intertidal snail Littorina saxatilis, which shows primary divergence between ecotypes associated with different shore habitats. We detect many SNPs with clinal patterns, most of which are consistent with neutrality. Among non-neutral SNPs, most are located within three large putative inversions differentiating ecotypes. Many non-neutral SNPs show relatively low levels of differentiation. We discuss potential reasons for this pattern, including loose linkage to selected variants, polygenic adaptation and a component of balancing selection within populations (which may be expected for inversions). Our work is in line with theory predicting a role for inversions in divergence, and emphasizes that genomic regions contributing to divergence may not always be accessible with methods purely based on allele frequency differences. These conclusions call for approaches that take spatial patterns of allele frequency change into account in other systems.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"department":[{"_id":"BeVi"}],"file_date_updated":"2021-08-16T07:48:03Z","date_updated":"2023-09-19T15:08:25Z","ddc":["570"],"article_type":"letter_note","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"9917","page":"297-309","date_published":"2018-08-20T00:00:00Z","doi":"10.1002/evl3.74","date_created":"2021-08-16T07:45:38Z","has_accepted_license":"1","isi":1,"year":"2018","day":"20","publication":"Evolution Letters","publisher":"Wiley","quality_controlled":"1","oa":1,"acknowledgement":"We are very grateful to people who helped with fieldwork, snail processing, and DNA extractions, particularly Laura Brettell, Mårten Duvetorp, Juan Galindo, Anne-Lise Liabot and Irena Senčić. We would also like to thank Magnus Alm Rosenblad and Mats Töpel for their contribution to assembling the Littorina saxatilis genome, Carl André, Pasi Rastas, and Romain Villoutreix for discussion, and two anonymous reviewers for their helpful comments on the manuscript. We are grateful to RapidGenomics for library preparation and sequencing. We thank the Natural Environment Research Council, the European Research Council and the Swedish Research Councils VR and Formas (Linnaeus grant to the Centre for Marine Evolutionary Biology and Tage Erlander Guest Professorship) for funding. P.C. was funded by the University of Sheffield Vice-chancellor's India scholarship. R.F. is funded by the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement no. 706376. M. Raf. was supported by the Adlerbert Research Foundation.","author":[{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M","last_name":"Westram","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M"},{"full_name":"Rafajlović, Marina","last_name":"Rafajlović","first_name":"Marina"},{"first_name":"Pragya","full_name":"Chaube, Pragya","last_name":"Chaube"},{"first_name":"Rui","full_name":"Faria, Rui","last_name":"Faria"},{"full_name":"Larsson, Tomas","last_name":"Larsson","first_name":"Tomas"},{"first_name":"Marina","full_name":"Panova, Marina","last_name":"Panova"},{"first_name":"Mark","last_name":"Ravinet","full_name":"Ravinet, Mark"},{"last_name":"Blomberg","full_name":"Blomberg, Anders","first_name":"Anders"},{"first_name":"Bernhard","last_name":"Mehlig","full_name":"Mehlig, Bernhard"},{"first_name":"Kerstin","full_name":"Johannesson, Kerstin","last_name":"Johannesson"},{"last_name":"Butlin","full_name":"Butlin, Roger","first_name":"Roger"}],"external_id":{"isi":["000446774400004"],"pmid":["30283683"]},"article_processing_charge":"Yes","title":"Clines on the seashore: The genomic architecture underlying rapid divergence in the face of gene flow","citation":{"short":"A.M. Westram, M. Rafajlović, P. Chaube, R. Faria, T. Larsson, M. Panova, M. Ravinet, A. Blomberg, B. Mehlig, K. Johannesson, R. Butlin, Evolution Letters 2 (2018) 297–309.","ieee":"A. M. Westram et al., “Clines on the seashore: The genomic architecture underlying rapid divergence in the face of gene flow,” Evolution Letters, vol. 2, no. 4. Wiley, pp. 297–309, 2018.","apa":"Westram, A. M., Rafajlović, M., Chaube, P., Faria, R., Larsson, T., Panova, M., … Butlin, R. (2018). Clines on the seashore: The genomic architecture underlying rapid divergence in the face of gene flow. Evolution Letters. Wiley. https://doi.org/10.1002/evl3.74","ama":"Westram AM, Rafajlović M, Chaube P, et al. Clines on the seashore: The genomic architecture underlying rapid divergence in the face of gene flow. Evolution Letters. 2018;2(4):297-309. doi:10.1002/evl3.74","mla":"Westram, Anja M., et al. “Clines on the Seashore: The Genomic Architecture Underlying Rapid Divergence in the Face of Gene Flow.” Evolution Letters, vol. 2, no. 4, Wiley, 2018, pp. 297–309, doi:10.1002/evl3.74.","ista":"Westram AM, Rafajlović M, Chaube P, Faria R, Larsson T, Panova M, Ravinet M, Blomberg A, Mehlig B, Johannesson K, Butlin R. 2018. Clines on the seashore: The genomic architecture underlying rapid divergence in the face of gene flow. Evolution Letters. 2(4), 297–309.","chicago":"Westram, Anja M, Marina Rafajlović, Pragya Chaube, Rui Faria, Tomas Larsson, Marina Panova, Mark Ravinet, et al. “Clines on the Seashore: The Genomic Architecture Underlying Rapid Divergence in the Face of Gene Flow.” Evolution Letters. Wiley, 2018. https://doi.org/10.1002/evl3.74."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"acknowledgement":"The authors express a special thanks to Dr Richard Willan at the Museum and Art Gallery of the Northern Territory for guidance and support in the field, and to Carole Smadja for reading and commenting on the manuscript. The authors thank the Government of Western Australia Department of Parks and Wildlife (license no. 009254) and Fishery Research Division (exemption no. 2262) for assistance with permits. Khalid Belkhir modified the coalescent sampler msnsam for the specific needs of this project and Martin Hirsch helped to set up the ABC pipeline and to modify the summary statistic calculator mscalc. The authors are grateful to the Crafoord Foundation for supporting this project. R.K.B., A.M.W., and L.D. were supported by grants from the Natural Environment Research Council, R.K.B. and A.M.W. were also supported by the European Research Council and R.K.B. and L.D. by the Leverhulme Trust. M.M.R. was supported by Consejo Nacional de Ciencia y Tecnología and Secretaría de Educación Pública, Mexico. G.B. was supported by the Centre for Animal Movement Research (CAnMove) financed by a Linnaeus grant (No. 349-2007-8690) from the Swedish Research Council and Lund University.","publisher":"Wiley","quality_controlled":"1","oa":1,"isi":1,"has_accepted_license":"1","year":"2018","day":"13","publication":"Evolution Letters","page":"557-566","doi":"10.1002/evl3.85","date_published":"2018-12-13T00:00:00Z","date_created":"2021-08-16T07:30:00Z","citation":{"chicago":"Hollander, Johan, Mauricio Montaño-Rendón, Giuseppe Bianco, Xi Yang, Anja M Westram, Ludovic Duvaux, David G. Reid, and Roger K. Butlin. “Are Assortative Mating and Genital Divergence Driven by Reinforcement?” Evolution Letters. Wiley, 2018. https://doi.org/10.1002/evl3.85.","ista":"Hollander J, Montaño-Rendón M, Bianco G, Yang X, Westram AM, Duvaux L, Reid DG, Butlin RK. 2018. Are assortative mating and genital divergence driven by reinforcement? Evolution Letters. 2(6), 557–566.","mla":"Hollander, Johan, et al. “Are Assortative Mating and Genital Divergence Driven by Reinforcement?” Evolution Letters, vol. 2, no. 6, Wiley, 2018, pp. 557–66, doi:10.1002/evl3.85.","apa":"Hollander, J., Montaño-Rendón, M., Bianco, G., Yang, X., Westram, A. M., Duvaux, L., … Butlin, R. K. (2018). Are assortative mating and genital divergence driven by reinforcement? Evolution Letters. Wiley. https://doi.org/10.1002/evl3.85","ama":"Hollander J, Montaño-Rendón M, Bianco G, et al. Are assortative mating and genital divergence driven by reinforcement? Evolution Letters. 2018;2(6):557-566. doi:10.1002/evl3.85","short":"J. Hollander, M. Montaño-Rendón, G. Bianco, X. Yang, A.M. Westram, L. Duvaux, D.G. Reid, R.K. Butlin, Evolution Letters 2 (2018) 557–566.","ieee":"J. Hollander et al., “Are assortative mating and genital divergence driven by reinforcement?,” Evolution Letters, vol. 2, no. 6. Wiley, pp. 557–566, 2018."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"last_name":"Hollander","full_name":"Hollander, Johan","first_name":"Johan"},{"first_name":"Mauricio","full_name":"Montaño-Rendón, Mauricio","last_name":"Montaño-Rendón"},{"last_name":"Bianco","full_name":"Bianco, Giuseppe","first_name":"Giuseppe"},{"full_name":"Yang, Xi","last_name":"Yang","first_name":"Xi"},{"first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","last_name":"Westram"},{"first_name":"Ludovic","last_name":"Duvaux","full_name":"Duvaux, Ludovic"},{"first_name":"David G.","last_name":"Reid","full_name":"Reid, David G."},{"first_name":"Roger K.","last_name":"Butlin","full_name":"Butlin, Roger K."}],"article_processing_charge":"Yes","external_id":{"isi":["000452990000002"],"pmid":["30564439"]},"title":"Are assortative mating and genital divergence driven by reinforcement?","abstract":[{"lang":"eng","text":"The evolution of assortative mating is a key part of the speciation process. Stronger assortment, or greater divergence in mating traits, between species pairs with overlapping ranges is commonly observed, but possible causes of this pattern of reproductive character displacement are difficult to distinguish. We use a multidisciplinary approach to provide a rare example where it is possible to distinguish among hypotheses concerning the evolution of reproductive character displacement. We build on an earlier comparative analysis that illustrated a strong pattern of greater divergence in penis form between pairs of sister species with overlapping ranges than between allopatric sister-species pairs, in a large clade of marine gastropods (Littorinidae). We investigate both assortative mating and divergence in male genitalia in one of the sister-species pairs, discriminating among three contrasting processes each of which can generate a pattern of reproductive character displacement: reinforcement, reproductive interference and the Templeton effect. We demonstrate reproductive character displacement in assortative mating, but not in genital form between this pair of sister species and use demographic models to distinguish among the different processes. Our results support a model with no gene flow since secondary contact and thus favor reproductive interference as the cause of reproductive character displacement for mate choice, rather than reinforcement. High gene flow within species argues against the Templeton effect. Secondary contact appears to have had little impact on genital divergence."}],"pmid":1,"oa_version":"Published Version","month":"12","intvolume":" 2","publication_identifier":{"eissn":["2056-3744"],"issn":[" 2056-3744"]},"publication_status":"published","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"9916","checksum":"997a78ac41c809975ca69cbdea441f88","file_size":584606,"date_updated":"2021-08-16T07:37:28Z","creator":"asandaue","file_name":"2018_EvolutionLetters_Hollander.pdf","date_created":"2021-08-16T07:37:28Z"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"id":"9929","status":"public","relation":"research_data"}]},"volume":2,"issue":"6","_id":"9915","type":"journal_article","article_type":"letter_note","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","date_updated":"2023-09-19T15:08:53Z","ddc":["570"],"department":[{"_id":"BeVi"}],"file_date_updated":"2021-08-16T07:37:28Z"},{"publication":"Scientific Reports","day":"09","year":"2018","has_accepted_license":"1","isi":1,"date_created":"2020-10-06T16:33:37Z","doi":"10.1038/s41598-018-19947-1","date_published":"2018-02-09T00:00:00Z","oa":1,"publisher":"Springer Nature","quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Gregor C, Sidenstein SC, Andresen M, Sahl SJ, Danzl JG, Hell SW. 2018. Novel reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered from the bacterial photoreceptor YtvA. Scientific Reports. 8, 2724.","chicago":"Gregor, Carola, Sven C. Sidenstein, Martin Andresen, Steffen J. Sahl, Johann G Danzl, and Stefan W. Hell. “Novel Reversibly Switchable Fluorescent Proteins for RESOLFT and STED Nanoscopy Engineered from the Bacterial Photoreceptor YtvA.” Scientific Reports. Springer Nature, 2018. https://doi.org/10.1038/s41598-018-19947-1.","ieee":"C. Gregor, S. C. Sidenstein, M. Andresen, S. J. Sahl, J. G. Danzl, and S. W. Hell, “Novel reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered from the bacterial photoreceptor YtvA,” Scientific Reports, vol. 8. Springer Nature, 2018.","short":"C. Gregor, S.C. Sidenstein, M. Andresen, S.J. Sahl, J.G. Danzl, S.W. Hell, Scientific Reports 8 (2018).","apa":"Gregor, C., Sidenstein, S. C., Andresen, M., Sahl, S. J., Danzl, J. G., & Hell, S. W. (2018). Novel reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered from the bacterial photoreceptor YtvA. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-018-19947-1","ama":"Gregor C, Sidenstein SC, Andresen M, Sahl SJ, Danzl JG, Hell SW. Novel reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered from the bacterial photoreceptor YtvA. Scientific Reports. 2018;8. doi:10.1038/s41598-018-19947-1","mla":"Gregor, Carola, et al. “Novel Reversibly Switchable Fluorescent Proteins for RESOLFT and STED Nanoscopy Engineered from the Bacterial Photoreceptor YtvA.” Scientific Reports, vol. 8, 2724, Springer Nature, 2018, doi:10.1038/s41598-018-19947-1."},"title":"Novel reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered from the bacterial photoreceptor YtvA","external_id":{"pmid":["29426833"],"isi":["000424630400037"]},"article_processing_charge":"No","author":[{"last_name":"Gregor","full_name":"Gregor, Carola","first_name":"Carola"},{"full_name":"Sidenstein, Sven C.","last_name":"Sidenstein","first_name":"Sven C."},{"first_name":"Martin","last_name":"Andresen","full_name":"Andresen, Martin"},{"first_name":"Steffen J.","last_name":"Sahl","full_name":"Sahl, Steffen J."},{"first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G"},{"last_name":"Hell","full_name":"Hell, Stefan W.","first_name":"Stefan W."}],"article_number":"2724","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"8619","checksum":"e642080fcbde9584c63544f587c74f03","file_size":2818077,"date_updated":"2020-10-06T16:35:16Z","creator":"dernst","file_name":"2018_ScientificReports_Gregor.pdf","date_created":"2020-10-06T16:35:16Z"}],"publication_status":"published","publication_identifier":{"issn":["2045-2322"]},"volume":8,"pmid":1,"oa_version":"Published Version","abstract":[{"text":"The reversibly switchable fluorescent proteins (RSFPs) commonly used for RESOLFT nanoscopy have been developed from fluorescent proteins of the GFP superfamily. These proteins are bright, but exhibit several drawbacks such as relatively large size, oxygen-dependence, sensitivity to low pH, and limited switching speed. Therefore, RSFPs from other origins with improved properties need to be explored. Here, we report the development of two RSFPs based on the LOV domain of the photoreceptor protein YtvA from Bacillus subtilis. LOV domains obtain their fluorescence by association with the abundant cellular cofactor flavin mononucleotide (FMN). Under illumination with blue and ultraviolet light, they undergo a photocycle, making these proteins inherently photoswitchable. Our first improved variant, rsLOV1, can be used for RESOLFT imaging, whereas rsLOV2 proved useful for STED nanoscopy of living cells with a resolution of down to 50 nm. In addition to their smaller size compared to GFP-related proteins (17 kDa instead of 27 kDa) and their usability at low pH, rsLOV1 and rsLOV2 exhibit faster switching kinetics, switching on and off 3 times faster than rsEGFP2, the fastest-switching RSFP reported to date. Therefore, LOV-domain-based RSFPs have potential for applications where the switching speed of GFP-based proteins is limiting.","lang":"eng"}],"intvolume":" 8","month":"02","ddc":["570"],"date_updated":"2023-09-19T15:04:49Z","department":[{"_id":"JoDa"}],"file_date_updated":"2020-10-06T16:35:16Z","_id":"8618","keyword":["Multidisciplinary"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article"},{"volume":69,"issue":"9","ec_funded":1,"publication_identifier":{"issn":["0022-0957"],"eissn":["1460-2431"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","month":"04","intvolume":" 69","abstract":[{"text":"Strigolactones (SLs) are a relatively recent addition to the list of plant hormones that control different aspects of plant development. SL signalling is perceived by an α/β hydrolase, DWARF 14 (D14). A close homolog of D14, KARRIKIN INSENSTIVE2 (KAI2), is involved in perception of an uncharacterized molecule called karrikin (KAR). Recent studies in Arabidopsis identified the SUPPRESSOR OF MAX2 1 (SMAX1) and SMAX1-LIKE 7 (SMXL7) to be potential SCF–MAX2 complex-mediated proteasome targets of KAI2 and D14, respectively. Genetic studies on SMXL7 and SMAX1 demonstrated distinct developmental roles for each, but very little is known about these repressors in terms of their sequence features. In this study, we performed an extensive comparative analysis of SMXLs and determined their phylogenetic and evolutionary history in the plant lineage. Our results show that SMXL family members can be sub-divided into four distinct phylogenetic clades/classes, with an ancient SMAX1. Further, we identified the clade-specific motifs that have evolved and that might act as determinants of SL-KAR signalling specificity. These specificities resulted from functional diversities among the clades. Our results suggest that a gradual co-evolution of SMXL members with their upstream receptors D14/KAI2 provided an increased specificity to both the SL perception and response in land plants.","lang":"eng"}],"oa_version":"None","pmid":1,"department":[{"_id":"JiFr"}],"date_updated":"2023-09-19T15:10:43Z","article_type":"original","type":"journal_article","status":"public","keyword":["Plant Science","Physiology"],"_id":"10881","page":"2367-2378","doi":"10.1093/jxb/ery097","date_published":"2018-04-13T00:00:00Z","date_created":"2022-03-18T12:43:22Z","isi":1,"year":"2018","day":"13","publication":"Journal of Experimental Botany","quality_controlled":"1","publisher":"Oxford University Press","acknowledgement":"This project received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Actions and it is co-financed by the South Moravian Region under grant agreement No. 665860 (SS). Access to computing and storage facilities owned by parties and projects contributing to the national grid infrastructure, MetaCentrum, provided under the program ‘Projects of Large Infrastructure for Research, Development, and Innovations’ (LM2010005) was greatly appreciated (RSV). The project was funded by The Ministry of Education, Youth and Sports/MES of the Czech Republic under the project CEITEC 2020 (LQ1601) (TN, TRM). JF was supported by the European Research Council (project ERC-2011-StG 20101109-PSDP) and the Czech Science Foundation GAČR (GA13-40637S). We thank Dr Kamel Chibani for active discussions on the evolutionary analysis and Nandan Mysore Vardarajan for his critical comments on the manuscript. This article reflects\r\nonly the authors’ views, and the EU is not responsible for any use that may be made of the information it contains. ","author":[{"first_name":"Taraka Ramji","full_name":"Moturu, Taraka Ramji","last_name":"Moturu"},{"full_name":"Thula, Sravankumar","last_name":"Thula","first_name":"Sravankumar"},{"first_name":"Ravi Kumar","full_name":"Singh, Ravi Kumar","last_name":"Singh"},{"first_name":"Tomasz","full_name":"Nodzyński, Tomasz","last_name":"Nodzyński"},{"first_name":"Radka Svobodová","full_name":"Vařeková, Radka Svobodová","last_name":"Vařeková"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml"},{"first_name":"Sibu","full_name":"Simon, Sibu","last_name":"Simon"}],"article_processing_charge":"No","external_id":{"isi":["000430727000016"],"pmid":["29538714"]},"title":"Molecular evolution and diversification of the SMXL gene family","citation":{"ista":"Moturu TR, Thula S, Singh RK, Nodzyński T, Vařeková RS, Friml J, Simon S. 2018. Molecular evolution and diversification of the SMXL gene family. Journal of Experimental Botany. 69(9), 2367–2378.","chicago":"Moturu, Taraka Ramji, Sravankumar Thula, Ravi Kumar Singh, Tomasz Nodzyński, Radka Svobodová Vařeková, Jiří Friml, and Sibu Simon. “Molecular Evolution and Diversification of the SMXL Gene Family.” Journal of Experimental Botany. Oxford University Press, 2018. https://doi.org/10.1093/jxb/ery097.","apa":"Moturu, T. R., Thula, S., Singh, R. K., Nodzyński, T., Vařeková, R. S., Friml, J., & Simon, S. (2018). Molecular evolution and diversification of the SMXL gene family. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/ery097","ama":"Moturu TR, Thula S, Singh RK, et al. Molecular evolution and diversification of the SMXL gene family. Journal of Experimental Botany. 2018;69(9):2367-2378. doi:10.1093/jxb/ery097","short":"T.R. Moturu, S. Thula, R.K. Singh, T. Nodzyński, R.S. Vařeková, J. Friml, S. Simon, Journal of Experimental Botany 69 (2018) 2367–2378.","ieee":"T. R. Moturu et al., “Molecular evolution and diversification of the SMXL gene family,” Journal of Experimental Botany, vol. 69, no. 9. Oxford University Press, pp. 2367–2378, 2018.","mla":"Moturu, Taraka Ramji, et al. “Molecular Evolution and Diversification of the SMXL Gene Family.” Journal of Experimental Botany, vol. 69, no. 9, Oxford University Press, 2018, pp. 2367–78, doi:10.1093/jxb/ery097."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"name":"Polarity and subcellular dynamics in plants","grant_number":"282300","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425"}]},{"page":"329-338","date_created":"2022-03-18T12:40:35Z","doi":"10.1093/bfgp/ely007","date_published":"2018-09-01T00:00:00Z","year":"2018","isi":1,"publication":"Briefings in Functional Genomics","day":"01","oa":1,"publisher":"Oxford University Press","quality_controlled":"1","acknowledgement":"This work was supported by JSPS overseas research fellowships (Y.M.) and SENSHIN Medical Research Foundation (K.K.T.).","external_id":{"isi":["000456054400004"],"pmid":["29579140"]},"article_processing_charge":"No","author":[{"last_name":"Yuuta","orcid":"0000-0002-2853-8051","full_name":"Yuuta, Moriyama","id":"4968E7C8-F248-11E8-B48F-1D18A9856A87","first_name":"Moriyama"},{"first_name":"Kazuko","last_name":"Koshiba-Takeuchi","full_name":"Koshiba-Takeuchi, Kazuko"}],"title":"Significance of whole-genome duplications on the emergence of evolutionary novelties","citation":{"ista":"Yuuta M, Koshiba-Takeuchi K. 2018. Significance of whole-genome duplications on the emergence of evolutionary novelties. Briefings in Functional Genomics. 17(5), 329–338.","chicago":"Yuuta, Moriyama, and Kazuko Koshiba-Takeuchi. “Significance of Whole-Genome Duplications on the Emergence of Evolutionary Novelties.” Briefings in Functional Genomics. Oxford University Press, 2018. https://doi.org/10.1093/bfgp/ely007.","apa":"Yuuta, M., & Koshiba-Takeuchi, K. (2018). Significance of whole-genome duplications on the emergence of evolutionary novelties. Briefings in Functional Genomics. Oxford University Press. https://doi.org/10.1093/bfgp/ely007","ama":"Yuuta M, Koshiba-Takeuchi K. Significance of whole-genome duplications on the emergence of evolutionary novelties. Briefings in Functional Genomics. 2018;17(5):329-338. doi:10.1093/bfgp/ely007","short":"M. Yuuta, K. Koshiba-Takeuchi, Briefings in Functional Genomics 17 (2018) 329–338.","ieee":"M. Yuuta and K. Koshiba-Takeuchi, “Significance of whole-genome duplications on the emergence of evolutionary novelties,” Briefings in Functional Genomics, vol. 17, no. 5. Oxford University Press, pp. 329–338, 2018.","mla":"Yuuta, Moriyama, and Kazuko Koshiba-Takeuchi. “Significance of Whole-Genome Duplications on the Emergence of Evolutionary Novelties.” Briefings in Functional Genomics, vol. 17, no. 5, Oxford University Press, 2018, pp. 329–38, doi:10.1093/bfgp/ely007."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":17,"issue":"5","publication_status":"published","publication_identifier":{"issn":["2041-2649"],"eissn":["2041-2657"]},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1093/bfgp/ely007","open_access":"1"}],"scopus_import":"1","intvolume":" 17","month":"09","abstract":[{"lang":"eng","text":"Acquisition of evolutionary novelties is a fundamental process for adapting to the external environment and invading new niches and results in the diversification of life, which we can see in the world today. How such novel phenotypic traits are acquired in the course of evolution and are built up in developing embryos has been a central question in biology. Whole-genome duplication (WGD) is a process of genome doubling that supplies raw genetic materials and increases genome complexity. Recently, it has been gradually revealed that WGD and subsequent fate changes of duplicated genes can facilitate phenotypic evolution. Here, we review the current understanding of the relationship between WGD and the acquisition of evolutionary novelties. We show some examples of this link and discuss how WGD and subsequent duplicated genes can facilitate phenotypic evolution as well as when such genomic doubling can be advantageous for adaptation."}],"pmid":1,"oa_version":"Published Version","department":[{"_id":"CaHe"}],"date_updated":"2023-09-19T15:11:22Z","article_type":"original","type":"journal_article","keyword":["Genetics","Molecular Biology","Biochemistry","General Medicine"],"status":"public","_id":"10880"},{"citation":{"mla":"Westram, Anja M., et al. Data from: Clines on the Seashore: The Genomic Architecture Underlying Rapid Divergence in the Face of Gene Flow. Dryad, 2018, doi:10.5061/dryad.bp25b65.","short":"A.M. Westram, M. Rafajlović, P. Chaube, R. Faria, T. Larsson, M. Panova, M. Ravinet, A. Blomberg, B. Mehlig, K. Johannesson, R. Butlin, (2018).","ieee":"A. M. Westram et al., “Data from: Clines on the seashore: the genomic architecture underlying rapid divergence in the face of gene flow.” Dryad, 2018.","ama":"Westram AM, Rafajlović M, Chaube P, et al. Data from: Clines on the seashore: the genomic architecture underlying rapid divergence in the face of gene flow. 2018. doi:10.5061/dryad.bp25b65","apa":"Westram, A. M., Rafajlović, M., Chaube, P., Faria, R., Larsson, T., Panova, M., … Butlin, R. (2018). Data from: Clines on the seashore: the genomic architecture underlying rapid divergence in the face of gene flow. Dryad. https://doi.org/10.5061/dryad.bp25b65","chicago":"Westram, Anja M, Marina Rafajlović, Pragya Chaube, Rui Faria, Tomas Larsson, Marina Panova, Mark Ravinet, et al. “Data from: Clines on the Seashore: The Genomic Architecture Underlying Rapid Divergence in the Face of Gene Flow.” Dryad, 2018. https://doi.org/10.5061/dryad.bp25b65.","ista":"Westram AM, Rafajlović M, Chaube P, Faria R, Larsson T, Panova M, Ravinet M, Blomberg A, Mehlig B, Johannesson K, Butlin R. 2018. Data from: Clines on the seashore: the genomic architecture underlying rapid divergence in the face of gene flow, Dryad, 10.5061/dryad.bp25b65."},"date_updated":"2023-09-19T15:08:24Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"last_name":"Westram","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M"},{"last_name":"Rafajlović","full_name":"Rafajlović, Marina","first_name":"Marina"},{"first_name":"Pragya","full_name":"Chaube, Pragya","last_name":"Chaube"},{"first_name":"Rui","full_name":"Faria, Rui","last_name":"Faria"},{"first_name":"Tomas","full_name":"Larsson, Tomas","last_name":"Larsson"},{"last_name":"Panova","full_name":"Panova, Marina","first_name":"Marina"},{"first_name":"Mark","last_name":"Ravinet","full_name":"Ravinet, Mark"},{"first_name":"Anders","last_name":"Blomberg","full_name":"Blomberg, Anders"},{"first_name":"Bernhard","last_name":"Mehlig","full_name":"Mehlig, Bernhard"},{"last_name":"Johannesson","full_name":"Johannesson, Kerstin","first_name":"Kerstin"},{"last_name":"Butlin","full_name":"Butlin, Roger","first_name":"Roger"}],"article_processing_charge":"No","department":[{"_id":"BeVi"}],"title":"Data from: Clines on the seashore: the genomic architecture underlying rapid divergence in the face of gene flow","_id":"9930","type":"research_data_reference","status":"public","year":"2018","day":"23","date_published":"2018-07-23T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"9917"}]},"doi":"10.5061/dryad.bp25b65","date_created":"2021-08-17T08:58:47Z","abstract":[{"text":"Adaptive divergence and speciation may happen despite opposition by gene flow. Identifying the genomic basis underlying divergence with gene flow is a major task in evolutionary genomics. Most approaches (e.g. outlier scans) focus on genomic regions of high differentiation. However, not all genomic architectures potentially underlying divergence are expected to show extreme differentiation. Here, we develop an approach that combines hybrid zone analysis (i.e. focuses on spatial patterns of allele frequency change) with system-specific simulations to identify loci inconsistent with neutral evolution. We apply this to a genome-wide SNP set from an ideally-suited study organism, the intertidal snail Littorina saxatilis, which shows primary divergence between ecotypes associated with different shore habitats. We detect many SNPs with clinal patterns, most of which are consistent with neutrality. Among non-neutral SNPs, most are located within three large putative inversions differentiating ecotypes. Many non-neutral SNPs show relatively low levels of differentiation. We discuss potential reasons for this pattern, including loose linkage to selected variants, polygenic adaptation and a component of balancing selection within populations (which may be expected for inversions). Our work is in line with theory predicting a role for inversions in divergence, and emphasises that genomic regions contributing to divergence may not always be accessible with methods purely based on allele frequency differences. These conclusions call for approaches that take spatial patterns of allele frequency change into account in other systems.","lang":"eng"}],"oa_version":"Published Version","publisher":"Dryad","main_file_link":[{"url":"https://doi.org/10.5061/dryad.bp25b65","open_access":"1"}],"oa":1,"month":"07"},{"_id":"9929","status":"public","type":"research_data_reference","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"ieee":"J. Hollander et al., “Data from: Are assortative mating and genital divergence driven by reinforcement?” Dryad, 2018.","short":"J. Hollander, M. Montaño-Rendón, G. Bianco, X. Yang, A.M. Westram, L. Duvaux, D.G. Reid, R.K. Butlin, (2018).","apa":"Hollander, J., Montaño-Rendón, M., Bianco, G., Yang, X., Westram, A. M., Duvaux, L., … Butlin, R. K. (2018). Data from: Are assortative mating and genital divergence driven by reinforcement? Dryad. https://doi.org/10.5061/dryad.51sd2p5","ama":"Hollander J, Montaño-Rendón M, Bianco G, et al. Data from: Are assortative mating and genital divergence driven by reinforcement? 2018. doi:10.5061/dryad.51sd2p5","mla":"Hollander, Johan, et al. Data from: Are Assortative Mating and Genital Divergence Driven by Reinforcement? Dryad, 2018, doi:10.5061/dryad.51sd2p5.","ista":"Hollander J, Montaño-Rendón M, Bianco G, Yang X, Westram AM, Duvaux L, Reid DG, Butlin RK. 2018. Data from: Are assortative mating and genital divergence driven by reinforcement?, Dryad, 10.5061/dryad.51sd2p5.","chicago":"Hollander, Johan, Mauricio Montaño-Rendón, Giuseppe Bianco, Xi Yang, Anja M Westram, Ludovic Duvaux, David G. Reid, and Roger K. Butlin. “Data from: Are Assortative Mating and Genital Divergence Driven by Reinforcement?” Dryad, 2018. https://doi.org/10.5061/dryad.51sd2p5."},"date_updated":"2023-09-19T15:08:53Z","title":"Data from: Are assortative mating and genital divergence driven by reinforcement?","department":[{"_id":"BeVi"}],"article_processing_charge":"No","author":[{"first_name":"Johan","last_name":"Hollander","full_name":"Hollander, Johan"},{"first_name":"Mauricio","last_name":"Montaño-Rendón","full_name":"Montaño-Rendón, Mauricio"},{"last_name":"Bianco","full_name":"Bianco, Giuseppe","first_name":"Giuseppe"},{"first_name":"Xi","full_name":"Yang, Xi","last_name":"Yang"},{"orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","last_name":"Westram","first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ludovic","full_name":"Duvaux, Ludovic","last_name":"Duvaux"},{"first_name":"David G.","last_name":"Reid","full_name":"Reid, David G."},{"first_name":"Roger K.","last_name":"Butlin","full_name":"Butlin, Roger K."}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"The evolution of assortative mating is a key part of the speciation process. Stronger assortment, or greater divergence in mating traits, between species pairs with overlapping ranges is commonly observed, but possible causes of this pattern of reproductive character displacement are difficult to distinguish. We use a multidisciplinary approach to provide a rare example where it is possible to distinguish among hypotheses concerning the evolution of reproductive character displacement. We build on an earlier comparative analysis that illustrated a strong pattern of greater divergence in penis form between pairs of sister species with overlapping ranges than between allopatric sister-species pairs, in a large clade of marine gastropods (Littorinidae). We investigate both assortative mating and divergence in male genitalia in one of the sister-species pairs, discriminating among three contrasting processes each of which can generate a pattern of reproductive character displacement: reinforcement, reproductive interference and the Templeton effect. We demonstrate reproductive character displacement in assortative mating, but not in genital form between this pair of sister species and use demographic models to distinguish among the different processes. Our results support a model with no gene flow since secondary contact and thus favour reproductive interference as the cause of reproductive character displacement for mate choice, rather than reinforcement. High gene flow within species argues against the Templeton effect. Secondary contact appears to have had little impact on genital divergence."}],"month":"10","main_file_link":[{"url":"https://doi.org/10.5061/dryad.51sd2p5","open_access":"1"}],"oa":1,"publisher":"Dryad","day":"17","year":"2018","date_created":"2021-08-17T08:51:06Z","doi":"10.5061/dryad.51sd2p5","date_published":"2018-10-17T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","id":"9915","status":"public"}]}},{"date_updated":"2023-09-19T15:11:49Z","department":[{"_id":"ChLa"}],"_id":"10882","type":"conference","conference":{"location":"Salt Lake City, UT, United States","end_date":"2018-06-23","start_date":"2018-06-18","name":"CVF: Conference on Computer Vision and Pattern Recognition"},"status":"public","publication_identifier":{"isbn":["9781538664209"],"eissn":["2575-7075"]},"publication_status":"published","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"We introduce Intelligent Annotation Dialogs for bounding box annotation. We train an agent to automatically choose a sequence of actions for a human annotator to produce a bounding box in a minimal amount of time. Specifically, we consider two actions: box verification [34], where the annotator verifies a box generated by an object detector, and manual box drawing. We explore two kinds of agents, one based on predicting the probability that a box will be positively verified, and the other based on reinforcement learning. We demonstrate that (1) our agents are able to learn efficient annotation strategies in several scenarios, automatically adapting to the image difficulty, the desired quality of the boxes, and the detector strength; (2) in all scenarios the resulting annotation dialogs speed up annotation compared to manual box drawing alone and box verification alone, while also outperforming any fixed combination of verification and drawing in most scenarios; (3) in a realistic scenario where the detector is iteratively re-trained, our agents evolve a series of strategies that reflect the shifting trade-off between verification and drawing as the detector grows stronger."}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.1712.08087","open_access":"1"}],"month":"12","citation":{"short":"J. Uijlings, K. Konyushkova, C. Lampert, V. Ferrari, in:, 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2018, pp. 9175–9184.","ieee":"J. Uijlings, K. Konyushkova, C. Lampert, and V. Ferrari, “Learning intelligent dialogs for bounding box annotation,” in 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, Salt Lake City, UT, United States, 2018, pp. 9175–9184.","ama":"Uijlings J, Konyushkova K, Lampert C, Ferrari V. Learning intelligent dialogs for bounding box annotation. In: 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition. IEEE; 2018:9175-9184. doi:10.1109/cvpr.2018.00956","apa":"Uijlings, J., Konyushkova, K., Lampert, C., & Ferrari, V. (2018). Learning intelligent dialogs for bounding box annotation. In 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition (pp. 9175–9184). Salt Lake City, UT, United States: IEEE. https://doi.org/10.1109/cvpr.2018.00956","mla":"Uijlings, Jasper, et al. “Learning Intelligent Dialogs for Bounding Box Annotation.” 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2018, pp. 9175–84, doi:10.1109/cvpr.2018.00956.","ista":"Uijlings J, Konyushkova K, Lampert C, Ferrari V. 2018. Learning intelligent dialogs for bounding box annotation. 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition. CVF: Conference on Computer Vision and Pattern Recognition, 9175–9184.","chicago":"Uijlings, Jasper, Ksenia Konyushkova, Christoph Lampert, and Vittorio Ferrari. “Learning Intelligent Dialogs for Bounding Box Annotation.” In 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, 9175–84. IEEE, 2018. https://doi.org/10.1109/cvpr.2018.00956."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"last_name":"Uijlings","full_name":"Uijlings, Jasper","first_name":"Jasper"},{"first_name":"Ksenia","full_name":"Konyushkova, Ksenia","last_name":"Konyushkova"},{"last_name":"Lampert","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ferrari, Vittorio","last_name":"Ferrari","first_name":"Vittorio"}],"article_processing_charge":"No","external_id":{"arxiv":["1712.08087"],"isi":["000457843609036"]},"title":"Learning intelligent dialogs for bounding box annotation","isi":1,"year":"2018","day":"17","publication":"2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition","page":"9175-9184","doi":"10.1109/cvpr.2018.00956","date_published":"2018-12-17T00:00:00Z","date_created":"2022-03-18T12:45:09Z","publisher":"IEEE","quality_controlled":"1","oa":1},{"citation":{"mla":"Alistarh, Dan-Adrian, et al. “Byzantine Stochastic Gradient Descent.” Advances in Neural Information Processing Systems, vol. 2018, Neural Information Processing Systems Foundation, 2018, pp. 4613–23.","ama":"Alistarh D-A, Allen-Zhu Z, Li J. Byzantine stochastic gradient descent. In: Advances in Neural Information Processing Systems. Vol 2018. Neural Information Processing Systems Foundation; 2018:4613-4623.","apa":"Alistarh, D.-A., Allen-Zhu, Z., & Li, J. (2018). Byzantine stochastic gradient descent. In Advances in Neural Information Processing Systems (Vol. 2018, pp. 4613–4623). Montreal, Canada: Neural Information Processing Systems Foundation.","short":"D.-A. Alistarh, Z. Allen-Zhu, J. Li, in:, Advances in Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2018, pp. 4613–4623.","ieee":"D.-A. Alistarh, Z. Allen-Zhu, and J. Li, “Byzantine stochastic gradient descent,” in Advances in Neural Information Processing Systems, Montreal, Canada, 2018, vol. 2018, pp. 4613–4623.","chicago":"Alistarh, Dan-Adrian, Zeyuan Allen-Zhu, and Jerry Li. “Byzantine Stochastic Gradient Descent.” In Advances in Neural Information Processing Systems, 2018:4613–23. Neural Information Processing Systems Foundation, 2018.","ista":"Alistarh D-A, Allen-Zhu Z, Li J. 2018. Byzantine stochastic gradient descent. Advances in Neural Information Processing Systems. NeurIPS: Conference on Neural Information Processing Systems vol. 2018, 4613–4623."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"last_name":"Alistarh","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Allen-Zhu, Zeyuan","last_name":"Allen-Zhu","first_name":"Zeyuan"},{"first_name":"Jerry","last_name":"Li","full_name":"Li, Jerry"}],"external_id":{"isi":["000461823304061"],"arxiv":["1803.08917"]},"article_processing_charge":"No","title":"Byzantine stochastic gradient descent","isi":1,"year":"2018","day":"01","publication":"Advances in Neural Information Processing Systems","page":"4613-4623","date_published":"2018-12-01T00:00:00Z","date_created":"2019-06-13T08:22:37Z","publisher":"Neural Information Processing Systems Foundation","quality_controlled":"1","oa":1,"date_updated":"2023-09-19T15:12:45Z","department":[{"_id":"DaAl"}],"_id":"6558","type":"conference","conference":{"name":"NeurIPS: Conference on Neural Information Processing Systems","end_date":"2018-12-08","location":"Montreal, Canada","start_date":"2018-12-02"},"status":"public","publication_status":"published","language":[{"iso":"eng"}],"volume":2018,"abstract":[{"lang":"eng","text":"This paper studies the problem of distributed stochastic optimization in an adversarial setting where, out of m machines which allegedly compute stochastic gradients every iteration, an α-fraction are Byzantine, and may behave adversarially. Our main result is a variant of stochastic gradient descent (SGD) which finds ε-approximate minimizers of convex functions in T=O~(1/ε²m+α²/ε²) iterations. In contrast, traditional mini-batch SGD needs T=O(1/ε²m) iterations, but cannot tolerate Byzantine failures. Further, we provide a lower bound showing that, up to logarithmic factors, our algorithm is information-theoretically optimal both in terms of sample complexity and time complexity."}],"oa_version":"Published Version","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1803.08917","open_access":"1"}],"month":"12","intvolume":" 2018"},{"status":"public","type":"journal_article","article_type":"original","_id":"6032","department":[{"_id":"VlKo"}],"date_updated":"2023-09-20T11:20:26Z","month":"12","intvolume":" 15","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1602.03124","open_access":"1"}],"oa_version":"Preprint","abstract":[{"text":"The main result of this article is a generalization of the classical blossom algorithm for finding perfect matchings. Our algorithm can efficiently solve Boolean CSPs where each variable appears in exactly two constraints (we call it edge CSP) and all constraints are even Δ-matroid relations (represented by lists of tuples). As a consequence of this, we settle the complexity classification of planar Boolean CSPs started by Dvorak and Kupec. Using a reduction to even Δ-matroids, we then extend the tractability result to larger classes of Δ-matroids that we call efficiently coverable. It properly includes classes that were known to be tractable before, namely, co-independent, compact, local, linear, and binary, with the following caveat:We represent Δ-matroids by lists of tuples, while the last two use a representation by matrices. Since an n ×n matrix can represent exponentially many tuples, our tractability result is not strictly stronger than the known algorithm for linear and binary Δ-matroids.","lang":"eng"}],"volume":15,"related_material":{"record":[{"relation":"earlier_version","id":"1192","status":"public"}]},"issue":"2","ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published","project":[{"call_identifier":"FP7","_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160","name":"Discrete Optimization in Computer Vision: Theory and Practice"}],"article_number":"22","title":"Even delta-matroids and the complexity of planar boolean CSPs","author":[{"first_name":"Alexandr","id":"3B32BAA8-F248-11E8-B48F-1D18A9856A87","last_name":"Kazda","full_name":"Kazda, Alexandr"},{"last_name":"Kolmogorov","full_name":"Kolmogorov, Vladimir","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Rolinek, Michal","last_name":"Rolinek","id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87","first_name":"Michal"}],"external_id":{"isi":["000468036500007"],"arxiv":["1602.03124"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Kazda A, Kolmogorov V, Rolinek M. 2018. Even delta-matroids and the complexity of planar boolean CSPs. ACM Transactions on Algorithms. 15(2), 22.","chicago":"Kazda, Alexandr, Vladimir Kolmogorov, and Michal Rolinek. “Even Delta-Matroids and the Complexity of Planar Boolean CSPs.” ACM Transactions on Algorithms. ACM, 2018. https://doi.org/10.1145/3230649.","ieee":"A. Kazda, V. Kolmogorov, and M. Rolinek, “Even delta-matroids and the complexity of planar boolean CSPs,” ACM Transactions on Algorithms, vol. 15, no. 2. ACM, 2018.","short":"A. Kazda, V. Kolmogorov, M. Rolinek, ACM Transactions on Algorithms 15 (2018).","ama":"Kazda A, Kolmogorov V, Rolinek M. Even delta-matroids and the complexity of planar boolean CSPs. ACM Transactions on Algorithms. 2018;15(2). doi:10.1145/3230649","apa":"Kazda, A., Kolmogorov, V., & Rolinek, M. (2018). Even delta-matroids and the complexity of planar boolean CSPs. ACM Transactions on Algorithms. ACM. https://doi.org/10.1145/3230649","mla":"Kazda, Alexandr, et al. “Even Delta-Matroids and the Complexity of Planar Boolean CSPs.” ACM Transactions on Algorithms, vol. 15, no. 2, 22, ACM, 2018, doi:10.1145/3230649."},"quality_controlled":"1","publisher":"ACM","oa":1,"doi":"10.1145/3230649","date_published":"2018-12-01T00:00:00Z","date_created":"2019-02-17T22:59:25Z","day":"01","publication":"ACM Transactions on Algorithms","isi":1,"year":"2018"},{"_id":"200","pubrep_id":"963","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"type":"dissertation","ddc":["576"],"date_updated":"2023-09-20T12:00:56Z","supervisor":[{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2020-07-14T12:45:23Z","department":[{"_id":"NiBa"}],"oa_version":"Published Version","abstract":[{"text":"This thesis is concerned with the inference of current population structure based on geo-referenced genetic data. The underlying idea is that population structure affects its spatial genetic structure. Therefore, genotype information can be utilized to estimate important demographic parameters such as migration rates. These indirect estimates of population structure have become very attractive, as genotype data is now widely available. However, there also has been much concern about these approaches. Importantly, genetic structure can be influenced by many complex patterns, which often cannot be disentangled. Moreover, many methods merely fit heuristic patterns of genetic structure, and do not build upon population genetics theory. Here, I describe two novel inference methods that address these shortcomings. In Chapter 2, I introduce an inference scheme based on a new type of signal, identity by descent (IBD) blocks. Recently, it has become feasible to detect such long blocks of genome shared between pairs of samples. These blocks are direct traces of recent coalescence events. As such, they contain ample signal for inferring recent demography. I examine sharing of IBD blocks in two-dimensional populations with local migration. Using a diffusion approximation, I derive formulas for an isolation by distance pattern of long IBD blocks and show that sharing of long IBD blocks approaches rapid exponential decay for growing sample distance. I describe an inference scheme based on these results. It can robustly estimate the dispersal rate and population density, which is demonstrated on simulated data. I also show an application to estimate mean migration and the rate of recent population growth within Eastern Europe. Chapter 3 is about a novel method to estimate barriers to gene flow in a two dimensional population. This inference scheme utilizes geographically localized allele frequency fluctuations - a classical isolation by distance signal. The strength of these local fluctuations increases on average next to a barrier, and there is less correlation across it. I again use a framework of diffusion of ancestral lineages to model this effect, and provide an efficient numerical implementation to fit the results to geo-referenced biallelic SNP data. This inference scheme is able to robustly estimate strong barriers to gene flow, as tests on simulated data confirm.","lang":"eng"}],"month":"02","alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"8cc534d2b528ae017acf80874cce48c9","file_id":"5111","creator":"system","date_updated":"2020-07-14T12:45:23Z","file_size":5792935,"date_created":"2018-12-12T10:14:55Z","file_name":"IST-2018-963-v1+1_thesis.pdf"},{"date_created":"2019-04-05T09:30:12Z","file_name":"2018_thesis_ringbauer_source.zip","date_updated":"2020-07-14T12:45:23Z","file_size":113365,"creator":"dernst","file_id":"6224","checksum":"6af18d7e5a7e2728ceda2f41ee24f628","content_type":"application/zip","access_level":"closed","relation":"source_file"}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"license":"https://creativecommons.org/licenses/by-nc/4.0/","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"563"},{"relation":"part_of_dissertation","id":"1074","status":"public"}]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Ringbauer, Harald. Inferring Recent Demography from Spatial Genetic Structure. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_963.","ieee":"H. Ringbauer, “Inferring recent demography from spatial genetic structure,” Institute of Science and Technology Austria, 2018.","short":"H. Ringbauer, Inferring Recent Demography from Spatial Genetic Structure, Institute of Science and Technology Austria, 2018.","apa":"Ringbauer, H. (2018). Inferring recent demography from spatial genetic structure. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_963","ama":"Ringbauer H. Inferring recent demography from spatial genetic structure. 2018. doi:10.15479/AT:ISTA:th_963","chicago":"Ringbauer, Harald. “Inferring Recent Demography from Spatial Genetic Structure.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_963.","ista":"Ringbauer H. 2018. Inferring recent demography from spatial genetic structure. Institute of Science and Technology Austria."},"title":"Inferring recent demography from spatial genetic structure","article_processing_charge":"No","publist_id":"7713","author":[{"id":"417FCFF4-F248-11E8-B48F-1D18A9856A87","first_name":"Harald","orcid":"0000-0002-4884-9682","full_name":"Ringbauer, Harald","last_name":"Ringbauer"}],"oa":1,"publisher":"Institute of Science and Technology Austria","day":"21","year":"2018","has_accepted_license":"1","date_created":"2018-12-11T11:45:10Z","date_published":"2018-02-21T00:00:00Z","doi":"10.15479/AT:ISTA:th_963","page":"146"},{"oa":1,"quality_controlled":"1","publisher":"Springer","date_created":"2018-12-11T11:49:57Z","date_published":"2018-06-01T00:00:00Z","doi":"10.1007/s00454-017-9883-x","page":"1001-1009","publication":"Discrete & Computational Geometry","day":"01","year":"2018","has_accepted_license":"1","isi":1,"project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"title":"On the circle covering theorem by A.W. Goodman and R.E. Goodman","external_id":{"isi":["000432205500011"]},"article_processing_charge":"Yes (via OA deal)","publist_id":"6324","author":[{"id":"430D2C90-F248-11E8-B48F-1D18A9856A87","first_name":"Arseniy","orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy","last_name":"Akopyan"},{"full_name":"Balitskiy, Alexey","last_name":"Balitskiy","first_name":"Alexey"},{"first_name":"Mikhail","full_name":"Grigorev, Mikhail","last_name":"Grigorev"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Akopyan, Arseniy, Alexey Balitskiy, and Mikhail Grigorev. “On the Circle Covering Theorem by A.W. Goodman and R.E. Goodman.” Discrete & Computational Geometry. Springer, 2018. https://doi.org/10.1007/s00454-017-9883-x.","ista":"Akopyan A, Balitskiy A, Grigorev M. 2018. On the circle covering theorem by A.W. Goodman and R.E. Goodman. Discrete & Computational Geometry. 59(4), 1001–1009.","mla":"Akopyan, Arseniy, et al. “On the Circle Covering Theorem by A.W. Goodman and R.E. Goodman.” Discrete & Computational Geometry, vol. 59, no. 4, Springer, 2018, pp. 1001–09, doi:10.1007/s00454-017-9883-x.","apa":"Akopyan, A., Balitskiy, A., & Grigorev, M. (2018). On the circle covering theorem by A.W. Goodman and R.E. Goodman. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-017-9883-x","ama":"Akopyan A, Balitskiy A, Grigorev M. On the circle covering theorem by A.W. Goodman and R.E. Goodman. Discrete & Computational Geometry. 2018;59(4):1001-1009. doi:10.1007/s00454-017-9883-x","ieee":"A. Akopyan, A. Balitskiy, and M. Grigorev, “On the circle covering theorem by A.W. Goodman and R.E. Goodman,” Discrete & Computational Geometry, vol. 59, no. 4. Springer, pp. 1001–1009, 2018.","short":"A. Akopyan, A. Balitskiy, M. Grigorev, Discrete & Computational Geometry 59 (2018) 1001–1009."},"intvolume":" 59","month":"06","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"In 1945, A.W. Goodman and R.E. Goodman proved the following conjecture by P. Erdős: Given a family of (round) disks of radii r1, … , rn in the plane, it is always possible to cover them by a disk of radius R= ∑ ri, provided they cannot be separated into two subfamilies by a straight line disjoint from the disks. In this note we show that essentially the same idea may work for different analogues and generalizations of their result. In particular, we prove the following: Given a family of positive homothetic copies of a fixed convex body K⊂ Rd with homothety coefficients τ1, … , τn> 0 , it is always possible to cover them by a translate of d+12(∑τi)K, provided they cannot be separated into two subfamilies by a hyperplane disjoint from the homothets.","lang":"eng"}],"ec_funded":1,"volume":59,"issue":"4","language":[{"iso":"eng"}],"file":[{"creator":"dernst","file_size":482518,"date_updated":"2019-01-18T09:27:36Z","file_name":"2018_DiscreteComp_Akopyan.pdf","date_created":"2019-01-18T09:27:36Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"5844"}],"publication_status":"published","publication_identifier":{"issn":["01795376"],"eissn":["14320444"]},"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","_id":"1064","department":[{"_id":"HeEd"}],"file_date_updated":"2019-01-18T09:27:36Z","ddc":["516","000"],"date_updated":"2023-09-20T12:08:51Z"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Gschaider-Reichhart, Eva. Optical and Optogenetic Control of Proliferation and Survival . Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_913.","ama":"Gschaider-Reichhart E. Optical and optogenetic control of proliferation and survival . 2018. doi:10.15479/AT:ISTA:th_913","apa":"Gschaider-Reichhart, E. (2018). Optical and optogenetic control of proliferation and survival . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_913","short":"E. Gschaider-Reichhart, Optical and Optogenetic Control of Proliferation and Survival , Institute of Science and Technology Austria, 2018.","ieee":"E. Gschaider-Reichhart, “Optical and optogenetic control of proliferation and survival ,” Institute of Science and Technology Austria, 2018.","chicago":"Gschaider-Reichhart, Eva. “Optical and Optogenetic Control of Proliferation and Survival .” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_913.","ista":"Gschaider-Reichhart E. 2018. Optical and optogenetic control of proliferation and survival . Institute of Science and Technology Austria."},"title":"Optical and optogenetic control of proliferation and survival ","publist_id":"7405","author":[{"last_name":"Gschaider-Reichhart","full_name":"Gschaider-Reichhart, Eva","orcid":"0000-0002-7218-7738","id":"3FEE232A-F248-11E8-B48F-1D18A9856A87","first_name":"Eva"}],"article_processing_charge":"No","day":"08","has_accepted_license":"1","year":"2018","doi":"10.15479/AT:ISTA:th_913","date_published":"2018-01-08T00:00:00Z","date_created":"2018-12-11T11:46:22Z","page":"107","publisher":"Institute of Science and Technology Austria","oa":1,"ddc":["571","570"],"supervisor":[{"first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315","last_name":"Janovjak"}],"date_updated":"2023-09-22T09:20:10Z","department":[{"_id":"HaJa"}],"file_date_updated":"2020-07-14T12:46:24Z","_id":"418","status":"public","pubrep_id":"913","type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","relation":"source_file","checksum":"697fa72ca36fb1b8ceabc133d58a73e5","file_id":"6222","date_updated":"2020-07-14T12:46:24Z","file_size":7012495,"creator":"dernst","date_created":"2019-04-05T09:28:03Z","file_name":"2018_THESIS_Gschaider-Reichhart_source.docx"},{"file_size":6355280,"date_updated":"2020-07-14T12:46:24Z","creator":"dernst","file_name":"2018_THESIS_Gschaider-Reichhart.pdf","date_created":"2019-04-05T09:28:03Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"58d7d1e9e58aeb7f061ab686b1d8a48c","file_id":"6223"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","related_material":{"record":[{"status":"public","id":"1441","relation":"part_of_dissertation"},{"status":"public","id":"1678","relation":"part_of_dissertation"},{"status":"public","id":"2084","relation":"part_of_dissertation"},{"status":"public","id":"1028","relation":"part_of_dissertation"}]},"oa_version":"Published Version","abstract":[{"text":"The aim of this thesis was the development of new strategies for optical and optogenetic control of proliferative and pro-survival signaling, and characterizing them from the molecular mechanism up to cellular effects. These new light-based methods have unique features, such as red light as an activator, or the avoidance of gene delivery, which enable to overcome current limitations, such as light delivery to target tissues and feasibility as therapeutic approach. A special focus was placed on implementing these new light-based approaches in pancreatic β-cells, as β-cells are the key players in diabetes and especially their loss in number negatively affects disease progression. Currently no treatment options are available to compensate the lack of functional β-cells in diabetic patients.\r\nIn a first approach, red-light-activated growth factor receptors, in particular receptor tyrosine kinases were engineered and characterized. Receptor activation with light allows spatio-temporal control compared to ligand-based activation, and especially red light exhibits deeper tissue penetration than other wavelengths of the visible spectrum. Red-light-activated receptor tyrosine kinases robustly activated major growth factor related signaling pathways with a high temporal resolution. Moreover, the remote activation of the proliferative MAPK/Erk pathway by red-light-activated receptor tyrosine kinases in a pancreatic β-cell line was also achieved, through one centimeter thick mouse tissue. Although red-light-activated receptor tyrosine kinases are particularly attractive for applications in animal models due to the deep tissue penetration of red light, a drawback, especially with regard to translation into humans, is the requirement of gene therapy.\r\nIn a second approach an endogenous light-sensitive mechanism was identified and its potential to promote proliferative and pro-survival signals was explored, towards light-based tissue regeneration without the need for gene transfer. Blue-green light illumination was found to be sufficient for the activation of proliferation and survival promoting signaling pathways in primary pancreatic murine and human islets. Blue-green light also led to an increase in proliferation of primary islet cells, an effect which was shown to be mostly β-cell specific in human islets. Moreover, it was demonstrated that this approach of pancreatic β-cell expansion did not have any negative effect on the β-cell function, in particular on their insulin secretion capacity. In contrast, a trend for enhanced insulin secretion under high glucose conditions after illumination was detected. In order to unravel the detailed characteristics of this endogenous light-sensitive mechanism, the precise light requirements were determined. In addition, the expression of light sensing proteins, OPN3 and rhodopsin, was detected. The observed effects were found to be independent of handling effects such as temperature differences and cytochrome c oxidase dependent ATP increase, but they were found to be enhanced through the knockout of OPN3. The exact mechanism of how islets cells sense light and the identity of the photoreceptor remains unknown.\r\nSummarized two new light-based systems with unique features were established that enable the activation of proliferative and pro-survival signaling pathways. While red-light-activated receptor tyrosine kinases open a new avenue for optogenetics research, by allowing non-invasive control of signaling in vivo, the identified endogenous light-sensitive mechanism has the potential to be the basis of a gene therapy-free therapeutical approach for light-based β-cell expansion.","lang":"eng"}],"month":"01","alternative_title":["ISTA Thesis"]},{"author":[{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","last_name":"Erdös","orcid":"0000-0001-5366-9603","full_name":"Erdös, László"},{"first_name":"Dominik J","id":"408ED176-F248-11E8-B48F-1D18A9856A87","last_name":"Schröder","full_name":"Schröder, Dominik J","orcid":"0000-0002-2904-1856"}],"publist_id":"6383","article_processing_charge":"No","external_id":{"arxiv":["1608.05163"],"isi":["000441668300009"]},"title":"Fluctuations of rectangular young diagrams of interlacing wigner eigenvalues","citation":{"short":"L. Erdös, D.J. Schröder, International Mathematics Research Notices 2018 (2018) 3255–3298.","ieee":"L. Erdös and D. J. Schröder, “Fluctuations of rectangular young diagrams of interlacing wigner eigenvalues,” International Mathematics Research Notices, vol. 2018, no. 10. Oxford University Press, pp. 3255–3298, 2018.","apa":"Erdös, L., & Schröder, D. J. (2018). Fluctuations of rectangular young diagrams of interlacing wigner eigenvalues. International Mathematics Research Notices. Oxford University Press. https://doi.org/10.1093/imrn/rnw330","ama":"Erdös L, Schröder DJ. Fluctuations of rectangular young diagrams of interlacing wigner eigenvalues. International Mathematics Research Notices. 2018;2018(10):3255-3298. doi:10.1093/imrn/rnw330","mla":"Erdös, László, and Dominik J. Schröder. “Fluctuations of Rectangular Young Diagrams of Interlacing Wigner Eigenvalues.” International Mathematics Research Notices, vol. 2018, no. 10, Oxford University Press, 2018, pp. 3255–98, doi:10.1093/imrn/rnw330.","ista":"Erdös L, Schröder DJ. 2018. Fluctuations of rectangular young diagrams of interlacing wigner eigenvalues. International Mathematics Research Notices. 2018(10), 3255–3298.","chicago":"Erdös, László, and Dominik J Schröder. “Fluctuations of Rectangular Young Diagrams of Interlacing Wigner Eigenvalues.” International Mathematics Research Notices. Oxford University Press, 2018. https://doi.org/10.1093/imrn/rnw330."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804","name":"Random matrices, universality and disordered quantum systems"}],"page":"3255-3298","doi":"10.1093/imrn/rnw330","date_published":"2018-05-18T00:00:00Z","date_created":"2018-12-11T11:49:41Z","isi":1,"year":"2018","day":"18","publication":"International Mathematics Research Notices","publisher":"Oxford University Press","quality_controlled":"1","oa":1,"department":[{"_id":"LaEr"}],"date_updated":"2023-09-22T09:44:21Z","type":"journal_article","status":"public","_id":"1012","issue":"10","volume":2018,"related_material":{"record":[{"id":"6179","status":"public","relation":"dissertation_contains"}]},"ec_funded":1,"publication_identifier":{"issn":["10737928"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1608.05163","open_access":"1"}],"month":"05","intvolume":" 2018","abstract":[{"lang":"eng","text":"We prove a new central limit theorem (CLT) for the difference of linear eigenvalue statistics of a Wigner random matrix H and its minor H and find that the fluctuation is much smaller than the fluctuations of the individual linear statistics, as a consequence of the strong correlation between the eigenvalues of H and H. In particular, our theorem identifies the fluctuation of Kerov's rectangular Young diagrams, defined by the interlacing eigenvalues ofH and H, around their asymptotic shape, the Vershik'Kerov'Logan'Shepp curve. Young diagrams equipped with the Plancherel measure follow the same limiting shape. For this, algebraically motivated, ensemble a CLT has been obtained in Ivanov and Olshanski [20] which is structurally similar to our result but the variance is different, indicating that the analogy between the two models has its limitations. Moreover, our theorem shows that Borodin's result [7] on the convergence of the spectral distribution of Wigner matrices to a Gaussian free field also holds in derivative sense."}],"oa_version":"Preprint"},{"project":[{"call_identifier":"FWF","_id":"264B3912-B435-11E9-9278-68D0E5697425","name":"Formal Methods meets Algorithmic Game Theory","grant_number":"M02369"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"name":"The Wittgenstein Prize","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"article_number":"39","title":"An abstraction-refinement methodology for reasoning about network games","author":[{"last_name":"Avni","full_name":"Avni, Guy","orcid":"0000-0001-5588-8287","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","first_name":"Guy"},{"full_name":"Guha, Shibashis","last_name":"Guha","first_name":"Shibashis"},{"last_name":"Kupferman","full_name":"Kupferman, Orna","first_name":"Orna"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"G. Avni, S. Guha, O. Kupferman, Games 9 (2018).","ieee":"G. Avni, S. Guha, and O. Kupferman, “An abstraction-refinement methodology for reasoning about network games,” Games, vol. 9, no. 3. MDPI AG, 2018.","apa":"Avni, G., Guha, S., & Kupferman, O. (2018). An abstraction-refinement methodology for reasoning about network games. Games. MDPI AG. https://doi.org/10.3390/g9030039","ama":"Avni G, Guha S, Kupferman O. An abstraction-refinement methodology for reasoning about network games. Games. 2018;9(3). doi:10.3390/g9030039","mla":"Avni, Guy, et al. “An Abstraction-Refinement Methodology for Reasoning about Network Games.” Games, vol. 9, no. 3, 39, MDPI AG, 2018, doi:10.3390/g9030039.","ista":"Avni G, Guha S, Kupferman O. 2018. An abstraction-refinement methodology for reasoning about network games. Games. 9(3), 39.","chicago":"Avni, Guy, Shibashis Guha, and Orna Kupferman. “An Abstraction-Refinement Methodology for Reasoning about Network Games.” Games. MDPI AG, 2018. https://doi.org/10.3390/g9030039."},"oa":1,"quality_controlled":"1","publisher":"MDPI AG","date_created":"2019-02-14T14:17:54Z","date_published":"2018-09-01T00:00:00Z","doi":"10.3390/g9030039","publication":"Games","day":"01","year":"2018","has_accepted_license":"1","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"6006","department":[{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:47:16Z","ddc":["004"],"date_updated":"2023-09-22T09:48:59Z","intvolume":" 9","month":"09","scopus_import":1,"oa_version":"Published Version","abstract":[{"text":"Network games (NGs) are played on directed graphs and are extensively used in network design and analysis. Search problems for NGs include finding special strategy profiles such as a Nash equilibrium and a globally-optimal solution. The networks modeled by NGs may be huge. In formal verification, abstraction has proven to be an extremely effective technique for reasoning about systems with big and even infinite state spaces. We describe an abstraction-refinement methodology for reasoning about NGs. Our methodology is based on an abstraction function that maps the state space of an NG to a much smaller state space. We search for a global optimum and a Nash equilibrium by reasoning on an under- and an over-approximation defined on top of this smaller state space. When the approximations are too coarse to find such profiles, we refine the abstraction function. We extend the abstraction-refinement methodology to labeled networks, where the objectives of the players are regular languages. Our experimental results demonstrate the effectiveness of the methodology. ","lang":"eng"}],"related_material":{"record":[{"status":"public","id":"1003","relation":"earlier_version"}]},"issue":"3","volume":9,"language":[{"iso":"eng"}],"file":[{"checksum":"749d65ca4ce74256a029d9644a1b1cb0","file_id":"6008","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2019-02-14T14:20:31Z","file_name":"2018_MDPI_Avni.pdf","creator":"kschuh","date_updated":"2020-07-14T12:47:16Z","file_size":505155}],"publication_status":"published","publication_identifier":{"issn":["2073-4336"]}}]