[{"license":"https://creativecommons.org/licenses/by/4.0/","year":"2021","_id":"9466","publication":"Public-Key Cryptography – PKC 2021","title":"The convergence of slide-type reductions","file_date_updated":"2022-05-27T09:48:31Z","conference":{"name":"PKC: IACR International Conference on Practice and Theory of Public Key Cryptography","start_date":"2021-05-10","end_date":"2021-05-13","location":"Virtual"},"doi":"10.1007/978-3-030-75245-3_3","month":"05","day":"01","volume":12710,"status":"public","publication_status":"published","article_processing_charge":"No","ddc":["000"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_identifier":{"issn":["03029743"],"eissn":["16113349"],"isbn":["9783030752446"]},"language":[{"iso":"eng"}],"quality_controlled":"1","date_updated":"2023-02-23T13:58:47Z","date_created":"2021-06-06T22:01:29Z","date_published":"2021-05-01T00:00:00Z","page":"45-67","alternative_title":["LNCS"],"publisher":"Springer Nature","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","oa_version":"Published Version","ec_funded":1,"author":[{"full_name":"Walter, Michael","first_name":"Michael","orcid":"0000-0003-3186-2482","id":"488F98B0-F248-11E8-B48F-1D18A9856A87","last_name":"Walter"}],"file":[{"creator":"dernst","success":1,"content_type":"application/pdf","checksum":"413e564d645ed93d7318672361d9d470","file_size":489017,"relation":"main_file","access_level":"open_access","date_updated":"2022-05-27T09:48:31Z","date_created":"2022-05-27T09:48:31Z","file_name":"2021_PKC_Walter.pdf","file_id":"11416"}],"project":[{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815","call_identifier":"H2020","name":"Teaching Old Crypto New Tricks"}],"scopus_import":"1","citation":{"ista":"Walter M. 2021. The convergence of slide-type reductions. Public-Key Cryptography – PKC 2021. PKC: IACR International Conference on Practice and Theory of Public Key Cryptography, LNCS, vol. 12710, 45–67.","ieee":"M. Walter, “The convergence of slide-type reductions,” in <i>Public-Key Cryptography – PKC 2021</i>, Virtual, 2021, vol. 12710, pp. 45–67.","mla":"Walter, Michael. “The Convergence of Slide-Type Reductions.” <i>Public-Key Cryptography – PKC 2021</i>, vol. 12710, Springer Nature, 2021, pp. 45–67, doi:<a href=\"https://doi.org/10.1007/978-3-030-75245-3_3\">10.1007/978-3-030-75245-3_3</a>.","short":"M. Walter, in:, Public-Key Cryptography – PKC 2021, Springer Nature, 2021, pp. 45–67.","chicago":"Walter, Michael. “The Convergence of Slide-Type Reductions.” In <i>Public-Key Cryptography – PKC 2021</i>, 12710:45–67. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/978-3-030-75245-3_3\">https://doi.org/10.1007/978-3-030-75245-3_3</a>.","apa":"Walter, M. (2021). The convergence of slide-type reductions. In <i>Public-Key Cryptography – PKC 2021</i> (Vol. 12710, pp. 45–67). Virtual: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-75245-3_3\">https://doi.org/10.1007/978-3-030-75245-3_3</a>","ama":"Walter M. The convergence of slide-type reductions. In: <i>Public-Key Cryptography – PKC 2021</i>. Vol 12710. Springer Nature; 2021:45-67. doi:<a href=\"https://doi.org/10.1007/978-3-030-75245-3_3\">10.1007/978-3-030-75245-3_3</a>"},"acknowledgement":"This work was initiated in discussions with Léo Ducas, when the author was visiting the Simons Institute for the Theory of Computation during the program “Lattices: Algorithms, Complexity, and Cryptography”. We thank Thomas Espitau for pointing out a bug in a proof in an earlier version of this manuscript.","intvolume":"     12710","has_accepted_license":"1","abstract":[{"text":"In this work, we apply the dynamical systems analysis of Hanrot et al. (CRYPTO’11) to a class of lattice block reduction algorithms that includes (natural variants of) slide reduction and block-Rankin reduction. This implies sharper bounds on the polynomial running times (in the query model) for these algorithms and opens the door to faster practical variants of slide reduction. We give heuristic arguments showing that such variants can indeed speed up slide reduction significantly in practice. This is confirmed by experimental evidence, which also shows that our variants are competitive with state-of-the-art reduction algorithms.","lang":"eng"}],"department":[{"_id":"KrPi"}]},{"publication":"Journal of Fluid Mechanics","_id":"9467","year":"2021","file_date_updated":"2021-08-03T09:53:28Z","title":"Suppression of turbulence and travelling waves in a vertical heated pipe","doi":"10.1017/jfm.2021.371","month":"07","day":"25","volume":919,"status":"public","publication_status":"published","article_number":"A17","isi":1,"article_processing_charge":"Yes (via OA deal)","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["530"],"publication_identifier":{"eissn":["14697645"],"issn":["00221120"]},"language":[{"iso":"eng"}],"arxiv":1,"quality_controlled":"1","date_updated":"2023-08-08T13:58:41Z","date_created":"2021-06-06T22:01:30Z","date_published":"2021-07-25T00:00:00Z","publisher":"Cambridge University Press","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","oa":1,"oa_version":"Published Version","author":[{"last_name":"Marensi","id":"0BE7553A-1004-11EA-B805-18983DDC885E","first_name":"Elena","full_name":"Marensi, Elena"},{"last_name":"He","first_name":"Shuisheng","full_name":"He, Shuisheng"},{"first_name":"Ashley P.","full_name":"Willis, Ashley P.","last_name":"Willis"}],"article_type":"original","file":[{"file_id":"9766","file_name":"2021_JournalFluidMechanics_Marensi.pdf","date_created":"2021-08-03T09:53:28Z","date_updated":"2021-08-03T09:53:28Z","access_level":"open_access","relation":"main_file","file_size":4087358,"checksum":"867ad077e45c181c2c5ec1311ba27c41","content_type":"application/pdf","success":1,"creator":"kschuh"}],"citation":{"ama":"Marensi E, He S, Willis AP. Suppression of turbulence and travelling waves in a vertical heated pipe. <i>Journal of Fluid Mechanics</i>. 2021;919. doi:<a href=\"https://doi.org/10.1017/jfm.2021.371\">10.1017/jfm.2021.371</a>","apa":"Marensi, E., He, S., &#38; Willis, A. P. (2021). Suppression of turbulence and travelling waves in a vertical heated pipe. <i>Journal of Fluid Mechanics</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/jfm.2021.371\">https://doi.org/10.1017/jfm.2021.371</a>","chicago":"Marensi, Elena, Shuisheng He, and Ashley P. Willis. “Suppression of Turbulence and Travelling Waves in a Vertical Heated Pipe.” <i>Journal of Fluid Mechanics</i>. Cambridge University Press, 2021. <a href=\"https://doi.org/10.1017/jfm.2021.371\">https://doi.org/10.1017/jfm.2021.371</a>.","short":"E. Marensi, S. He, A.P. Willis, Journal of Fluid Mechanics 919 (2021).","ieee":"E. Marensi, S. He, and A. P. Willis, “Suppression of turbulence and travelling waves in a vertical heated pipe,” <i>Journal of Fluid Mechanics</i>, vol. 919. Cambridge University Press, 2021.","mla":"Marensi, Elena, et al. “Suppression of Turbulence and Travelling Waves in a Vertical Heated Pipe.” <i>Journal of Fluid Mechanics</i>, vol. 919, A17, Cambridge University Press, 2021, doi:<a href=\"https://doi.org/10.1017/jfm.2021.371\">10.1017/jfm.2021.371</a>.","ista":"Marensi E, He S, Willis AP. 2021. Suppression of turbulence and travelling waves in a vertical heated pipe. Journal of Fluid Mechanics. 919, A17."},"acknowledgement":"The anonymous referees are kindly acknowledged for their useful suggestions andcomments.","scopus_import":"1","has_accepted_license":"1","abstract":[{"text":"Turbulence in the flow of fluid through a pipe can be suppressed by buoyancy forces. As the suppression of turbulence leads to severe heat transfer deterioration, this is an important and undesirable phenomenon in both heating and cooling applications. Vertical flow is often considered, as the axial buoyancy force can help drive the flow. With heating measured by the buoyancy parameter 𝐶, our direct numerical simulations show that shear-driven turbulence may either be completely laminarised or it transitions to a relatively quiescent convection-driven state. Buoyancy forces cause a flattening of the base flow profile, which in isothermal pipe flow has recently been linked to complete suppression of turbulence (Kühnen et al., Nat. Phys., vol. 14, 2018, pp. 386–390), and the flattened laminar base profile has enhanced nonlinear stability (Marensi et al., J. Fluid Mech., vol. 863, 2019, pp. 50–875). In agreement with these findings, the nonlinear lower-branch travelling-wave solution analysed here, which is believed to mediate transition to turbulence in isothermal pipe flow, is shown to be suppressed by buoyancy. A linear instability of the laminar base flow is responsible for the appearance of the relatively quiescent convection driven state for 𝐶≳4 across the range of Reynolds numbers considered. In the suppression of turbulence, however, i.e. in the transition from turbulence, we find clearer association with the analysis of He et al. (J. Fluid Mech., vol. 809, 2016, pp. 31–71) than with the above dynamical systems approach, which describes better the transition to turbulence. The laminarisation criterion He et al. propose, based on an apparent Reynolds number of the flow as measured by its driving pressure gradient, is found to capture the critical 𝐶=𝐶𝑐𝑟(𝑅𝑒) above which the flow will be laminarised or switch to the convection-driven type. Our analysis suggests that it is the weakened rolls, rather than the streaks, which appear to be critical for laminarisation.","lang":"eng"}],"intvolume":"       919","external_id":{"arxiv":["2008.13486"],"isi":["000653785000001"]},"department":[{"_id":"BjHo"}]},{"intvolume":"        35","abstract":[{"text":"Motivated by the successful application of geometry to proving the Harary--Hill conjecture for “pseudolinear” drawings of $K_n$, we introduce “pseudospherical” drawings of graphs. A spherical drawing of a graph $G$ is a drawing in the unit sphere $\\mathbb{S}^2$ in which the vertices of $G$ are represented as points---no three on a great circle---and the edges of $G$ are shortest-arcs in $\\mathbb{S}^2$ connecting pairs of vertices. Such a drawing has three properties: (1) every edge $e$ is contained in a simple closed curve $\\gamma_e$ such that the only vertices in $\\gamma_e$ are the ends of $e$; (2) if $e\\ne f$, then $\\gamma_e\\cap\\gamma_f$ has precisely two crossings; and (3) if $e\\ne f$, then $e$ intersects $\\gamma_f$ at most once, in either a crossing or an end of $e$. We use properties (1)--(3) to define a pseudospherical drawing of $G$. Our main result is that for the complete graph, properties (1)--(3) are equivalent to the same three properties but with “precisely two crossings” in (2) replaced by “at most two crossings.” The proof requires a result in the geometric transversal theory of arrangements of pseudocircles. This is proved using the surprising result that the absence of special arcs (coherent spirals) in an arrangement of simple closed curves characterizes the fact that any two curves in the arrangement have at most two crossings. Our studies provide the necessary ideas for exhibiting a drawing of $K_{10}$ that has no extension to an arrangement of pseudocircles and a drawing of $K_9$ that does extend to an arrangement of pseudocircles, but no such extension has all pairs of pseudocircles crossing twice.\r\n","lang":"eng"}],"department":[{"_id":"UlWa"}],"external_id":{"isi":["000674142200022"],"arxiv":["2001.06053"]},"scopus_import":"1","citation":{"ieee":"A. M. Arroyo Guevara, R. B. Richter, and M. Sunohara, “Extending drawings of complete graphs into arrangements of pseudocircles,” <i>SIAM Journal on Discrete Mathematics</i>, vol. 35, no. 2. Society for Industrial and Applied Mathematics, pp. 1050–1076, 2021.","mla":"Arroyo Guevara, Alan M., et al. “Extending Drawings of Complete Graphs into Arrangements of Pseudocircles.” <i>SIAM Journal on Discrete Mathematics</i>, vol. 35, no. 2, Society for Industrial and Applied Mathematics, 2021, pp. 1050–76, doi:<a href=\"https://doi.org/10.1137/20M1313234\">10.1137/20M1313234</a>.","ista":"Arroyo Guevara AM, Richter RB, Sunohara M. 2021. Extending drawings of complete graphs into arrangements of pseudocircles. SIAM Journal on Discrete Mathematics. 35(2), 1050–1076.","ama":"Arroyo Guevara AM, Richter RB, Sunohara M. Extending drawings of complete graphs into arrangements of pseudocircles. <i>SIAM Journal on Discrete Mathematics</i>. 2021;35(2):1050-1076. doi:<a href=\"https://doi.org/10.1137/20M1313234\">10.1137/20M1313234</a>","apa":"Arroyo Guevara, A. M., Richter, R. B., &#38; Sunohara, M. (2021). Extending drawings of complete graphs into arrangements of pseudocircles. <i>SIAM Journal on Discrete Mathematics</i>. Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/20M1313234\">https://doi.org/10.1137/20M1313234</a>","short":"A.M. Arroyo Guevara, R.B. Richter, M. Sunohara, SIAM Journal on Discrete Mathematics 35 (2021) 1050–1076.","chicago":"Arroyo Guevara, Alan M, R. Bruce Richter, and Matthew Sunohara. “Extending Drawings of Complete Graphs into Arrangements of Pseudocircles.” <i>SIAM Journal on Discrete Mathematics</i>. Society for Industrial and Applied Mathematics, 2021. <a href=\"https://doi.org/10.1137/20M1313234\">https://doi.org/10.1137/20M1313234</a>."},"project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"author":[{"orcid":"0000-0003-2401-8670","last_name":"Arroyo Guevara","id":"3207FDC6-F248-11E8-B48F-1D18A9856A87","full_name":"Arroyo Guevara, Alan M","first_name":"Alan M"},{"full_name":"Richter, R. Bruce","first_name":"R. Bruce","last_name":"Richter"},{"last_name":"Sunohara","first_name":"Matthew","full_name":"Sunohara, Matthew"}],"ec_funded":1,"article_type":"original","oa":1,"issue":"2","type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Society for Industrial and Applied Mathematics","oa_version":"Preprint","arxiv":1,"quality_controlled":"1","language":[{"iso":"eng"}],"date_published":"2021-05-20T00:00:00Z","page":"1050-1076","date_updated":"2023-08-08T13:58:12Z","date_created":"2021-06-06T22:01:30Z","article_processing_charge":"No","isi":1,"publication_status":"published","publication_identifier":{"issn":["08954801"]},"month":"05","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2001.06053"}],"status":"public","volume":35,"day":"20","title":"Extending drawings of complete graphs into arrangements of pseudocircles","_id":"9468","year":"2021","publication":"SIAM Journal on Discrete Mathematics","doi":"10.1137/20M1313234"},{"date_published":"2021-05-12T00:00:00Z","date_created":"2021-06-06T22:01:30Z","date_updated":"2023-08-08T13:57:43Z","quality_controlled":"1","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1055-6788"],"eissn":["1029-4937"]},"article_processing_charge":"No","isi":1,"publication_status":"published","status":"public","day":"12","month":"05","doi":"10.1080/10556788.2021.1924715","title":"Reflected three-operator splitting method for monotone inclusion problem","_id":"9469","year":"2021","publication":"Optimization Methods and Software","department":[{"_id":"VlKo"}],"external_id":{"isi":["000650507600001"]},"abstract":[{"text":"In this paper, we consider reflected three-operator splitting methods for monotone inclusion problems in real Hilbert spaces. To do this, we first obtain weak convergence analysis and nonasymptotic O(1/n) convergence rate of the reflected Krasnosel'skiĭ-Mann iteration for finding a fixed point of nonexpansive mapping in real Hilbert spaces under some seemingly easy to implement conditions on the iterative parameters. We then apply our results to three-operator splitting for the monotone inclusion problem and consequently obtain the corresponding convergence analysis. Furthermore, we derive reflected primal-dual algorithms for highly structured monotone inclusion problems. Some numerical implementations are drawn from splitting methods to support the theoretical analysis.","lang":"eng"}],"scopus_import":"1","citation":{"ista":"Iyiola OS, Enyi CD, Shehu Y. 2021. Reflected three-operator splitting method for monotone inclusion problem. Optimization Methods and Software.","mla":"Iyiola, Olaniyi S., et al. “Reflected Three-Operator Splitting Method for Monotone Inclusion Problem.” <i>Optimization Methods and Software</i>, Taylor and Francis, 2021, doi:<a href=\"https://doi.org/10.1080/10556788.2021.1924715\">10.1080/10556788.2021.1924715</a>.","ieee":"O. S. Iyiola, C. D. Enyi, and Y. Shehu, “Reflected three-operator splitting method for monotone inclusion problem,” <i>Optimization Methods and Software</i>. Taylor and Francis, 2021.","chicago":"Iyiola, Olaniyi S., Cyril D. Enyi, and Yekini Shehu. “Reflected Three-Operator Splitting Method for Monotone Inclusion Problem.” <i>Optimization Methods and Software</i>. Taylor and Francis, 2021. <a href=\"https://doi.org/10.1080/10556788.2021.1924715\">https://doi.org/10.1080/10556788.2021.1924715</a>.","short":"O.S. Iyiola, C.D. Enyi, Y. Shehu, Optimization Methods and Software (2021).","ama":"Iyiola OS, Enyi CD, Shehu Y. Reflected three-operator splitting method for monotone inclusion problem. <i>Optimization Methods and Software</i>. 2021. doi:<a href=\"https://doi.org/10.1080/10556788.2021.1924715\">10.1080/10556788.2021.1924715</a>","apa":"Iyiola, O. S., Enyi, C. D., &#38; Shehu, Y. (2021). Reflected three-operator splitting method for monotone inclusion problem. <i>Optimization Methods and Software</i>. Taylor and Francis. <a href=\"https://doi.org/10.1080/10556788.2021.1924715\">https://doi.org/10.1080/10556788.2021.1924715</a>"},"acknowledgement":"The authors are grateful to the anonymous referees and the handling Editor for their insightful comments which have improved the earlier version of the manuscript greatly. The second author is grateful to the University of Hafr Al Batin. The last author has received funding from the European Research Council (ERC) under the European Union's Seventh Framework Program (FP7-2007-2013) (Grant agreement No. 616160).","project":[{"grant_number":"616160","call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice","_id":"25FBA906-B435-11E9-9278-68D0E5697425"}],"article_type":"original","author":[{"full_name":"Iyiola, Olaniyi S.","first_name":"Olaniyi S.","last_name":"Iyiola"},{"last_name":"Enyi","full_name":"Enyi, Cyril D.","first_name":"Cyril D."},{"first_name":"Yekini","full_name":"Shehu, Yekini","id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87","last_name":"Shehu","orcid":"0000-0001-9224-7139"}],"ec_funded":1,"oa_version":"None","type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Taylor and Francis"},{"publisher":"Wiley","oa":1,"issue":"12","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","oa_version":"Published Version","ec_funded":1,"author":[{"first_name":"Emma L.","full_name":"Berdan, Emma L.","last_name":"Berdan"},{"first_name":"Alexandre","full_name":"Blanckaert, Alexandre","last_name":"Blanckaert"},{"full_name":"Slotte, Tanja","first_name":"Tanja","last_name":"Slotte"},{"last_name":"Suh","full_name":"Suh, Alexander","first_name":"Alexander"},{"orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","full_name":"Westram, Anja M","first_name":"Anja M"},{"full_name":"Fragata, Inês","first_name":"Inês","last_name":"Fragata"}],"file":[{"file_name":"2021_MolecularEcology_Berdan.pdf","file_id":"9545","success":1,"creator":"kschuh","checksum":"e6f4731365bde2614b333040a08265d8","content_type":"application/pdf","relation":"main_file","date_updated":"2021-06-11T15:34:53Z","access_level":"open_access","date_created":"2021-06-11T15:34:53Z","file_size":1031978}],"project":[{"_id":"265B41B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"797747","name":"Theoretical and empirical approaches to understanding Parallel Adaptation"}],"scopus_import":"1","acknowledgement":"We thank the editor, two helpful reviewers, Roger Butlin, Kerstin Johannesson, Valentina Peona, Rike Stelkens, Julie Blommaert, Nick Barton, and João Alpedrinha for helpful comments that improved the manuscript. The authors acknowledge funding from the Swedish Research Council Formas (2017-01597 to AS), the Swedish Research Council Vetenskapsrådet (2016-05139 to AS, 2019-04452 to TS) and from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 757451 to TS). ELB was funded by a Carl Tryggers grant awarded to Tanja Slotte. Anja M. Westram was funded by the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 797747. Inês Fragata was funded by a Junior Researcher contract from FCT (CEECIND/02616/2018).","citation":{"ista":"Berdan EL, Blanckaert A, Slotte T, Suh A, Westram AM, Fragata I. 2021. Unboxing mutations: Connecting mutation types with evolutionary consequences. Molecular Ecology. 30(12), 2710–2723.","ieee":"E. L. Berdan, A. Blanckaert, T. Slotte, A. Suh, A. M. Westram, and I. Fragata, “Unboxing mutations: Connecting mutation types with evolutionary consequences,” <i>Molecular Ecology</i>, vol. 30, no. 12. Wiley, pp. 2710–2723, 2021.","mla":"Berdan, Emma L., et al. “Unboxing Mutations: Connecting Mutation Types with Evolutionary Consequences.” <i>Molecular Ecology</i>, vol. 30, no. 12, Wiley, 2021, pp. 2710–23, doi:<a href=\"https://doi.org/10.1111/mec.15936\">10.1111/mec.15936</a>.","chicago":"Berdan, Emma L., Alexandre Blanckaert, Tanja Slotte, Alexander Suh, Anja M Westram, and Inês Fragata. “Unboxing Mutations: Connecting Mutation Types with Evolutionary Consequences.” <i>Molecular Ecology</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/mec.15936\">https://doi.org/10.1111/mec.15936</a>.","short":"E.L. Berdan, A. Blanckaert, T. Slotte, A. Suh, A.M. Westram, I. Fragata, Molecular Ecology 30 (2021) 2710–2723.","ama":"Berdan EL, Blanckaert A, Slotte T, Suh A, Westram AM, Fragata I. Unboxing mutations: Connecting mutation types with evolutionary consequences. <i>Molecular Ecology</i>. 2021;30(12):2710-2723. doi:<a href=\"https://doi.org/10.1111/mec.15936\">10.1111/mec.15936</a>","apa":"Berdan, E. L., Blanckaert, A., Slotte, T., Suh, A., Westram, A. M., &#38; Fragata, I. (2021). Unboxing mutations: Connecting mutation types with evolutionary consequences. <i>Molecular Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/mec.15936\">https://doi.org/10.1111/mec.15936</a>"},"intvolume":"        30","has_accepted_license":"1","abstract":[{"lang":"eng","text":"A key step in understanding the genetic basis of different evolutionary outcomes (e.g., adaptation) is to determine the roles played by different mutation types (e.g., SNPs, translocations and inversions). To do this we must simultaneously consider different mutation types in an evolutionary framework. Here, we propose a research framework that directly utilizes the most important characteristics of mutations, their population genetic effects, to determine their relative evolutionary significance in a given scenario. We review known population genetic effects of different mutation types and show how these may be connected to different evolutionary outcomes. We provide examples of how to implement this framework and pinpoint areas where more data, theory and synthesis are needed. Linking experimental and theoretical approaches to examine different mutation types simultaneously is a critical step towards understanding their evolutionary significance."}],"department":[{"_id":"NiBa"}],"external_id":{"isi":["000652056400001"]},"_id":"9470","license":"https://creativecommons.org/licenses/by-nc/4.0/","year":"2021","publication":"Molecular Ecology","title":"Unboxing mutations: Connecting mutation types with evolutionary consequences","file_date_updated":"2021-06-11T15:34:53Z","doi":"10.1111/mec.15936","month":"06","volume":30,"day":"01","status":"public","isi":1,"publication_status":"published","article_processing_charge":"No","ddc":["570"],"tmp":{"image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"publication_identifier":{"issn":["09621083"],"eissn":["1365294X"]},"language":[{"iso":"eng"}],"quality_controlled":"1","date_created":"2021-06-06T22:01:31Z","date_updated":"2023-08-08T13:59:18Z","date_published":"2021-06-01T00:00:00Z","page":"2710-2723"},{"publication_identifier":{"eissn":["2041-1723"]},"ddc":["570"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"No","isi":1,"publication_status":"published","article_number":"3483","date_published":"2021-06-09T00:00:00Z","date_created":"2021-06-10T14:57:45Z","date_updated":"2023-08-08T14:05:26Z","quality_controlled":"1","language":[{"iso":"eng"}],"pmid":1,"doi":"10.1038/s41467-021-23854-x","title":"Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine","file_date_updated":"2021-06-15T18:55:59Z","_id":"9540","year":"2021","publication":"Nature Communications","status":"public","day":"09","volume":12,"month":"06","acknowledgement":"We are deeply grateful to the late Gregor Högenauer who built the foundation for this study with his visionary work on the inhibitor diazaborine and its bacterial target. We thank Rolf Breinbauer for insightful discussions on boron chemistry. We thank Anton Meinhart and Tim Clausen for the valuable discussion of the manuscript. We are indebted to Thomas Köcher for the MS measurement of the diazaborine-ATPγS adduct. We thank the team of the VBCF for support during early phases of this work and the IST Austria Electron Microscopy Facility for providing equipment. The lab of D.H. is supported by Boehringer Ingelheim. The work was funded by FWF projects P32536 and P32977 (to H.B.).","citation":{"apa":"Prattes, M., Grishkovskaya, I., Hodirnau, V.-V., Rössler, I., Klein, I., Hetzmannseder, C., … Bergler, H. (2021). Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-021-23854-x\">https://doi.org/10.1038/s41467-021-23854-x</a>","ama":"Prattes M, Grishkovskaya I, Hodirnau V-V, et al. Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine. <i>Nature Communications</i>. 2021;12(1). doi:<a href=\"https://doi.org/10.1038/s41467-021-23854-x\">10.1038/s41467-021-23854-x</a>","short":"M. Prattes, I. Grishkovskaya, V.-V. Hodirnau, I. Rössler, I. Klein, C. Hetzmannseder, G. Zisser, C.C. Gruber, K. Gruber, D. Haselbach, H. Bergler, Nature Communications 12 (2021).","chicago":"Prattes, Michael, Irina Grishkovskaya, Victor-Valentin Hodirnau, Ingrid Rössler, Isabella Klein, Christina Hetzmannseder, Gertrude Zisser, et al. “Structural Basis for Inhibition of the AAA-ATPase Drg1 by Diazaborine.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-021-23854-x\">https://doi.org/10.1038/s41467-021-23854-x</a>.","mla":"Prattes, Michael, et al. “Structural Basis for Inhibition of the AAA-ATPase Drg1 by Diazaborine.” <i>Nature Communications</i>, vol. 12, no. 1, 3483, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-23854-x\">10.1038/s41467-021-23854-x</a>.","ieee":"M. Prattes <i>et al.</i>, “Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine,” <i>Nature Communications</i>, vol. 12, no. 1. Springer Nature, 2021.","ista":"Prattes M, Grishkovskaya I, Hodirnau V-V, Rössler I, Klein I, Hetzmannseder C, Zisser G, Gruber CC, Gruber K, Haselbach D, Bergler H. 2021. Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine. Nature Communications. 12(1), 3483."},"keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"department":[{"_id":"EM-Fac"}],"external_id":{"isi":["000664874700014"],"pmid":["34108481"]},"intvolume":"        12","abstract":[{"text":"The hexameric AAA-ATPase Drg1 is a key factor in eukaryotic ribosome biogenesis and initiates cytoplasmic maturation of the large ribosomal subunit by releasing the shuttling maturation factor Rlp24. Drg1 monomers contain two AAA-domains (D1 and D2) that act in a concerted manner. Rlp24 release is inhibited by the drug diazaborine which blocks ATP hydrolysis in D2. The mode of inhibition was unknown. Here we show the first cryo-EM structure of Drg1 revealing the inhibitory mechanism. Diazaborine forms a covalent bond to the 2′-OH of the nucleotide in D2, explaining its specificity for this site. As a consequence, the D2 domain is locked in a rigid, inactive state, stalling the whole Drg1 hexamer. Resistance mechanisms identified include abolished drug binding and altered positioning of the nucleotide. Our results suggest nucleotide-modifying compounds as potential novel inhibitors for AAA-ATPases.","lang":"eng"}],"has_accepted_license":"1","acknowledged_ssus":[{"_id":"EM-Fac"}],"oa_version":"Published Version","oa":1,"issue":"1","type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Springer Nature","file":[{"success":1,"creator":"cziletti","checksum":"40fc24c1310930990b52a8ad1142ee97","content_type":"application/pdf","file_size":3397292,"date_updated":"2021-06-15T18:55:59Z","relation":"main_file","access_level":"open_access","date_created":"2021-06-15T18:55:59Z","file_name":"2021_NatureComm_Prattes.pdf","file_id":"9556"}],"article_type":"original","author":[{"last_name":"Prattes","full_name":"Prattes, Michael","first_name":"Michael"},{"first_name":"Irina","full_name":"Grishkovskaya, Irina","last_name":"Grishkovskaya"},{"first_name":"Victor-Valentin","full_name":"Hodirnau, Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87","last_name":"Hodirnau"},{"last_name":"Rössler","first_name":"Ingrid","full_name":"Rössler, Ingrid"},{"full_name":"Klein, Isabella","first_name":"Isabella","last_name":"Klein"},{"first_name":"Christina","full_name":"Hetzmannseder, Christina","last_name":"Hetzmannseder"},{"last_name":"Zisser","first_name":"Gertrude","full_name":"Zisser, Gertrude"},{"last_name":"Gruber","first_name":"Christian C.","full_name":"Gruber, Christian C."},{"last_name":"Gruber","first_name":"Karl","full_name":"Gruber, Karl"},{"full_name":"Haselbach, David","first_name":"David","last_name":"Haselbach"},{"first_name":"Helmut","full_name":"Bergler, Helmut","last_name":"Bergler"}]},{"status":"public","main_file_link":[{"url":"https://arxiv.org/abs/1912.05390","open_access":"1"}],"volume":17,"day":"01","month":"06","doi":"10.1145/3451992","file_date_updated":"2021-06-10T19:33:56Z","title":"Graph sparsification for derandomizing massively parallel computation with low space","publication":"ACM Transactions on Algorithms","year":"2021","_id":"9541","date_published":"2021-06-01T00:00:00Z","date_updated":"2024-02-28T12:53:09Z","date_created":"2021-06-10T19:31:05Z","arxiv":1,"quality_controlled":"1","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1549-6333"],"issn":["1549-6325"]},"ddc":["000"],"article_processing_charge":"No","article_number":"16","publication_status":"published","isi":1,"article_type":"original","file":[{"file_id":"9542","file_name":"MISMM-arxiv.pdf","file_size":587404,"date_created":"2021-06-10T19:33:56Z","relation":"main_file","access_level":"open_access","date_updated":"2021-06-10T19:33:56Z","checksum":"a21c627683890c309a68f6389302c408","content_type":"application/pdf","creator":"pdavies","success":1}],"author":[{"full_name":"Czumaj, Artur","first_name":"Artur","last_name":"Czumaj"},{"orcid":"0000-0002-5646-9524","id":"11396234-BB50-11E9-B24C-90FCE5697425","last_name":"Davies","full_name":"Davies, Peter","first_name":"Peter"},{"last_name":"Parter","first_name":"Merav","full_name":"Parter, Merav"}],"ec_funded":1,"oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","issue":"2","oa":1,"publisher":"Association for Computing Machinery","external_id":{"arxiv":["1912.05390"],"isi":["000661311300006"]},"department":[{"_id":"DaAl"}],"has_accepted_license":"1","abstract":[{"lang":"eng","text":"The Massively Parallel Computation (MPC) model is an emerging model that distills core aspects of distributed and parallel computation, developed as a tool to solve combinatorial (typically graph) problems in systems of many machines with limited space. Recent work has focused on the regime in which machines have sublinear (in n, the number of nodes in the input graph) space, with randomized algorithms presented for the fundamental problems of Maximal Matching and Maximal Independent Set. However, there have been no prior corresponding deterministic algorithms. A major challenge underlying the sublinear space setting is that the local space of each machine might be too small to store all edges incident to a single node. This poses a considerable obstacle compared to classical models in which each node is assumed to know and have easy access to its incident edges. To overcome this barrier, we introduce a new graph sparsification technique that deterministically computes a low-degree subgraph, with the additional property that solving the problem on this subgraph provides significant progress towards solving the problem for the original input graph. Using this framework to derandomize the well-known algorithm of Luby [SICOMP’86], we obtain O(log Δ + log log n)-round deterministic MPC algorithms for solving the problems of Maximal Matching and Maximal Independent Set with O(nɛ) space on each machine for any constant ɛ > 0. These algorithms also run in O(log Δ) rounds in the closely related model of CONGESTED CLIQUE, improving upon the state-of-the-art bound of O(log 2Δ) rounds by Censor-Hillel et al. [DISC’17]."}],"intvolume":"        17","citation":{"chicago":"Czumaj, Artur, Peter Davies, and Merav Parter. “Graph Sparsification for Derandomizing Massively Parallel Computation with Low Space.” <i>ACM Transactions on Algorithms</i>. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3451992\">https://doi.org/10.1145/3451992</a>.","short":"A. Czumaj, P. Davies, M. Parter, ACM Transactions on Algorithms 17 (2021).","ama":"Czumaj A, Davies P, Parter M. Graph sparsification for derandomizing massively parallel computation with low space. <i>ACM Transactions on Algorithms</i>. 2021;17(2). doi:<a href=\"https://doi.org/10.1145/3451992\">10.1145/3451992</a>","apa":"Czumaj, A., Davies, P., &#38; Parter, M. (2021). Graph sparsification for derandomizing massively parallel computation with low space. <i>ACM Transactions on Algorithms</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3451992\">https://doi.org/10.1145/3451992</a>","ista":"Czumaj A, Davies P, Parter M. 2021. Graph sparsification for derandomizing massively parallel computation with low space. ACM Transactions on Algorithms. 17(2), 16.","mla":"Czumaj, Artur, et al. “Graph Sparsification for Derandomizing Massively Parallel Computation with Low Space.” <i>ACM Transactions on Algorithms</i>, vol. 17, no. 2, 16, Association for Computing Machinery, 2021, doi:<a href=\"https://doi.org/10.1145/3451992\">10.1145/3451992</a>.","ieee":"A. Czumaj, P. Davies, and M. Parter, “Graph sparsification for derandomizing massively parallel computation with low space,” <i>ACM Transactions on Algorithms</i>, vol. 17, no. 2. Association for Computing Machinery, 2021."},"acknowledgement":"Institute of Science and Technology Austria (IST Austria). Email: peter.davies@ist.ac.at. Work partially\r\ndone at the Department of Computer Science and Centre for Discrete Mathematics and its Applications (DIMAP),University of Warwick. Research partially supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 754411, the Centre for Discrete Mathematics and its Applications, a Weizmann-UK Making Connections Grant, and EPSRC award EP/N011163/1.","related_material":{"record":[{"id":"7802","status":"public","relation":"earlier_version"}]},"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020"}]},{"ec_funded":1,"author":[{"full_name":"Davies, Peter","first_name":"Peter","orcid":"0000-0002-5646-9524","last_name":"Davies","id":"11396234-BB50-11E9-B24C-90FCE5697425"},{"first_name":"Vijaykrishna","full_name":"Gurunanthan, Vijaykrishna","last_name":"Gurunanthan"},{"full_name":"Moshrefi, Niusha ","first_name":"Niusha ","id":"4db776ff-ce15-11eb-96e3-bc2b90b01c16","last_name":"Moshrefi"},{"last_name":"Ashkboos","id":"0D0A9058-257B-11EA-A937-9341C3D8BC8A","first_name":"Saleh","full_name":"Ashkboos, Saleh"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian"}],"month":"05","day":"01","main_file_link":[{"url":"https://openreview.net/pdf?id=t86MwoUCCNe","open_access":"1"}],"status":"public","_id":"9543","year":"2021","publication":"9th International Conference on Learning Representations","title":"New bounds for distributed mean estimation and variance reduction","oa":1,"type":"conference","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","conference":{"location":"Virtual","end_date":"2021-05-07","start_date":"2021-05-03","name":" ICLR: International Conference on Learning Representations"},"oa_version":"Published Version","language":[{"iso":"eng"}],"quality_controlled":"1","arxiv":1,"abstract":[{"lang":"eng","text":"We consider the problem ofdistributed mean estimation (DME), in which n machines are each given a local d-dimensional vector xv∈Rd, and must cooperate to estimate the mean of their inputs μ=1n∑nv=1xv, while minimizing total communication cost. DME is a fundamental construct in distributed machine learning, and there has been considerable work on variants of this problem, especially in the context of distributed variance reduction for stochastic gradients in parallel SGD. Previous work typically assumes an upper bound on the norm of the input vectors, and achieves an error bound in terms of this norm. However, in many real applications, the input vectors are concentrated around the correct output μ, but μ itself has large norm. In such cases, previous output error bounds perform poorly. In this paper, we show that output error bounds need not depend on input norm. We provide a method of quantization which allows distributed mean estimation to be performed with solution quality dependent only on the distance between inputs, not on input norm, and show an analogous result for distributed variance reduction. The technique is based on a new connection with lattice theory. We also provide lower bounds showing that the communication to error trade-off of our algorithms is asymptotically optimal. As the lattices achieving optimal bounds under l2-norm can be computationally impractical, we also present an extension which leverages easy-to-use cubic lattices, and is loose only up to a logarithmic factor ind. We show experimentally that our method yields practical improvements for common applications, relative to prior approaches."}],"date_updated":"2023-02-23T14:00:40Z","date_created":"2021-06-10T19:46:08Z","department":[{"_id":"DaAl"}],"external_id":{"arxiv":["2002.09268"]},"date_published":"2021-05-01T00:00:00Z","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411"}],"publication_status":"published","citation":{"ista":"Davies P, Gurunanthan V, Moshrefi N, Ashkboos S, Alistarh D-A. 2021. New bounds for distributed mean estimation and variance reduction. 9th International Conference on Learning Representations.  ICLR: International Conference on Learning Representations.","ieee":"P. Davies, V. Gurunanthan, N. Moshrefi, S. Ashkboos, and D.-A. Alistarh, “New bounds for distributed mean estimation and variance reduction,” in <i>9th International Conference on Learning Representations</i>, Virtual, 2021.","mla":"Davies, Peter, et al. “New Bounds for Distributed Mean Estimation and Variance Reduction.” <i>9th International Conference on Learning Representations</i>, 2021.","short":"P. Davies, V. Gurunanthan, N. Moshrefi, S. Ashkboos, D.-A. Alistarh, in:, 9th International Conference on Learning Representations, 2021.","chicago":"Davies, Peter, Vijaykrishna Gurunanthan, Niusha  Moshrefi, Saleh Ashkboos, and Dan-Adrian Alistarh. “New Bounds for Distributed Mean Estimation and Variance Reduction.” In <i>9th International Conference on Learning Representations</i>, 2021.","ama":"Davies P, Gurunanthan V, Moshrefi N, Ashkboos S, Alistarh D-A. New bounds for distributed mean estimation and variance reduction. In: <i>9th International Conference on Learning Representations</i>. ; 2021.","apa":"Davies, P., Gurunanthan, V., Moshrefi, N., Ashkboos, S., &#38; Alistarh, D.-A. (2021). New bounds for distributed mean estimation and variance reduction. In <i>9th International Conference on Learning Representations</i>. Virtual."},"article_processing_charge":"No"},{"ddc":["004"],"publication_identifier":{"eissn":["1467-8659"],"issn":["0167-7055"]},"publication_status":"published","isi":1,"article_processing_charge":"No","date_updated":"2023-08-14T08:01:50Z","date_created":"2021-06-13T22:01:32Z","page":"205-219","date_published":"2021-05-01T00:00:00Z","language":[{"iso":"eng"}],"quality_controlled":"1","doi":"10.1111/cgf.142626","publication":"Computer Graphics Forum","_id":"9547","year":"2021","file_date_updated":"2021-10-11T12:06:50Z","title":"Neural acceleration of scattering-aware color 3D printing","day":"01","volume":40,"status":"public","month":"05","project":[{"_id":"2508E324-B435-11E9-9278-68D0E5697425","name":"Distributed 3D Object Design","grant_number":"642841","call_identifier":"H2020"},{"_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling"}],"acknowledgement":"We thank Sebastian Cucerca for processing and capturing the phys-cal printouts. This work was supported by the Charles University grant SVV-260588 and Czech Science Foundation grant 19-07626S. This project has received funding from the European Union’s Horizon 2020 research and innovation programme, under the Marie Skłodowska Curie grant agreements No 642841 (DISTRO) and No765911 (RealVision), and under the European Research Council grant agreement No 715767 (MATERIALIZABLE).","citation":{"ista":"Rittig T, Sumin D, Babaei V, Didyk P, Voloboy A, Wilkie A, Bickel B, Myszkowski K, Weyrich T, Křivánek J. 2021. Neural acceleration of scattering-aware color 3D printing. Computer Graphics Forum. 40(2), 205–219.","mla":"Rittig, Tobias, et al. “Neural Acceleration of Scattering-Aware Color 3D Printing.” <i>Computer Graphics Forum</i>, vol. 40, no. 2, Wiley, 2021, pp. 205–19, doi:<a href=\"https://doi.org/10.1111/cgf.142626\">10.1111/cgf.142626</a>.","ieee":"T. Rittig <i>et al.</i>, “Neural acceleration of scattering-aware color 3D printing,” <i>Computer Graphics Forum</i>, vol. 40, no. 2. Wiley, pp. 205–219, 2021.","chicago":"Rittig, Tobias, Denis Sumin, Vahid Babaei, Piotr Didyk, Alexey Voloboy, Alexander Wilkie, Bernd Bickel, Karol Myszkowski, Tim Weyrich, and Jaroslav Křivánek. “Neural Acceleration of Scattering-Aware Color 3D Printing.” <i>Computer Graphics Forum</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/cgf.142626\">https://doi.org/10.1111/cgf.142626</a>.","short":"T. Rittig, D. Sumin, V. Babaei, P. Didyk, A. Voloboy, A. Wilkie, B. Bickel, K. Myszkowski, T. Weyrich, J. Křivánek, Computer Graphics Forum 40 (2021) 205–219.","apa":"Rittig, T., Sumin, D., Babaei, V., Didyk, P., Voloboy, A., Wilkie, A., … Křivánek, J. (2021). Neural acceleration of scattering-aware color 3D printing. <i>Computer Graphics Forum</i>. Wiley. <a href=\"https://doi.org/10.1111/cgf.142626\">https://doi.org/10.1111/cgf.142626</a>","ama":"Rittig T, Sumin D, Babaei V, et al. Neural acceleration of scattering-aware color 3D printing. <i>Computer Graphics Forum</i>. 2021;40(2):205-219. doi:<a href=\"https://doi.org/10.1111/cgf.142626\">10.1111/cgf.142626</a>"},"scopus_import":"1","external_id":{"isi":["000657959600017"]},"department":[{"_id":"BeBi"}],"abstract":[{"text":"With the wider availability of full-color 3D printers, color-accurate 3D-print preparation has received increased attention. A key challenge lies in the inherent translucency of commonly used print materials that blurs out details of the color texture. Previous work tries to compensate for these scattering effects through strategic assignment of colored primary materials to printer voxels. To date, the highest-quality approach uses iterative optimization that relies on computationally expensive Monte Carlo light transport simulation to predict the surface appearance from subsurface scattering within a given print material distribution; that optimization, however, takes in the order of days on a single machine. In our work, we dramatically speed up the process by replacing the light transport simulation with a data-driven approach. Leveraging a deep neural network to predict the scattering within a highly heterogeneous medium, our method performs around two orders of magnitude faster than Monte Carlo rendering while yielding optimization results of similar quality level. The network is based on an established method from atmospheric cloud rendering, adapted to our domain and extended by a physically motivated weight sharing scheme that substantially reduces the network size. We analyze its performance in an end-to-end print preparation pipeline and compare quality and runtime to alternative approaches, and demonstrate its generalization to unseen geometry and material values. This for the first time enables full heterogenous material optimization for 3D-print preparation within time frames in the order of the actual printing time.","lang":"eng"}],"has_accepted_license":"1","intvolume":"        40","oa_version":"Submitted Version","publisher":"Wiley","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","oa":1,"issue":"2","article_type":"original","file":[{"creator":"bbickel","success":1,"file_size":26026501,"date_updated":"2021-10-11T12:06:50Z","date_created":"2021-10-11T12:06:50Z","relation":"main_file","access_level":"open_access","checksum":"33271724215f54a75c39d2ed40f2c502","content_type":"application/pdf","file_name":"ScatteringAwareColor3DPrinting_authorVersion.pdf","file_id":"10120"}],"ec_funded":1,"author":[{"last_name":"Rittig","first_name":"Tobias","full_name":"Rittig, Tobias"},{"last_name":"Sumin","full_name":"Sumin, Denis","first_name":"Denis"},{"last_name":"Babaei","full_name":"Babaei, Vahid","first_name":"Vahid"},{"last_name":"Didyk","full_name":"Didyk, Piotr","first_name":"Piotr"},{"first_name":"Alexey","full_name":"Voloboy, Alexey","last_name":"Voloboy"},{"full_name":"Wilkie, Alexander","first_name":"Alexander","last_name":"Wilkie"},{"first_name":"Bernd","full_name":"Bickel, Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","orcid":"0000-0001-6511-9385"},{"last_name":"Myszkowski","first_name":"Karol","full_name":"Myszkowski, Karol"},{"last_name":"Weyrich","full_name":"Weyrich, Tim","first_name":"Tim"},{"last_name":"Křivánek","full_name":"Křivánek, Jaroslav","first_name":"Jaroslav"}]},{"external_id":{"isi":["000656507500001"],"arxiv":["2008.09543"]},"department":[{"_id":"UlWa"}],"abstract":[{"text":"We extend the notion of the minimal volume ellipsoid containing a convex body in Rd to the setting of logarithmically concave functions. We consider a vast class of logarithmically concave functions whose superlevel sets are concentric ellipsoids. For a fixed function from this class, we consider the set of all its “affine” positions. For any log-concave function f on Rd, we consider functions belonging to this set of “affine” positions, and find the one with the minimal integral under the condition that it is pointwise greater than or equal to f. We study the properties of existence and uniqueness of the solution to this problem. For any s∈[0,+∞), we consider the construction dual to the recently defined John s-function (Ivanov and Naszódi in Functional John ellipsoids. arXiv preprint: arXiv:2006.09934, 2020). We prove that such a construction determines a unique function and call it the Löwner s-function of f. We study the Löwner s-functions as s tends to zero and to infinity. Finally, extending the notion of the outer volume ratio, we define the outer integral ratio of a log-concave function and give an asymptotically tight bound on it.","lang":"eng"}],"intvolume":"        31","citation":{"ista":"Ivanov G, Tsiutsiurupa I. 2021. Functional Löwner ellipsoids. Journal of Geometric Analysis. 31, 11493–11528.","mla":"Ivanov, Grigory, and Igor Tsiutsiurupa. “Functional Löwner Ellipsoids.” <i>Journal of Geometric Analysis</i>, vol. 31, Springer, 2021, pp. 11493–528, doi:<a href=\"https://doi.org/10.1007/s12220-021-00691-4\">10.1007/s12220-021-00691-4</a>.","ieee":"G. Ivanov and I. Tsiutsiurupa, “Functional Löwner ellipsoids,” <i>Journal of Geometric Analysis</i>, vol. 31. Springer, pp. 11493–11528, 2021.","short":"G. Ivanov, I. Tsiutsiurupa, Journal of Geometric Analysis 31 (2021) 11493–11528.","chicago":"Ivanov, Grigory, and Igor Tsiutsiurupa. “Functional Löwner Ellipsoids.” <i>Journal of Geometric Analysis</i>. Springer, 2021. <a href=\"https://doi.org/10.1007/s12220-021-00691-4\">https://doi.org/10.1007/s12220-021-00691-4</a>.","apa":"Ivanov, G., &#38; Tsiutsiurupa, I. (2021). Functional Löwner ellipsoids. <i>Journal of Geometric Analysis</i>. Springer. <a href=\"https://doi.org/10.1007/s12220-021-00691-4\">https://doi.org/10.1007/s12220-021-00691-4</a>","ama":"Ivanov G, Tsiutsiurupa I. Functional Löwner ellipsoids. <i>Journal of Geometric Analysis</i>. 2021;31:11493-11528. doi:<a href=\"https://doi.org/10.1007/s12220-021-00691-4\">10.1007/s12220-021-00691-4</a>"},"acknowledgement":"The authors acknowledge the support of the grant of the Russian Government N 075-15-2019-1926.","scopus_import":"1","article_type":"original","author":[{"id":"87744F66-5C6F-11EA-AFE0-D16B3DDC885E","last_name":"Ivanov","first_name":"Grigory","full_name":"Ivanov, Grigory"},{"last_name":"Tsiutsiurupa","full_name":"Tsiutsiurupa, Igor","first_name":"Igor"}],"oa_version":"Preprint","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","oa":1,"publisher":"Springer","page":"11493-11528","date_published":"2021-05-31T00:00:00Z","date_updated":"2023-08-08T14:04:49Z","date_created":"2021-06-13T22:01:32Z","arxiv":1,"quality_controlled":"1","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1559-002X"],"issn":["1050-6926"]},"article_processing_charge":"No","publication_status":"published","isi":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2008.09543"}],"status":"public","day":"31","volume":31,"month":"05","doi":"10.1007/s12220-021-00691-4","title":"Functional Löwner ellipsoids","publication":"Journal of Geometric Analysis","_id":"9548","year":"2021"},{"article_type":"original","author":[{"first_name":"Danyang","full_name":"Zhang, Danyang","last_name":"Zhang"},{"id":"63836096-4690-11EA-BD4E-32803DDC885E","orcid":"0000-0002-8698-3823","last_name":"Watson","full_name":"Watson, Jake","first_name":"Jake"},{"last_name":"Matthews","full_name":"Matthews, Peter M.","first_name":"Peter M."},{"last_name":"Cais","full_name":"Cais, Ondrej","first_name":"Ondrej"},{"last_name":"Greger","full_name":"Greger, Ingo H.","first_name":"Ingo H."}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","oa":1,"publisher":"Springer Nature","external_id":{"pmid":["34079129"],"isi":["000657238100003"]},"department":[{"_id":"PeJo"}],"abstract":[{"text":"AMPA receptors (AMPARs) mediate the majority of excitatory transmission in the brain and enable the synaptic plasticity that underlies learning1. A diverse array of AMPAR signalling complexes are established by receptor auxiliary subunits, which associate with the AMPAR in various combinations to modulate trafficking, gating and synaptic strength2. However, their mechanisms of action are poorly understood. Here we determine cryo-electron microscopy structures of the heteromeric GluA1–GluA2 receptor assembled with both TARP-γ8 and CNIH2, the predominant AMPAR complex in the forebrain, in both resting and active states. Two TARP-γ8 and two CNIH2 subunits insert at distinct sites beneath the ligand-binding domains of the receptor, with site-specific lipids shaping each interaction and affecting the gating regulation of the AMPARs. Activation of the receptor leads to asymmetry between GluA1 and GluA2 along the ion conduction path and an outward expansion of the channel triggers counter-rotations of both auxiliary subunit pairs, promoting the active-state conformation. In addition, both TARP-γ8 and CNIH2 pivot towards the pore exit upon activation, extending their reach for cytoplasmic receptor elements. CNIH2 achieves this through its uniquely extended M2 helix, which has transformed this endoplasmic reticulum-export factor into a powerful AMPAR modulator that is capable of providing hippocampal pyramidal neurons with their integrative synaptic properties. ","lang":"eng"}],"intvolume":"       594","citation":{"mla":"Zhang, Danyang, et al. “Gating and Modulation of a Hetero-Octameric AMPA Glutamate Receptor.” <i>Nature</i>, vol. 594, Springer Nature, 2021, pp. 454–58, doi:<a href=\"https://doi.org/10.1038/s41586-021-03613-0\">10.1038/s41586-021-03613-0</a>.","ieee":"D. Zhang, J. Watson, P. M. Matthews, O. Cais, and I. H. Greger, “Gating and modulation of a hetero-octameric AMPA glutamate receptor,” <i>Nature</i>, vol. 594. Springer Nature, pp. 454–458, 2021.","ista":"Zhang D, Watson J, Matthews PM, Cais O, Greger IH. 2021. Gating and modulation of a hetero-octameric AMPA glutamate receptor. Nature. 594, 454–458.","apa":"Zhang, D., Watson, J., Matthews, P. M., Cais, O., &#38; Greger, I. H. (2021). Gating and modulation of a hetero-octameric AMPA glutamate receptor. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-021-03613-0\">https://doi.org/10.1038/s41586-021-03613-0</a>","ama":"Zhang D, Watson J, Matthews PM, Cais O, Greger IH. Gating and modulation of a hetero-octameric AMPA glutamate receptor. <i>Nature</i>. 2021;594:454-458. doi:<a href=\"https://doi.org/10.1038/s41586-021-03613-0\">10.1038/s41586-021-03613-0</a>","short":"D. Zhang, J. Watson, P.M. Matthews, O. Cais, I.H. Greger, Nature 594 (2021) 454–458.","chicago":"Zhang, Danyang, Jake Watson, Peter M. Matthews, Ondrej Cais, and Ingo H. Greger. “Gating and Modulation of a Hetero-Octameric AMPA Glutamate Receptor.” <i>Nature</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41586-021-03613-0\">https://doi.org/10.1038/s41586-021-03613-0</a>."},"acknowledgement":"We thank members of the Greger laboratory, B. Herguedas, J. Krieger and J.-N. Dohrke for comments on the manuscript; J. Krieger and J.-N. Dohrke for discussion, J. Krieger for help with the normal mode analysis, B. Köhegyi for help with cryo-EM imaging, V. Chang and K. Suzuki for helping to generate the CNIH2-1D4-HA stable cell line, M. Carvalho for assistance at early stages of this project, the LMB scientific computing and the cryo-EM facility for support, P. Emsley for help with model building, T. Nakane for helpful comments with RELION 3.1 and R. Warshamanage for helping with EMDA cryo-EM-map processing. We acknowledge the Diamond Light Source for access and support of the Cryo-EM facilities at the UK national electron bio10 imaging centre (eBIC), proposal EM17434, funded by the Wellcome Trust, MRC and BBSRC. This work was supported by grants from the Medical Research Council, as part of United Kingdom Research and Innovation (also known as UK Research and Innovation) (MC_U105174197) and BBSRC (BB/N002113/1) to I.H.G.","scopus_import":"1","status":"public","main_file_link":[{"url":"https://doi.org/10.1038/s41586-021-03613-0","open_access":"1"}],"volume":594,"day":"02","month":"06","doi":"10.1038/s41586-021-03613-0","pmid":1,"title":"Gating and modulation of a hetero-octameric AMPA glutamate receptor","publication":"Nature","_id":"9549","year":"2021","page":"454-458","date_published":"2021-06-02T00:00:00Z","date_updated":"2023-08-08T13:59:51Z","date_created":"2021-06-13T22:01:33Z","quality_controlled":"1","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"article_processing_charge":"No","publication_status":"published","isi":1},{"language":[{"iso":"eng"}],"arxiv":1,"quality_controlled":"1","date_updated":"2023-08-08T14:03:40Z","date_created":"2021-06-13T22:01:33Z","date_published":"2021-05-27T00:00:00Z","isi":1,"publication_status":"published","article_number":"e44","article_processing_charge":"No","ddc":["510"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_identifier":{"eissn":["20505094"]},"month":"05","day":"27","volume":9,"status":"public","year":"2021","_id":"9550","publication":"Forum of Mathematics, Sigma","title":"Equipartition principle for Wigner matrices","file_date_updated":"2021-06-15T14:40:45Z","doi":"10.1017/fms.2021.38","intvolume":"         9","has_accepted_license":"1","abstract":[{"text":"We prove that the energy of any eigenvector of a sum of several independent large Wigner matrices is equally distributed among these matrices with very high precision. This shows a particularly strong microcanonical form of the equipartition principle for quantum systems whose components are modelled by Wigner matrices. ","lang":"eng"}],"department":[{"_id":"LaEr"}],"external_id":{"isi":["000654960800001"],"arxiv":["2008.07061"]},"project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","call_identifier":"FP7"}],"scopus_import":"1","citation":{"chicago":"Bao, Zhigang, László Erdös, and Kevin Schnelli. “Equipartition Principle for Wigner Matrices.” <i>Forum of Mathematics, Sigma</i>. Cambridge University Press, 2021. <a href=\"https://doi.org/10.1017/fms.2021.38\">https://doi.org/10.1017/fms.2021.38</a>.","short":"Z. Bao, L. Erdös, K. Schnelli, Forum of Mathematics, Sigma 9 (2021).","ama":"Bao Z, Erdös L, Schnelli K. Equipartition principle for Wigner matrices. <i>Forum of Mathematics, Sigma</i>. 2021;9. doi:<a href=\"https://doi.org/10.1017/fms.2021.38\">10.1017/fms.2021.38</a>","apa":"Bao, Z., Erdös, L., &#38; Schnelli, K. (2021). Equipartition principle for Wigner matrices. <i>Forum of Mathematics, Sigma</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/fms.2021.38\">https://doi.org/10.1017/fms.2021.38</a>","ista":"Bao Z, Erdös L, Schnelli K. 2021. Equipartition principle for Wigner matrices. Forum of Mathematics, Sigma. 9, e44.","mla":"Bao, Zhigang, et al. “Equipartition Principle for Wigner Matrices.” <i>Forum of Mathematics, Sigma</i>, vol. 9, e44, Cambridge University Press, 2021, doi:<a href=\"https://doi.org/10.1017/fms.2021.38\">10.1017/fms.2021.38</a>.","ieee":"Z. Bao, L. Erdös, and K. Schnelli, “Equipartition principle for Wigner matrices,” <i>Forum of Mathematics, Sigma</i>, vol. 9. Cambridge University Press, 2021."},"acknowledgement":"The first author is supported in part by Hong Kong RGC Grant GRF 16301519 and NSFC 11871425. The second author is supported in part by ERC Advanced Grant RANMAT 338804. The third author is supported in part by Swedish Research Council Grant VR-2017-05195 and the Knut and Alice Wallenberg Foundation","ec_funded":1,"author":[{"first_name":"Zhigang","full_name":"Bao, Zhigang","id":"442E6A6C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3036-1475","last_name":"Bao"},{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","orcid":"0000-0001-5366-9603","full_name":"Erdös, László","first_name":"László"},{"last_name":"Schnelli","orcid":"0000-0003-0954-3231","id":"434AD0AE-F248-11E8-B48F-1D18A9856A87","full_name":"Schnelli, Kevin","first_name":"Kevin"}],"file":[{"file_id":"9555","file_name":"2021_ForumMath_Bao.pdf","checksum":"47c986578de132200d41e6d391905519","content_type":"application/pdf","date_created":"2021-06-15T14:40:45Z","access_level":"open_access","relation":"main_file","date_updated":"2021-06-15T14:40:45Z","file_size":483458,"success":1,"creator":"cziletti"}],"article_type":"original","publisher":"Cambridge University Press","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","oa_version":"Published Version"},{"type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"issue":"24","publisher":"American Physical Society","oa_version":"Preprint","author":[{"last_name":"Yalniz","id":"66E74FA2-D8BF-11E9-8249-8DE2E5697425","orcid":"0000-0002-8490-9312","first_name":"Gökhan","full_name":"Yalniz, Gökhan"},{"full_name":"Hof, Björn","first_name":"Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754"},{"last_name":"Budanur","orcid":"0000-0003-0423-5010","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","full_name":"Budanur, Nazmi B","first_name":"Nazmi B"}],"article_type":"letter_note","citation":{"ieee":"G. Yalniz, B. Hof, and N. B. Budanur, “Coarse graining the state space of a turbulent flow using periodic orbits,” <i>Physical Review Letters</i>, vol. 126, no. 24. American Physical Society, 2021.","mla":"Yalniz, Gökhan, et al. “Coarse Graining the State Space of a Turbulent Flow Using Periodic Orbits.” <i>Physical Review Letters</i>, vol. 126, no. 24, 244502, American Physical Society, 2021, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.126.244502\">10.1103/PhysRevLett.126.244502</a>.","ista":"Yalniz G, Hof B, Budanur NB. 2021. Coarse graining the state space of a turbulent flow using periodic orbits. Physical Review Letters. 126(24), 244502.","apa":"Yalniz, G., Hof, B., &#38; Budanur, N. B. (2021). Coarse graining the state space of a turbulent flow using periodic orbits. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.126.244502\">https://doi.org/10.1103/PhysRevLett.126.244502</a>","ama":"Yalniz G, Hof B, Budanur NB. Coarse graining the state space of a turbulent flow using periodic orbits. <i>Physical Review Letters</i>. 2021;126(24). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.126.244502\">10.1103/PhysRevLett.126.244502</a>","short":"G. Yalniz, B. Hof, N.B. Budanur, Physical Review Letters 126 (2021).","chicago":"Yalniz, Gökhan, Björn Hof, and Nazmi B Budanur. “Coarse Graining the State Space of a Turbulent Flow Using Periodic Orbits.” <i>Physical Review Letters</i>. American Physical Society, 2021. <a href=\"https://doi.org/10.1103/PhysRevLett.126.244502\">https://doi.org/10.1103/PhysRevLett.126.244502</a>."},"acknowledgement":"We thank the referees for improving this Letter with their comments. We acknowledge stimulating discussions with\r\nH. Edelsbrunner. This work was supported by Grant No. 662960 from the Simons Foundation (B. H.). The numerical calculations were performed at TUBITAK ULAKBIM High Performance and Grid Computing Center (TRUBA resources) and IST Austria High Performance Computing cluster.","related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/turbulent-flow-simplified/","relation":"press_release"}]},"project":[{"grant_number":"662960","name":"Revisiting the Turbulence Problem Using Statistical Mechanics: Experimental Studies on Transitional and Turbulent Flows","_id":"238598C6-32DE-11EA-91FC-C7463DDC885E"}],"abstract":[{"lang":"eng","text":"We show that turbulent dynamics that arise in simulations of the three-dimensional Navier--Stokes equations in a triply-periodic domain under sinusoidal forcing can be described as transient visits to the neighborhoods of unstable time-periodic solutions. Based on this description, we reduce the original system with more than 10^5 degrees of freedom to a 17-node Markov chain where each node corresponds to the neighborhood of a periodic orbit. The model accurately reproduces long-term averages of the system's observables as weighted sums over the periodic orbits.\r\n"}],"intvolume":"       126","acknowledged_ssus":[{"_id":"ScienComp"}],"external_id":{"arxiv":["2007.02584"],"isi":["000663310100008"]},"department":[{"_id":"GradSch"},{"_id":"BjHo"}],"title":"Coarse graining the state space of a turbulent flow using periodic orbits","publication":"Physical Review Letters","_id":"9558","year":"2021","doi":"10.1103/PhysRevLett.126.244502","month":"06","status":"public","main_file_link":[{"url":"https://arxiv.org/abs/2007.02584","open_access":"1"}],"volume":126,"day":"18","article_processing_charge":"No","article_number":"244502","publication_status":"published","isi":1,"publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"arxiv":1,"quality_controlled":"1","language":[{"iso":"eng"}],"date_published":"2021-06-18T00:00:00Z","date_updated":"2023-08-08T14:08:36Z","date_created":"2021-06-16T15:45:36Z"},{"year":"2021","_id":"9562","degree_awarded":"PhD","file_date_updated":"2022-07-02T22:30:04Z","title":"2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning","doi":"10.15479/at:ista:9562","month":"06","day":"01","status":"public","publication_status":"published","article_processing_charge":"No","ddc":["570"],"publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"supervisor":[{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi"}],"date_created":"2021-06-17T14:10:47Z","date_updated":"2023-09-11T12:55:53Z","page":"124","date_published":"2021-06-01T00:00:00Z","publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"type":"dissertation","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"oa_version":"Published Version","author":[{"full_name":"Kleindienst, David","first_name":"David","id":"42E121A4-F248-11E8-B48F-1D18A9856A87","last_name":"Kleindienst"}],"file":[{"content_type":"application/pdf","checksum":"659df5518db495f679cb1df9e9bd1d94","file_size":77299142,"access_level":"open_access","date_created":"2021-06-17T14:03:14Z","date_updated":"2022-07-02T22:30:04Z","relation":"main_file","creator":"dkleindienst","file_id":"9563","embargo":"2022-07-01","file_name":"Thesis.pdf"},{"file_name":"Thesis_source.zip","file_id":"9564","creator":"dkleindienst","embargo_to":"open_access","checksum":"3bcf63a2b19e5b6663be051bea332748","content_type":"application/zip","file_size":369804895,"relation":"source_file","access_level":"closed","date_updated":"2022-07-02T22:30:04Z","date_created":"2021-06-17T14:04:30Z"}],"citation":{"mla":"Kleindienst, David. <i>2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:9562\">10.15479/at:ista:9562</a>.","ieee":"D. Kleindienst, “2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning,” Institute of Science and Technology Austria, 2021.","ista":"Kleindienst D. 2021. 2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning. Institute of Science and Technology Austria.","apa":"Kleindienst, D. (2021). <i>2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:9562\">https://doi.org/10.15479/at:ista:9562</a>","ama":"Kleindienst D. 2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:9562\">10.15479/at:ista:9562</a>","short":"D. Kleindienst, 2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning, Institute of Science and Technology Austria, 2021.","chicago":"Kleindienst, David. “2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:9562\">https://doi.org/10.15479/at:ista:9562</a>."},"related_material":{"record":[{"status":"public","id":"9756","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"9437","status":"public"},{"relation":"part_of_dissertation","id":"8532","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"612"}]},"acknowledged_ssus":[{"_id":"EM-Fac"}],"abstract":[{"text":"Left-right asymmetries can be considered a fundamental organizational principle of the vertebrate central nervous system. The hippocampal CA3-CA1 pyramidal cell synaptic connection shows an input-side dependent asymmetry where the hemispheric location of the presynaptic CA3 neuron determines the synaptic properties. Left-input synapses terminating on apical dendrites in stratum radiatum have a higher density of NMDA receptor subunit GluN2B, a lower density of AMPA receptor subunit GluA1 and smaller areas with less often perforated PSDs. On the other hand, left-input synapses terminating on basal dendrites in stratum oriens have lower GluN2B densities than right-input ones. Apical and basal synapses further employ different signaling pathways involved in LTP. SDS-digested freeze-fracture replica labeling can visualize synaptic membrane proteins with high sensitivity and resolution, and has been used to reveal the asymmetry at the electron microscopic level. However, it requires time-consuming manual demarcation of the synaptic surface for quantitative measurements. To facilitate the analysis of replica labeling, I first developed a software named Darea, which utilizes deep-learning to automatize this demarcation. With Darea I characterized the synaptic distribution of NMDA and AMPA receptors as well as the voltage-gated Ca2+ channels in CA1 stratum radiatum and oriens. Second, I explored the role of GluN2B and its carboxy-terminus in the establishment of input-side dependent hippocampal asymmetry. In conditional knock-out mice lacking GluN2B expression in CA1 and GluN2B-2A swap mice, where GluN2B carboxy-terminus was exchanged to that of GluN2A, no significant asymmetries of GluN2B, GluA1 and PSD area were detected. We further discovered a previously unknown functional asymmetry of GluN2A, which was also lost in the swap mouse. These results demonstrate that GluN2B carboxy-terminus plays a critical role in normal formation of input-side dependent asymmetry.","lang":"eng"}],"has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"RySh"}]},{"doi":"10.1039/d1ra03428f","title":"Heat induction in two-dimensional graphene–Fe3O4 nanohybrids for magnetic hyperthermia applications with artificial neural network modeling","file_date_updated":"2021-06-23T13:09:34Z","license":"https://creativecommons.org/licenses/by/3.0/","_id":"9569","year":"2021","publication":"RSC Advances","status":"public","day":"18","volume":11,"month":"06","publication_identifier":{"eissn":["2046-2069"]},"ddc":["540"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","short":"CC BY (3.0)"},"article_processing_charge":"No","isi":1,"publication_status":"published","date_published":"2021-06-18T00:00:00Z","page":"21702-21715","date_updated":"2023-08-08T14:23:21Z","date_created":"2021-06-19T07:27:45Z","quality_controlled":"1","language":[{"iso":"eng"}],"oa_version":"Published Version","issue":"35","oa":1,"type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Royal Society of Chemistry","file":[{"file_id":"9596","file_name":"2021_RSCAdvances_Dar.pdf","date_updated":"2021-06-23T13:09:34Z","date_created":"2021-06-23T13:09:34Z","access_level":"open_access","relation":"main_file","file_size":2114557,"checksum":"cd582d67ace7151078e46b3a896871a9","content_type":"application/pdf","success":1,"creator":"asandaue"}],"article_type":"original","author":[{"last_name":"Dar","first_name":"M. S.","full_name":"Dar, M. S."},{"first_name":"Khush Bakhat","full_name":"Akram, Khush Bakhat","last_name":"Akram"},{"full_name":"Sohail, Ayesha","first_name":"Ayesha","last_name":"Sohail"},{"last_name":"Arif","full_name":"Arif, Fatima","first_name":"Fatima"},{"last_name":"Zabihi","full_name":"Zabihi, Fatemeh","first_name":"Fatemeh"},{"last_name":"Yang","full_name":"Yang, Shengyuan","first_name":"Shengyuan"},{"first_name":"Shamsa","full_name":"Munir, Shamsa","last_name":"Munir"},{"first_name":"Meifang","full_name":"Zhu, Meifang","last_name":"Zhu"},{"first_name":"M.","full_name":"Abid, M.","last_name":"Abid"},{"full_name":"Nauman, Muhammad","first_name":"Muhammad","last_name":"Nauman","orcid":"0000-0002-2111-4846","id":"32c21954-2022-11eb-9d5f-af9f93c24e71"}],"acknowledgement":"The research is funded by Higher Education Commission (HEC) Pakistan under start-up research grant program (SRGP) Project no. 2454.","citation":{"ista":"Dar MS, Akram KB, Sohail A, Arif F, Zabihi F, Yang S, Munir S, Zhu M, Abid M, Nauman M. 2021. Heat induction in two-dimensional graphene–Fe3O4 nanohybrids for magnetic hyperthermia applications with artificial neural network modeling. RSC Advances. 11(35), 21702–21715.","mla":"Dar, M. S., et al. “Heat Induction in Two-Dimensional Graphene–Fe3O4 Nanohybrids for Magnetic Hyperthermia Applications with Artificial Neural Network Modeling.” <i>RSC Advances</i>, vol. 11, no. 35, Royal Society of Chemistry, 2021, pp. 21702–15, doi:<a href=\"https://doi.org/10.1039/d1ra03428f\">10.1039/d1ra03428f</a>.","ieee":"M. S. Dar <i>et al.</i>, “Heat induction in two-dimensional graphene–Fe3O4 nanohybrids for magnetic hyperthermia applications with artificial neural network modeling,” <i>RSC Advances</i>, vol. 11, no. 35. Royal Society of Chemistry, pp. 21702–21715, 2021.","chicago":"Dar, M. S., Khush Bakhat Akram, Ayesha Sohail, Fatima Arif, Fatemeh Zabihi, Shengyuan Yang, Shamsa Munir, Meifang Zhu, M. Abid, and Muhammad Nauman. “Heat Induction in Two-Dimensional Graphene–Fe3O4 Nanohybrids for Magnetic Hyperthermia Applications with Artificial Neural Network Modeling.” <i>RSC Advances</i>. Royal Society of Chemistry, 2021. <a href=\"https://doi.org/10.1039/d1ra03428f\">https://doi.org/10.1039/d1ra03428f</a>.","short":"M.S. Dar, K.B. Akram, A. Sohail, F. Arif, F. Zabihi, S. Yang, S. Munir, M. Zhu, M. Abid, M. Nauman, RSC Advances 11 (2021) 21702–21715.","apa":"Dar, M. S., Akram, K. B., Sohail, A., Arif, F., Zabihi, F., Yang, S., … Nauman, M. (2021). Heat induction in two-dimensional graphene–Fe3O4 nanohybrids for magnetic hyperthermia applications with artificial neural network modeling. <i>RSC Advances</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/d1ra03428f\">https://doi.org/10.1039/d1ra03428f</a>","ama":"Dar MS, Akram KB, Sohail A, et al. Heat induction in two-dimensional graphene–Fe3O4 nanohybrids for magnetic hyperthermia applications with artificial neural network modeling. <i>RSC Advances</i>. 2021;11(35):21702-21715. doi:<a href=\"https://doi.org/10.1039/d1ra03428f\">10.1039/d1ra03428f</a>"},"department":[{"_id":"KiMo"}],"external_id":{"isi":["000665644000048"]},"intvolume":"        11","abstract":[{"lang":"eng","text":"We report the synthesis and characterization of graphene functionalized with iron (Fe3+) oxide (G-Fe3O4) nanohybrids for radio-frequency magnetic hyperthermia application. We adopted the wet chemical procedure, using various contents of Fe3O4 (magnetite) from 0–100% for making two-dimensional graphene–Fe3O4 nanohybrids. The homogeneous dispersal of Fe3O4 nanoparticles decorated on the graphene surface combined with their biocompatibility and high thermal conductivity make them an excellent material for magnetic hyperthermia. The morphological and magnetic properties of the nanohybrids were studied using scanning electron microscopy (SEM) and a vibrating sample magnetometer (VSM), respectively. The smart magnetic platforms were exposed to an alternating current (AC) magnetic field of 633 kHz and of strength 9.1 mT for studying their hyperthermic performance. The localized antitumor effects were investigated with artificial neural network modeling. A neural net time-series model was developed for the assessment of the best nanohybrid composition to serve the purpose with an accuracy close to 100%. Six Nonlinear Autoregressive with External Input (NARX) models were obtained, one for each of the components. The assessment of the accuracy of the predicted results has been done on the basis of Mean Squared Error (MSE). The highest Mean Squared Error value was obtained for the nanohybrid containing 45% magnetite and 55% graphene (F45G55) in the training phase i.e., 0.44703, which is where the model achieved optimal results after 71 epochs. The F45G55 nanohybrid was found to be the best for hyperthermia applications in low dosage with the highest specific absorption rate (SAR) and mean squared error values."}],"has_accepted_license":"1"},{"month":"06","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2006.01275"}],"status":"public","day":"15","volume":103,"title":"Closing of the induced gap in a hybrid superconductor-semiconductor nanowire","_id":"9570","year":"2021","publication":"Physical Review B","doi":"10.1103/PhysRevB.103.235201","arxiv":1,"quality_controlled":"1","language":[{"iso":"eng"}],"date_published":"2021-06-15T00:00:00Z","date_updated":"2023-08-08T14:08:08Z","date_created":"2021-06-20T22:01:33Z","article_processing_charge":"No","isi":1,"publication_status":"published","article_number":"235201","publication_identifier":{"issn":["24699950"],"eissn":["24699969"]},"author":[{"last_name":"Puglia","id":"4D495994-AE37-11E9-AC72-31CAE5697425","first_name":"Denise","full_name":"Puglia, Denise"},{"last_name":"Martinez","full_name":"Martinez, E. A.","first_name":"E. A."},{"full_name":"Ménard, G. C.","first_name":"G. C.","last_name":"Ménard"},{"full_name":"Pöschl, A.","first_name":"A.","last_name":"Pöschl"},{"full_name":"Gronin, S.","first_name":"S.","last_name":"Gronin"},{"last_name":"Gardner","full_name":"Gardner, G. C.","first_name":"G. C."},{"first_name":"R.","full_name":"Kallaher, R.","last_name":"Kallaher"},{"first_name":"M. J.","full_name":"Manfra, M. J.","last_name":"Manfra"},{"first_name":"C. M.","full_name":"Marcus, C. M.","last_name":"Marcus"},{"full_name":"Higginbotham, Andrew P","first_name":"Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","last_name":"Higginbotham","orcid":"0000-0003-2607-2363"},{"full_name":"Casparis, L.","first_name":"L.","last_name":"Casparis"}],"article_type":"original","oa":1,"issue":"23","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","publisher":"American Physical Society","oa_version":"Preprint","intvolume":"       103","abstract":[{"text":"We present conductance-matrix measurements in long, three-terminal hybrid superconductor-semiconductor nanowires, and compare with theoretical predictions of a magnetic-field-driven, topological quantum phase transition. By examining the nonlocal conductance, we identify the closure of the excitation gap in the bulk of the semiconductor before the emergence of zero-bias peaks, ruling out spurious gap-closure signatures from localized states. We observe that after the gap closes, nonlocal signals and zero-bias peaks fluctuate strongly at both ends, inconsistent with a simple picture of clean topological superconductivity.","lang":"eng"}],"department":[{"_id":"AnHi"}],"external_id":{"arxiv":["2006.01275"],"isi":["000661512500002"]},"scopus_import":"1","related_material":{"record":[{"status":"public","id":"13080","relation":"research_data"}]},"citation":{"short":"D. Puglia, E.A. Martinez, G.C. Ménard, A. Pöschl, S. Gronin, G.C. Gardner, R. Kallaher, M.J. Manfra, C.M. Marcus, A.P. Higginbotham, L. Casparis, Physical Review B 103 (2021).","chicago":"Puglia, Denise, E. A. Martinez, G. C. Ménard, A. Pöschl, S. Gronin, G. C. Gardner, R. Kallaher, et al. “Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire.” <i>Physical Review B</i>. American Physical Society, 2021. <a href=\"https://doi.org/10.1103/PhysRevB.103.235201\">https://doi.org/10.1103/PhysRevB.103.235201</a>.","apa":"Puglia, D., Martinez, E. A., Ménard, G. C., Pöschl, A., Gronin, S., Gardner, G. C., … Casparis, L. (2021). Closing of the induced gap in a hybrid superconductor-semiconductor nanowire. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.103.235201\">https://doi.org/10.1103/PhysRevB.103.235201</a>","ama":"Puglia D, Martinez EA, Ménard GC, et al. Closing of the induced gap in a hybrid superconductor-semiconductor nanowire. <i>Physical Review B</i>. 2021;103(23). doi:<a href=\"https://doi.org/10.1103/PhysRevB.103.235201\">10.1103/PhysRevB.103.235201</a>","ista":"Puglia D, Martinez EA, Ménard GC, Pöschl A, Gronin S, Gardner GC, Kallaher R, Manfra MJ, Marcus CM, Higginbotham AP, Casparis L. 2021. Closing of the induced gap in a hybrid superconductor-semiconductor nanowire. Physical Review B. 103(23), 235201.","ieee":"D. Puglia <i>et al.</i>, “Closing of the induced gap in a hybrid superconductor-semiconductor nanowire,” <i>Physical Review B</i>, vol. 103, no. 23. American Physical Society, 2021.","mla":"Puglia, Denise, et al. “Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire.” <i>Physical Review B</i>, vol. 103, no. 23, 235201, American Physical Society, 2021, doi:<a href=\"https://doi.org/10.1103/PhysRevB.103.235201\">10.1103/PhysRevB.103.235201</a>."},"acknowledgement":"We acknowledge insightful discussions with K. Flensberg, E. B. Hansen, T. Karzig, R. Lutchyn, D. Pikulin, E. Prada, and R. Aguado. This work was supported by Microsoft Project Q and the Danmarks Grundforskningsfond. C.M.M. acknowledges support from the Villum Fonden. A.P.H. and L.C. contributed equally to this work."},{"date_published":"2021-04-01T00:00:00Z","page":"1−43","date_updated":"2024-03-06T12:22:07Z","date_created":"2021-06-20T22:01:33Z","arxiv":1,"quality_controlled":"1","language":[{"iso":"eng"}],"publication_identifier":{"issn":["15324435"],"eissn":["15337928"]},"ddc":["000"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"No","publication_status":"published","status":"public","main_file_link":[{"open_access":"1","url":"https://www.jmlr.org/papers/v22/20-255.html"}],"volume":22,"day":"01","month":"04","title":"NUQSGD: Provably communication-efficient data-parallel SGD via nonuniform quantization","file_date_updated":"2021-06-23T07:09:41Z","_id":"9571","year":"2021","publication":"Journal of Machine Learning Research","department":[{"_id":"DaAl"}],"external_id":{"arxiv":["1908.06077"]},"intvolume":"        22","abstract":[{"text":"As the size and complexity of models and datasets grow, so does the need for communication-efficient variants of stochastic gradient descent that can be deployed to perform parallel model training. One popular communication-compression method for data-parallel SGD is QSGD (Alistarh et al., 2017), which quantizes and encodes gradients to reduce communication costs. The baseline variant of QSGD provides strong theoretical guarantees, however, for practical purposes, the authors proposed a heuristic variant which we call QSGDinf, which demonstrated impressive empirical gains for distributed training of large neural networks. In this paper, we build on this work to propose a new gradient quantization scheme, and show that it has both stronger theoretical guarantees than QSGD, and matches and exceeds the empirical performance of the QSGDinf heuristic and of other compression methods.","lang":"eng"}],"has_accepted_license":"1","scopus_import":"1","citation":{"chicago":"Ramezani-Kebrya, Ali, Fartash Faghri, Ilya Markov, Vitalii Aksenov, Dan-Adrian Alistarh, and Daniel M. Roy. “NUQSGD: Provably Communication-Efficient Data-Parallel SGD via Nonuniform Quantization.” <i>Journal of Machine Learning Research</i>. Journal of Machine Learning Research, 2021.","short":"A. Ramezani-Kebrya, F. Faghri, I. Markov, V. Aksenov, D.-A. Alistarh, D.M. Roy, Journal of Machine Learning Research 22 (2021) 1−43.","ama":"Ramezani-Kebrya A, Faghri F, Markov I, Aksenov V, Alistarh D-A, Roy DM. NUQSGD: Provably communication-efficient data-parallel SGD via nonuniform quantization. <i>Journal of Machine Learning Research</i>. 2021;22(114):1−43.","apa":"Ramezani-Kebrya, A., Faghri, F., Markov, I., Aksenov, V., Alistarh, D.-A., &#38; Roy, D. M. (2021). NUQSGD: Provably communication-efficient data-parallel SGD via nonuniform quantization. <i>Journal of Machine Learning Research</i>. Journal of Machine Learning Research.","ista":"Ramezani-Kebrya A, Faghri F, Markov I, Aksenov V, Alistarh D-A, Roy DM. 2021. NUQSGD: Provably communication-efficient data-parallel SGD via nonuniform quantization. Journal of Machine Learning Research. 22(114), 1−43.","mla":"Ramezani-Kebrya, Ali, et al. “NUQSGD: Provably Communication-Efficient Data-Parallel SGD via Nonuniform Quantization.” <i>Journal of Machine Learning Research</i>, vol. 22, no. 114, Journal of Machine Learning Research, 2021, p. 1−43.","ieee":"A. Ramezani-Kebrya, F. Faghri, I. Markov, V. Aksenov, D.-A. Alistarh, and D. M. Roy, “NUQSGD: Provably communication-efficient data-parallel SGD via nonuniform quantization,” <i>Journal of Machine Learning Research</i>, vol. 22, no. 114. Journal of Machine Learning Research, p. 1−43, 2021."},"file":[{"file_id":"9595","file_name":"2021_JournalOfMachineLearningResearch_Ramezani-Kebrya.pdf","checksum":"6428aa8bcb67768b6949c99b55d5281d","content_type":"application/pdf","access_level":"open_access","date_updated":"2021-06-23T07:09:41Z","date_created":"2021-06-23T07:09:41Z","relation":"main_file","file_size":11237154,"success":1,"creator":"asandaue"}],"article_type":"original","author":[{"last_name":"Ramezani-Kebrya","full_name":"Ramezani-Kebrya, Ali","first_name":"Ali"},{"first_name":"Fartash","full_name":"Faghri, Fartash","last_name":"Faghri"},{"full_name":"Markov, Ilya","first_name":"Ilya","last_name":"Markov"},{"full_name":"Aksenov, Vitalii","first_name":"Vitalii","id":"2980135A-F248-11E8-B48F-1D18A9856A87","last_name":"Aksenov"},{"first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X"},{"last_name":"Roy","first_name":"Daniel M.","full_name":"Roy, Daniel M."}],"oa_version":"Published Version","oa":1,"issue":"114","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","publisher":"Journal of Machine Learning Research"},{"day":"29","status":"public","month":"06","conference":{"location":"Halifax, NS, Canada","name":"CCCG: Canadian Conference on Computational Geometry","end_date":"2021-08-12","start_date":"2021-08-10"},"publication":"Proceedings of the 33rd Canadian Conference on Computational Geometry","year":"2021","license":"https://creativecommons.org/licenses/by-nd/4.0/","_id":"9592","file_date_updated":"2021-08-12T10:57:21Z","title":"Massively winning configurations in the convex grabbing game on the plane","date_created":"2021-06-22T15:57:11Z","date_updated":"2021-08-12T10:57:39Z","date_published":"2021-06-29T00:00:00Z","language":[{"iso":"eng"}],"quality_controlled":"1","arxiv":1,"tmp":{"image":"/image/cc_by_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","short":"CC BY-ND (4.0)","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)"},"ddc":["516"],"publication_status":"accepted","article_processing_charge":"No","file":[{"file_id":"9616","file_name":"Convex-Grabbing-Game_CCCG_proc_version.pdf","date_updated":"2021-06-28T20:23:13Z","relation":"main_file","date_created":"2021-06-28T20:23:13Z","access_level":"open_access","file_size":381306,"content_type":"application/pdf","checksum":"45accb1de9b7e0e4bb2fbfe5fd3e6239","creator":"mdvorak","success":1},{"content_type":"application/pdf","checksum":"9199cf18c65658553487458cc24d0ab2","relation":"main_file","access_level":"open_access","date_updated":"2021-08-12T10:57:21Z","date_created":"2021-08-12T10:57:21Z","file_size":403645,"creator":"kschuh","success":1,"file_id":"9902","file_name":"Convex-Grabbing-Game_FULL-VERSION.pdf"}],"author":[{"first_name":"Martin","full_name":"Dvorak, Martin","last_name":"Dvorak","orcid":"0000-0001-5293-214X","id":"40ED02A8-C8B4-11E9-A9C0-453BE6697425"},{"first_name":"Sara","full_name":"Nicholson, Sara","last_name":"Nicholson"}],"oa_version":"Submitted Version","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","type":"conference","oa":1,"external_id":{"arxiv":["2106.11247"]},"department":[{"_id":"GradSch"},{"_id":"VlKo"}],"keyword":["convex grabbing game","graph grabbing game","combinatorial game","convex geometry"],"has_accepted_license":"1","abstract":[{"text":"The convex grabbing game is a game where two players, Alice and Bob, alternate taking extremal points from the convex hull of a point set on the plane. Rational weights are given to the points. The goal of each player is to maximize the total weight over all points that they obtain. We restrict the setting to the case of binary weights. We show a construction of an arbitrarily large odd-sized point set that allows Bob to obtain almost 3/4 of the total weight. This construction answers a question asked by Matsumoto, Nakamigawa, and Sakuma in [Graphs and Combinatorics, 36/1 (2020)]. We also present an arbitrarily large even-sized point set where Bob can obtain the entirety of the total weight. Finally, we discuss conjectures about optimum moves in the convex grabbing game for both players in general.","lang":"eng"}],"citation":{"short":"M. Dvorak, S. Nicholson, in:, Proceedings of the 33rd Canadian Conference on Computational Geometry, n.d.","chicago":"Dvorak, Martin, and Sara Nicholson. “Massively Winning Configurations in the Convex Grabbing Game on the Plane.” In <i>Proceedings of the 33rd Canadian Conference on Computational Geometry</i>, n.d.","ama":"Dvorak M, Nicholson S. Massively winning configurations in the convex grabbing game on the plane. In: <i>Proceedings of the 33rd Canadian Conference on Computational Geometry</i>.","apa":"Dvorak, M., &#38; Nicholson, S. (n.d.). Massively winning configurations in the convex grabbing game on the plane. In <i>Proceedings of the 33rd Canadian Conference on Computational Geometry</i>. Halifax, NS, Canada.","ista":"Dvorak M, Nicholson S. Massively winning configurations in the convex grabbing game on the plane. Proceedings of the 33rd Canadian Conference on Computational Geometry. CCCG: Canadian Conference on Computational Geometry.","ieee":"M. Dvorak and S. Nicholson, “Massively winning configurations in the convex grabbing game on the plane,” in <i>Proceedings of the 33rd Canadian Conference on Computational Geometry</i>, Halifax, NS, Canada.","mla":"Dvorak, Martin, and Sara Nicholson. “Massively Winning Configurations in the Convex Grabbing Game on the Plane.” <i>Proceedings of the 33rd Canadian Conference on Computational Geometry</i>."}},{"language":[{"iso":"eng"}],"quality_controlled":"1","date_updated":"2023-08-10T13:53:23Z","date_created":"2021-06-27T22:01:46Z","date_published":"2021-07-12T00:00:00Z","article_number":"3804","publication_status":"published","isi":1,"article_processing_charge":"No","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["570"],"publication_identifier":{"eissn":["20411723"]},"month":"07","day":"12","volume":12,"status":"public","publication":"Nature Communications","year":"2021","_id":"9601","file_date_updated":"2021-06-28T08:04:22Z","title":"Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3","doi":"10.1038/s41467-021-23510-4","abstract":[{"text":"In mammalian genomes, differentially methylated regions (DMRs) and histone marks including trimethylation of histone 3 lysine 27 (H3K27me3) at imprinted genes are asymmetrically inherited to control parentally-biased gene expression. However, neither parent-of-origin-specific transcription nor imprints have been comprehensively mapped at the blastocyst stage of preimplantation development. Here, we address this by integrating transcriptomic and epigenomic approaches in mouse preimplantation embryos. We find that seventy-one genes exhibit previously unreported parent-of-origin-specific expression in blastocysts (nBiX: novel blastocyst-imprinted expressed). Uniparental expression of nBiX genes disappears soon after implantation. Micro-whole-genome bisulfite sequencing (µWGBS) of individual uniparental blastocysts detects 859 DMRs. We further find that 16% of nBiX genes are associated with a DMR, whereas most are associated with parentally-biased H3K27me3, suggesting a role for Polycomb-mediated imprinting in blastocysts. nBiX genes are clustered: five clusters contained at least one published imprinted gene, and five clusters exclusively contained nBiX genes. These data suggest that early development undergoes a complex program of stage-specific imprinting involving different tiers of regulation.","lang":"eng"}],"has_accepted_license":"1","intvolume":"        12","external_id":{"isi":["000667248600005"]},"department":[{"_id":"SiHi"}],"citation":{"apa":"Santini, L., Halbritter, F., Titz-Teixeira, F., Suzuki, T., Asami, M., Ma, X., … Leeb, M. (2021). Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-021-23510-4\">https://doi.org/10.1038/s41467-021-23510-4</a>","ama":"Santini L, Halbritter F, Titz-Teixeira F, et al. Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3. <i>Nature Communications</i>. 2021;12(1). doi:<a href=\"https://doi.org/10.1038/s41467-021-23510-4\">10.1038/s41467-021-23510-4</a>","chicago":"Santini, Laura, Florian Halbritter, Fabian Titz-Teixeira, Toru Suzuki, Maki Asami, Xiaoyan Ma, Julia Ramesmayer, et al. “Genomic Imprinting in Mouse Blastocysts Is Predominantly Associated with H3K27me3.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-021-23510-4\">https://doi.org/10.1038/s41467-021-23510-4</a>.","short":"L. Santini, F. Halbritter, F. Titz-Teixeira, T. Suzuki, M. Asami, X. Ma, J. Ramesmayer, A. Lackner, N. Warr, F. Pauler, S. Hippenmeyer, E. Laue, M. Farlik, C. Bock, A. Beyer, A.C.F. Perry, M. Leeb, Nature Communications 12 (2021).","ieee":"L. Santini <i>et al.</i>, “Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3,” <i>Nature Communications</i>, vol. 12, no. 1. Springer Nature, 2021.","mla":"Santini, Laura, et al. “Genomic Imprinting in Mouse Blastocysts Is Predominantly Associated with H3K27me3.” <i>Nature Communications</i>, vol. 12, no. 1, 3804, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-23510-4\">10.1038/s41467-021-23510-4</a>.","ista":"Santini L, Halbritter F, Titz-Teixeira F, Suzuki T, Asami M, Ma X, Ramesmayer J, Lackner A, Warr N, Pauler F, Hippenmeyer S, Laue E, Farlik M, Bock C, Beyer A, Perry ACF, Leeb M. 2021. Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3. Nature Communications. 12(1), 3804."},"acknowledgement":"The authors thank Robert Feil and Anton Wutz for helpful discussions and comments, Samuel Collombet and Peter Fraser for sharing embryo TAD coordinates, and Andy Riddel at the Cambridge Stem Cell Institute and Thomas Sauer at the Max Perutz Laboratories FACS facility for flow-sorting. We thank the team of the Biomedical Sequencing Facility at the CeMM and the Vienna Biocenter Core Facilities (VBCF) for support with next-generation sequencing. We are grateful to animal care teams at the University of Bath and MRC Harwell. A.C.F.P. acknowledges support from the UK Medical Research Council (MR/N000080/1 and MR/N020294/1) and Biotechnology and Biological Sciences Research Council (BB/P009506/1). L.S. is part of the FWF doctoral programme SMICH and supported by an Austrian Academy of Sciences DOC Fellowship. M.L. is funded by a Vienna Research Group for Young Investigators grant (VRG14-006) by the Vienna Science and Technology Fund (WWTF) and by the Austrian Science Fund FWF (I3786 and P31334).","scopus_import":"1","author":[{"full_name":"Santini, Laura","first_name":"Laura","last_name":"Santini"},{"full_name":"Halbritter, Florian","first_name":"Florian","last_name":"Halbritter"},{"last_name":"Titz-Teixeira","first_name":"Fabian","full_name":"Titz-Teixeira, Fabian"},{"last_name":"Suzuki","full_name":"Suzuki, Toru","first_name":"Toru"},{"full_name":"Asami, Maki","first_name":"Maki","last_name":"Asami"},{"last_name":"Ma","full_name":"Ma, Xiaoyan","first_name":"Xiaoyan"},{"last_name":"Ramesmayer","first_name":"Julia","full_name":"Ramesmayer, Julia"},{"last_name":"Lackner","full_name":"Lackner, Andreas","first_name":"Andreas"},{"full_name":"Warr, Nick","first_name":"Nick","last_name":"Warr"},{"id":"48EA0138-F248-11E8-B48F-1D18A9856A87","last_name":"Pauler","orcid":"0000-0002-7462-0048","full_name":"Pauler, Florian","first_name":"Florian"},{"orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","full_name":"Hippenmeyer, Simon"},{"first_name":"Ernest","full_name":"Laue, Ernest","last_name":"Laue"},{"full_name":"Farlik, Matthias","first_name":"Matthias","last_name":"Farlik"},{"last_name":"Bock","full_name":"Bock, Christoph","first_name":"Christoph"},{"first_name":"Andreas","full_name":"Beyer, Andreas","last_name":"Beyer"},{"last_name":"Perry","first_name":"Anthony C.F.","full_name":"Perry, Anthony C.F."},{"first_name":"Martin","full_name":"Leeb, Martin","last_name":"Leeb"}],"article_type":"original","file":[{"success":1,"creator":"asandaue","date_updated":"2021-06-28T08:04:22Z","date_created":"2021-06-28T08:04:22Z","access_level":"open_access","relation":"main_file","file_size":2156554,"content_type":"application/pdf","checksum":"75dd89d09945185b2d14b2434a0bcb50","file_name":"2021_NatureCommunications_Santini.pdf","file_id":"9608"}],"publisher":"Springer Nature","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","issue":"1","oa":1,"oa_version":"Published Version"},{"file":[{"checksum":"15fbc9064cd9d1c777ac0043b78c8f12","content_type":"application/pdf","file_size":418168,"relation":"main_file","date_updated":"2021-06-28T13:33:23Z","access_level":"open_access","date_created":"2021-06-28T13:33:23Z","creator":"asandaue","success":1,"file_id":"9612","file_name":"2021_JournalOfCombinatorialTheory_Pach.pdf"}],"article_type":"original","author":[{"id":"E62E3130-B088-11EA-B919-BF823C25FEA4","last_name":"Pach","first_name":"János","full_name":"Pach, János"},{"full_name":"Tomon, István","first_name":"István","last_name":"Tomon"}],"oa_version":"Published Version","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","publisher":"Elsevier","department":[{"_id":"HeEd"}],"external_id":{"isi":["000702280800002"]},"intvolume":"       151","has_accepted_license":"1","abstract":[{"text":"An ordered graph is a graph with a linear ordering on its vertex set. We prove that for every positive integer k, there exists a constant ck > 0 such that any ordered graph G on n vertices with the property that neither G nor its complement contains an induced monotone path of size k, has either a clique or an independent set of size at least n^ck . This strengthens a result of Bousquet, Lagoutte, and Thomassé, who proved the analogous result for unordered graphs.\r\nA key idea of the above paper was to show that any unordered graph on n vertices that does not contain an induced path of size k, and whose maximum degree is at most c(k)n for some small c(k) > 0, contains two disjoint linear size subsets with no edge between them. This approach fails for ordered graphs, because the analogous statement is false for k ≥ 3, by a construction of Fox. We provide some further examples showing that this statement also fails for ordered graphs avoiding other ordered trees.","lang":"eng"}],"scopus_import":"1","acknowledgement":"We would like to thank the anonymous referees for their useful comments and suggestions. János Pach is partially supported by Austrian Science Fund (FWF) grant Z 342-N31 and by ERC Advanced grant “GeoScape.” István Tomon is partially supported by Swiss National Science Foundation grant no. 200021_196965, and thanks the support of MIPT Moscow. Both authors are partially supported by The Russian Government in the framework of MegaGrant no. 075-15-2019-1926.","citation":{"chicago":"Pach, János, and István Tomon. “Erdős-Hajnal-Type Results for Monotone Paths.” <i>Journal of Combinatorial Theory. Series B</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.jctb.2021.05.004\">https://doi.org/10.1016/j.jctb.2021.05.004</a>.","short":"J. Pach, I. Tomon, Journal of Combinatorial Theory. Series B 151 (2021) 21–37.","apa":"Pach, J., &#38; Tomon, I. (2021). Erdős-Hajnal-type results for monotone paths. <i>Journal of Combinatorial Theory. Series B</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jctb.2021.05.004\">https://doi.org/10.1016/j.jctb.2021.05.004</a>","ama":"Pach J, Tomon I. Erdős-Hajnal-type results for monotone paths. <i>Journal of Combinatorial Theory Series B</i>. 2021;151:21-37. doi:<a href=\"https://doi.org/10.1016/j.jctb.2021.05.004\">10.1016/j.jctb.2021.05.004</a>","ista":"Pach J, Tomon I. 2021. Erdős-Hajnal-type results for monotone paths. Journal of Combinatorial Theory. Series B. 151, 21–37.","ieee":"J. Pach and I. Tomon, “Erdős-Hajnal-type results for monotone paths,” <i>Journal of Combinatorial Theory. Series B</i>, vol. 151. Elsevier, pp. 21–37, 2021.","mla":"Pach, János, and István Tomon. “Erdős-Hajnal-Type Results for Monotone Paths.” <i>Journal of Combinatorial Theory. Series B</i>, vol. 151, Elsevier, 2021, pp. 21–37, doi:<a href=\"https://doi.org/10.1016/j.jctb.2021.05.004\">10.1016/j.jctb.2021.05.004</a>."},"project":[{"_id":"268116B8-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z00342"}],"status":"public","volume":151,"day":"09","month":"06","doi":"10.1016/j.jctb.2021.05.004","title":"Erdős-Hajnal-type results for monotone paths","file_date_updated":"2021-06-28T13:33:23Z","_id":"9602","year":"2021","publication":"Journal of Combinatorial Theory. Series B","date_published":"2021-06-09T00:00:00Z","page":"21-37","date_created":"2021-06-27T22:01:47Z","date_updated":"2023-08-10T13:38:00Z","quality_controlled":"1","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0095-8956"]},"ddc":["510"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"No","isi":1,"publication_status":"published"}]