[{"main_file_link":[{"url":"https://arxiv.org/abs/2007.14879","open_access":"1"}],"intvolume":"       103","publisher":"American Physical Society","isi":1,"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"department":[{"_id":"MaSe"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000664429700005"],"arxiv":["2007.14879"]},"date_published":"2021-06-21T00:00:00Z","date_created":"2020-08-04T13:03:40Z","publication":"Physical Review B","date_updated":"2023-08-04T10:56:33Z","article_type":"original","article_number":"214204","oa":1,"year":"2021","arxiv":1,"article_processing_charge":"No","volume":103,"day":"21","citation":{"chicago":"Diringer, Asaf A., and Tobias Gulden. “Impact of Drive Harmonics on the Stability of Floquet Many-Body Localization.” <i>Physical Review B</i>. American Physical Society, 2021. <a href=\"https://doi.org/10.1103/PhysRevB.103.214204\">https://doi.org/10.1103/PhysRevB.103.214204</a>.","mla":"Diringer, Asaf A., and Tobias Gulden. “Impact of Drive Harmonics on the Stability of Floquet Many-Body Localization.” <i>Physical Review B</i>, vol. 103, no. 21, 214204, American Physical Society, 2021, doi:<a href=\"https://doi.org/10.1103/PhysRevB.103.214204\">10.1103/PhysRevB.103.214204</a>.","ieee":"A. A. Diringer and T. Gulden, “Impact of drive harmonics on the stability of Floquet many-body localization,” <i>Physical Review B</i>, vol. 103, no. 21. American Physical Society, 2021.","apa":"Diringer, A. A., &#38; Gulden, T. (2021). Impact of drive harmonics on the stability of Floquet many-body localization. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.103.214204\">https://doi.org/10.1103/PhysRevB.103.214204</a>","short":"A.A. Diringer, T. Gulden, Physical Review B 103 (2021).","ama":"Diringer AA, Gulden T. Impact of drive harmonics on the stability of Floquet many-body localization. <i>Physical Review B</i>. 2021;103(21). doi:<a href=\"https://doi.org/10.1103/PhysRevB.103.214204\">10.1103/PhysRevB.103.214204</a>","ista":"Diringer AA, Gulden T. 2021. Impact of drive harmonics on the stability of Floquet many-body localization. Physical Review B. 103(21), 214204."},"month":"06","oa_version":"Preprint","publication_identifier":{"eissn":["24699969"],"issn":["24699950"]},"project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"acknowledgement":"We thank Y. Bar Lev, T. Biadse, and, particularly, E. Bairey and B. Katzir for illuminating discussions and their many insights and help. The authors thank N. Lindner for his support throughout this project. We are further grateful to M. Serbyn, A. Kamenev, A. Turner, and S. de Nicola for reading the manuscript and providing good feedback and suggestions. We acknowledge financial support from the Defense Advanced Research Projects Agency through the DRINQS program, Grant No. D18AC00025. T.G. was in part supported by an Aly Kaufman Fellowship at the Technion. T.G. acknowledges funding from the Institute of Science and Technology (IST) Austria and from the European Union’s Horizon 2020 research and innovation program under Marie SkłodowskaCurie Grant Agreement No. 754411.under the Marie Skłodowska-Curie Grant Agreement No.754411.","publication_status":"published","status":"public","ec_funded":1,"author":[{"first_name":"Asaf A.","full_name":"Diringer, Asaf A.","last_name":"Diringer"},{"orcid":"0000-0001-6814-7541","full_name":"Gulden, Tobias","last_name":"Gulden","id":"1083E038-9F73-11E9-A4B5-532AE6697425","first_name":"Tobias"}],"title":"Impact of drive harmonics on the stability of Floquet many-body localization","_id":"8198","issue":"21","abstract":[{"text":"We investigate how the critical driving amplitude at the Floquet many-body localized (MBL) to ergodic phase transition differs between smooth and nonsmooth drives. To this end, we numerically study a disordered spin-1/2 chain which is periodically driven by a sine or square-wave drive over a wide range of driving frequencies. In both cases the critical driving amplitude increases monotonically with the frequency, and at large frequencies it is identical for the two drives. However, at low and intermediate frequencies the critical amplitude of the square-wave drive depends strongly on the frequency, while that of the sinusoidal drive is almost constant over a wide frequency range. By analyzing the density of drive-induced resonances we conclude that this difference is due to resonances induced by the higher harmonics which are present (absent) in the Fourier spectrum of the square-wave (sine) drive. Furthermore, we suggest a numerically efficient method for estimating the frequency dependence of the critical driving amplitudes for different drives which is based on calculating the density of drive-induced resonances. We conclude that delocalization occurs once the density of drive-induced resonances reaches a critical value determined only by the static system.","lang":"eng"}],"doi":"10.1103/PhysRevB.103.214204"},{"page":"666-686","article_type":"original","date_updated":"2024-03-07T14:54:59Z","publication":"Discrete and Computational Geometry","year":"2021","oa":1,"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","isi":1,"publisher":"Springer Nature","intvolume":"        66","main_file_link":[{"url":"https://doi.org/10.1007/s00454-020-00233-9","open_access":"1"}],"date_created":"2020-08-11T07:11:51Z","scopus_import":"1","date_published":"2021-09-01T00:00:00Z","external_id":{"isi":["000558119300001"]},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"HeEd"}],"ec_funded":1,"status":"public","acknowledgement":"Open access funding provided by the Institute of Science and Technology (IST Austria). Arijit Ghosh is supported by the Ramanujan Fellowship (No. SB/S2/RJN-064/2015), India.\r\nThis work has been funded by the European Research Council under the European Union’s ERC Grant Agreement number 339025 GUDHI (Algorithmic Foundations of Geometric Understanding in Higher Dimensions). The third author is supported by Ramanujan Fellowship (No. SB/S2/RJN-064/2015), India. The fifth author also received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411.","publication_status":"published","project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"publication_identifier":{"issn":["0179-5376"],"eissn":["1432-0444"]},"doi":"10.1007/s00454-020-00233-9","abstract":[{"lang":"eng","text":"We consider the following setting: suppose that we are given a manifold M in Rd with positive reach. Moreover assume that we have an embedded simplical complex A without boundary, whose vertex set lies on the manifold, is sufficiently dense and such that all simplices in A have sufficient quality. We prove that if, locally, interiors of the projection of the simplices onto the tangent space do not intersect, then A is a triangulation of the manifold, that is, they are homeomorphic."}],"_id":"8248","title":"Local conditions for triangulating submanifolds of Euclidean space","author":[{"full_name":"Boissonnat, Jean-Daniel","last_name":"Boissonnat","first_name":"Jean-Daniel"},{"full_name":"Dyer, Ramsay","last_name":"Dyer","first_name":"Ramsay"},{"first_name":"Arijit","full_name":"Ghosh, Arijit","last_name":"Ghosh"},{"full_name":"Lieutier, Andre","last_name":"Lieutier","first_name":"Andre"},{"orcid":"0000-0002-7472-2220","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","first_name":"Mathijs","full_name":"Wintraecken, Mathijs","last_name":"Wintraecken"}],"volume":66,"article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa_version":"Published Version","month":"09","ddc":["510"],"citation":{"short":"J.-D. Boissonnat, R. Dyer, A. Ghosh, A. Lieutier, M. Wintraecken, Discrete and Computational Geometry 66 (2021) 666–686.","ista":"Boissonnat J-D, Dyer R, Ghosh A, Lieutier A, Wintraecken M. 2021. Local conditions for triangulating submanifolds of Euclidean space. Discrete and Computational Geometry. 66, 666–686.","ama":"Boissonnat J-D, Dyer R, Ghosh A, Lieutier A, Wintraecken M. Local conditions for triangulating submanifolds of Euclidean space. <i>Discrete and Computational Geometry</i>. 2021;66:666-686. doi:<a href=\"https://doi.org/10.1007/s00454-020-00233-9\">10.1007/s00454-020-00233-9</a>","apa":"Boissonnat, J.-D., Dyer, R., Ghosh, A., Lieutier, A., &#38; Wintraecken, M. (2021). Local conditions for triangulating submanifolds of Euclidean space. <i>Discrete and Computational Geometry</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00454-020-00233-9\">https://doi.org/10.1007/s00454-020-00233-9</a>","ieee":"J.-D. Boissonnat, R. Dyer, A. Ghosh, A. Lieutier, and M. Wintraecken, “Local conditions for triangulating submanifolds of Euclidean space,” <i>Discrete and Computational Geometry</i>, vol. 66. Springer Nature, pp. 666–686, 2021.","mla":"Boissonnat, Jean-Daniel, et al. “Local Conditions for Triangulating Submanifolds of Euclidean Space.” <i>Discrete and Computational Geometry</i>, vol. 66, Springer Nature, 2021, pp. 666–86, doi:<a href=\"https://doi.org/10.1007/s00454-020-00233-9\">10.1007/s00454-020-00233-9</a>.","chicago":"Boissonnat, Jean-Daniel, Ramsay Dyer, Arijit Ghosh, Andre Lieutier, and Mathijs Wintraecken. “Local Conditions for Triangulating Submanifolds of Euclidean Space.” <i>Discrete and Computational Geometry</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s00454-020-00233-9\">https://doi.org/10.1007/s00454-020-00233-9</a>."},"day":"01"},{"year":"2021","oa":1,"page":"899-925","article_type":"original","date_updated":"2023-08-04T10:53:14Z","publication":"Neural Computation","date_created":"2020-08-12T12:08:24Z","scopus_import":"1","date_published":"2021-03-01T00:00:00Z","external_id":{"pmid":["33513328"],"isi":["000663433900003"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"TiVo"}],"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","isi":1,"publisher":"MIT Press","intvolume":"        33","doi":"10.1162/neco_a_01367","abstract":[{"lang":"eng","text":"Brains process information in spiking neural networks. Their intricate connections shape the diverse functions these networks perform. In comparison, the functional capabilities of models of spiking networks are still rudimentary. This shortcoming is mainly due to the lack of insight and practical algorithms to construct the necessary connectivity. Any such algorithm typically attempts to build networks by iteratively reducing the error compared to a desired output. But assigning credit to hidden units in multi-layered spiking networks has remained challenging due to the non-differentiable nonlinearity of spikes. To avoid this issue, one can employ surrogate gradients to discover the required connectivity in spiking network models. However, the choice of a surrogate is not unique, raising the question of how its implementation influences the effectiveness of the method. Here, we use numerical simulations to systematically study how essential design parameters of surrogate gradients impact learning performance on a range of classification problems. We show that surrogate gradient learning is robust to different shapes of underlying surrogate derivatives, but the choice of the derivative’s scale can substantially affect learning performance. When we combine surrogate gradients with a suitable activity regularization technique, robust information processing can be achieved in spiking networks even at the sparse activity limit. Our study provides a systematic account of the remarkable robustness of surrogate gradient learning and serves as a practical guide to model functional spiking neural networks."}],"issue":"4","_id":"8253","title":"The remarkable robustness of surrogate gradient learning for instilling complex function in spiking neural networks","author":[{"orcid":"0000-0003-1883-644X","full_name":"Zenke, Friedemann","last_name":"Zenke","first_name":"Friedemann"},{"orcid":"0000-0003-3295-6181","last_name":"Vogels","full_name":"Vogels, Tim P","first_name":"Tim P","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425"}],"ec_funded":1,"status":"public","acknowledgement":"F.Z. was supported by the Wellcome Trust (110124/Z/15/Z) and the Novartis Research Foundation. T.P.V. was supported by a Wellcome Trust Sir Henry Dale Research fellowship (WT100000), a Wellcome Trust Senior Research Fellowship (214316/Z/18/Z), and an ERC Consolidator Grant SYNAPSEEK.","publication_status":"published","project":[{"name":"Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning.","call_identifier":"H2020","grant_number":"819603","_id":"0aacfa84-070f-11eb-9043-d7eb2c709234"},{"name":"What’s in a memory? Spatiotemporal dynamics in strongly coupled recurrent neuronal networks.","grant_number":"214316/Z/18/Z","_id":"c084a126-5a5b-11eb-8a69-d75314a70a87"}],"publication_identifier":{"issn":["0899-7667"],"eissn":["1530-888X"]},"oa_version":"Published Version","file_date_updated":"2022-04-08T06:05:39Z","month":"03","pmid":1,"ddc":["000","570"],"citation":{"chicago":"Zenke, Friedemann, and Tim P Vogels. “The Remarkable Robustness of Surrogate Gradient Learning for Instilling Complex Function in Spiking Neural Networks.” <i>Neural Computation</i>. MIT Press, 2021. <a href=\"https://doi.org/10.1162/neco_a_01367\">https://doi.org/10.1162/neco_a_01367</a>.","mla":"Zenke, Friedemann, and Tim P. Vogels. “The Remarkable Robustness of Surrogate Gradient Learning for Instilling Complex Function in Spiking Neural Networks.” <i>Neural Computation</i>, vol. 33, no. 4, MIT Press, 2021, pp. 899–925, doi:<a href=\"https://doi.org/10.1162/neco_a_01367\">10.1162/neco_a_01367</a>.","apa":"Zenke, F., &#38; Vogels, T. P. (2021). The remarkable robustness of surrogate gradient learning for instilling complex function in spiking neural networks. <i>Neural Computation</i>. MIT Press. <a href=\"https://doi.org/10.1162/neco_a_01367\">https://doi.org/10.1162/neco_a_01367</a>","ieee":"F. Zenke and T. P. Vogels, “The remarkable robustness of surrogate gradient learning for instilling complex function in spiking neural networks,” <i>Neural Computation</i>, vol. 33, no. 4. MIT Press, pp. 899–925, 2021.","ama":"Zenke F, Vogels TP. The remarkable robustness of surrogate gradient learning for instilling complex function in spiking neural networks. <i>Neural Computation</i>. 2021;33(4):899-925. doi:<a href=\"https://doi.org/10.1162/neco_a_01367\">10.1162/neco_a_01367</a>","short":"F. Zenke, T.P. Vogels, Neural Computation 33 (2021) 899–925.","ista":"Zenke F, Vogels TP. 2021. The remarkable robustness of surrogate gradient learning for instilling complex function in spiking neural networks. Neural Computation. 33(4), 899–925."},"day":"01","volume":33,"article_processing_charge":"No","has_accepted_license":"1","file":[{"file_id":"11131","date_created":"2022-04-08T06:05:39Z","success":1,"date_updated":"2022-04-08T06:05:39Z","access_level":"open_access","content_type":"application/pdf","checksum":"eac5a51c24c8989ae7cf9ae32ec3bc95","file_name":"2021_NeuralComputation_Zenke.pdf","creator":"dernst","file_size":1611614,"relation":"main_file"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}},{"department":[{"_id":"DaAl"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2021-12-24T00:00:00Z","external_id":{"isi":["000734004600001"],"arxiv":["2003.09297"]},"scopus_import":"1","date_created":"2020-08-24T06:24:04Z","publisher":"Springer Nature","isi":1,"quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"oa":1,"year":"2021","publication":"Algorithmica","date_updated":"2024-03-05T07:35:53Z","related_material":{"record":[{"id":"15077","status":"public","relation":"earlier_version"}],"link":[{"url":"https://doi.org/10.4230/LIPIcs.ICALP.2020.7","relation":"earlier_version"}]},"article_type":"original","day":"24","citation":{"ama":"Alistarh D-A, Nadiradze G, Sabour A. Dynamic averaging load balancing on cycles. <i>Algorithmica</i>. 2021. doi:<a href=\"https://doi.org/10.1007/s00453-021-00905-9\">10.1007/s00453-021-00905-9</a>","ista":"Alistarh D-A, Nadiradze G, Sabour A. 2021. Dynamic averaging load balancing on cycles. Algorithmica.","short":"D.-A. Alistarh, G. Nadiradze, A. Sabour, Algorithmica (2021).","apa":"Alistarh, D.-A., Nadiradze, G., &#38; Sabour, A. (2021). Dynamic averaging load balancing on cycles. <i>Algorithmica</i>. Virtual, Online; Germany: Springer Nature. <a href=\"https://doi.org/10.1007/s00453-021-00905-9\">https://doi.org/10.1007/s00453-021-00905-9</a>","ieee":"D.-A. Alistarh, G. Nadiradze, and A. Sabour, “Dynamic averaging load balancing on cycles,” <i>Algorithmica</i>. Springer Nature, 2021.","mla":"Alistarh, Dan-Adrian, et al. “Dynamic Averaging Load Balancing on Cycles.” <i>Algorithmica</i>, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1007/s00453-021-00905-9\">10.1007/s00453-021-00905-9</a>.","chicago":"Alistarh, Dan-Adrian, Giorgi Nadiradze, and Amirmojtaba Sabour. “Dynamic Averaging Load Balancing on Cycles.” <i>Algorithmica</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s00453-021-00905-9\">https://doi.org/10.1007/s00453-021-00905-9</a>."},"month":"12","ddc":["000"],"file_date_updated":"2021-12-27T10:36:40Z","conference":{"name":"ICALP: International Colloquium on Automata, Languages, and Programming ","end_date":"2020-07-11","start_date":"2020-07-08","location":"Virtual, Online; Germany"},"oa_version":"Published Version","file":[{"file_name":"2021_Algorithmica_Alistarh.pdf","file_size":525950,"creator":"cchlebak","relation":"main_file","success":1,"date_updated":"2021-12-27T10:36:40Z","access_level":"open_access","checksum":"21169b25b0c8e17b21e12af22bff9870","content_type":"application/pdf","file_id":"10577","date_created":"2021-12-27T10:36:40Z"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"arxiv":1,"has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","author":[{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","orcid":"0000-0003-3650-940X"},{"orcid":"0000-0001-5634-0731","last_name":"Nadiradze","full_name":"Nadiradze, Giorgi","first_name":"Giorgi","id":"3279A00C-F248-11E8-B48F-1D18A9856A87"},{"id":"bcc145fd-e77f-11ea-ae8b-80d661dbff67","first_name":"Amirmojtaba","full_name":"Sabour, Amirmojtaba","last_name":"Sabour"}],"title":"Dynamic averaging load balancing on cycles","_id":"8286","abstract":[{"lang":"eng","text":"We consider the following dynamic load-balancing process: given an underlying graph G with n nodes, in each step t≥ 0, one unit of load is created, and placed at a randomly chosen graph node. In the same step, the chosen node picks a random neighbor, and the two nodes balance their loads by averaging them. We are interested in the expected gap between the minimum and maximum loads at nodes as the process progresses, and its dependence on n and on the graph structure. Variants of the above graphical balanced allocation process have been studied previously by Peres, Talwar, and Wieder [Peres et al., 2015], and by Sauerwald and Sun [Sauerwald and Sun, 2015]. These authors left as open the question of characterizing the gap in the case of cycle graphs in the dynamic case, where weights are created during the algorithm’s execution. For this case, the only known upper bound is of 𝒪(n log n), following from a majorization argument due to [Peres et al., 2015], which analyzes a related graphical allocation process. In this paper, we provide an upper bound of 𝒪 (√n log n) on the expected gap of the above process for cycles of length n. We introduce a new potential analysis technique, which enables us to bound the difference in load between k-hop neighbors on the cycle, for any k ≤ n/2. We complement this with a \"gap covering\" argument, which bounds the maximum value of the gap by bounding its value across all possible subsets of a certain structure, and recursively bounding the gaps within each subset. We provide analytical and experimental evidence that our upper bound on the gap is tight up to a logarithmic factor. "}],"doi":"10.1007/s00453-021-00905-9","publication_identifier":{"eissn":["1432-0541"],"issn":["0178-4617"]},"project":[{"name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020","grant_number":"805223","_id":"268A44D6-B435-11E9-9278-68D0E5697425"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"publication_status":"published","acknowledgement":"The authors sincerely thank Thomas Sauerwald and George Giakkoupis for insightful discussions, and Mohsen Ghaffari, Yuval Peres, and Udi Wieder for feedback on earlier versions of this draft. We also thank the ICALP anonymous reviewers for their very useful comments. Open access funding provided by Institute of Science and Technology (IST Austria). Funding was provided by European Research Council (Grant No. PR1042ERC01).","status":"public","ec_funded":1},{"oa_version":"Preprint","month":"02","day":"01","citation":{"mla":"Aichholzer, Oswin, et al. “Folding Polyominoes with Holes into a Cube.” <i>Computational Geometry: Theory and Applications</i>, vol. 93, 101700, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.comgeo.2020.101700\">10.1016/j.comgeo.2020.101700</a>.","chicago":"Aichholzer, Oswin, Hugo A. Akitaya, Kenneth C. Cheung, Erik D. Demaine, Martin L. Demaine, Sándor P. Fekete, Linda Kleist, et al. “Folding Polyominoes with Holes into a Cube.” <i>Computational Geometry: Theory and Applications</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.comgeo.2020.101700\">https://doi.org/10.1016/j.comgeo.2020.101700</a>.","apa":"Aichholzer, O., Akitaya, H. A., Cheung, K. C., Demaine, E. D., Demaine, M. L., Fekete, S. P., … Schmidt, C. (2021). Folding polyominoes with holes into a cube. <i>Computational Geometry: Theory and Applications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.comgeo.2020.101700\">https://doi.org/10.1016/j.comgeo.2020.101700</a>","ieee":"O. Aichholzer <i>et al.</i>, “Folding polyominoes with holes into a cube,” <i>Computational Geometry: Theory and Applications</i>, vol. 93. Elsevier, 2021.","ista":"Aichholzer O, Akitaya HA, Cheung KC, Demaine ED, Demaine ML, Fekete SP, Kleist L, Kostitsyna I, Löffler M, Masárová Z, Mundilova K, Schmidt C. 2021. Folding polyominoes with holes into a cube. Computational Geometry: Theory and Applications. 93, 101700.","short":"O. Aichholzer, H.A. Akitaya, K.C. Cheung, E.D. Demaine, M.L. Demaine, S.P. Fekete, L. Kleist, I. Kostitsyna, M. Löffler, Z. Masárová, K. Mundilova, C. Schmidt, Computational Geometry: Theory and Applications 93 (2021).","ama":"Aichholzer O, Akitaya HA, Cheung KC, et al. Folding polyominoes with holes into a cube. <i>Computational Geometry: Theory and Applications</i>. 2021;93. doi:<a href=\"https://doi.org/10.1016/j.comgeo.2020.101700\">10.1016/j.comgeo.2020.101700</a>"},"article_processing_charge":"No","volume":93,"arxiv":1,"doi":"10.1016/j.comgeo.2020.101700","abstract":[{"lang":"eng","text":"When can a polyomino piece of paper be folded into a unit cube? Prior work studied tree-like polyominoes, but polyominoes with holes remain an intriguing open problem. We present sufficient conditions for a polyomino with one or several holes to fold into a cube, and conditions under which cube folding is impossible. In particular, we show that all but five special “basic” holes guarantee foldability."}],"_id":"8317","author":[{"first_name":"Oswin","full_name":"Aichholzer, Oswin","last_name":"Aichholzer"},{"first_name":"Hugo A.","full_name":"Akitaya, Hugo A.","last_name":"Akitaya"},{"first_name":"Kenneth C.","full_name":"Cheung, Kenneth C.","last_name":"Cheung"},{"first_name":"Erik D.","last_name":"Demaine","full_name":"Demaine, Erik D."},{"full_name":"Demaine, Martin L.","last_name":"Demaine","first_name":"Martin L."},{"last_name":"Fekete","full_name":"Fekete, Sándor P.","first_name":"Sándor P."},{"first_name":"Linda","last_name":"Kleist","full_name":"Kleist, Linda"},{"first_name":"Irina","last_name":"Kostitsyna","full_name":"Kostitsyna, Irina"},{"first_name":"Maarten","last_name":"Löffler","full_name":"Löffler, Maarten"},{"orcid":"0000-0002-6660-1322","last_name":"Masárová","full_name":"Masárová, Zuzana","first_name":"Zuzana","id":"45CFE238-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Mundilova, Klara","last_name":"Mundilova","first_name":"Klara"},{"last_name":"Schmidt","full_name":"Schmidt, Christiane","first_name":"Christiane"}],"title":"Folding polyominoes with holes into a cube","acknowledgement":"This research was performed in part at the 33rd Bellairs Winter Workshop on Computational Geometry. We thank all other participants for a fruitful atmosphere. H. Akitaya was supported by NSF CCF-1422311 & 1423615. Z. Masárová was partially funded by Wittgenstein Prize, Austrian Science Fund (FWF), grant no. Z 342-N31.","publication_status":"published","status":"public","project":[{"name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z00342","_id":"268116B8-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"issn":["09257721"]},"scopus_import":"1","date_created":"2020-08-30T22:01:09Z","external_id":{"arxiv":["1910.09917"],"isi":["000579185100004"]},"date_published":"2021-02-01T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"HeEd"}],"quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"isi":1,"intvolume":"        93","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1910.09917v3"}],"publisher":"Elsevier","year":"2021","oa":1,"article_type":"original","article_number":"101700","related_material":{"record":[{"relation":"shorter_version","status":"public","id":"6989"}]},"date_updated":"2023-08-04T10:57:42Z","publication":"Computational Geometry: Theory and Applications"},{"year":"2021","oa":1,"article_type":"original","page":"938-976","date_updated":"2024-03-07T14:51:11Z","publication":"Discrete and Computational Geometry","scopus_import":"1","date_created":"2020-09-06T22:01:13Z","external_id":{"isi":["000564488500002"],"arxiv":["1908.00856"]},"date_published":"2021-10-01T00:00:00Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"HeEd"}],"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","isi":1,"intvolume":"        66","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1908.00856"}],"publisher":"Springer Nature","doi":"10.1007/s00454-020-00240-w","abstract":[{"lang":"eng","text":"Canonical parametrisations of classical confocal coordinate systems are introduced and exploited to construct non-planar analogues of incircular (IC) nets on individual quadrics and systems of confocal quadrics. Intimate connections with classical deformations of quadrics that are isometric along asymptotic lines and circular cross-sections of quadrics are revealed. The existence of octahedral webs of surfaces of Blaschke type generated by asymptotic and characteristic lines that are diagonally related to lines of curvature is proved theoretically and established constructively. Appropriate samplings (grids) of these webs lead to three-dimensional extensions of non-planar IC nets. Three-dimensional octahedral grids composed of planes and spatially extending (checkerboard) IC-nets are shown to arise in connection with systems of confocal quadrics in Minkowski space. In this context, the Laguerre geometric notion of conical octahedral grids of planes is introduced. The latter generalise the octahedral grids derived from systems of confocal quadrics in Minkowski space. An explicit construction of conical octahedral grids is presented. The results are accompanied by various illustrations which are based on the explicit formulae provided by the theory."}],"_id":"8338","author":[{"orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy","last_name":"Akopyan","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","first_name":"Arseniy"},{"first_name":"Alexander I.","last_name":"Bobenko","full_name":"Bobenko, Alexander I."},{"first_name":"Wolfgang K.","full_name":"Schief, Wolfgang K.","last_name":"Schief"},{"first_name":"Jan","full_name":"Techter, Jan","last_name":"Techter"}],"title":"On mutually diagonal nets on (confocal) quadrics and 3-dimensional webs","ec_funded":1,"publication_status":"published","status":"public","acknowledgement":"This research was supported by the DFG Collaborative Research Center TRR 109 “Discretization in Geometry and Dynamics”. W.K.S. was also supported by the Australian Research Council (DP1401000851). A.V.A. was also supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 78818 Alpha).","project":[{"call_identifier":"H2020","name":"Alpha Shape Theory Extended","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","grant_number":"788183"}],"publication_identifier":{"issn":["0179-5376"],"eissn":["1432-0444"]},"oa_version":"Preprint","month":"10","day":"01","citation":{"short":"A. Akopyan, A.I. Bobenko, W.K. Schief, J. Techter, Discrete and Computational Geometry 66 (2021) 938–976.","ista":"Akopyan A, Bobenko AI, Schief WK, Techter J. 2021. On mutually diagonal nets on (confocal) quadrics and 3-dimensional webs. Discrete and Computational Geometry. 66, 938–976.","ama":"Akopyan A, Bobenko AI, Schief WK, Techter J. On mutually diagonal nets on (confocal) quadrics and 3-dimensional webs. <i>Discrete and Computational Geometry</i>. 2021;66:938-976. doi:<a href=\"https://doi.org/10.1007/s00454-020-00240-w\">10.1007/s00454-020-00240-w</a>","ieee":"A. Akopyan, A. I. Bobenko, W. K. Schief, and J. Techter, “On mutually diagonal nets on (confocal) quadrics and 3-dimensional webs,” <i>Discrete and Computational Geometry</i>, vol. 66. Springer Nature, pp. 938–976, 2021.","apa":"Akopyan, A., Bobenko, A. I., Schief, W. K., &#38; Techter, J. (2021). On mutually diagonal nets on (confocal) quadrics and 3-dimensional webs. <i>Discrete and Computational Geometry</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00454-020-00240-w\">https://doi.org/10.1007/s00454-020-00240-w</a>","chicago":"Akopyan, Arseniy, Alexander I. Bobenko, Wolfgang K. Schief, and Jan Techter. “On Mutually Diagonal Nets on (Confocal) Quadrics and 3-Dimensional Webs.” <i>Discrete and Computational Geometry</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s00454-020-00240-w\">https://doi.org/10.1007/s00454-020-00240-w</a>.","mla":"Akopyan, Arseniy, et al. “On Mutually Diagonal Nets on (Confocal) Quadrics and 3-Dimensional Webs.” <i>Discrete and Computational Geometry</i>, vol. 66, Springer Nature, 2021, pp. 938–76, doi:<a href=\"https://doi.org/10.1007/s00454-020-00240-w\">10.1007/s00454-020-00240-w</a>."},"volume":66,"article_processing_charge":"No","arxiv":1},{"publication_identifier":{"issn":["0024-3795"]},"project":[{"grant_number":"846294","_id":"26A455A6-B435-11E9-9278-68D0E5697425","name":"Geometric study of Wasserstein spaces and free probability","call_identifier":"H2020"},{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"acknowledgement":"The authors are grateful to Milán Mosonyi for fruitful discussions on the topic, and to the anonymous referee for his/her comments and suggestions.\r\nJ. Pitrik was supported by the Hungarian Academy of Sciences Lendület-Momentum Grant for Quantum Information Theory, No. 96 141, and by Hungarian National Research, Development and Innovation Office (NKFIH) via grants no. K119442, no. K124152, and no. KH129601. D. Virosztek was supported by the ISTFELLOW program of the Institute of Science and Technology Austria (project code IC1027FELL01), by the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement No. 846294, and partially supported by the Hungarian National Research, Development and Innovation Office (NKFIH) via grants no. K124152, and no. KH129601.","publication_status":"published","status":"public","ec_funded":1,"title":"A divergence center interpretation of general symmetric Kubo-Ando means, and related weighted multivariate operator means","author":[{"full_name":"Pitrik, József","last_name":"Pitrik","first_name":"József"},{"first_name":"Daniel","id":"48DB45DA-F248-11E8-B48F-1D18A9856A87","last_name":"Virosztek","full_name":"Virosztek, Daniel","orcid":"0000-0003-1109-5511"}],"_id":"8373","abstract":[{"text":"It is well known that special Kubo-Ando operator means admit divergence center interpretations, moreover, they are also mean squared error estimators for certain metrics on positive definite operators. In this paper we give a divergence center interpretation for every symmetric Kubo-Ando mean. This characterization of the symmetric means naturally leads to a definition of weighted and multivariate versions of a large class of symmetric Kubo-Ando means. We study elementary properties of these weighted multivariate means, and note in particular that in the special case of the geometric mean we recover the weighted A#H-mean introduced by Kim, Lawson, and Lim.","lang":"eng"}],"doi":"10.1016/j.laa.2020.09.007","arxiv":1,"article_processing_charge":"No","volume":609,"citation":{"mla":"Pitrik, József, and Daniel Virosztek. “A Divergence Center Interpretation of General Symmetric Kubo-Ando Means, and Related Weighted Multivariate Operator Means.” <i>Linear Algebra and Its Applications</i>, vol. 609, Elsevier, 2021, pp. 203–17, doi:<a href=\"https://doi.org/10.1016/j.laa.2020.09.007\">10.1016/j.laa.2020.09.007</a>.","chicago":"Pitrik, József, and Daniel Virosztek. “A Divergence Center Interpretation of General Symmetric Kubo-Ando Means, and Related Weighted Multivariate Operator Means.” <i>Linear Algebra and Its Applications</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.laa.2020.09.007\">https://doi.org/10.1016/j.laa.2020.09.007</a>.","ieee":"J. Pitrik and D. Virosztek, “A divergence center interpretation of general symmetric Kubo-Ando means, and related weighted multivariate operator means,” <i>Linear Algebra and its Applications</i>, vol. 609. Elsevier, pp. 203–217, 2021.","apa":"Pitrik, J., &#38; Virosztek, D. (2021). A divergence center interpretation of general symmetric Kubo-Ando means, and related weighted multivariate operator means. <i>Linear Algebra and Its Applications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.laa.2020.09.007\">https://doi.org/10.1016/j.laa.2020.09.007</a>","ista":"Pitrik J, Virosztek D. 2021. A divergence center interpretation of general symmetric Kubo-Ando means, and related weighted multivariate operator means. Linear Algebra and its Applications. 609, 203–217.","short":"J. Pitrik, D. Virosztek, Linear Algebra and Its Applications 609 (2021) 203–217.","ama":"Pitrik J, Virosztek D. A divergence center interpretation of general symmetric Kubo-Ando means, and related weighted multivariate operator means. <i>Linear Algebra and its Applications</i>. 2021;609:203-217. doi:<a href=\"https://doi.org/10.1016/j.laa.2020.09.007\">10.1016/j.laa.2020.09.007</a>"},"day":"15","month":"01","oa_version":"Preprint","publication":"Linear Algebra and its Applications","date_updated":"2023-08-04T10:58:14Z","page":"203-217","article_type":"original","oa":1,"year":"2021","keyword":["Kubo-Ando mean","weighted multivariate mean","barycenter"],"publisher":"Elsevier","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2002.11678"}],"intvolume":"       609","isi":1,"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","department":[{"_id":"LaEr"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000581730500011"],"arxiv":["2002.11678"]},"date_published":"2021-01-15T00:00:00Z","date_created":"2020-09-11T08:35:50Z"},{"date_updated":"2023-09-26T10:36:14Z","publication":"Nature Communications","article_type":"original","article_number":"6972","related_material":{"record":[{"relation":"research_data","status":"public","id":"13063"}]},"oa":1,"year":"2021","intvolume":"        12","publisher":"Springer Nature","language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","isi":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"MaRo"}],"scopus_import":"1","date_created":"2020-09-17T10:52:38Z","external_id":{"isi":["000724450600023"]},"date_published":"2021-11-30T00:00:00Z","publication_identifier":{"eissn":["2041-1723"]},"publication_status":"published","acknowledgement":"This project was funded by an SNSF Eccellenza Grant to MRR (PCEGP3-181181), and by core funding from the Institute of Science and Technology Austria. We would like to thank the participants of the cohort studies, and the Ecole Polytechnique Federal Lausanne (EPFL) SCITAS for their excellent compute resources, their generosity with their time and the kindness of their support. P.M.V. acknowledges funding from the Australian National Health and Medical Research Council (1113400) and the Australian Research Council (FL180100072). L.R. acknowledges funding from the Kjell & Märta Beijer Foundation (Stockholm, Sweden). We also would like to acknowledge Simone Rubinacci, Oliver Delanau, Alexander Terenin, Eleonora Porcu, and Mike Goddard for their useful comments and suggestions.","status":"public","_id":"8429","author":[{"first_name":"Marion","full_name":"Patxot, Marion","last_name":"Patxot"},{"last_name":"Trejo Banos","full_name":"Trejo Banos, Daniel","first_name":"Daniel"},{"last_name":"Kousathanas","full_name":"Kousathanas, Athanasios","first_name":"Athanasios"},{"full_name":"Orliac, Etienne J","last_name":"Orliac","first_name":"Etienne J"},{"full_name":"Ojavee, Sven E","last_name":"Ojavee","first_name":"Sven E"},{"first_name":"Gerhard","last_name":"Moser","full_name":"Moser, Gerhard"},{"first_name":"Julia","last_name":"Sidorenko","full_name":"Sidorenko, Julia"},{"full_name":"Kutalik, Zoltan","last_name":"Kutalik","first_name":"Zoltan"},{"last_name":"Magi","full_name":"Magi, Reedik","first_name":"Reedik"},{"last_name":"Visscher","full_name":"Visscher, Peter M","first_name":"Peter M"},{"full_name":"Ronnegard, Lars","last_name":"Ronnegard","first_name":"Lars"},{"orcid":"0000-0001-8982-8813","last_name":"Robinson","full_name":"Robinson, Matthew Richard","first_name":"Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425"}],"title":"Probabilistic inference of the genetic architecture underlying functional enrichment of complex traits","doi":"10.1038/s41467-021-27258-9","issue":"1","abstract":[{"lang":"eng","text":"We develop a Bayesian model (BayesRR-RC) that provides robust SNP-heritability estimation, an alternative to marker discovery, and accurate genomic prediction, taking 22 seconds per iteration to estimate 8.4 million SNP-effects and 78 SNP-heritability parameters in the UK Biobank. We find that only ≤10% of the genetic variation captured for height, body mass index, cardiovascular disease, and type 2 diabetes is attributable to proximal regulatory regions within 10kb upstream of genes, while 12-25% is attributed to coding regions, 32–44% to introns, and 22-28% to distal 10-500kb upstream regions. Up to 24% of all cis and coding regions of each chromosome are associated with each trait, with over 3,100 independent exonic and intronic regions and over 5,400 independent regulatory regions having ≥95% probability of contributing ≥0.001% to the genetic variance of these four traits. Our open-source software (GMRM) provides a scalable alternative to current approaches for biobank data."}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"date_created":"2021-12-06T07:47:11Z","file_id":"10419","content_type":"application/pdf","checksum":"384681be17aff902c149a48f52d13d4f","access_level":"open_access","date_updated":"2021-12-06T07:47:11Z","success":1,"relation":"main_file","file_size":6519771,"creator":"cchlebak","file_name":"2021_NatComm_Paxtot.pdf"}],"article_processing_charge":"No","volume":12,"has_accepted_license":"1","file_date_updated":"2021-12-06T07:47:11Z","month":"11","ddc":["610"],"day":"30","citation":{"mla":"Patxot, Marion, et al. “Probabilistic Inference of the Genetic Architecture Underlying Functional Enrichment of Complex Traits.” <i>Nature Communications</i>, vol. 12, no. 1, 6972, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-27258-9\">10.1038/s41467-021-27258-9</a>.","chicago":"Patxot, Marion, Daniel Trejo Banos, Athanasios Kousathanas, Etienne J Orliac, Sven E Ojavee, Gerhard Moser, Julia Sidorenko, et al. “Probabilistic Inference of the Genetic Architecture Underlying Functional Enrichment of Complex Traits.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-021-27258-9\">https://doi.org/10.1038/s41467-021-27258-9</a>.","ista":"Patxot M, Trejo Banos D, Kousathanas A, Orliac EJ, Ojavee SE, Moser G, Sidorenko J, Kutalik Z, Magi R, Visscher PM, Ronnegard L, Robinson MR. 2021. Probabilistic inference of the genetic architecture underlying functional enrichment of complex traits. Nature Communications. 12(1), 6972.","ama":"Patxot M, Trejo Banos D, Kousathanas A, et al. Probabilistic inference of the genetic architecture underlying functional enrichment of complex traits. <i>Nature Communications</i>. 2021;12(1). doi:<a href=\"https://doi.org/10.1038/s41467-021-27258-9\">10.1038/s41467-021-27258-9</a>","short":"M. Patxot, D. Trejo Banos, A. Kousathanas, E.J. Orliac, S.E. Ojavee, G. Moser, J. Sidorenko, Z. Kutalik, R. Magi, P.M. Visscher, L. Ronnegard, M.R. Robinson, Nature Communications 12 (2021).","ieee":"M. Patxot <i>et al.</i>, “Probabilistic inference of the genetic architecture underlying functional enrichment of complex traits,” <i>Nature Communications</i>, vol. 12, no. 1. Springer Nature, 2021.","apa":"Patxot, M., Trejo Banos, D., Kousathanas, A., Orliac, E. J., Ojavee, S. E., Moser, G., … Robinson, M. R. (2021). Probabilistic inference of the genetic architecture underlying functional enrichment of complex traits. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-021-27258-9\">https://doi.org/10.1038/s41467-021-27258-9</a>"},"oa_version":"Published Version"},{"publication_identifier":{"eissn":["20411723"]},"project":[{"grant_number":"PCEGP3_181181","_id":"9B8D11D6-BA93-11EA-9121-9846C619BF3A","name":"Improving estimation and prediction of common complex disease risk"}],"publication_status":"published","acknowledgement":"This project was funded by an SNSF Eccellenza Grant to MRR (PCEGP3-181181), and by core funding from the Institute of Science and Technology Austria and the University of Lausanne; the work of KF was supported by the grant PUT1665 by the Estonian Research Council. We would like to thank Mike Goddard for comments which greatly improved the work, the participants of the cohort studies, and the Ecole Polytechnique Federal Lausanne (EPFL) SCITAS for their excellent compute resources, their generosity with their time and the kindness of their support.","status":"public","title":"Genomic architecture and prediction of censored time-to-event phenotypes with a Bayesian genome-wide analysis","author":[{"first_name":"Sven E","full_name":"Ojavee, Sven E","last_name":"Ojavee"},{"full_name":"Kousathanas, Athanasios","last_name":"Kousathanas","first_name":"Athanasios"},{"full_name":"Trejo Banos, Daniel","last_name":"Trejo Banos","first_name":"Daniel"},{"last_name":"Orliac","full_name":"Orliac, Etienne J","first_name":"Etienne J"},{"full_name":"Patxot, Marion","last_name":"Patxot","first_name":"Marion"},{"last_name":"Lall","full_name":"Lall, Kristi","first_name":"Kristi"},{"full_name":"Magi, Reedik","last_name":"Magi","first_name":"Reedik"},{"first_name":"Krista","full_name":"Fischer, Krista","last_name":"Fischer"},{"last_name":"Kutalik","full_name":"Kutalik, Zoltan","first_name":"Zoltan"},{"last_name":"Robinson","full_name":"Robinson, Matthew Richard","first_name":"Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","orcid":"0000-0001-8982-8813"}],"_id":"8430","abstract":[{"text":"While recent advancements in computation and modelling have improved the analysis of complex traits, our understanding of the genetic basis of the time at symptom onset remains limited. Here, we develop a Bayesian approach (BayesW) that provides probabilistic inference of the genetic architecture of age-at-onset phenotypes in a sampling scheme that facilitates biobank-scale time-to-event analyses. We show in extensive simulation work the benefits BayesW provides in terms of number of discoveries, model performance and genomic prediction. In the UK Biobank, we find many thousands of common genomic regions underlying the age-at-onset of high blood pressure (HBP), cardiac disease (CAD), and type-2 diabetes (T2D), and for the genetic basis of onset reflecting the underlying genetic liability to disease. Age-at-menopause and age-at-menarche are also highly polygenic, but with higher variance contributed by low frequency variants. Genomic prediction into the Estonian Biobank data shows that BayesW gives higher prediction accuracy than other approaches.","lang":"eng"}],"issue":"1","doi":"10.1038/s41467-021-22538-w","file":[{"creator":"kschuh","relation":"main_file","file_size":6474239,"file_name":"2021_nature_communications_Ojavee.pdf","date_updated":"2021-05-04T15:07:50Z","success":1,"checksum":"eca8b9ae713835c5b785211dd08d8a2e","content_type":"application/pdf","access_level":"open_access","date_created":"2021-05-04T15:07:50Z","file_id":"9372"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","article_processing_charge":"No","volume":12,"citation":{"chicago":"Ojavee, Sven E, Athanasios Kousathanas, Daniel Trejo Banos, Etienne J Orliac, Marion Patxot, Kristi Lall, Reedik Magi, Krista Fischer, Zoltan Kutalik, and Matthew Richard Robinson. “Genomic Architecture and Prediction of Censored Time-to-Event Phenotypes with a Bayesian Genome-Wide Analysis.” <i>Nature Communications</i>. Nature Research, 2021. <a href=\"https://doi.org/10.1038/s41467-021-22538-w\">https://doi.org/10.1038/s41467-021-22538-w</a>.","mla":"Ojavee, Sven E., et al. “Genomic Architecture and Prediction of Censored Time-to-Event Phenotypes with a Bayesian Genome-Wide Analysis.” <i>Nature Communications</i>, vol. 12, no. 1, 2337, Nature Research, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-22538-w\">10.1038/s41467-021-22538-w</a>.","ieee":"S. E. Ojavee <i>et al.</i>, “Genomic architecture and prediction of censored time-to-event phenotypes with a Bayesian genome-wide analysis,” <i>Nature Communications</i>, vol. 12, no. 1. Nature Research, 2021.","apa":"Ojavee, S. E., Kousathanas, A., Trejo Banos, D., Orliac, E. J., Patxot, M., Lall, K., … Robinson, M. R. (2021). Genomic architecture and prediction of censored time-to-event phenotypes with a Bayesian genome-wide analysis. <i>Nature Communications</i>. Nature Research. <a href=\"https://doi.org/10.1038/s41467-021-22538-w\">https://doi.org/10.1038/s41467-021-22538-w</a>","short":"S.E. Ojavee, A. Kousathanas, D. Trejo Banos, E.J. Orliac, M. Patxot, K. Lall, R. Magi, K. Fischer, Z. Kutalik, M.R. Robinson, Nature Communications 12 (2021).","ama":"Ojavee SE, Kousathanas A, Trejo Banos D, et al. Genomic architecture and prediction of censored time-to-event phenotypes with a Bayesian genome-wide analysis. <i>Nature Communications</i>. 2021;12(1). doi:<a href=\"https://doi.org/10.1038/s41467-021-22538-w\">10.1038/s41467-021-22538-w</a>","ista":"Ojavee SE, Kousathanas A, Trejo Banos D, Orliac EJ, Patxot M, Lall K, Magi R, Fischer K, Kutalik Z, Robinson MR. 2021. Genomic architecture and prediction of censored time-to-event phenotypes with a Bayesian genome-wide analysis. Nature Communications. 12(1), 2337."},"day":"20","month":"04","ddc":["570"],"file_date_updated":"2021-05-04T15:07:50Z","oa_version":"Published Version","publication":"Nature Communications","date_updated":"2023-08-04T11:00:17Z","related_material":{"link":[{"url":"https://ist.ac.at/en/news/predicting-the-onset-of-diseases/","description":"News on IST Homepage","relation":"press_release"}]},"article_number":"2337","oa":1,"year":"2021","publisher":"Nature Research","intvolume":"        12","isi":1,"quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","department":[{"_id":"MaRo"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2021-04-20T00:00:00Z","external_id":{"isi":["000642509600006"]},"date_created":"2020-09-17T10:53:00Z","scopus_import":"1"},{"abstract":[{"text":"The synaptotrophic hypothesis posits that synapse formation stabilizes dendritic branches, yet this hypothesis has not been causally tested in vivo in the mammalian brain. Presynaptic ligand cerebellin-1 (Cbln1) and postsynaptic receptor GluD2 mediate synaptogenesis between granule cells and Purkinje cells in the molecular layer of the cerebellar cortex. Here we show that sparse but not global knockout of GluD2 causes under-elaboration of Purkinje cell dendrites in the deep molecular layer and overelaboration in the superficial molecular layer. Developmental, overexpression, structure-function, and genetic epistasis analyses indicate that dendrite morphogenesis defects result from competitive synaptogenesis in a Cbln1/GluD2-dependent manner. A generative model of dendritic growth based on competitive synaptogenesis largely recapitulates GluD2 sparse and global knockout phenotypes. Our results support the synaptotrophic hypothesis at initial stages of dendrite development, suggest a second mode in which cumulative synapse formation inhibits further dendrite growth, and highlight the importance of competition in dendrite morphogenesis.","lang":"eng"}],"issue":"4","doi":"10.1016/j.neuron.2020.11.028","title":"GluD2- and Cbln1-mediated competitive synaptogenesis shapes the dendritic arbors of cerebellar Purkinje cells","author":[{"full_name":"Takeo, Yukari H.","last_name":"Takeo","first_name":"Yukari H."},{"first_name":"S. Andrew","last_name":"Shuster","full_name":"Shuster, S. Andrew"},{"full_name":"Jiang, Linnie","last_name":"Jiang","first_name":"Linnie"},{"first_name":"Miley","last_name":"Hu","full_name":"Hu, Miley"},{"last_name":"Luginbuhl","full_name":"Luginbuhl, David J.","first_name":"David J."},{"first_name":"Thomas","full_name":"Rülicke, Thomas","last_name":"Rülicke"},{"id":"475990FE-F248-11E8-B48F-1D18A9856A87","first_name":"Ximena","full_name":"Contreras, Ximena","last_name":"Contreras"},{"full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","orcid":"0000-0003-2279-1061"},{"first_name":"Mark J.","last_name":"Wagner","full_name":"Wagner, Mark J."},{"last_name":"Ganguli","full_name":"Ganguli, Surya","first_name":"Surya"},{"first_name":"Liqun","last_name":"Luo","full_name":"Luo, Liqun"}],"_id":"8544","acknowledgement":"We thank M. Mishina for GluD2fl frozen embryos, T.C. Südhof and J.I. Morgan for Cbln1fl mice, L. Anderson for help in generating the MADM alleles, W. Joo for a previously unpublished construct, M. Yuzaki, K. Shen, J. Ding, and members of the Luo lab, including J.M. Kebschull, H. Li, J. Li, T. Li, C.M. McLaughlin, D. Pederick, J. Ren, D.C. Wang and C. Xu for discussions and critiques of the manuscript, and M. Yuzaki for supporting Y.H.T. during the final phase of this project. Y.H.T. was supported by a JSPS fellowship; S.A.S. was supported by a Stanford Graduate Fellowship and an NSF Predoctoral Fellowship; L.J. is supported by a Stanford Graduate Fellowship and an NSF Predoctoral Fellowship; M.J.W. is supported by a Burroughs Wellcome Fund CASI Award. This work was supported by an NIH grant (R01-NS050538) to L.L.; the European Research Council (ERC) under the European Union's Horizon 2020 research and innovations programme (No. 725780 LinPro) to S.H.; and Simons and James S. McDonnell Foundations and an NSF CAREER award to S.G.; L.L. is an HHMI investigator.","publication_status":"published","status":"public","ec_funded":1,"publication_identifier":{"eissn":["1097-4199"]},"project":[{"grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020"}],"oa_version":"Preprint","citation":{"chicago":"Takeo, Yukari H., S. Andrew Shuster, Linnie Jiang, Miley Hu, David J. Luginbuhl, Thomas Rülicke, Ximena Contreras, et al. “GluD2- and Cbln1-Mediated Competitive Synaptogenesis Shapes the Dendritic Arbors of Cerebellar Purkinje Cells.” <i>Neuron</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.neuron.2020.11.028\">https://doi.org/10.1016/j.neuron.2020.11.028</a>.","mla":"Takeo, Yukari H., et al. “GluD2- and Cbln1-Mediated Competitive Synaptogenesis Shapes the Dendritic Arbors of Cerebellar Purkinje Cells.” <i>Neuron</i>, vol. 109, no. 4, Elsevier, 2021, p. P629–644.E8, doi:<a href=\"https://doi.org/10.1016/j.neuron.2020.11.028\">10.1016/j.neuron.2020.11.028</a>.","apa":"Takeo, Y. H., Shuster, S. A., Jiang, L., Hu, M., Luginbuhl, D. J., Rülicke, T., … Luo, L. (2021). GluD2- and Cbln1-mediated competitive synaptogenesis shapes the dendritic arbors of cerebellar Purkinje cells. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2020.11.028\">https://doi.org/10.1016/j.neuron.2020.11.028</a>","ieee":"Y. H. Takeo <i>et al.</i>, “GluD2- and Cbln1-mediated competitive synaptogenesis shapes the dendritic arbors of cerebellar Purkinje cells,” <i>Neuron</i>, vol. 109, no. 4. Elsevier, p. P629–644.E8, 2021.","ama":"Takeo YH, Shuster SA, Jiang L, et al. GluD2- and Cbln1-mediated competitive synaptogenesis shapes the dendritic arbors of cerebellar Purkinje cells. <i>Neuron</i>. 2021;109(4):P629-644.E8. doi:<a href=\"https://doi.org/10.1016/j.neuron.2020.11.028\">10.1016/j.neuron.2020.11.028</a>","ista":"Takeo YH, Shuster SA, Jiang L, Hu M, Luginbuhl DJ, Rülicke T, Contreras X, Hippenmeyer S, Wagner MJ, Ganguli S, Luo L. 2021. GluD2- and Cbln1-mediated competitive synaptogenesis shapes the dendritic arbors of cerebellar Purkinje cells. Neuron. 109(4), P629–644.E8.","short":"Y.H. Takeo, S.A. Shuster, L. Jiang, M. Hu, D.J. Luginbuhl, T. Rülicke, X. Contreras, S. Hippenmeyer, M.J. Wagner, S. Ganguli, L. Luo, Neuron 109 (2021) P629–644.E8."},"day":"17","month":"02","article_processing_charge":"No","volume":109,"year":"2021","oa":1,"page":"P629-644.E8","article_type":"original","publication":"Neuron","date_updated":"2024-03-06T12:12:48Z","date_published":"2021-02-17T00:00:00Z","date_created":"2020-09-21T11:59:47Z","scopus_import":"1","department":[{"_id":"SiHi"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"publisher":"Elsevier","main_file_link":[{"url":"https://doi.org/10.1101/2020.06.14.151258","open_access":"1"}],"intvolume":"       109"},{"date_created":"2020-09-21T12:00:48Z","scopus_import":"1","date_published":"2021-06-08T00:00:00Z","external_id":{"pmid":["34107249 "],"isi":["000659894300001"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"SiHi"}],"quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"isi":1,"publisher":"Elsevier","intvolume":"        35","year":"2021","oa":1,"article_number":"109208","article_type":"original","related_material":{"link":[{"url":"https://doi.org/10.1101/2020.03.18.997205","relation":"earlier_version"}]},"date_updated":"2023-08-04T11:00:48Z","publication":"Cell Reports","oa_version":"Published Version","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","file_date_updated":"2021-06-15T14:01:35Z","ddc":["570"],"month":"06","pmid":1,"citation":{"chicago":"Zhang, Tingting, Tengyuan Liu, Natalia Mora, Justine Guegan, Mathilde Bertrand, Ximena Contreras, Andi H Hansen, et al. “Generation of Excitatory and Inhibitory Neurons from Common Progenitors via Notch Signaling in the Cerebellum.” <i>Cell Reports</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.celrep.2021.109208\">https://doi.org/10.1016/j.celrep.2021.109208</a>.","mla":"Zhang, Tingting, et al. “Generation of Excitatory and Inhibitory Neurons from Common Progenitors via Notch Signaling in the Cerebellum.” <i>Cell Reports</i>, vol. 35, no. 10, 109208, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.celrep.2021.109208\">10.1016/j.celrep.2021.109208</a>.","apa":"Zhang, T., Liu, T., Mora, N., Guegan, J., Bertrand, M., Contreras, X., … Hassan, B. A. (2021). Generation of excitatory and inhibitory neurons from common progenitors via Notch signaling in the cerebellum. <i>Cell Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.celrep.2021.109208\">https://doi.org/10.1016/j.celrep.2021.109208</a>","ieee":"T. Zhang <i>et al.</i>, “Generation of excitatory and inhibitory neurons from common progenitors via Notch signaling in the cerebellum,” <i>Cell Reports</i>, vol. 35, no. 10. Elsevier, 2021.","ista":"Zhang T, Liu T, Mora N, Guegan J, Bertrand M, Contreras X, Hansen AH, Streicher C, Anderle M, Danda N, Tiberi L, Hippenmeyer S, Hassan BA. 2021. Generation of excitatory and inhibitory neurons from common progenitors via Notch signaling in the cerebellum. Cell Reports. 35(10), 109208.","ama":"Zhang T, Liu T, Mora N, et al. Generation of excitatory and inhibitory neurons from common progenitors via Notch signaling in the cerebellum. <i>Cell Reports</i>. 2021;35(10). doi:<a href=\"https://doi.org/10.1016/j.celrep.2021.109208\">10.1016/j.celrep.2021.109208</a>","short":"T. Zhang, T. Liu, N. Mora, J. Guegan, M. Bertrand, X. Contreras, A.H. Hansen, C. Streicher, M. Anderle, N. Danda, L. Tiberi, S. Hippenmeyer, B.A. Hassan, Cell Reports 35 (2021)."},"day":"08","article_processing_charge":"No","volume":35,"has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"file":[{"success":1,"date_updated":"2021-06-15T14:01:35Z","access_level":"open_access","checksum":"7def3d42ebc8f5675efb6f38819e3e2e","content_type":"application/pdf","file_name":"2021_CellReports_Zhang.pdf","file_size":8900385,"relation":"main_file","creator":"cziletti","file_id":"9554","date_created":"2021-06-15T14:01:35Z"}],"doi":"10.1016/j.celrep.2021.109208","abstract":[{"text":"Brain neurons arise from relatively few progenitors generating an enormous diversity of neuronal types. Nonetheless, a cardinal feature of mammalian brain neurogenesis is thought to be that excitatory and inhibitory neurons derive from separate, spatially segregated progenitors. Whether bi-potential progenitors with an intrinsic capacity to generate both lineages exist and how such a fate decision may be regulated are unknown. Using cerebellar development as a model, we discover that individual progenitors can give rise to both inhibitory and excitatory lineages. Gradations of Notch activity determine the fates of the progenitors and their daughters. Daughters with the highest levels of Notch activity retain the progenitor fate, while intermediate levels of Notch activity generate inhibitory neurons, and daughters with very low levels of Notch signaling adopt the excitatory fate. Therefore, Notch-mediated binary cell fate choice is a mechanism for regulating the ratio of excitatory to inhibitory neurons from common progenitors.","lang":"eng"}],"issue":"10","_id":"8546","title":"Generation of excitatory and inhibitory neurons from common progenitors via Notch signaling in the cerebellum","author":[{"full_name":"Zhang, Tingting","last_name":"Zhang","first_name":"Tingting"},{"last_name":"Liu","full_name":"Liu, Tengyuan","first_name":"Tengyuan"},{"last_name":"Mora","full_name":"Mora, Natalia","first_name":"Natalia"},{"full_name":"Guegan, Justine","last_name":"Guegan","first_name":"Justine"},{"full_name":"Bertrand, Mathilde","last_name":"Bertrand","first_name":"Mathilde"},{"last_name":"Contreras","full_name":"Contreras, Ximena","first_name":"Ximena","id":"475990FE-F248-11E8-B48F-1D18A9856A87"},{"id":"38853E16-F248-11E8-B48F-1D18A9856A87","first_name":"Andi H","full_name":"Hansen, Andi H","last_name":"Hansen"},{"last_name":"Streicher","full_name":"Streicher, Carmen","first_name":"Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Marica","last_name":"Anderle","full_name":"Anderle, Marica"},{"first_name":"Natasha","full_name":"Danda, Natasha","last_name":"Danda"},{"first_name":"Luca","last_name":"Tiberi","full_name":"Tiberi, Luca"},{"orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon"},{"first_name":"Bassem A.","full_name":"Hassan, Bassem A.","last_name":"Hassan"}],"ec_funded":1,"status":"public","publication_status":"published","acknowledgement":"This work was supported by the program “Investissements d’avenir” ANR-10-IAIHU-06 , ICM , a Sorbonne Université Emergence grant, an Allen Distinguished Investigator Award , and the Roger De Spoelberch Foundation Prize (to B.A.H.); Armenise-Harvard Foundation , AIRC , and CARITRO (to L.T.); and the European Research Council under the European Union’s Horizon 2020 research and innovation programme grant agreement no. 725780 LinPro (to S.H.). T.Z. and T.L. were supported by doctoral fellowships from the China Scholarship Council and A.H.H. by a doctoral DOC fellowship of the Austrian Academy of Sciences ( 24812 ). All animal work was conducted at the PHENO-ICMice facility. The Core is supported by 2 “Investissements d’avenir” (ANR-10- IAIHU-06 and ANR-11-INBS-0011-NeurATRIS) and the “Fondation pour la Recherche Médicale.” Light microscopy work was carried out at ICM’s imaging core facility, ICM.Quant, and analysis of scRNA-seq data was carried out at ICM’s bioinformatics core facility, iCONICS. We thank Paulina Ejsmont, Natalia Danda, and Nathalie De Geest for technical support. We are grateful to Dr. Shahragim TAJBAKHSH for providing R26Rstop-NICD-nGFP transgenic mice, Dr. Bart De Strooper for Psn1-deficient mice, Dr. Jean-Christophe Marine for Gt(ROSA)26SortdTom reporter mice, and Dr. Martinez Barbera for Sox2CreERT2 mice. We also give thanks to Dr. Mikio Hoshino for providing Atoh1 and Ptf1a antibodies. B.A.H. is an Einstein Visiting Fellow of the Berlin Institute of Health .","project":[{"call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425"},{"_id":"2625A13E-B435-11E9-9278-68D0E5697425","grant_number":"24812","name":"Molecular Mechanisms of Radial Neuronal Migration"}],"publication_identifier":{"eissn":[" 22111247"]}},{"date_published":"2021-01-01T00:00:00Z","external_id":{"isi":["000570187900001"]},"date_created":"2020-09-28T08:59:28Z","acknowledged_ssus":[{"_id":"Bio"}],"scopus_import":"1","department":[{"_id":"JiFr"},{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"EvBe"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","publisher":"Wiley","intvolume":"       229","year":"2021","oa":1,"page":"351-369","article_type":"original","publication":"New Phytologist","date_updated":"2023-08-04T11:01:21Z","oa_version":"Published Version","citation":{"chicago":"Li, Hongjiang, Daniel von Wangenheim, Xixi Zhang, Shutang Tan, Nasser Darwish-Miranda, Satoshi Naramoto, Krzysztof T Wabnik, et al. “Cellular Requirements for PIN Polar Cargo Clustering in Arabidopsis Thaliana.” <i>New Phytologist</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/nph.16887\">https://doi.org/10.1111/nph.16887</a>.","mla":"Li, Hongjiang, et al. “Cellular Requirements for PIN Polar Cargo Clustering in Arabidopsis Thaliana.” <i>New Phytologist</i>, vol. 229, no. 1, Wiley, 2021, pp. 351–69, doi:<a href=\"https://doi.org/10.1111/nph.16887\">10.1111/nph.16887</a>.","ama":"Li H, von Wangenheim D, Zhang X, et al. Cellular requirements for PIN polar cargo clustering in Arabidopsis thaliana. <i>New Phytologist</i>. 2021;229(1):351-369. doi:<a href=\"https://doi.org/10.1111/nph.16887\">10.1111/nph.16887</a>","short":"H. Li, D. von Wangenheim, X. Zhang, S. Tan, N. Darwish-Miranda, S. Naramoto, K.T. Wabnik, R. de Rycke, W. Kaufmann, D.J. Gütl, R. Tejos, P. Grones, M. Ke, X. Chen, J. Dettmer, J. Friml, New Phytologist 229 (2021) 351–369.","ista":"Li H, von Wangenheim D, Zhang X, Tan S, Darwish-Miranda N, Naramoto S, Wabnik KT, de Rycke R, Kaufmann W, Gütl DJ, Tejos R, Grones P, Ke M, Chen X, Dettmer J, Friml J. 2021. Cellular requirements for PIN polar cargo clustering in Arabidopsis thaliana. New Phytologist. 229(1), 351–369.","ieee":"H. Li <i>et al.</i>, “Cellular requirements for PIN polar cargo clustering in Arabidopsis thaliana,” <i>New Phytologist</i>, vol. 229, no. 1. Wiley, pp. 351–369, 2021.","apa":"Li, H., von Wangenheim, D., Zhang, X., Tan, S., Darwish-Miranda, N., Naramoto, S., … Friml, J. (2021). Cellular requirements for PIN polar cargo clustering in Arabidopsis thaliana. <i>New Phytologist</i>. Wiley. <a href=\"https://doi.org/10.1111/nph.16887\">https://doi.org/10.1111/nph.16887</a>"},"day":"01","ddc":["580"],"file_date_updated":"2021-02-04T09:44:17Z","month":"01","has_accepted_license":"1","volume":229,"article_processing_charge":"Yes (via OA deal)","file":[{"file_size":4061962,"relation":"main_file","creator":"dernst","file_name":"2021_NewPhytologist_Li.pdf","date_updated":"2021-02-04T09:44:17Z","success":1,"content_type":"application/pdf","checksum":"b45621607b4cab97eeb1605ab58e896e","access_level":"open_access","date_created":"2021-02-04T09:44:17Z","file_id":"9084"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"abstract":[{"lang":"eng","text":"Cell and tissue polarization is fundamental for plant growth and morphogenesis. The polar, cellular localization of Arabidopsis PIN‐FORMED (PIN) proteins is crucial for their function in directional auxin transport. The clustering of PIN polar cargoes within the plasma membrane has been proposed to be important for the maintenance of their polar distribution. However, the more detailed features of PIN clusters and the cellular requirements of cargo clustering remain unclear.\r\nHere, we characterized PIN clusters in detail by means of multiple advanced microscopy and quantification methods, such as 3D quantitative imaging or freeze‐fracture replica labeling. The size and aggregation types of PIN clusters were determined by electron microscopy at the nanometer level at different polar domains and at different developmental stages, revealing a strong preference for clustering at the polar domains.\r\nPharmacological and genetic studies revealed that PIN clusters depend on phosphoinositol pathways, cytoskeletal structures and specific cell‐wall components as well as connections between the cell wall and the plasma membrane.\r\nThis study identifies the role of different cellular processes and structures in polar cargo clustering and provides initial mechanistic insight into the maintenance of polarity in plants and other systems."}],"issue":"1","doi":"10.1111/nph.16887","title":"Cellular requirements for PIN polar cargo clustering in Arabidopsis thaliana","author":[{"orcid":"0000-0001-5039-9660","last_name":"Li","full_name":"Li, Hongjiang","first_name":"Hongjiang","id":"33CA54A6-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-6862-1247","id":"49E91952-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel","full_name":"von Wangenheim, Daniel","last_name":"von Wangenheim"},{"orcid":"0000-0001-7048-4627","first_name":"Xixi","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","last_name":"Zhang","full_name":"Zhang, Xixi"},{"first_name":"Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","last_name":"Tan","full_name":"Tan, Shutang","orcid":"0000-0002-0471-8285"},{"full_name":"Darwish-Miranda, Nasser","last_name":"Darwish-Miranda","id":"39CD9926-F248-11E8-B48F-1D18A9856A87","first_name":"Nasser","orcid":"0000-0002-8821-8236"},{"full_name":"Naramoto, Satoshi","last_name":"Naramoto","first_name":"Satoshi"},{"full_name":"Wabnik, Krzysztof T","last_name":"Wabnik","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof T","orcid":"0000-0001-7263-0560"},{"first_name":"Riet","last_name":"de Rycke","full_name":"de Rycke, Riet"},{"full_name":"Kaufmann, Walter","last_name":"Kaufmann","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","first_name":"Walter","orcid":"0000-0001-9735-5315"},{"first_name":"Daniel J","id":"381929CE-F248-11E8-B48F-1D18A9856A87","last_name":"Gütl","full_name":"Gütl, Daniel J"},{"last_name":"Tejos","full_name":"Tejos, Ricardo","first_name":"Ricardo"},{"full_name":"Grones, Peter","last_name":"Grones","id":"399876EC-F248-11E8-B48F-1D18A9856A87","first_name":"Peter"},{"first_name":"Meiyu","full_name":"Ke, Meiyu","last_name":"Ke"},{"full_name":"Chen, Xu","last_name":"Chen","id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87","first_name":"Xu"},{"last_name":"Dettmer","full_name":"Dettmer, Jan","first_name":"Jan"},{"full_name":"Friml, Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596"}],"_id":"8582","publication_status":"published","status":"public","acknowledgement":"We thank Dr Ingo Heilmann (Martin‐Luther‐University Halle‐Wittenberg) for the XVE>>PIP5K1‐YFP line, Dr Brad Day (Michigan State University) for the ndr1‐1 mutant and the complementation lines, and Dr Patricia C. Zambryski (University of California, Berkeley) for the 35S::P30‐GFP line, the Bioimaging team (IST Austria) for assistance with imaging, group members for discussions, Martine De Cock for help in preparing the manuscript and Nataliia Gnyliukh for critical reading and revision of the manuscript. This project received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (grant agreement No. 742985) and Comisión Nacional de Investigación Científica y Tecnológica (Project CONICYT‐PAI 82130047). DvW received funding from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007‐2013) under REA grant agreement no. 291734.","ec_funded":1,"publication_identifier":{"eissn":["14698137"],"issn":["0028646X"]},"project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985"},{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}]},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"LaEr"}],"date_created":"2020-10-04T22:01:37Z","scopus_import":"1","date_published":"2021-02-01T00:00:00Z","external_id":{"arxiv":["1908.00969"],"isi":["000572724600002"]},"publisher":"Springer Nature","type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","isi":1,"oa":1,"year":"2021","date_updated":"2024-03-07T15:07:53Z","publication":"Probability Theory and Related Fields","article_type":"original","file_date_updated":"2020-10-05T14:53:40Z","month":"02","ddc":["510"],"citation":{"apa":"Cipolloni, G., Erdös, L., &#38; Schröder, D. J. (2021). Edge universality for non-Hermitian random matrices. <i>Probability Theory and Related Fields</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00440-020-01003-7\">https://doi.org/10.1007/s00440-020-01003-7</a>","ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “Edge universality for non-Hermitian random matrices,” <i>Probability Theory and Related Fields</i>. Springer Nature, 2021.","ista":"Cipolloni G, Erdös L, Schröder DJ. 2021. Edge universality for non-Hermitian random matrices. Probability Theory and Related Fields.","ama":"Cipolloni G, Erdös L, Schröder DJ. Edge universality for non-Hermitian random matrices. <i>Probability Theory and Related Fields</i>. 2021. doi:<a href=\"https://doi.org/10.1007/s00440-020-01003-7\">10.1007/s00440-020-01003-7</a>","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Probability Theory and Related Fields (2021).","chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Edge Universality for Non-Hermitian Random Matrices.” <i>Probability Theory and Related Fields</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s00440-020-01003-7\">https://doi.org/10.1007/s00440-020-01003-7</a>.","mla":"Cipolloni, Giorgio, et al. “Edge Universality for Non-Hermitian Random Matrices.” <i>Probability Theory and Related Fields</i>, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1007/s00440-020-01003-7\">10.1007/s00440-020-01003-7</a>."},"day":"01","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"arxiv":1,"file":[{"file_id":"8612","date_created":"2020-10-05T14:53:40Z","success":1,"date_updated":"2020-10-05T14:53:40Z","access_level":"open_access","checksum":"611ae28d6055e1e298d53a57beb05ef4","content_type":"application/pdf","file_name":"2020_ProbTheory_Cipolloni.pdf","creator":"dernst","file_size":497032,"relation":"main_file"}],"article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","_id":"8601","title":"Edge universality for non-Hermitian random matrices","author":[{"full_name":"Cipolloni, Giorgio","last_name":"Cipolloni","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","first_name":"Giorgio","orcid":"0000-0002-4901-7992"},{"last_name":"Erdös","full_name":"Erdös, László","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603"},{"orcid":"0000-0002-2904-1856","full_name":"Schröder, Dominik J","last_name":"Schröder","id":"408ED176-F248-11E8-B48F-1D18A9856A87","first_name":"Dominik J"}],"doi":"10.1007/s00440-020-01003-7","abstract":[{"lang":"eng","text":"We consider large non-Hermitian real or complex random matrices X with independent, identically distributed centred entries. We prove that their local eigenvalue statistics near the spectral edge, the unit circle, coincide with those of the Ginibre ensemble, i.e. when the matrix elements of X are Gaussian. This result is the non-Hermitian counterpart of the universality of the Tracy–Widom distribution at the spectral edges of the Wigner ensemble."}],"project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"},{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804","name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7"},{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"}],"publication_identifier":{"eissn":["14322064"],"issn":["01788051"]},"ec_funded":1,"status":"public","publication_status":"published"},{"status":"public","publication_status":"published","acknowledgement":"We would like to thank G. Tkacik and all of the members of the Hannezo and Hirashima groups for useful discussions, X. Trepat for help on traction force microscopy and M. Matsuda for use of the lab facility. E.H. acknowledges grants from the Austrian Science Fund (FWF) (P 31639) and the European Research Council (851288). T.H. acknowledges a grant from JST, PRESTO (JPMJPR1949). This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 665385 (to D.B.), from JSPS KAKENHI grant no. 17J02107 (to N.H.) and from the SPIRITS 2018 of Kyoto University (to E.H. and T.H.).","ec_funded":1,"publication_identifier":{"eissn":["17452481"],"issn":["17452473"]},"project":[{"_id":"268294B6-B435-11E9-9278-68D0E5697425","grant_number":"P31639","call_identifier":"FWF","name":"Active mechano-chemical description of the cell cytoskeleton"},{"name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020","_id":"05943252-7A3F-11EA-A408-12923DDC885E","grant_number":"851288"},{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"abstract":[{"text":"Collective cell migration offers a rich field of study for non-equilibrium physics and cellular biology, revealing phenomena such as glassy dynamics, pattern formation and active turbulence. However, how mechanical and chemical signalling are integrated at the cellular level to give rise to such collective behaviours remains unclear. We address this by focusing on the highly conserved phenomenon of spatiotemporal waves of density and extracellular signal-regulated kinase (ERK) activation, which appear both in vitro and in vivo during collective cell migration and wound healing. First, we propose a biophysical theory, backed by mechanical and optogenetic perturbation experiments, showing that patterns can be quantitatively explained by a mechanochemical coupling between active cellular tensions and the mechanosensitive ERK pathway. Next, we demonstrate how this biophysical mechanism can robustly induce long-ranged order and migration in a desired orientation, and we determine the theoretically optimal wavelength and period for inducing maximal migration towards free edges, which fits well with experimentally observed dynamics. We thereby provide a bridge between the biophysical origin of spatiotemporal instabilities and the design principles of robust and efficient long-ranged migration.","lang":"eng"}],"doi":"10.1038/s41567-020-01037-7","author":[{"first_name":"Daniel R","id":"453AF628-F248-11E8-B48F-1D18A9856A87","last_name":"Boocock","full_name":"Boocock, Daniel R","orcid":"0000-0002-1585-2631"},{"full_name":"Hino, Naoya","last_name":"Hino","first_name":"Naoya"},{"last_name":"Ruzickova","full_name":"Ruzickova, Natalia","first_name":"Natalia","id":"D2761128-D73D-11E9-A1BF-BA0DE6697425"},{"first_name":"Tsuyoshi","full_name":"Hirashima, Tsuyoshi","last_name":"Hirashima"},{"orcid":"0000-0001-6005-1561","last_name":"Hannezo","full_name":"Hannezo, Edouard B","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"}],"title":"Theory of mechanochemical patterning and optimal migration in cell monolayers","_id":"8602","article_processing_charge":"No","volume":17,"oa_version":"Preprint","day":"01","citation":{"mla":"Boocock, Daniel R., et al. “Theory of Mechanochemical Patterning and Optimal Migration in Cell Monolayers.” <i>Nature Physics</i>, vol. 17, Springer Nature, 2021, pp. 267–74, doi:<a href=\"https://doi.org/10.1038/s41567-020-01037-7\">10.1038/s41567-020-01037-7</a>.","chicago":"Boocock, Daniel R, Naoya Hino, Natalia Ruzickova, Tsuyoshi Hirashima, and Edouard B Hannezo. “Theory of Mechanochemical Patterning and Optimal Migration in Cell Monolayers.” <i>Nature Physics</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41567-020-01037-7\">https://doi.org/10.1038/s41567-020-01037-7</a>.","short":"D.R. Boocock, N. Hino, N. Ruzickova, T. Hirashima, E.B. Hannezo, Nature Physics 17 (2021) 267–274.","ama":"Boocock DR, Hino N, Ruzickova N, Hirashima T, Hannezo EB. Theory of mechanochemical patterning and optimal migration in cell monolayers. <i>Nature Physics</i>. 2021;17:267-274. doi:<a href=\"https://doi.org/10.1038/s41567-020-01037-7\">10.1038/s41567-020-01037-7</a>","ista":"Boocock DR, Hino N, Ruzickova N, Hirashima T, Hannezo EB. 2021. Theory of mechanochemical patterning and optimal migration in cell monolayers. Nature Physics. 17, 267–274.","ieee":"D. R. Boocock, N. Hino, N. Ruzickova, T. Hirashima, and E. B. Hannezo, “Theory of mechanochemical patterning and optimal migration in cell monolayers,” <i>Nature Physics</i>, vol. 17. Springer Nature, pp. 267–274, 2021.","apa":"Boocock, D. R., Hino, N., Ruzickova, N., Hirashima, T., &#38; Hannezo, E. B. (2021). Theory of mechanochemical patterning and optimal migration in cell monolayers. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-020-01037-7\">https://doi.org/10.1038/s41567-020-01037-7</a>"},"month":"02","related_material":{"record":[{"id":"12964","status":"public","relation":"dissertation_contains"}],"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/wound-healing-waves/","relation":"press_release"}]},"article_type":"original","page":"267-274","publication":"Nature Physics","date_updated":"2023-08-04T11:02:41Z","year":"2021","oa":1,"isi":1,"language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","intvolume":"        17","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.05.15.096479"}],"publisher":"Springer Nature","external_id":{"isi":["000573519500002"]},"date_published":"2021-02-01T00:00:00Z","scopus_import":"1","date_created":"2020-10-04T22:01:37Z","department":[{"_id":"EdHa"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"checksum":"5f665ffa6e6dd958aec5c3040cbcfa84","content_type":"application/pdf","access_level":"open_access","date_updated":"2021-03-11T10:03:30Z","success":1,"file_size":334987,"relation":"main_file","creator":"dernst","file_name":"2021_CommPureApplMath_Frank.pdf","date_created":"2021-03-11T10:03:30Z","file_id":"9236"}],"has_accepted_license":"1","volume":74,"article_processing_charge":"No","day":"01","citation":{"mla":"Frank, Rupert, and Robert Seiringer. “Quantum Corrections to the Pekar Asymptotics of a Strongly Coupled Polaron.” <i>Communications on Pure and Applied Mathematics</i>, vol. 74, no. 3, Wiley, 2021, pp. 544–88, doi:<a href=\"https://doi.org/10.1002/cpa.21944\">10.1002/cpa.21944</a>.","chicago":"Frank, Rupert, and Robert Seiringer. “Quantum Corrections to the Pekar Asymptotics of a Strongly Coupled Polaron.” <i>Communications on Pure and Applied Mathematics</i>. Wiley, 2021. <a href=\"https://doi.org/10.1002/cpa.21944\">https://doi.org/10.1002/cpa.21944</a>.","ama":"Frank R, Seiringer R. Quantum corrections to the Pekar asymptotics of a strongly coupled polaron. <i>Communications on Pure and Applied Mathematics</i>. 2021;74(3):544-588. doi:<a href=\"https://doi.org/10.1002/cpa.21944\">10.1002/cpa.21944</a>","ista":"Frank R, Seiringer R. 2021. Quantum corrections to the Pekar asymptotics of a strongly coupled polaron. Communications on Pure and Applied Mathematics. 74(3), 544–588.","short":"R. Frank, R. Seiringer, Communications on Pure and Applied Mathematics 74 (2021) 544–588.","ieee":"R. Frank and R. Seiringer, “Quantum corrections to the Pekar asymptotics of a strongly coupled polaron,” <i>Communications on Pure and Applied Mathematics</i>, vol. 74, no. 3. Wiley, pp. 544–588, 2021.","apa":"Frank, R., &#38; Seiringer, R. (2021). Quantum corrections to the Pekar asymptotics of a strongly coupled polaron. <i>Communications on Pure and Applied Mathematics</i>. Wiley. <a href=\"https://doi.org/10.1002/cpa.21944\">https://doi.org/10.1002/cpa.21944</a>"},"file_date_updated":"2021-03-11T10:03:30Z","month":"03","ddc":["510"],"oa_version":"Published Version","publication_identifier":{"issn":["00103640"],"eissn":["10970312"]},"project":[{"name":"Analysis of quantum many-body systems","call_identifier":"H2020","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"status":"public","publication_status":"published","acknowledgement":"Partial support through National Science Foundation GrantDMS-1363432 (R.L.F.) and the European Research Council (ERC) under the Euro-pean Union’s Horizon 2020 research and innovation programme (grant agreementNo 694227; R.S.), is acknowledged. Open access funding enabled and organizedby Projekt DEAL.","ec_funded":1,"author":[{"full_name":"Frank, Rupert","last_name":"Frank","first_name":"Rupert"},{"orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","full_name":"Seiringer, Robert","last_name":"Seiringer"}],"title":"Quantum corrections to the Pekar asymptotics of a strongly coupled polaron","_id":"8603","issue":"3","abstract":[{"lang":"eng","text":"We consider the Fröhlich polaron model in the strong coupling limit. It is well‐known that to leading order the ground state energy is given by the (classical) Pekar energy. In this work, we establish the subleading correction, describing quantum fluctuation about the classical limit. Our proof applies to a model of a confined polaron, where both the electron and the polarization field are restricted to a set of finite volume, with linear size determined by the natural length scale of the Pekar problem."}],"doi":"10.1002/cpa.21944","intvolume":"        74","publisher":"Wiley","isi":1,"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","department":[{"_id":"RoSe"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000572991500001"]},"date_published":"2021-03-01T00:00:00Z","scopus_import":"1","date_created":"2020-10-04T22:01:37Z","publication":"Communications on Pure and Applied Mathematics","date_updated":"2023-08-04T11:02:16Z","article_type":"original","page":"544-588","oa":1,"year":"2021"},{"oa":1,"year":"2021","publication":"Plant Biotechnology Journal","date_updated":"2023-08-04T11:03:10Z","article_type":"original","page":"548-562","department":[{"_id":"JiFr"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2021-03-01T00:00:00Z","external_id":{"pmid":["32981232"],"isi":["000577682300001"]},"scopus_import":"1","date_created":"2020-10-05T12:44:33Z","intvolume":"        19","publisher":"Wiley","isi":1,"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","author":[{"first_name":"P","last_name":"He","full_name":"He, P"},{"orcid":"0000-0003-2627-6956","last_name":"Zhang","full_name":"Zhang, Yuzhou","first_name":"Yuzhou","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Li","full_name":"Li, H","first_name":"H"},{"first_name":"X","full_name":"Fu, X","last_name":"Fu"},{"full_name":"Shang, H","last_name":"Shang","first_name":"H"},{"full_name":"Zou, C","last_name":"Zou","first_name":"C"},{"full_name":"Friml, Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596"},{"last_name":"Xiao","full_name":"Xiao, G","first_name":"G"}],"title":"GhARF16-1 modulates leaf development by transcriptionally regulating the GhKNOX2-1 gene in cotton","_id":"8606","issue":"3","abstract":[{"text":"The leaf is a crucial organ evolved with remarkable morphological diversity to maximize plant photosynthesis. The leaf shape is a key trait that affects photosynthesis, flowering rates, disease resistance, and yield. Although many genes regulating leaf development have been identified in the past years, the precise regulatory architecture underlying the generation of diverse leaf shapes remains to be elucidated. We used cotton as a reference model to probe the genetic framework underlying divergent leaf forms. Comparative transcriptome analysis revealed that the GhARF16‐1 and GhKNOX2‐1 genes might be potential regulators of leaf shape. We functionally characterized the auxin‐responsive factor ARF16‐1 acting upstream of GhKNOX2‐1 to determine leaf morphology in cotton. The transcription of GhARF16‐1 was significantly higher in lobed‐leaved cotton than in smooth‐leaved cotton. Furthermore, the overexpression of GhARF16‐1 led to the upregulation of GhKNOX2‐1 and resulted in more and deeper serrations in cotton leaves, similar to the leaf shape of cotton plants overexpressing GhKNOX2‐1. We found that GhARF16‐1 specifically bound to the promoter of GhKNOX2‐1 to induce its expression. The heterologous expression of GhARF16‐1 and GhKNOX2‐1 in Arabidopsis led to lobed and curly leaves, and a genetic analysis revealed that GhKNOX2‐1 is epistatic to GhARF16‐1 in Arabidopsis, suggesting that the GhARF16‐1 and GhKNOX2‐1 interaction paradigm also functions to regulate leaf shape in Arabidopsis. To our knowledge, our results uncover a novel mechanism by which auxin, through the key component ARF16‐1 and its downstream‐activated gene KNOX2‐1, determines leaf morphology in eudicots.","lang":"eng"}],"doi":"10.1111/pbi.13484","publication_identifier":{"issn":["1467-7644","1467-7652"]},"status":"public","publication_status":"published","acknowledgement":"We are thankful to Professor Yuxian Zhu from Wuhan University for his extremely valuable remarks and helpful comments on the manuscript. This work was supported by the Shaanxi Natural Science Foundation (2019JQ‐062 and 2020JQ‐410), Shaanxi Youth Entrusted Talents Program (20190205), China Postdoctoral Science Foundation (2018M640947, 2020T130394), Shaanxi Postdoctoral Project (2018BSHYDZZ76), Natural Science Basic Research Plan in Shaanxi Province of China (2018JZ3006), Fundamental Research Funds for the Central Universities (GK201903064, GK201901004, GK202002005 and GK202001004), and State Key Laboratory of Cotton Biology Open Fund (CB2020A12).","day":"01","citation":{"ieee":"P. He <i>et al.</i>, “GhARF16-1 modulates leaf development by transcriptionally regulating the GhKNOX2-1 gene in cotton,” <i>Plant Biotechnology Journal</i>, vol. 19, no. 3. Wiley, pp. 548–562, 2021.","apa":"He, P., Zhang, Y., Li, H., Fu, X., Shang, H., Zou, C., … Xiao, G. (2021). GhARF16-1 modulates leaf development by transcriptionally regulating the GhKNOX2-1 gene in cotton. <i>Plant Biotechnology Journal</i>. Wiley. <a href=\"https://doi.org/10.1111/pbi.13484\">https://doi.org/10.1111/pbi.13484</a>","short":"P. He, Y. Zhang, H. Li, X. Fu, H. Shang, C. Zou, J. Friml, G. Xiao, Plant Biotechnology Journal 19 (2021) 548–562.","ista":"He P, Zhang Y, Li H, Fu X, Shang H, Zou C, Friml J, Xiao G. 2021. GhARF16-1 modulates leaf development by transcriptionally regulating the GhKNOX2-1 gene in cotton. Plant Biotechnology Journal. 19(3), 548–562.","ama":"He P, Zhang Y, Li H, et al. GhARF16-1 modulates leaf development by transcriptionally regulating the GhKNOX2-1 gene in cotton. <i>Plant Biotechnology Journal</i>. 2021;19(3):548-562. doi:<a href=\"https://doi.org/10.1111/pbi.13484\">10.1111/pbi.13484</a>","mla":"He, P., et al. “GhARF16-1 Modulates Leaf Development by Transcriptionally Regulating the GhKNOX2-1 Gene in Cotton.” <i>Plant Biotechnology Journal</i>, vol. 19, no. 3, Wiley, 2021, pp. 548–62, doi:<a href=\"https://doi.org/10.1111/pbi.13484\">10.1111/pbi.13484</a>.","chicago":"He, P, Yuzhou Zhang, H Li, X Fu, H Shang, C Zou, Jiří Friml, and G Xiao. “GhARF16-1 Modulates Leaf Development by Transcriptionally Regulating the GhKNOX2-1 Gene in Cotton.” <i>Plant Biotechnology Journal</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/pbi.13484\">https://doi.org/10.1111/pbi.13484</a>."},"file_date_updated":"2021-04-12T12:29:07Z","month":"03","ddc":["580"],"pmid":1,"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_id":"9321","date_created":"2021-04-12T12:29:07Z","file_name":"2021_PlantBiotechJournal_He.pdf","creator":"dernst","relation":"main_file","file_size":15691871,"access_level":"open_access","checksum":"63845be37fb962586e0c7773f2355970","content_type":"application/pdf","success":1,"date_updated":"2021-04-12T12:29:07Z"}],"has_accepted_license":"1","article_processing_charge":"No","volume":19},{"doi":"10.1111/nph.16915","abstract":[{"text":"To adapt to the diverse array of biotic and abiotic cues, plants have evolved sophisticated mechanisms to sense changes in environmental conditions and modulate their growth. Growth-promoting hormones and defence signalling fine tune plant development antagonistically. During host-pathogen interactions, this defence-growth trade-off is mediated by the counteractive effects of the defence hormone salicylic acid (SA) and the growth hormone auxin. Here we revealed an underlying mechanism of SA regulating auxin signalling by constraining the plasma membrane dynamics of PIN2 auxin efflux transporter in Arabidopsis thaliana roots. The lateral diffusion of PIN2 proteins is constrained by SA signalling, during which PIN2 proteins are condensed into hyperclusters depending on REM1.2-mediated nanodomain compartmentalisation. Furthermore, membrane nanodomain compartmentalisation by SA or Remorin (REM) assembly significantly suppressed clathrin-mediated endocytosis. Consequently, SA-induced heterogeneous surface condensation disrupted asymmetric auxin distribution and the resultant gravitropic response. Our results demonstrated a defence-growth trade-off mechanism by which SA signalling crosstalked with auxin transport by concentrating membrane-resident PIN2 into heterogeneous compartments.","lang":"eng"}],"issue":"2","_id":"8608","title":"Salicylic acid regulates PIN2 auxin transporter hyper-clustering and root gravitropic growth via Remorin-dependent lipid nanodomain organization in Arabidopsis thaliana","author":[{"first_name":"M","last_name":"Ke","full_name":"Ke, M"},{"first_name":"Z","full_name":"Ma, Z","last_name":"Ma"},{"first_name":"D","last_name":"Wang","full_name":"Wang, D"},{"first_name":"Y","full_name":"Sun, Y","last_name":"Sun"},{"last_name":"Wen","full_name":"Wen, C","first_name":"C"},{"first_name":"D","last_name":"Huang","full_name":"Huang, D"},{"last_name":"Chen","full_name":"Chen, Z","first_name":"Z"},{"first_name":"L","full_name":"Yang, L","last_name":"Yang"},{"full_name":"Tan, Shutang","last_name":"Tan","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","first_name":"Shutang","orcid":"0000-0002-0471-8285"},{"last_name":"Li","full_name":"Li, R","first_name":"R"},{"full_name":"Friml, Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596"},{"first_name":"Y","last_name":"Miao","full_name":"Miao, Y"},{"full_name":"Chen, X","last_name":"Chen","first_name":"X"}],"acknowledgement":"This work was supported by the National Key Research andDevelopment Programme of China (2017YFA0506100), theNational Natural Science Foundation of China (31870170 and31701168), and the Fok Ying Tung Education Foundation(161027) to XC; NTU startup grant (M4081533) and NIM/01/2016 (NTU, Singapore) to YM. We thank Lei Shi andZhongquan Lin for microscopy assistance.","publication_status":"published","status":"public","publication_identifier":{"issn":["0028-646x"],"eissn":["1469-8137"]},"oa_version":"Published Version","month":"01","file_date_updated":"2021-02-04T09:53:16Z","pmid":1,"ddc":["580"],"citation":{"apa":"Ke, M., Ma, Z., Wang, D., Sun, Y., Wen, C., Huang, D., … Chen, X. (2021). Salicylic acid regulates PIN2 auxin transporter hyper-clustering and root gravitropic growth via Remorin-dependent lipid nanodomain organization in Arabidopsis thaliana. <i>New Phytologist</i>. Wiley. <a href=\"https://doi.org/10.1111/nph.16915\">https://doi.org/10.1111/nph.16915</a>","ieee":"M. Ke <i>et al.</i>, “Salicylic acid regulates PIN2 auxin transporter hyper-clustering and root gravitropic growth via Remorin-dependent lipid nanodomain organization in Arabidopsis thaliana,” <i>New Phytologist</i>, vol. 229, no. 2. Wiley, pp. 963–978, 2021.","short":"M. Ke, Z. Ma, D. Wang, Y. Sun, C. Wen, D. Huang, Z. Chen, L. Yang, S. Tan, R. Li, J. Friml, Y. Miao, X. Chen, New Phytologist 229 (2021) 963–978.","ista":"Ke M, Ma Z, Wang D, Sun Y, Wen C, Huang D, Chen Z, Yang L, Tan S, Li R, Friml J, Miao Y, Chen X. 2021. Salicylic acid regulates PIN2 auxin transporter hyper-clustering and root gravitropic growth via Remorin-dependent lipid nanodomain organization in Arabidopsis thaliana. New Phytologist. 229(2), 963–978.","ama":"Ke M, Ma Z, Wang D, et al. Salicylic acid regulates PIN2 auxin transporter hyper-clustering and root gravitropic growth via Remorin-dependent lipid nanodomain organization in Arabidopsis thaliana. <i>New Phytologist</i>. 2021;229(2):963-978. doi:<a href=\"https://doi.org/10.1111/nph.16915\">10.1111/nph.16915</a>","mla":"Ke, M., et al. “Salicylic Acid Regulates PIN2 Auxin Transporter Hyper-Clustering and Root Gravitropic Growth via Remorin-Dependent Lipid Nanodomain Organization in Arabidopsis Thaliana.” <i>New Phytologist</i>, vol. 229, no. 2, Wiley, 2021, pp. 963–78, doi:<a href=\"https://doi.org/10.1111/nph.16915\">10.1111/nph.16915</a>.","chicago":"Ke, M, Z Ma, D Wang, Y Sun, C Wen, D Huang, Z Chen, et al. “Salicylic Acid Regulates PIN2 Auxin Transporter Hyper-Clustering and Root Gravitropic Growth via Remorin-Dependent Lipid Nanodomain Organization in Arabidopsis Thaliana.” <i>New Phytologist</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/nph.16915\">https://doi.org/10.1111/nph.16915</a>."},"day":"01","volume":229,"article_processing_charge":"No","has_accepted_license":"1","file":[{"file_size":3674502,"creator":"dernst","relation":"main_file","file_name":"2021_NewPhytologist_Ke.pdf","date_updated":"2021-02-04T09:53:16Z","success":1,"content_type":"application/pdf","checksum":"d36b6a8c6fafab66264e0d27114dae63","access_level":"open_access","date_created":"2021-02-04T09:53:16Z","file_id":"9085"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2021","oa":1,"page":"963-978","article_type":"original","date_updated":"2023-09-05T16:06:24Z","publication":"New Phytologist","date_created":"2020-10-05T12:45:36Z","scopus_import":"1","external_id":{"isi":["000573568000001"],"pmid":["32901934"]},"date_published":"2021-01-01T00:00:00Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"JiFr"}],"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","isi":1,"publisher":"Wiley","intvolume":"       229"},{"arxiv":1,"article_processing_charge":"No","volume":17,"month":"02","day":"01","citation":{"apa":"Modic, K. A., McDonald, R. D., Ruff, J. P. C., Bachmann, M. D., Lai, Y., Palmstrom, J. C., … Shekhter, A. (2021). Scale-invariant magnetic anisotropy in RuCl3 at high magnetic fields. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-020-1028-0\">https://doi.org/10.1038/s41567-020-1028-0</a>","ieee":"K. A. Modic <i>et al.</i>, “Scale-invariant magnetic anisotropy in RuCl3 at high magnetic fields,” <i>Nature Physics</i>, vol. 17. Springer Nature, pp. 240–244, 2021.","short":"K.A. Modic, R.D. McDonald, J.P.C. Ruff, M.D. Bachmann, Y. Lai, J.C. Palmstrom, D. Graf, M.K. Chan, F.F. Balakirev, J.B. Betts, G.S. Boebinger, M. Schmidt, M.J. Lawler, D.A. Sokolov, P.J.W. Moll, B.J. Ramshaw, A. Shekhter, Nature Physics 17 (2021) 240–244.","ista":"Modic KA, McDonald RD, Ruff JPC, Bachmann MD, Lai Y, Palmstrom JC, Graf D, Chan MK, Balakirev FF, Betts JB, Boebinger GS, Schmidt M, Lawler MJ, Sokolov DA, Moll PJW, Ramshaw BJ, Shekhter A. 2021. Scale-invariant magnetic anisotropy in RuCl3 at high magnetic fields. Nature Physics. 17, 240–244.","ama":"Modic KA, McDonald RD, Ruff JPC, et al. Scale-invariant magnetic anisotropy in RuCl3 at high magnetic fields. <i>Nature Physics</i>. 2021;17:240-244. doi:<a href=\"https://doi.org/10.1038/s41567-020-1028-0\">10.1038/s41567-020-1028-0</a>","chicago":"Modic, Kimberly A, Ross D. McDonald, J.P.C. Ruff, Maja D. Bachmann, You Lai, Johanna C. Palmstrom, David Graf, et al. “Scale-Invariant Magnetic Anisotropy in RuCl3 at High Magnetic Fields.” <i>Nature Physics</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41567-020-1028-0\">https://doi.org/10.1038/s41567-020-1028-0</a>.","mla":"Modic, Kimberly A., et al. “Scale-Invariant Magnetic Anisotropy in RuCl3 at High Magnetic Fields.” <i>Nature Physics</i>, vol. 17, Springer Nature, 2021, pp. 240–44, doi:<a href=\"https://doi.org/10.1038/s41567-020-1028-0\">10.1038/s41567-020-1028-0</a>."},"oa_version":"Preprint","publication_identifier":{"eissn":["17452481"],"issn":["17452473"]},"status":"public","acknowledgement":"We thank M. Baenitz, A. Bangura, R. Coldea, G. Jackeli, S. Kivelson, S. Nagler, R. Valenti, C. Varma, S. Winter and J. Zaanen for insightful discussions. Samples were grown at the Max Planck Institute for Chemical Physics of Solids. The d.c.-field measurements were made at the National High Magnetic Field Laboratory (NHMFL) in Tallahassee, FL. The pulsed-field measurements were made in the Pulsed Field Facility of the NHMFL in Los Alamos, NM. All work at the NHMFL is supported through the National Science Foundation Cooperative Agreement nos. DMR-1157490 and DMR-1644779, the US Department of Energy and the State of Florida. R.D.M. acknowledges support from LANL LDRD-DR 20160085 Topology and Strong Correlations. M.C. acknowledges support from the Department of Energy ‘Science of 100 tesla’ BES programme for high-field experiments. X-ray data acquisition and analysis was performed at Cornell University. Research conducted at the Cornell High Energy Synchrotron Source (CHESS) is supported by the National Science Foundation under award no. DMR-1332208. B.J.R. acknowledges support from the Institute for Quantum Matter, an Energy Frontier Research Center funded by the US Department of Energy, Office of Science, Office of Basic Energy Sciences under award no. DE-SC0019331. Y.L. acknowledges support from the US Department of Energy through the LANL/LDRD programme and the G.T. Seaborg institute. J.C.P. is supported by a Gabilan Stanford Graduate Fellowship and an NSF Graduate Research Fellowship (grant no. DGE-114747). P.J.W.M. acknowledges funding from the Swiss National Science Foundation through project no. PP00P2-176789.","publication_status":"published","_id":"8673","author":[{"id":"13C26AC0-EB69-11E9-87C6-5F3BE6697425","first_name":"Kimberly A","full_name":"Modic, Kimberly A","last_name":"Modic","orcid":"0000-0001-9760-3147"},{"last_name":"McDonald","full_name":"McDonald, Ross D.","first_name":"Ross D."},{"last_name":"Ruff","full_name":"Ruff, J.P.C.","first_name":"J.P.C."},{"last_name":"Bachmann","full_name":"Bachmann, Maja D.","first_name":"Maja D."},{"full_name":"Lai, You","last_name":"Lai","first_name":"You"},{"full_name":"Palmstrom, Johanna C.","last_name":"Palmstrom","first_name":"Johanna C."},{"last_name":"Graf","full_name":"Graf, David","first_name":"David"},{"full_name":"Chan, Mun K.","last_name":"Chan","first_name":"Mun K."},{"first_name":"F.F.","full_name":"Balakirev, F.F.","last_name":"Balakirev"},{"first_name":"J.B.","full_name":"Betts, J.B.","last_name":"Betts"},{"first_name":"G.S.","last_name":"Boebinger","full_name":"Boebinger, G.S."},{"first_name":"Marcus","last_name":"Schmidt","full_name":"Schmidt, Marcus"},{"first_name":"Michael J.","last_name":"Lawler","full_name":"Lawler, Michael J."},{"last_name":"Sokolov","full_name":"Sokolov, D.A.","first_name":"D.A."},{"full_name":"Moll, Philip J.W.","last_name":"Moll","first_name":"Philip J.W."},{"first_name":"B.J.","last_name":"Ramshaw","full_name":"Ramshaw, B.J."},{"full_name":"Shekhter, Arkady","last_name":"Shekhter","first_name":"Arkady"}],"title":"Scale-invariant magnetic anisotropy in RuCl3 at high magnetic fields","doi":"10.1038/s41567-020-1028-0","abstract":[{"lang":"eng","text":"In RuCl3, inelastic neutron scattering and Raman spectroscopy reveal a continuum of non-spin-wave excitations that persists to high temperature, suggesting the presence of a spin liquid state on a honeycomb lattice. In the context of the Kitaev model, finite magnetic fields introduce interactions between the elementary excitations, and thus the effects of high magnetic fields that are comparable to the spin-exchange energy scale must be explored. Here, we report measurements of the magnetotropic coefficient—the thermodynamic coefficient associated with magnetic anisotropy—over a wide range of magnetic fields and temperatures. We find that magnetic field and temperature compete to determine the magnetic response in a way that is independent of the large intrinsic exchange-interaction energy. This emergent scale-invariant magnetic anisotropy provides evidence for a high degree of exchange frustration that favours the formation of a spin liquid state in RuCl3."}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2005.04228"}],"intvolume":"        17","publisher":"Springer Nature","language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","isi":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"KiMo"}],"scopus_import":"1","date_created":"2020-10-18T22:01:37Z","external_id":{"isi":["000575344700003"],"arxiv":["2005.04228"]},"date_published":"2021-02-01T00:00:00Z","date_updated":"2023-08-04T11:03:39Z","publication":"Nature Physics","article_type":"original","page":"240-244","oa":1,"year":"2021"},{"status":"public","publication_status":"published","publication_identifier":{"issn":["1560-3547"]},"doi":"10.1134/S1560354721010044","abstract":[{"text":"This paper continues the discussion started in [CK19] concerning Arnold's legacy on classical KAM theory and (some of) its modern developments. We prove a detailed and explicit `global' Arnold's KAM Theorem, which yields, in particular, the Whitney conjugacy of a non{degenerate, real{analytic, nearly-integrable Hamiltonian system to an integrable system on a closed, nowhere dense, positive measure subset of the phase space. Detailed measure estimates on the Kolmogorov's set are provided in the case the phase space is: (A) a uniform neighbourhood of an arbitrary (bounded) set times the d-torus and (B) a domain with C2 boundary times the d-torus. All constants are explicitly given.","lang":"eng"}],"issue":"1","_id":"8689","title":"V.I. Arnold's ''Global'' KAM theorem and geometric measure estimates","author":[{"last_name":"Chierchia","full_name":"Chierchia, Luigi","first_name":"Luigi"},{"id":"52DF3E68-AEFA-11EA-95A4-124A3DDC885E","first_name":"Edmond","full_name":"Koudjinan, Edmond","last_name":"Koudjinan","orcid":"0000-0003-2640-4049"}],"article_processing_charge":"No","volume":26,"arxiv":1,"oa_version":"Preprint","ddc":["515"],"month":"02","citation":{"chicago":"Chierchia, Luigi, and Edmond Koudjinan. “V.I. Arnold’s ‘“Global”’ KAM Theorem and Geometric Measure Estimates.” <i>Regular and Chaotic Dynamics</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1134/S1560354721010044\">https://doi.org/10.1134/S1560354721010044</a>.","mla":"Chierchia, Luigi, and Edmond Koudjinan. “V.I. Arnold’s ‘“Global”’ KAM Theorem and Geometric Measure Estimates.” <i>Regular and Chaotic Dynamics</i>, vol. 26, no. 1, Springer Nature, 2021, pp. 61–88, doi:<a href=\"https://doi.org/10.1134/S1560354721010044\">10.1134/S1560354721010044</a>.","ama":"Chierchia L, Koudjinan E. V.I. Arnold’s “‘Global’” KAM theorem and geometric measure estimates. <i>Regular and Chaotic Dynamics</i>. 2021;26(1):61-88. doi:<a href=\"https://doi.org/10.1134/S1560354721010044\">10.1134/S1560354721010044</a>","ista":"Chierchia L, Koudjinan E. 2021. V.I. Arnold’s ‘“Global”’ KAM theorem and geometric measure estimates. Regular and Chaotic Dynamics. 26(1), 61–88.","short":"L. Chierchia, E. Koudjinan, Regular and Chaotic Dynamics 26 (2021) 61–88.","ieee":"L. Chierchia and E. Koudjinan, “V.I. Arnold’s ‘“Global”’ KAM theorem and geometric measure estimates,” <i>Regular and Chaotic Dynamics</i>, vol. 26, no. 1. Springer Nature, pp. 61–88, 2021.","apa":"Chierchia, L., &#38; Koudjinan, E. (2021). V.I. Arnold’s “‘Global’” KAM theorem and geometric measure estimates. <i>Regular and Chaotic Dynamics</i>. Springer Nature. <a href=\"https://doi.org/10.1134/S1560354721010044\">https://doi.org/10.1134/S1560354721010044</a>"},"day":"03","page":"61-88","article_type":"original","date_updated":"2023-08-07T13:37:27Z","publication":"Regular and Chaotic Dynamics","keyword":["Nearly{integrable Hamiltonian systems","perturbation theory","KAM Theory","Arnold's scheme","Kolmogorov's set","primary invariant tori","Lagrangian tori","measure estimates","small divisors","integrability on nowhere dense sets","Diophantine frequencies."],"year":"2021","oa":1,"quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"isi":1,"publisher":"Springer Nature","main_file_link":[{"url":"https://arxiv.org/abs/2010.13243","open_access":"1"}],"intvolume":"        26","date_created":"2020-10-21T14:56:47Z","scopus_import":"1","external_id":{"isi":["000614454700004"],"arxiv":["2010.13243"]},"date_published":"2021-02-03T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"VaKa"}]},{"article_processing_charge":"No","volume":34,"oa_version":"Preprint","citation":{"chicago":"Simon, Alexis, Christelle Fraisse, Tahani El Ayari, Cathy Liautard‐Haag, Petr Strelkov, John J Welch, and Nicolas Bierne. “How Do Species Barriers Decay? Concordance and Local Introgression in Mosaic Hybrid Zones of Mussels.” <i>Journal of Evolutionary Biology</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/jeb.13709\">https://doi.org/10.1111/jeb.13709</a>.","mla":"Simon, Alexis, et al. “How Do Species Barriers Decay? Concordance and Local Introgression in Mosaic Hybrid Zones of Mussels.” <i>Journal of Evolutionary Biology</i>, vol. 34, no. 1, Wiley, 2021, pp. 208–23, doi:<a href=\"https://doi.org/10.1111/jeb.13709\">10.1111/jeb.13709</a>.","short":"A. Simon, C. Fraisse, T. El Ayari, C. Liautard‐Haag, P. Strelkov, J.J. Welch, N. Bierne, Journal of Evolutionary Biology 34 (2021) 208–223.","ama":"Simon A, Fraisse C, El Ayari T, et al. How do species barriers decay? Concordance and local introgression in mosaic hybrid zones of mussels. <i>Journal of Evolutionary Biology</i>. 2021;34(1):208-223. doi:<a href=\"https://doi.org/10.1111/jeb.13709\">10.1111/jeb.13709</a>","ista":"Simon A, Fraisse C, El Ayari T, Liautard‐Haag C, Strelkov P, Welch JJ, Bierne N. 2021. How do species barriers decay? Concordance and local introgression in mosaic hybrid zones of mussels. Journal of Evolutionary Biology. 34(1), 208–223.","apa":"Simon, A., Fraisse, C., El Ayari, T., Liautard‐Haag, C., Strelkov, P., Welch, J. J., &#38; Bierne, N. (2021). How do species barriers decay? Concordance and local introgression in mosaic hybrid zones of mussels. <i>Journal of Evolutionary Biology</i>. Wiley. <a href=\"https://doi.org/10.1111/jeb.13709\">https://doi.org/10.1111/jeb.13709</a>","ieee":"A. Simon <i>et al.</i>, “How do species barriers decay? Concordance and local introgression in mosaic hybrid zones of mussels,” <i>Journal of Evolutionary Biology</i>, vol. 34, no. 1. Wiley, pp. 208–223, 2021."},"day":"01","pmid":1,"month":"01","status":"public","publication_status":"published","acknowledgement":"Data used in this work were partly produced through the genotyping and sequencing facilities of ISEM and LabEx CeMEB, an ANR ‘Investissements d'avenir’ program (ANR‐10‐LABX‐04‐01) This project benefited from the Montpellier Bioinformatics Biodiversity platform supported by the LabEx CeMEB. We thank Norah Saarman, Grant Pogson, Célia Gosset and Pierre‐Alexandre Gagnaire for providing samples. This work was funded by a Languedoc‐Roussillon ‘Chercheur(se)s d'Avenir’ grant (Connect7 project). P. Strelkov was supported by the Russian Science Foundation project 19‐74‐20024. This is article 2020‐240 of Institut des Sciences de l'Evolution de Montpellier.","publication_identifier":{"issn":["1010061X"],"eissn":["14209101"]},"abstract":[{"text":"The Mytilus complex of marine mussel species forms a mosaic of hybrid zones, found across temperate regions of the globe. This allows us to study ‘replicated’ instances of secondary contact between closely related species. Previous work on this complex has shown that local introgression is both widespread and highly heterogeneous, and has identified SNPs that are outliers of differentiation between lineages. Here, we developed an ancestry‐informative panel of such SNPs. We then compared their frequencies in newly sampled populations, including samples from within the hybrid zones, and parental populations at different distances from the contact. Results show that close to the hybrid zones, some outlier loci are near to fixation for the heterospecific allele, suggesting enhanced local introgression, or the local sweep of a shared ancestral allele. Conversely, genomic cline analyses, treating local parental populations as the reference, reveal a globally high concordance among loci, albeit with a few signals of asymmetric introgression. Enhanced local introgression at specific loci is consistent with the early transfer of adaptive variants after contact, possibly including asymmetric bi‐stable variants (Dobzhansky‐Muller incompatibilities), or haplotypes loaded with fewer deleterious mutations. Having escaped one barrier, however, these variants can be trapped or delayed at the next barrier, confining the introgression locally. These results shed light on the decay of species barriers during phases of contact.","lang":"eng"}],"issue":"1","doi":"10.1111/jeb.13709","title":"How do species barriers decay? Concordance and local introgression in mosaic hybrid zones of mussels","author":[{"last_name":"Simon","full_name":"Simon, Alexis","first_name":"Alexis"},{"first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse","full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075"},{"first_name":"Tahani","last_name":"El Ayari","full_name":"El Ayari, Tahani"},{"first_name":"Cathy","last_name":"Liautard‐Haag","full_name":"Liautard‐Haag, Cathy"},{"last_name":"Strelkov","full_name":"Strelkov, Petr","first_name":"Petr"},{"first_name":"John J","full_name":"Welch, John J","last_name":"Welch"},{"last_name":"Bierne","full_name":"Bierne, Nicolas","first_name":"Nicolas"}],"_id":"8708","isi":1,"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"publisher":"Wiley","main_file_link":[{"url":"https://doi.org/10.1101/818559","open_access":"1"}],"intvolume":"        34","date_published":"2021-01-01T00:00:00Z","external_id":{"isi":["000579599700001"],"pmid":["33045123"]},"date_created":"2020-10-25T23:01:20Z","scopus_import":"1","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","related_material":{"record":[{"status":"public","relation":"research_data","id":"13073"}]},"page":"208-223","article_type":"original","publication":"Journal of Evolutionary Biology","date_updated":"2023-08-04T11:04:11Z","year":"2021","oa":1}]