[{"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","publisher":"IEEE","scopus_import":"1","quality_controlled":"1","month":"09","isi":1,"publication_identifier":{"isbn":["9781538630815"]},"year":"2018","publication_status":"published","day":"10","language":[{"iso":"eng"}],"doi":"10.1109/icra.2018.8461106","date_published":"2018-09-10T00:00:00Z","date_created":"2019-04-04T09:50:38Z","_id":"6195","article_number":"8461106","type":"conference","conference":{"name":"ICRA: International Conference on Robotics and Automation","start_date":"2018-05-21","end_date":"2018-05-25","location":"Brisbane, Australia"},"status":"public","citation":{"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.","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.","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.","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.","short":"M. Pozzi, E. Miguel Villalba, R. Deimel, M. Malvezzi, B. Bickel, O. Brock, D. Prattichizzo, in:, IEEE, 2018.","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","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"},"date_updated":"2023-09-19T14:49:03Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"last_name":"Pozzi","full_name":"Pozzi, Maria","first_name":"Maria"},{"full_name":"Miguel Villalba, Eder","orcid":"0000-0001-5665-0430","last_name":"Miguel Villalba","id":"3FB91342-F248-11E8-B48F-1D18A9856A87","first_name":"Eder"},{"first_name":"Raphael","last_name":"Deimel","full_name":"Deimel, Raphael"},{"first_name":"Monica","last_name":"Malvezzi","full_name":"Malvezzi, Monica"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd","last_name":"Bickel","full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385"},{"first_name":"Oliver","last_name":"Brock","full_name":"Brock, Oliver"},{"full_name":"Prattichizzo, Domenico","last_name":"Prattichizzo","first_name":"Domenico"}],"external_id":{"isi":["000446394503031"]},"article_processing_charge":"No","department":[{"_id":"BeBi"}],"title":"Efficient FEM-based simulation of soft robots modeled as kinematic chains"},{"date_updated":"2023-09-19T15:02:13Z","department":[{"_id":"KrPi"}],"_id":"6941","type":"conference","conference":{"name":"FC: Financial Cryptography and Data Security","start_date":"2018-02-26","end_date":"2018-03-02","location":"Nieuwpoort, Curacao"},"status":"public","publication_identifier":{"issn":["0302-9743"],"isbn":["9783662583869","9783662583876"],"eissn":["1611-3349"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":10957,"ec_funded":1,"abstract":[{"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.","lang":"eng"}],"oa_version":"Submitted Version","scopus_import":"1","alternative_title":["LNCS"],"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2015/528"}],"month":"12","intvolume":" 10957","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Sunoo","last_name":"Park","full_name":"Park, Sunoo"},{"first_name":"Albert","full_name":"Kwon, Albert","last_name":"Kwon"},{"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"},{"id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","first_name":"Joel F","last_name":"Alwen","full_name":"Alwen, Joel F"},{"first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak"}],"external_id":{"isi":["000540656400026"]},"article_processing_charge":"No","title":"SpaceMint: A cryptocurrency based on proofs of space","project":[{"name":"Teaching Old Crypto New Tricks","grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"isi":1,"year":"2018","day":"07","publication":"22nd International Conference on Financial Cryptography and Data Security","page":"480-499","doi":"10.1007/978-3-662-58387-6_26","date_published":"2018-12-07T00:00:00Z","date_created":"2019-10-14T06:35:38Z","publisher":"Springer Nature","quality_controlled":"1","oa":1},{"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)"},"type":"journal_article","status":"public","_id":"6497","department":[{"_id":"MiSi"}],"file_date_updated":"2020-07-14T12:47:32Z","date_updated":"2023-09-19T14:52:08Z","ddc":["570"],"scopus_import":"1","intvolume":" 2015","month":"06","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","volume":2015,"issue":"7","publication_status":"published","publication_identifier":{"issn":["0022-1007"],"eissn":["1540-9538"]},"language":[{"iso":"eng"}],"file":[{"file_name":"2018_rupress_Moalli.pdf","date_created":"2019-05-28T12:40:05Z","creator":"kschuh","file_size":3841660,"date_updated":"2020-07-14T12:47:32Z","checksum":"86ae5331f9bfced9a6358a790a04bef4","file_id":"6498","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"article_processing_charge":"No","external_id":{"isi":["000440822900011"]},"author":[{"first_name":"Federica","last_name":"Moalli","full_name":"Moalli, Federica"},{"first_name":"Xenia","last_name":"Ficht","full_name":"Ficht, Xenia"},{"last_name":"Germann","full_name":"Germann, Philipp","first_name":"Philipp"},{"last_name":"Vladymyrov","full_name":"Vladymyrov, Mykhailo","first_name":"Mykhailo"},{"first_name":"Bettina","last_name":"Stolp","full_name":"Stolp, Bettina"},{"last_name":"de Vries","full_name":"de Vries, Ingrid","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","first_name":"Ingrid"},{"last_name":"Lyck","full_name":"Lyck, Ruth","first_name":"Ruth"},{"first_name":"Jasmin","full_name":"Balmer, Jasmin","last_name":"Balmer"},{"first_name":"Amleto","full_name":"Fiocchi, Amleto","last_name":"Fiocchi"},{"first_name":"Mario","last_name":"Kreutzfeldt","full_name":"Kreutzfeldt, Mario"},{"full_name":"Merkler, Doron","last_name":"Merkler","first_name":"Doron"},{"first_name":"Matteo","full_name":"Iannacone, Matteo","last_name":"Iannacone"},{"first_name":"Akitaka","last_name":"Ariga","full_name":"Ariga, Akitaka"},{"first_name":"Michael H.","last_name":"Stoffel","full_name":"Stoffel, Michael H."},{"first_name":"James","last_name":"Sharpe","full_name":"Sharpe, James"},{"first_name":"Martin","last_name":"Bähler","full_name":"Bähler, Martin"},{"first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt"},{"last_name":"Diz-Muñoz","full_name":"Diz-Muñoz, Alba","first_name":"Alba"},{"full_name":"Stein, Jens V.","last_name":"Stein","first_name":"Jens V."}],"title":"The Rho regulator Myosin IXb enables nonlymphoid tissue seeding of protective CD8+T cells","citation":{"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","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.","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.","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.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"quality_controlled":"1","publisher":"Rockefeller University Press","page":"1869–1890","date_created":"2019-05-28T12:36:47Z","doi":"10.1084/jem.20170896","date_published":"2018-06-06T00:00:00Z","year":"2018","isi":1,"has_accepted_license":"1","publication":"The Journal of Experimental Medicine","day":"06"},{"publication_identifier":{"eissn":["1469-3178"],"issn":["1469-221X"]},"publication_status":"published","file":[{"date_created":"2019-05-28T13:17:19Z","file_name":"2018_embo_Truckenbrodt.pdf","creator":"kschuh","date_updated":"2020-07-14T12:47:32Z","file_size":2005572,"file_id":"6500","checksum":"6ec90abc637f09cca3a7b6424d7e7a26","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"volume":19,"issue":"9","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","date_updated":"2023-09-19T14:52:32Z","ddc":["580"],"file_date_updated":"2020-07-14T12:47:32Z","department":[{"_id":"JoDa"}],"_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","isi":1,"has_accepted_license":"1","year":"2018","day":"01","publication":"EMBO reports","doi":"10.15252/embr.201845836","date_published":"2018-09-01T00:00:00Z","date_created":"2019-05-28T13:16:08Z","quality_controlled":"1","publisher":"EMBO","oa":1,"citation":{"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.","short":"S.M. Truckenbrodt, M. Maidorn, D. Crzan, H. Wildhagen, S. Kabatas, S.O. Rizzoli, EMBO Reports 19 (2018).","ieee":"S. M. Truckenbrodt, M. Maidorn, D. Crzan, H. Wildhagen, S. Kabatas, and S. O. Rizzoli, “X10 expansion microscopy enables 25‐nm resolution on conventional microscopes,” EMBO reports, vol. 19, no. 9. EMBO, 2018.","ama":"Truckenbrodt SM, Maidorn M, Crzan D, Wildhagen H, Kabatas S, Rizzoli SO. X10 expansion microscopy enables 25‐nm resolution on conventional microscopes. EMBO reports. 2018;19(9). doi:10.15252/embr.201845836","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","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."},"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"},{"first_name":"Manuel","last_name":"Maidorn","full_name":"Maidorn, Manuel"},{"first_name":"Dagmar","full_name":"Crzan, Dagmar","last_name":"Crzan"},{"first_name":"Hanna","last_name":"Wildhagen","full_name":"Wildhagen, Hanna"},{"first_name":"Selda","full_name":"Kabatas, Selda","last_name":"Kabatas"},{"full_name":"Rizzoli, Silvio O","last_name":"Rizzoli","first_name":"Silvio O"}],"external_id":{"isi":["000443682200009"]},"article_processing_charge":"No","title":"X10 expansion microscopy enables 25‐nm resolution on conventional microscopes","article_number":"e45836"},{"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","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1704.04947"}],"oa":1,"publisher":"ACM","quality_controlled":"1","month":"01","year":"2018","publication_status":"published","isi":1,"publication_identifier":{"isbn":["9781611975031"]},"language":[{"iso":"eng"}],"publication":"Proceedings of the 29th Annual ACM-SIAM Symposium on Discrete Algorithms","day":"30","page":"2221-2239","date_created":"2019-11-26T15:10:55Z","doi":"10.1137/1.9781611975031.144","date_published":"2018-01-30T00:00:00Z","_id":"7123","conference":{"name":"SODA: Symposium on Discrete Algorithms","start_date":"2018-01-07","end_date":"2018-01-10","location":"New Orleans, LA, United States"},"type":"conference","status":"public","date_updated":"2023-09-19T15:03:16Z","citation":{"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.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000483921200145"],"arxiv":["1704.04947"]},"article_processing_charge":"No","author":[{"first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X"},{"first_name":"James","full_name":"Aspnes, James","last_name":"Aspnes"},{"first_name":"Rati","last_name":"Gelashvili","full_name":"Gelashvili, Rati"}],"department":[{"_id":"DaAl"}],"title":"Space-optimal majority in population protocols"},{"intvolume":" 2","month":"08","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,"issue":"4","related_material":{"record":[{"relation":"research_data","status":"public","id":"9930"}]},"volume":2,"publication_status":"published","publication_identifier":{"issn":["2056-3744"],"eissn":["2056-3744"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"8524e72507d521416be3f8ccfcd5e3f5","file_id":"9918","success":1,"date_updated":"2021-08-16T07:48:03Z","file_size":764299,"creator":"asandaue","date_created":"2021-08-16T07:48:03Z","file_name":"2018_EvolutionLetters_Westram.pdf"}],"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","article_type":"letter_note","status":"public","_id":"9917","file_date_updated":"2021-08-16T07:48:03Z","department":[{"_id":"BeVi"}],"date_updated":"2023-09-19T15:08:25Z","ddc":["570"],"oa":1,"quality_controlled":"1","publisher":"Wiley","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.","page":"297-309","date_created":"2021-08-16T07:45:38Z","date_published":"2018-08-20T00:00:00Z","doi":"10.1002/evl3.74","year":"2018","has_accepted_license":"1","isi":1,"publication":"Evolution Letters","day":"20","article_processing_charge":"Yes","external_id":{"pmid":["30283683"],"isi":["000446774400004"]},"author":[{"first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","last_name":"Westram"},{"first_name":"Marina","full_name":"Rafajlović, Marina","last_name":"Rafajlović"},{"first_name":"Pragya","last_name":"Chaube","full_name":"Chaube, Pragya"},{"first_name":"Rui","full_name":"Faria, Rui","last_name":"Faria"},{"last_name":"Larsson","full_name":"Larsson, Tomas","first_name":"Tomas"},{"last_name":"Panova","full_name":"Panova, Marina","first_name":"Marina"},{"last_name":"Ravinet","full_name":"Ravinet, Mark","first_name":"Mark"},{"first_name":"Anders","last_name":"Blomberg","full_name":"Blomberg, Anders"},{"first_name":"Bernhard","last_name":"Mehlig","full_name":"Mehlig, Bernhard"},{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"},{"full_name":"Butlin, Roger","last_name":"Butlin","first_name":"Roger"}],"title":"Clines on the seashore: The genomic architecture underlying rapid divergence in the face of gene flow","citation":{"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.","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.","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","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","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"},{"file_date_updated":"2021-08-16T07:37:28Z","department":[{"_id":"BeVi"}],"ddc":["570"],"date_updated":"2023-09-19T15:08:53Z","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","article_type":"letter_note","_id":"9915","related_material":{"record":[{"relation":"research_data","status":"public","id":"9929"}]},"issue":"6","volume":2,"language":[{"iso":"eng"}],"file":[{"date_created":"2021-08-16T07:37:28Z","file_name":"2018_EvolutionLetters_Hollander.pdf","creator":"asandaue","date_updated":"2021-08-16T07:37:28Z","file_size":584606,"checksum":"997a78ac41c809975ca69cbdea441f88","file_id":"9916","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"eissn":["2056-3744"],"issn":[" 2056-3744"]},"intvolume":" 2","month":"12","pmid":1,"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 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."}],"title":"Are assortative mating and genital divergence driven by reinforcement?","article_processing_charge":"Yes","external_id":{"isi":["000452990000002"],"pmid":["30564439"]},"author":[{"full_name":"Hollander, Johan","last_name":"Hollander","first_name":"Johan"},{"first_name":"Mauricio","full_name":"Montaño-Rendón, Mauricio","last_name":"Montaño-Rendón"},{"first_name":"Giuseppe","last_name":"Bianco","full_name":"Bianco, Giuseppe"},{"first_name":"Xi","full_name":"Yang, Xi","last_name":"Yang"},{"first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","last_name":"Westram"},{"first_name":"Ludovic","last_name":"Duvaux","full_name":"Duvaux, Ludovic"},{"last_name":"Reid","full_name":"Reid, David G.","first_name":"David G."},{"first_name":"Roger K.","last_name":"Butlin","full_name":"Butlin, Roger K."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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","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","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.","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.","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.","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."},"date_created":"2021-08-16T07:30:00Z","doi":"10.1002/evl3.85","date_published":"2018-12-13T00:00:00Z","page":"557-566","publication":"Evolution Letters","day":"13","year":"2018","isi":1,"has_accepted_license":"1","oa":1,"publisher":"Wiley","quality_controlled":"1","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."},{"month":"02","intvolume":" 8","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"}],"oa_version":"Published Version","pmid":1,"volume":8,"publication_identifier":{"issn":["2045-2322"]},"publication_status":"published","file":[{"checksum":"e642080fcbde9584c63544f587c74f03","file_id":"8619","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2020-10-06T16:35:16Z","file_name":"2018_ScientificReports_Gregor.pdf","date_updated":"2020-10-06T16:35:16Z","file_size":2818077,"creator":"dernst"}],"language":[{"iso":"eng"}],"article_type":"original","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","keyword":["Multidisciplinary"],"_id":"8618","department":[{"_id":"JoDa"}],"file_date_updated":"2020-10-06T16:35:16Z","date_updated":"2023-09-19T15:04:49Z","ddc":["570"],"quality_controlled":"1","publisher":"Springer Nature","oa":1,"doi":"10.1038/s41598-018-19947-1","date_published":"2018-02-09T00:00:00Z","date_created":"2020-10-06T16:33:37Z","isi":1,"has_accepted_license":"1","year":"2018","day":"09","publication":"Scientific Reports","article_number":"2724","author":[{"first_name":"Carola","full_name":"Gregor, Carola","last_name":"Gregor"},{"last_name":"Sidenstein","full_name":"Sidenstein, Sven C.","first_name":"Sven C."},{"full_name":"Andresen, Martin","last_name":"Andresen","first_name":"Martin"},{"full_name":"Sahl, Steffen J.","last_name":"Sahl","first_name":"Steffen J."},{"orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G"},{"first_name":"Stefan W.","full_name":"Hell, Stefan W.","last_name":"Hell"}],"external_id":{"isi":["000424630400037"],"pmid":["29426833"]},"article_processing_charge":"No","title":"Novel reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered from the bacterial photoreceptor YtvA","citation":{"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.","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).","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","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","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.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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.","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","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","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.","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."},"title":"Molecular evolution and diversification of the SMXL gene family","author":[{"first_name":"Taraka Ramji","last_name":"Moturu","full_name":"Moturu, Taraka Ramji"},{"last_name":"Thula","full_name":"Thula, Sravankumar","first_name":"Sravankumar"},{"first_name":"Ravi Kumar","full_name":"Singh, Ravi Kumar","last_name":"Singh"},{"first_name":"Tomasz","last_name":"Nodzyński","full_name":"Nodzyński, Tomasz"},{"last_name":"Vařeková","full_name":"Vařeková, Radka Svobodová","first_name":"Radka Svobodová"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"},{"first_name":"Sibu","last_name":"Simon","full_name":"Simon, Sibu"}],"article_processing_charge":"No","external_id":{"isi":["000430727000016"],"pmid":["29538714"]},"project":[{"call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","name":"Polarity and subcellular dynamics in plants"}],"day":"13","publication":"Journal of Experimental Botany","isi":1,"year":"2018","doi":"10.1093/jxb/ery097","date_published":"2018-04-13T00:00:00Z","date_created":"2022-03-18T12:43:22Z","page":"2367-2378","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. ","quality_controlled":"1","publisher":"Oxford University Press","date_updated":"2023-09-19T15:10:43Z","department":[{"_id":"JiFr"}],"_id":"10881","status":"public","keyword":["Plant Science","Physiology"],"type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0022-0957"],"eissn":["1460-2431"]},"publication_status":"published","issue":"9","volume":69,"ec_funded":1,"oa_version":"None","pmid":1,"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"}],"month":"04","intvolume":" 69","scopus_import":"1"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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","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","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.","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."},"title":"Significance of whole-genome duplications on the emergence of evolutionary novelties","author":[{"orcid":"0000-0002-2853-8051","full_name":"Yuuta, Moriyama","last_name":"Yuuta","id":"4968E7C8-F248-11E8-B48F-1D18A9856A87","first_name":"Moriyama"},{"first_name":"Kazuko","full_name":"Koshiba-Takeuchi, Kazuko","last_name":"Koshiba-Takeuchi"}],"external_id":{"isi":["000456054400004"],"pmid":["29579140"]},"article_processing_charge":"No","acknowledgement":"This work was supported by JSPS overseas research fellowships (Y.M.) and SENSHIN Medical Research Foundation (K.K.T.).","publisher":"Oxford University Press","quality_controlled":"1","oa":1,"day":"01","publication":"Briefings in Functional Genomics","isi":1,"year":"2018","doi":"10.1093/bfgp/ely007","date_published":"2018-09-01T00:00:00Z","date_created":"2022-03-18T12:40:35Z","page":"329-338","_id":"10880","status":"public","keyword":["Genetics","Molecular Biology","Biochemistry","General Medicine"],"article_type":"original","type":"journal_article","date_updated":"2023-09-19T15:11:22Z","department":[{"_id":"CaHe"}],"pmid":1,"oa_version":"Published Version","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."}],"month":"09","intvolume":" 17","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/bfgp/ely007"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2041-2657"],"issn":["2041-2649"]},"publication_status":"published","issue":"5","volume":17}]