[{"oa_version":"Submitted Version","article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","date_updated":"2025-04-14T07:43:52Z","author":[{"full_name":"Zhang, Yu","last_name":"Zhang","first_name":"Yu"},{"full_name":"Xing, Congcong","last_name":"Xing","first_name":"Congcong"},{"first_name":"Yu","orcid":"0000-0001-7313-6740","full_name":"Liu, Yu","last_name":"Liu","id":"2A70014E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Maria Chiara","last_name":"Spadaro","full_name":"Spadaro, Maria Chiara"},{"full_name":"Wang, Xiang","last_name":"Wang","first_name":"Xiang"},{"last_name":"Li","full_name":"Li, Mengyao","first_name":"Mengyao"},{"full_name":"Xiao, Ke","last_name":"Xiao","first_name":"Ke"},{"first_name":"Ting","last_name":"Zhang","full_name":"Zhang, Ting"},{"first_name":"Pablo","full_name":"Guardia, Pablo","last_name":"Guardia"},{"full_name":"Lim, Khak Ho","last_name":"Lim","first_name":"Khak Ho"},{"first_name":"Ahmad Ostovari","full_name":"Moghaddam, Ahmad Ostovari","last_name":"Moghaddam"},{"last_name":"Llorca","full_name":"Llorca, Jordi","first_name":"Jordi"},{"last_name":"Arbiol","full_name":"Arbiol, Jordi","first_name":"Jordi"},{"first_name":"Maria","last_name":"Ibáñez","full_name":"Ibáñez, Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843"},{"last_name":"Cabot","full_name":"Cabot, Andreu","first_name":"Andreu"}],"title":"Doping-mediated stabilization of copper vacancies to promote thermoelectric properties of Cu2-xS","article_type":"original","year":"2021","acknowledgement":"This work was supported by the European Regional Development Fund and by the Spanish Ministerio de Economía y Competitividad through the project SEHTOP (ENE2016-77798-C4-3-R). MI acknowledges financial support from IST Austria. YL acknowledges funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No. 754411. YZ, CX, XW, KX and TZ thank the China Scholarship Council for the scholarship support. ICN2 acknowledges funding from Generalitat de Catalunya 2017 SGR 327 and the Spanish MINECO project ENE2017-85087-C3. ICN2 is supported by the Severo Ochoa program from the Spanish MINECO (grant no. SEV-2017-0706) and is funded by the CERCA program/Generalitat de Catalunya. Part of the present work has been performed in the framework of Universitat Autònoma de Barcelona Materials Science Ph.D. program. M.C.S. has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754510 (PROBIST) and the Severo Ochoa programme. P.G. acknowledges financial support from the Spanish government (MICIU) through the RTI2018-102006-J-I00 project and the Catalan Agency of Competitiveness (ACCIO) through the TecnioSpring+ Marie Sklodowska-Curie action TECSPR16-1-0082. YZ and CX contributed equally to this work.","publication_identifier":{"issn":["2211-2855"]},"ec_funded":1,"article_number":"105991","date_published":"2021-07-01T00:00:00Z","intvolume":"        85","oa":1,"doi":"10.1016/j.nanoen.2021.105991","day":"01","project":[{"call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"publication":"Nano Energy","external_id":{"isi":["000663442200004"]},"date_created":"2021-04-04T22:01:21Z","publication_status":"published","scopus_import":"1","issue":"7","month":"07","_id":"9305","quality_controlled":"1","citation":{"mla":"Zhang, Yu, et al. “Doping-Mediated Stabilization of Copper Vacancies to Promote Thermoelectric Properties of Cu2-XS.” <i>Nano Energy</i>, vol. 85, no. 7, 105991, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.nanoen.2021.105991\">10.1016/j.nanoen.2021.105991</a>.","ista":"Zhang Y, Xing C, Liu Y, Spadaro MC, Wang X, Li M, Xiao K, Zhang T, Guardia P, Lim KH, Moghaddam AO, Llorca J, Arbiol J, Ibáñez M, Cabot A. 2021. Doping-mediated stabilization of copper vacancies to promote thermoelectric properties of Cu2-xS. Nano Energy. 85(7), 105991.","chicago":"Zhang, Yu, Congcong Xing, Yu Liu, Maria Chiara Spadaro, Xiang Wang, Mengyao Li, Ke Xiao, et al. “Doping-Mediated Stabilization of Copper Vacancies to Promote Thermoelectric Properties of Cu2-XS.” <i>Nano Energy</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.nanoen.2021.105991\">https://doi.org/10.1016/j.nanoen.2021.105991</a>.","apa":"Zhang, Y., Xing, C., Liu, Y., Spadaro, M. C., Wang, X., Li, M., … Cabot, A. (2021). Doping-mediated stabilization of copper vacancies to promote thermoelectric properties of Cu2-xS. <i>Nano Energy</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.nanoen.2021.105991\">https://doi.org/10.1016/j.nanoen.2021.105991</a>","ama":"Zhang Y, Xing C, Liu Y, et al. Doping-mediated stabilization of copper vacancies to promote thermoelectric properties of Cu2-xS. <i>Nano Energy</i>. 2021;85(7). doi:<a href=\"https://doi.org/10.1016/j.nanoen.2021.105991\">10.1016/j.nanoen.2021.105991</a>","ieee":"Y. Zhang <i>et al.</i>, “Doping-mediated stabilization of copper vacancies to promote thermoelectric properties of Cu2-xS,” <i>Nano Energy</i>, vol. 85, no. 7. Elsevier, 2021.","short":"Y. Zhang, C. Xing, Y. Liu, M.C. Spadaro, X. Wang, M. Li, K. Xiao, T. Zhang, P. Guardia, K.H. Lim, A.O. Moghaddam, J. Llorca, J. Arbiol, M. Ibáñez, A. Cabot, Nano Energy 85 (2021)."},"abstract":[{"text":"Copper chalcogenides are outstanding thermoelectric materials for applications in the medium-high temperature range. Among different chalcogenides, while Cu2−xSe is characterized by higher thermoelectric figures of merit, Cu2−xS provides advantages in terms of low cost and element abundance. In the present work, we investigate the effect of different dopants to enhance the Cu2−xS performance and also its thermal stability. Among the tested options, Pb-doped Cu2−xS shows the highest improvement in stability against sulfur volatilization. Additionally, Pb incorporation allows tuning charge carrier concentration, which enables a significant improvement of the power factor. We demonstrate here that the introduction of an optimal additive amount of just 0.3% results in a threefold increase of the power factor in the middle-temperature range (500–800 K) and a record dimensionless thermoelectric figure of merit above 2 at 880 K.","lang":"eng"}],"type":"journal_article","main_file_link":[{"url":"https://ddd.uab.cat/record/271947","open_access":"1"}],"publisher":"Elsevier","corr_author":"1","department":[{"_id":"MaIb"}],"volume":85},{"publisher":"Springer Nature","department":[{"_id":"JuFi"}],"volume":9,"quality_controlled":"1","citation":{"short":"S. Hensel, Stochastics and Partial Differential Equations: Analysis and Computations 9 (2021) 892–939.","mla":"Hensel, Sebastian. “Finite Time Extinction for the 1D Stochastic Porous Medium Equation with Transport Noise.” <i>Stochastics and Partial Differential Equations: Analysis and Computations</i>, vol. 9, Springer Nature, 2021, pp. 892–939, doi:<a href=\"https://doi.org/10.1007/s40072-021-00188-9\">10.1007/s40072-021-00188-9</a>.","ista":"Hensel S. 2021. Finite time extinction for the 1D stochastic porous medium equation with transport noise. Stochastics and Partial Differential Equations: Analysis and Computations. 9, 892–939.","chicago":"Hensel, Sebastian. “Finite Time Extinction for the 1D Stochastic Porous Medium Equation with Transport Noise.” <i>Stochastics and Partial Differential Equations: Analysis and Computations</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s40072-021-00188-9\">https://doi.org/10.1007/s40072-021-00188-9</a>.","ieee":"S. Hensel, “Finite time extinction for the 1D stochastic porous medium equation with transport noise,” <i>Stochastics and Partial Differential Equations: Analysis and Computations</i>, vol. 9. Springer Nature, pp. 892–939, 2021.","ama":"Hensel S. Finite time extinction for the 1D stochastic porous medium equation with transport noise. <i>Stochastics and Partial Differential Equations: Analysis and Computations</i>. 2021;9:892–939. doi:<a href=\"https://doi.org/10.1007/s40072-021-00188-9\">10.1007/s40072-021-00188-9</a>","apa":"Hensel, S. (2021). Finite time extinction for the 1D stochastic porous medium equation with transport noise. <i>Stochastics and Partial Differential Equations: Analysis and Computations</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s40072-021-00188-9\">https://doi.org/10.1007/s40072-021-00188-9</a>"},"abstract":[{"lang":"eng","text":"We establish finite time extinction with probability one for weak solutions of the Cauchy–Dirichlet problem for the 1D stochastic porous medium equation with Stratonovich transport noise and compactly supported smooth initial datum. Heuristically, this is expected to hold because Brownian motion has average spread rate O(t12) whereas the support of solutions to the deterministic PME grows only with rate O(t1m+1). The rigorous proof relies on a contraction principle up to time-dependent shift for Wong–Zakai type approximations, the transformation to a deterministic PME with two copies of a Brownian path as the lateral boundary, and techniques from the theory of viscosity solutions."}],"type":"journal_article","scopus_import":"1","month":"03","_id":"9307","external_id":{"isi":["000631001700001"]},"date_created":"2021-04-04T22:01:21Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"published","ddc":["510"],"project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"license":"https://creativecommons.org/licenses/by/4.0/","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"publication":"Stochastics and Partial Differential Equations: Analysis and Computations","publication_identifier":{"issn":["2194-0401"],"eissn":["2194-041X"]},"article_type":"original","year":"2021","acknowledgement":"This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385 . I am very grateful to M. Gerencsér and J. Maas for proposing this problem as well as helpful discussions. Special thanks go to F. Cornalba for suggesting the additional κ-truncation in Proposition 5. I am also indebted to an anonymous referee for pointing out a gap in a previous version of the proof of Lemma 9 (concerning the treatment of the noise term). The issue is resolved in this version.","ec_funded":1,"date_published":"2021-03-21T00:00:00Z","intvolume":"         9","file":[{"content_type":"application/pdf","checksum":"6529b609c9209861720ffa4685111bc6","relation":"main_file","date_updated":"2021-04-06T09:31:28Z","file_id":"9309","access_level":"open_access","creator":"dernst","file_size":727005,"success":1,"date_created":"2021-04-06T09:31:28Z","file_name":"2021_StochPartDiffEquation_Hensel.pdf"}],"oa":1,"day":"21","doi":"10.1007/s40072-021-00188-9","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","file_date_updated":"2021-04-06T09:31:28Z","status":"public","language":[{"iso":"eng"}],"date_updated":"2025-03-31T16:00:58Z","page":"892–939","author":[{"first_name":"Sebastian","orcid":"0000-0001-7252-8072","full_name":"Hensel, Sebastian","last_name":"Hensel","id":"4D23B7DA-F248-11E8-B48F-1D18A9856A87"}],"title":"Finite time extinction for the 1D stochastic porous medium equation with transport noise","oa_version":"Published Version"},{"corr_author":"1","publisher":"Springer Nature","volume":76,"department":[{"_id":"VlKo"}],"citation":{"ama":"Iyiola OS, Shehu Y. New convergence results for inertial Krasnoselskii–Mann iterations in Hilbert spaces with applications. <i>Results in Mathematics</i>. 2021;76(2). doi:<a href=\"https://doi.org/10.1007/s00025-021-01381-x\">10.1007/s00025-021-01381-x</a>","apa":"Iyiola, O. S., &#38; Shehu, Y. (2021). New convergence results for inertial Krasnoselskii–Mann iterations in Hilbert spaces with applications. <i>Results in Mathematics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00025-021-01381-x\">https://doi.org/10.1007/s00025-021-01381-x</a>","ieee":"O. S. Iyiola and Y. Shehu, “New convergence results for inertial Krasnoselskii–Mann iterations in Hilbert spaces with applications,” <i>Results in Mathematics</i>, vol. 76, no. 2. Springer Nature, 2021.","mla":"Iyiola, Olaniyi S., and Yekini Shehu. “New Convergence Results for Inertial Krasnoselskii–Mann Iterations in Hilbert Spaces with Applications.” <i>Results in Mathematics</i>, vol. 76, no. 2, 75, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1007/s00025-021-01381-x\">10.1007/s00025-021-01381-x</a>.","chicago":"Iyiola, Olaniyi S., and Yekini Shehu. “New Convergence Results for Inertial Krasnoselskii–Mann Iterations in Hilbert Spaces with Applications.” <i>Results in Mathematics</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s00025-021-01381-x\">https://doi.org/10.1007/s00025-021-01381-x</a>.","ista":"Iyiola OS, Shehu Y. 2021. New convergence results for inertial Krasnoselskii–Mann iterations in Hilbert spaces with applications. Results in Mathematics. 76(2), 75.","short":"O.S. Iyiola, Y. Shehu, Results in Mathematics 76 (2021)."},"abstract":[{"text":"We consider inertial iteration methods for Fermat–Weber location problem and primal–dual three-operator splitting in real Hilbert spaces. To do these, we first obtain weak convergence analysis and nonasymptotic O(1/n) convergence rate of the inertial Krasnoselskii–Mann iteration for fixed point of nonexpansive operators in infinite dimensional real Hilbert spaces under some seemingly easy to implement conditions on the iterative parameters. One of our contributions is that the convergence analysis and rate of convergence results are obtained using conditions which appear not complicated and restrictive as assumed in other previous related results in the literature. We then show that Fermat–Weber location problem and primal–dual three-operator splitting are special cases of fixed point problem of nonexpansive mapping and consequently obtain the convergence analysis of inertial iteration methods for Fermat–Weber location problem and primal–dual three-operator splitting in real Hilbert spaces. Some numerical implementations are drawn from primal–dual three-operator splitting to support the theoretical analysis.","lang":"eng"}],"type":"journal_article","quality_controlled":"1","month":"03","issue":"2","scopus_import":"1","_id":"9315","external_id":{"isi":["000632917700001"]},"publication_status":"published","date_created":"2021-04-11T22:01:14Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"publication":"Results in Mathematics","article_number":"75","acknowledgement":"The research of this author is supported by the Postdoctoral Fellowship from Institute of Science and Technology (IST), Austria.","year":"2021","publication_identifier":{"eissn":["1420-9012"],"issn":["1422-6383"]},"article_type":"original","doi":"10.1007/s00025-021-01381-x","day":"25","date_published":"2021-03-25T00:00:00Z","intvolume":"        76","language":[{"iso":"eng"}],"status":"public","article_processing_charge":"No","author":[{"first_name":"Olaniyi S.","full_name":"Iyiola, Olaniyi S.","last_name":"Iyiola"},{"first_name":"Yekini","full_name":"Shehu, Yekini","last_name":"Shehu","id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9224-7139"}],"title":"New convergence results for inertial Krasnoselskii–Mann iterations in Hilbert spaces with applications","date_updated":"2024-10-09T21:00:33Z","oa_version":"None"},{"publisher":"Elsevier","corr_author":"1","department":[{"_id":"CaHe"},{"_id":"EdHa"}],"volume":184,"quality_controlled":"1","abstract":[{"text":"Embryo morphogenesis is impacted by dynamic changes in tissue material properties, which have been proposed to occur via processes akin to phase transitions (PTs). Here, we show that rigidity percolation provides a simple and robust theoretical framework to predict material/structural PTs of embryonic tissues from local cell connectivity. By using percolation theory, combined with directly monitoring dynamic changes in tissue rheology and cell contact mechanics, we demonstrate that the zebrafish blastoderm undergoes a genuine rigidity PT, brought about by a small reduction in adhesion-dependent cell connectivity below a critical value. We quantitatively predict and experimentally verify hallmarks of PTs, including power-law exponents and associated discontinuities of macroscopic observables. Finally, we show that this uniform PT depends on blastoderm cells undergoing meta-synchronous divisions causing random and, consequently, uniform changes in cell connectivity. Collectively, our theoretical and experimental findings reveal the structural basis of material PTs in an organismal context.","lang":"eng"}],"type":"journal_article","pmid":1,"citation":{"chicago":"Petridou, Nicoletta, Bernat Corominas-Murtra, Carl-Philipp J Heisenberg, and Edouard B Hannezo. “Rigidity Percolation Uncovers a Structural Basis for Embryonic Tissue Phase Transitions.” <i>Cell</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.cell.2021.02.017\">https://doi.org/10.1016/j.cell.2021.02.017</a>.","ista":"Petridou N, Corominas-Murtra B, Heisenberg C-PJ, Hannezo EB. 2021. Rigidity percolation uncovers a structural basis for embryonic tissue phase transitions. Cell. 184(7), 1914–1928.e19.","mla":"Petridou, Nicoletta, et al. “Rigidity Percolation Uncovers a Structural Basis for Embryonic Tissue Phase Transitions.” <i>Cell</i>, vol. 184, no. 7, Elsevier, 2021, p. 1914–1928.e19, doi:<a href=\"https://doi.org/10.1016/j.cell.2021.02.017\">10.1016/j.cell.2021.02.017</a>.","ieee":"N. Petridou, B. Corominas-Murtra, C.-P. J. Heisenberg, and E. B. Hannezo, “Rigidity percolation uncovers a structural basis for embryonic tissue phase transitions,” <i>Cell</i>, vol. 184, no. 7. Elsevier, p. 1914–1928.e19, 2021.","ama":"Petridou N, Corominas-Murtra B, Heisenberg C-PJ, Hannezo EB. Rigidity percolation uncovers a structural basis for embryonic tissue phase transitions. <i>Cell</i>. 2021;184(7):1914-1928.e19. doi:<a href=\"https://doi.org/10.1016/j.cell.2021.02.017\">10.1016/j.cell.2021.02.017</a>","apa":"Petridou, N., Corominas-Murtra, B., Heisenberg, C.-P. J., &#38; Hannezo, E. B. (2021). Rigidity percolation uncovers a structural basis for embryonic tissue phase transitions. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2021.02.017\">https://doi.org/10.1016/j.cell.2021.02.017</a>","short":"N. Petridou, B. Corominas-Murtra, C.-P.J. Heisenberg, E.B. Hannezo, Cell 184 (2021) 1914–1928.e19."},"issue":"7","scopus_import":"1","month":"04","_id":"9316","external_id":{"isi":["000636734000022"],"pmid":["33730596"]},"date_created":"2021-04-11T22:01:14Z","publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"ddc":["570"],"project":[{"grant_number":"742573","_id":"260F1432-B435-11E9-9278-68D0E5697425","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","call_identifier":"H2020"},{"call_identifier":"H2020","grant_number":"851288","name":"Design Principles of Branching Morphogenesis","_id":"05943252-7A3F-11EA-A408-12923DDC885E"},{"call_identifier":"FWF","_id":"2693FD8C-B435-11E9-9278-68D0E5697425","name":"Tissue material properties in embryonic development","grant_number":"V00736"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Cell","isi":1,"ec_funded":1,"acknowledgement":"We thank Carl Goodrich and the members of the Heisenberg and Hannezo groups, in particular Reka Korei, for help, technical advice, and discussions; and the Bioimaging and zebrafish facilities of the IST Austria for continuous support. This work was supported by the Elise Richter Program of Austrian Science Fund (FWF) to N.I.P. ( V 736-B26 ) and the European Union (European Research Council Advanced Grant 742573 to C.-P.H. and European Research Council Starting Grant 851288 to E.H.).","publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]},"article_type":"original","year":"2021","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"intvolume":"       184","date_published":"2021-04-01T00:00:00Z","doi":"10.1016/j.cell.2021.02.017","day":"01","oa":1,"file":[{"success":1,"file_name":"2021_Cell_Petridou.pdf","date_created":"2021-06-08T10:04:10Z","creator":"cziletti","file_size":11405875,"access_level":"open_access","date_updated":"2021-06-08T10:04:10Z","file_id":"9534","checksum":"1e5295fbd9c2a459173ec45a0e8a7c2e","content_type":"application/pdf","relation":"main_file"}],"file_date_updated":"2021-06-08T10:04:10Z","has_accepted_license":"1","article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","date_updated":"2025-07-10T12:01:42Z","related_material":{"link":[{"url":"https://ist.ac.at/en/news/embryonic-tissue-undergoes-phase-transition/","description":"News on IST Homepage","relation":"press_release"}]},"page":"1914-1928.e19","title":"Rigidity percolation uncovers a structural basis for embryonic tissue phase transitions","author":[{"first_name":"Nicoletta","id":"2A003F6C-F248-11E8-B48F-1D18A9856A87","last_name":"Petridou","full_name":"Petridou, Nicoletta","orcid":"0000-0002-8451-1195"},{"last_name":"Corominas-Murtra","full_name":"Corominas-Murtra, Bernat","id":"43BE2298-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9806-5643","first_name":"Bernat"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J"},{"orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","full_name":"Hannezo, Edouard B","first_name":"Edouard B"}],"oa_version":"Published Version"},{"citation":{"short":"H. Edelsbrunner, G.F. Osang, Discrete and Computational Geometry 65 (2021) 1296–1313.","mla":"Edelsbrunner, Herbert, and Georg F. Osang. “The Multi-Cover Persistence of Euclidean Balls.” <i>Discrete and Computational Geometry</i>, vol. 65, Springer Nature, 2021, pp. 1296–1313, doi:<a href=\"https://doi.org/10.1007/s00454-021-00281-9\">10.1007/s00454-021-00281-9</a>.","ista":"Edelsbrunner H, Osang GF. 2021. The multi-cover persistence of Euclidean balls. Discrete and Computational Geometry. 65, 1296–1313.","chicago":"Edelsbrunner, Herbert, and Georg F Osang. “The Multi-Cover Persistence of Euclidean Balls.” <i>Discrete and Computational Geometry</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s00454-021-00281-9\">https://doi.org/10.1007/s00454-021-00281-9</a>.","ieee":"H. Edelsbrunner and G. F. Osang, “The multi-cover persistence of Euclidean balls,” <i>Discrete and Computational Geometry</i>, vol. 65. Springer Nature, pp. 1296–1313, 2021.","ama":"Edelsbrunner H, Osang GF. The multi-cover persistence of Euclidean balls. <i>Discrete and Computational Geometry</i>. 2021;65:1296–1313. doi:<a href=\"https://doi.org/10.1007/s00454-021-00281-9\">10.1007/s00454-021-00281-9</a>","apa":"Edelsbrunner, H., &#38; Osang, G. F. (2021). The multi-cover persistence of Euclidean balls. <i>Discrete and Computational Geometry</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00454-021-00281-9\">https://doi.org/10.1007/s00454-021-00281-9</a>"},"type":"journal_article","abstract":[{"lang":"eng","text":"Given a locally finite X⊆Rd and a radius r≥0, the k-fold cover of X and r consists of all points in Rd that have k or more points of X within distance r. We consider two filtrations—one in scale obtained by fixing k and increasing r, and the other in depth obtained by fixing r and decreasing k—and we compute the persistence diagrams of both. While standard methods suffice for the filtration in scale, we need novel geometric and topological concepts for the filtration in depth. In particular, we introduce a rhomboid tiling in Rd+1 whose horizontal integer slices are the order-k Delaunay mosaics of X, and construct a zigzag module of Delaunay mosaics that is isomorphic to the persistence module of the multi-covers."}],"pmid":1,"quality_controlled":"1","corr_author":"1","publisher":"Springer Nature","volume":65,"department":[{"_id":"HeEd"}],"external_id":{"pmid":["34720303"],"isi":["000635460400001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"published","date_created":"2021-04-11T22:01:15Z","month":"03","scopus_import":"1","_id":"9317","publication_identifier":{"eissn":["1432-0444"],"issn":["0179-5376"]},"year":"2021","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 78818 Alpha), and by the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, through Grant No. I02979-N35 of the Austrian Science Fund (FWF)\r\nOpen Access funding provided by the Institute of Science and Technology (IST Austria).","article_type":"original","ec_funded":1,"file":[{"creator":"cchlebak","file_size":677704,"success":1,"file_name":"2021_DisCompGeo_Edelsbrunner_Osang.pdf","date_created":"2021-12-01T10:56:53Z","access_level":"open_access","date_updated":"2021-12-01T10:56:53Z","file_id":"10394","checksum":"59b4e1e827e494209bcb4aae22e1d347","content_type":"application/pdf","relation":"main_file"}],"oa":1,"doi":"10.1007/s00454-021-00281-9","day":"31","date_published":"2021-03-31T00:00:00Z","intvolume":"        65","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"788183","name":"Alpha Shape Theory Extended","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"I02979-N35","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","name":"Persistence and stability of geometric complexes","call_identifier":"FWF"}],"ddc":["516"],"isi":1,"publication":"Discrete and Computational Geometry","oa_version":"Published Version","status":"public","language":[{"iso":"eng"}],"has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","file_date_updated":"2021-12-01T10:56:53Z","title":"The multi-cover persistence of Euclidean balls","author":[{"orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert"},{"id":"464B40D6-F248-11E8-B48F-1D18A9856A87","full_name":"Osang, Georg F","last_name":"Osang","orcid":"0000-0002-8882-5116","first_name":"Georg F"}],"page":"1296–1313","related_material":{"record":[{"relation":"earlier_version","id":"187","status":"public"}]},"date_updated":"2025-06-12T06:36:54Z"},{"department":[{"_id":"GradSch"},{"_id":"GeKa"}],"publisher":"Institute of Science and Technology Austria","license":"https://creativecommons.org/publicdomain/zero/1.0/","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["530"],"oa":1,"citation":{"ama":"Jirovec D. Research data for “A singlet-triplet hole spin qubit planar Ge.” 2021. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9323\">10.15479/AT:ISTA:9323</a>","ieee":"D. Jirovec, “Research data for ‘A singlet-triplet hole spin qubit planar Ge.’” Institute of Science and Technology Austria, 2021.","apa":"Jirovec, D. (2021). Research data for “A singlet-triplet hole spin qubit planar Ge.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:9323\">https://doi.org/10.15479/AT:ISTA:9323</a>","mla":"Jirovec, Daniel. <i>Research Data for “A Singlet-Triplet Hole Spin Qubit Planar Ge.”</i> Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9323\">10.15479/AT:ISTA:9323</a>.","chicago":"Jirovec, Daniel. “Research Data for ‘A Singlet-Triplet Hole Spin Qubit Planar Ge.’” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/AT:ISTA:9323\">https://doi.org/10.15479/AT:ISTA:9323</a>.","ista":"Jirovec D. 2021. Research data for ‘A singlet-triplet hole spin qubit planar Ge’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:9323\">10.15479/AT:ISTA:9323</a>.","short":"D. Jirovec, (2021)."},"file":[{"creator":"djirovec","file_size":221832287,"success":1,"file_name":"DataRepositorySTqubit.zip","date_created":"2021-04-14T09:48:47Z","access_level":"open_access","date_updated":"2021-04-14T09:48:47Z","file_id":"9324","checksum":"c569d2a2ce1694445cdbca19cf8ae023","content_type":"application/x-zip-compressed","relation":"main_file"},{"access_level":"open_access","file_name":"ReadMe","date_created":"2021-04-14T09:49:30Z","success":1,"file_size":4323,"creator":"djirovec","relation":"main_file","checksum":"845bdf87430718ad6aff47eda7b5fc92","content_type":"application/octet-stream","file_id":"9325","date_updated":"2021-04-14T09:49:30Z"}],"day":"14","type":"research_data","doi":"10.15479/AT:ISTA:9323","abstract":[{"lang":"eng","text":"This .zip File contains the data for figures presented in the main text and supplementary material of \"A singlet triplet hole spin qubit in planar Ge\" by D. Jirovec, et. al. The measurements were done using Labber Software and the data is stored in the hdf5 file format. The files can be opened using either the Labber Log Browser (https://labber.org/overview/) or Labber Python API (http://labber.org/online-doc/api/LogFile.html). A single file is acquired with QCodes and features the corresponding data type. XRD data are in .dat format and a code to open the data is provided. The code for simulations is as well provided in Python."}],"date_published":"2021-04-14T00:00:00Z","year":"2021","author":[{"first_name":"Daniel","orcid":"0000-0002-7197-4801","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","last_name":"Jirovec","full_name":"Jirovec, Daniel"}],"title":"Research data for \"A singlet-triplet hole spin qubit planar Ge\"","date_updated":"2025-06-12T06:57:18Z","_id":"9323","contributor":[{"first_name":"Daniel","last_name":"Jirovec","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member"}],"related_material":{"record":[{"status":"public","id":"8909","relation":"used_in_publication"}]},"status":"public","month":"04","article_processing_charge":"No","has_accepted_license":"1","file_date_updated":"2021-04-14T09:49:30Z","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa_version":"Published Version","date_created":"2021-04-14T09:50:22Z"},{"issue":"6","scopus_import":"1","month":"03","_id":"9329","external_id":{"pmid":["33711356"],"isi":["000661088500005"]},"date_created":"2021-04-18T22:01:39Z","publication_status":"published","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"publisher":"Elsevier","department":[{"_id":"PeJo"},{"_id":"ScienComp"}],"volume":357,"quality_controlled":"1","pmid":1,"abstract":[{"text":"Background: To understand information coding in single neurons, it is necessary to analyze subthreshold synaptic events, action potentials (APs), and their interrelation in different behavioral states. However, detecting excitatory postsynaptic potentials (EPSPs) or currents (EPSCs) in behaving animals remains challenging, because of unfavorable signal-to-noise ratio, high frequency, fluctuating amplitude, and variable time course of synaptic events.\r\nNew method: We developed a method for synaptic event detection, termed MOD (Machine-learning Optimal-filtering Detection-procedure), which combines concepts of supervised machine learning and optimal Wiener filtering. Experts were asked to manually score short epochs of data. The algorithm was trained to obtain the optimal filter coefficients of a Wiener filter and the optimal detection threshold. Scored and unscored data were then processed with the optimal filter, and events were detected as peaks above threshold.\r\nResults: We challenged MOD with EPSP traces in vivo in mice during spatial navigation and EPSC traces in vitro in slices under conditions of enhanced transmitter release. The area under the curve (AUC) of the receiver operating characteristics (ROC) curve was, on average, 0.894 for in vivo and 0.969 for in vitro data sets, indicating high detection accuracy and efficiency.\r\nComparison with existing methods: When benchmarked using a (1 − AUC)−1 metric, MOD outperformed previous methods (template-fit, deconvolution, and Bayesian methods) by an average factor of 3.13 for in vivo data sets, but showed comparable (template-fit, deconvolution) or higher (Bayesian) computational efficacy.\r\nConclusions: MOD may become an important new tool for large-scale, real-time analysis of synaptic activity.","lang":"eng"}],"type":"journal_article","citation":{"ieee":"X. Zhang, A. Schlögl, D. H. Vandael, and P. M. Jonas, “MOD: A novel machine-learning optimal-filtering method for accurate and efficient detection of subthreshold synaptic events in vivo,” <i>Journal of Neuroscience Methods</i>, vol. 357, no. 6. Elsevier, 2021.","apa":"Zhang, X., Schlögl, A., Vandael, D. H., &#38; Jonas, P. M. (2021). MOD: A novel machine-learning optimal-filtering method for accurate and efficient detection of subthreshold synaptic events in vivo. <i>Journal of Neuroscience Methods</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jneumeth.2021.109125\">https://doi.org/10.1016/j.jneumeth.2021.109125</a>","ama":"Zhang X, Schlögl A, Vandael DH, Jonas PM. MOD: A novel machine-learning optimal-filtering method for accurate and efficient detection of subthreshold synaptic events in vivo. <i>Journal of Neuroscience Methods</i>. 2021;357(6). doi:<a href=\"https://doi.org/10.1016/j.jneumeth.2021.109125\">10.1016/j.jneumeth.2021.109125</a>","chicago":"Zhang, Xiaomin, Alois Schlögl, David H Vandael, and Peter M Jonas. “MOD: A Novel Machine-Learning Optimal-Filtering Method for Accurate and Efficient Detection of Subthreshold Synaptic Events in Vivo.” <i>Journal of Neuroscience Methods</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.jneumeth.2021.109125\">https://doi.org/10.1016/j.jneumeth.2021.109125</a>.","ista":"Zhang X, Schlögl A, Vandael DH, Jonas PM. 2021. MOD: A novel machine-learning optimal-filtering method for accurate and efficient detection of subthreshold synaptic events in vivo. Journal of Neuroscience Methods. 357(6), 109125.","mla":"Zhang, Xiaomin, et al. “MOD: A Novel Machine-Learning Optimal-Filtering Method for Accurate and Efficient Detection of Subthreshold Synaptic Events in Vivo.” <i>Journal of Neuroscience Methods</i>, vol. 357, no. 6, 109125, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.jneumeth.2021.109125\">10.1016/j.jneumeth.2021.109125</a>.","short":"X. Zhang, A. Schlögl, D.H. Vandael, P.M. Jonas, Journal of Neuroscience Methods 357 (2021)."},"file_date_updated":"2021-04-19T08:30:22Z","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","language":[{"iso":"eng"}],"status":"public","date_updated":"2025-06-12T06:39:15Z","title":"MOD: A novel machine-learning optimal-filtering method for accurate and efficient detection of subthreshold synaptic events in vivo","author":[{"first_name":"Xiaomin","id":"423EC9C2-F248-11E8-B48F-1D18A9856A87","full_name":"Zhang, Xiaomin","last_name":"Zhang"},{"full_name":"Schlögl, Alois","last_name":"Schlögl","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5621-8100","first_name":"Alois"},{"first_name":"David H","orcid":"0000-0001-7577-1676","full_name":"Vandael, David H","last_name":"Vandael","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Peter M","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Published Version","ddc":["570"],"project":[{"call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","grant_number":"692692"},{"name":"Synaptic communication in neuronal microcircuits","_id":"25C5A090-B435-11E9-9278-68D0E5697425","grant_number":"Z00312","call_identifier":"FWF"}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Journal of Neuroscience Methods","isi":1,"ec_funded":1,"acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement number 692692 to P.J.) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award to P.J.). We thank Drs. Jozsef Csicsvari, Christoph Lampert, and Federico Stella for critically reading previous manuscript versions. We are also grateful to Drs. Josh Merel and Ben Shababo for their help with applying the Bayesian detection method to our data. We also thank Florian Marr for technical assistance, Eleftheria Kralli-Beller for manuscript editing, and the Scientific Service Units of IST Austria for efficient support.","publication_identifier":{"eissn":["1872-678X"],"issn":["0165-0270"]},"article_type":"original","year":"2021","acknowledged_ssus":[{"_id":"SSU"}],"article_number":"109125","intvolume":"       357","date_published":"2021-03-09T00:00:00Z","doi":"10.1016/j.jneumeth.2021.109125","day":"09","file":[{"date_updated":"2021-04-19T08:30:22Z","file_id":"9339","content_type":"application/pdf","checksum":"2a5800d91b96d08b525e17319dcd5e44","relation":"main_file","creator":"dernst","file_size":6924738,"date_created":"2021-04-19T08:30:22Z","success":1,"file_name":"2021_JourNeuroscienceMeth_Zhang.pdf","access_level":"open_access"}],"oa":1},{"publisher":"National Academy of Sciences","volume":118,"department":[{"_id":"EM-Fac"},{"_id":"RySh"}],"citation":{"short":"C.L. Schöpf, C. Ablinger, S.M. Geisler, R.I. Stanika, M. Campiglio, W. Kaufmann, B. Nimmervoll, B. Schlick, J. Brockhaus, M. Missler, R. Shigemoto, G.J. Obermair, Proceedings of the National Academy of Sciences of the United States of America 118 (2021).","apa":"Schöpf, C. L., Ablinger, C., Geisler, S. M., Stanika, R. I., Campiglio, M., Kaufmann, W., … Obermair, G. J. (2021). Presynaptic α2δ subunits are key organizers of glutamatergic synapses. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1920827118\">https://doi.org/10.1073/pnas.1920827118</a>","ieee":"C. L. Schöpf <i>et al.</i>, “Presynaptic α2δ subunits are key organizers of glutamatergic synapses,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 118, no. 14. National Academy of Sciences, 2021.","ama":"Schöpf CL, Ablinger C, Geisler SM, et al. Presynaptic α2δ subunits are key organizers of glutamatergic synapses. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2021;118(14). doi:<a href=\"https://doi.org/10.1073/pnas.1920827118\">10.1073/pnas.1920827118</a>","mla":"Schöpf, Clemens L., et al. “Presynaptic Α2δ Subunits Are Key Organizers of Glutamatergic Synapses.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 118, no. 14, National Academy of Sciences, 2021, doi:<a href=\"https://doi.org/10.1073/pnas.1920827118\">10.1073/pnas.1920827118</a>.","chicago":"Schöpf, Clemens L., Cornelia Ablinger, Stefanie M. Geisler, Ruslan I. Stanika, Marta Campiglio, Walter Kaufmann, Benedikt Nimmervoll, et al. “Presynaptic Α2δ Subunits Are Key Organizers of Glutamatergic Synapses.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2021. <a href=\"https://doi.org/10.1073/pnas.1920827118\">https://doi.org/10.1073/pnas.1920827118</a>.","ista":"Schöpf CL, Ablinger C, Geisler SM, Stanika RI, Campiglio M, Kaufmann W, Nimmervoll B, Schlick B, Brockhaus J, Missler M, Shigemoto R, Obermair GJ. 2021. Presynaptic α2δ subunits are key organizers of glutamatergic synapses. Proceedings of the National Academy of Sciences of the United States of America. 118(14)."},"pmid":1,"abstract":[{"lang":"eng","text":"In nerve cells the genes encoding for α2δ subunits of voltage-gated calcium channels have been linked to synaptic functions and neurological disease. Here we show that α2δ subunits are essential for the formation and organization of glutamatergic synapses. Using a cellular α2δ subunit triple-knockout/knockdown model, we demonstrate a failure in presynaptic differentiation evidenced by defective presynaptic calcium channel clustering and calcium influx, smaller presynaptic active zones, and a strongly reduced accumulation of presynaptic vesicle-associated proteins (synapsin and vGLUT). The presynaptic defect is associated with the downscaling of postsynaptic AMPA receptors and the postsynaptic density. The role of α2δ isoforms as synaptic organizers is highly redundant, as each individual α2δ isoform can rescue presynaptic calcium channel trafficking and expression of synaptic proteins. Moreover, α2δ-2 and α2δ-3 with mutated metal ion-dependent adhesion sites can fully rescue presynaptic synapsin expression but only partially calcium channel trafficking, suggesting that the regulatory role of α2δ subunits is independent from its role as a calcium channel subunit. Our findings influence the current view on excitatory synapse formation. First, our study suggests that postsynaptic differentiation is secondary to presynaptic differentiation. Second, the dependence of presynaptic differentiation on α2δ implicates α2δ subunits as potential nucleation points for the organization of synapses. Finally, our results suggest that α2δ subunits act as transsynaptic organizers of glutamatergic synapses, thereby aligning the synaptic active zone with the postsynaptic density."}],"type":"journal_article","quality_controlled":"1","month":"04","issue":"14","scopus_import":"1","_id":"9330","external_id":{"isi":["000637398300002"],"pmid":["33782113"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"published","date_created":"2021-04-18T22:01:40Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"call_identifier":"H2020","_id":"25CA28EA-B435-11E9-9278-68D0E5697425","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","grant_number":"694539"}],"ddc":["570"],"isi":1,"publication":"Proceedings of the National Academy of Sciences of the United States of America","acknowledged_ssus":[{"_id":"EM-Fac"}],"year":"2021","acknowledgement":"We thank Arnold Schwartz for providing α2δ-1 knockout mice; Ariane Benedetti, Sabine Baumgartner, Sandra Demetz, and Irene Mahlknecht for technical support; Nadine Ortner and Andreas Lieb for electrophysiological experiments; the team of the Electron Microscopy Facility at the Institute of Science and Technology Austria for technical support related to ultrastructural analysis; Hermann Dietrich and Anja Beierfuß and her team for animal care; Jutta Engel and Jörg Striessnig for critical discussions; and Bruno Benedetti and Bernhard Flucher for critical discussions and reading the manuscript. This study was supported by Austrian Science Fund Grants P24079, F44060, F44150, and DOC30-B30 (to G.J.O.) and T855 (to M.C.), European Research Council Grant AdG 694539 (to R.S.), Deutsche Forschungsgemeinschaft\r\nGrant SFB1348-TP A03 (to M.M.), and Interdisziplinäre Zentrum für Klinische Forschung Münster Grant Mi3/004/19 (to M.M.). This work is part of the PhD theses of C.L.S., S.M.G., and C.A.","article_type":"original","publication_identifier":{"eissn":["1091-6490"]},"ec_funded":1,"oa":1,"file":[{"content_type":"application/pdf","checksum":"dd014f68ae9d7d8d8fc4139a24e04506","relation":"main_file","date_updated":"2021-04-19T10:10:56Z","file_id":"9340","access_level":"open_access","creator":"dernst","file_size":2603911,"date_created":"2021-04-19T10:10:56Z","success":1,"file_name":"2021_PNAS_Schoepf.pdf"}],"doi":"10.1073/pnas.1920827118","day":"06","date_published":"2021-04-06T00:00:00Z","intvolume":"       118","status":"public","language":[{"iso":"eng"}],"has_accepted_license":"1","article_processing_charge":"No","file_date_updated":"2021-04-19T10:10:56Z","author":[{"first_name":"Clemens L.","last_name":"Schöpf","full_name":"Schöpf, Clemens L."},{"first_name":"Cornelia","last_name":"Ablinger","full_name":"Ablinger, Cornelia"},{"full_name":"Geisler, Stefanie M.","last_name":"Geisler","first_name":"Stefanie M."},{"first_name":"Ruslan I.","full_name":"Stanika, Ruslan I.","last_name":"Stanika"},{"last_name":"Campiglio","full_name":"Campiglio, Marta","first_name":"Marta"},{"id":"3F99E422-F248-11E8-B48F-1D18A9856A87","full_name":"Kaufmann, Walter","last_name":"Kaufmann","orcid":"0000-0001-9735-5315","first_name":"Walter"},{"first_name":"Benedikt","full_name":"Nimmervoll, Benedikt","last_name":"Nimmervoll"},{"first_name":"Bettina","full_name":"Schlick, Bettina","last_name":"Schlick"},{"last_name":"Brockhaus","full_name":"Brockhaus, Johannes","first_name":"Johannes"},{"full_name":"Missler, Markus","last_name":"Missler","first_name":"Markus"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","orcid":"0000-0001-8761-9444","first_name":"Ryuichi"},{"last_name":"Obermair","full_name":"Obermair, Gerald J.","first_name":"Gerald J."}],"title":"Presynaptic α2δ subunits are key organizers of glutamatergic synapses","date_updated":"2025-06-12T06:56:21Z","oa_version":"Published Version"},{"arxiv":1,"publication":"Applied Physics Letters","isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1063/5.0050235","day":"07","oa":1,"intvolume":"       118","date_published":"2021-04-07T00:00:00Z","article_number":"140501","publication_identifier":{"issn":["0003-6951"]},"acknowledgement":"We acknowledge fruitful discussions with John Close, Chris Freier, Kyle Hardman, Joseph Hope, and Paul Wigley, and insightful suggestions made by Franck Pereira dos Santos on behalf of the Atom Interferometry and Inertial Sensors team at SYRTE. S.S.S. was supported by an Australian Research Council Discovery Early Career Researcher Award (DECRA), Project No. DE200100495. O.H. was supported by IST Austria.","article_type":"original","year":"2021","author":[{"full_name":"Szigeti, Stuart S.","last_name":"Szigeti","first_name":"Stuart S."},{"orcid":"0000-0002-2031-204X","last_name":"Hosten","full_name":"Hosten, Onur","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","first_name":"Onur"},{"last_name":"Haine","full_name":"Haine, Simon A.","first_name":"Simon A."}],"title":"Improving cold-atom sensors with quantum entanglement: Prospects and challenges","date_updated":"2025-07-10T12:01:43Z","language":[{"iso":"eng"}],"status":"public","article_processing_charge":"No","oa_version":"Preprint","volume":118,"department":[{"_id":"OnHo"}],"publisher":"AIP Publishing","corr_author":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2010.09168"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Quantum entanglement has been generated and verified in cold-atom experiments and used to make atom-interferometric measurements below the shot-noise limit. However, current state-of-the-art cold-atom devices exploit separable (i.e., unentangled) atomic states. This perspective piece asks the question: can entanglement usefully improve cold-atom sensors, in the sense that it gives new sensing capabilities unachievable with current state-of-the-art devices? We briefly review the state-of-the-art in precision cold-atom sensing, focusing on clocks and inertial sensors, identifying the potential benefits entanglement could bring to these devices, and the challenges that need to be overcome to realize these benefits. We survey demonstrated methods of generating metrologically useful entanglement in cold-atom systems, note their relative strengths and weaknesses, and assess their prospects for near-to-medium term quantum-enhanced cold-atom sensing."}],"citation":{"short":"S.S. Szigeti, O. Hosten, S.A. Haine, Applied Physics Letters 118 (2021).","mla":"Szigeti, Stuart S., et al. “Improving Cold-Atom Sensors with Quantum Entanglement: Prospects and Challenges.” <i>Applied Physics Letters</i>, vol. 118, no. 14, 140501, AIP Publishing, 2021, doi:<a href=\"https://doi.org/10.1063/5.0050235\">10.1063/5.0050235</a>.","ista":"Szigeti SS, Hosten O, Haine SA. 2021. Improving cold-atom sensors with quantum entanglement: Prospects and challenges. Applied Physics Letters. 118(14), 140501.","chicago":"Szigeti, Stuart S., Onur Hosten, and Simon A. Haine. “Improving Cold-Atom Sensors with Quantum Entanglement: Prospects and Challenges.” <i>Applied Physics Letters</i>. AIP Publishing, 2021. <a href=\"https://doi.org/10.1063/5.0050235\">https://doi.org/10.1063/5.0050235</a>.","ama":"Szigeti SS, Hosten O, Haine SA. Improving cold-atom sensors with quantum entanglement: Prospects and challenges. <i>Applied Physics Letters</i>. 2021;118(14). doi:<a href=\"https://doi.org/10.1063/5.0050235\">10.1063/5.0050235</a>","apa":"Szigeti, S. S., Hosten, O., &#38; Haine, S. A. (2021). Improving cold-atom sensors with quantum entanglement: Prospects and challenges. <i>Applied Physics Letters</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0050235\">https://doi.org/10.1063/5.0050235</a>","ieee":"S. S. Szigeti, O. Hosten, and S. A. Haine, “Improving cold-atom sensors with quantum entanglement: Prospects and challenges,” <i>Applied Physics Letters</i>, vol. 118, no. 14. AIP Publishing, 2021."},"quality_controlled":"1","_id":"9331","month":"04","issue":"14","scopus_import":"1","publication_status":"published","date_created":"2021-04-18T22:01:40Z","external_id":{"arxiv":["2010.09168"],"isi":["000637702100001"]}},{"_id":"9332","scopus_import":"1","issue":"8","month":"04","date_created":"2021-04-18T22:01:41Z","publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000644394800001"],"pmid":["33917959"]},"department":[{"_id":"EvBe"}],"volume":22,"publisher":"MDPI","quality_controlled":"1","type":"journal_article","pmid":1,"abstract":[{"text":"Lateral root (LR) formation is an example of a plant post-embryonic organogenesis event. LRs are issued from non-dividing cells entering consecutive steps of formative divisions, proliferation and elongation. The chromatin remodeling protein PICKLE (PKL) negatively regulates auxin-mediated LR formation through a mechanism that is not yet known. Here we show that PKL interacts with RETINOBLASTOMA-RELATED 1 (RBR1) to repress the LATERAL ORGAN BOUNDARIES-DOMAIN 16 (LBD16) promoter activity. Since LBD16 function is required for the formative division of LR founder cells, repression mediated by the PKL–RBR1 complex negatively regulates formative division and LR formation. Inhibition of LR formation by PKL–RBR1 is counteracted by auxin, indicating that, in addition to auxin-mediated transcriptional responses, the fine-tuned process of LR formation is also controlled at the chromatin level in an auxin-signaling dependent manner.","lang":"eng"}],"citation":{"ama":"Ötvös K, Miskolczi P, Marhavý P, et al. Pickle recruits retinoblastoma related 1 to control lateral root formation in arabidopsis. <i>International Journal of Molecular Sciences</i>. 2021;22(8). doi:<a href=\"https://doi.org/10.3390/ijms22083862\">10.3390/ijms22083862</a>","ieee":"K. Ötvös <i>et al.</i>, “Pickle recruits retinoblastoma related 1 to control lateral root formation in arabidopsis,” <i>International Journal of Molecular Sciences</i>, vol. 22, no. 8. MDPI, 2021.","apa":"Ötvös, K., Miskolczi, P., Marhavý, P., Cruz-Ramírez, A., Benková, E., Robert, S., &#38; Bakó, L. (2021). Pickle recruits retinoblastoma related 1 to control lateral root formation in arabidopsis. <i>International Journal of Molecular Sciences</i>. MDPI. <a href=\"https://doi.org/10.3390/ijms22083862\">https://doi.org/10.3390/ijms22083862</a>","mla":"Ötvös, Krisztina, et al. “Pickle Recruits Retinoblastoma Related 1 to Control Lateral Root Formation in Arabidopsis.” <i>International Journal of Molecular Sciences</i>, vol. 22, no. 8, 3862, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/ijms22083862\">10.3390/ijms22083862</a>.","ista":"Ötvös K, Miskolczi P, Marhavý P, Cruz-Ramírez A, Benková E, Robert S, Bakó L. 2021. Pickle recruits retinoblastoma related 1 to control lateral root formation in arabidopsis. International Journal of Molecular Sciences. 22(8), 3862.","chicago":"Ötvös, Krisztina, Pál Miskolczi, Peter Marhavý, Alfredo Cruz-Ramírez, Eva Benková, Stéphanie Robert, and László Bakó. “Pickle Recruits Retinoblastoma Related 1 to Control Lateral Root Formation in Arabidopsis.” <i>International Journal of Molecular Sciences</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/ijms22083862\">https://doi.org/10.3390/ijms22083862</a>.","short":"K. Ötvös, P. Miskolczi, P. Marhavý, A. Cruz-Ramírez, E. Benková, S. Robert, L. Bakó, International Journal of Molecular Sciences 22 (2021)."},"date_updated":"2025-06-12T06:39:41Z","title":"Pickle recruits retinoblastoma related 1 to control lateral root formation in arabidopsis","author":[{"orcid":"0000-0002-5503-4983","full_name":"Ötvös, Krisztina","last_name":"Ötvös","id":"29B901B0-F248-11E8-B48F-1D18A9856A87","first_name":"Krisztina"},{"first_name":"Pál","full_name":"Miskolczi, Pál","last_name":"Miskolczi"},{"first_name":"Peter","orcid":"0000-0001-5227-5741","id":"3F45B078-F248-11E8-B48F-1D18A9856A87","last_name":"Marhavý","full_name":"Marhavý, Peter"},{"first_name":"Alfredo","last_name":"Cruz-Ramírez","full_name":"Cruz-Ramírez, Alfredo"},{"first_name":"Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","full_name":"Benková, Eva"},{"full_name":"Robert, Stéphanie","last_name":"Robert","first_name":"Stéphanie"},{"first_name":"László","full_name":"Bakó, László","last_name":"Bakó"}],"file_date_updated":"2021-04-19T10:54:55Z","has_accepted_license":"1","article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","oa_version":"Published Version","publication":"International Journal of Molecular Sciences","isi":1,"ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        22","date_published":"2021-04-08T00:00:00Z","day":"08","doi":"10.3390/ijms22083862","file":[{"date_updated":"2021-04-19T10:54:55Z","file_id":"9342","content_type":"application/pdf","checksum":"26ada2531ad1f9c01a1664de0431f1fe","relation":"main_file","date_created":"2021-04-19T10:54:55Z","success":1,"file_name":"2021_JourMolecularScience_Oetvoes.pdf","creator":"dernst","file_size":2769717,"access_level":"open_access"}],"oa":1,"publication_identifier":{"issn":["1661-6596"],"eissn":["1422-0067"]},"article_type":"original","acknowledgement":"This research was supported by a postdoctoral fellowship of the Carl Tryggers Foundation (to K.Ö.) and by grants from Vetenskapsrådet (Nr.: 621-2004-2921 to L.B.) and VINNOVA (to L.B. and S.R.).\r\nWe thank Frederic Berger, Hidehiro Fukaki, Malcolm Bennett, Claudia Köhler, Jiri Friml for providing pRBR1::RBR1-RFP, ssl2-1, slr-1, pPKL::PKL-GFP seeds and the DR5 expressing vector, respectively. Authors are grateful to Hayashi Kenichiro for providing the auxinol compound and to Rishi Bhalerao for stimulating discussions. The technical help of Adeline Rigal and Thomas Vain with the auxinol experiments is much appreciated.","year":"2021","article_number":"3862"},{"quality_controlled":"1","type":"journal_article","abstract":[{"text":"Various degenerate diffusion equations exhibit a waiting time phenomenon: depending on the “flatness” of the compactly supported initial datum at the boundary of the support, the support of the solution may not expand for a certain amount of time. We show that this phenomenon is captured by particular Lagrangian discretizations of the porous medium and the thin film equations, and we obtain sufficient criteria for the occurrence of waiting times that are consistent with the known ones for the original PDEs. For the spatially discrete solution, the waiting time phenomenon refers to a deviation of the edge of support from its original position by a quantity comparable to the mesh width, over a mesh-independent time interval. Our proof is based on estimates on the fluid velocity in Lagrangian coordinates. Combining weighted entropy estimates with an iteration technique à la Stampacchia leads to upper bounds on free boundary propagation. Numerical simulations show that the phenomenon is already clearly visible for relatively coarse discretizations.","lang":"eng"}],"citation":{"ieee":"J. L. Fischer and D. Matthes, “The waiting time phenomenon in spatially discretized porous medium and thin film equations,” <i>SIAM Journal on Numerical Analysis</i>, vol. 59, no. 1. Society for Industrial and Applied Mathematics, pp. 60–87, 2021.","ama":"Fischer JL, Matthes D. The waiting time phenomenon in spatially discretized porous medium and thin film equations. <i>SIAM Journal on Numerical Analysis</i>. 2021;59(1):60-87. doi:<a href=\"https://doi.org/10.1137/19M1300017\">10.1137/19M1300017</a>","apa":"Fischer, J. L., &#38; Matthes, D. (2021). The waiting time phenomenon in spatially discretized porous medium and thin film equations. <i>SIAM Journal on Numerical Analysis</i>. Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/19M1300017\">https://doi.org/10.1137/19M1300017</a>","chicago":"Fischer, Julian L, and Daniel Matthes. “The Waiting Time Phenomenon in Spatially Discretized Porous Medium and Thin Film Equations.” <i>SIAM Journal on Numerical Analysis</i>. Society for Industrial and Applied Mathematics, 2021. <a href=\"https://doi.org/10.1137/19M1300017\">https://doi.org/10.1137/19M1300017</a>.","ista":"Fischer JL, Matthes D. 2021. The waiting time phenomenon in spatially discretized porous medium and thin film equations. SIAM Journal on Numerical Analysis. 59(1), 60–87.","mla":"Fischer, Julian L., and Daniel Matthes. “The Waiting Time Phenomenon in Spatially Discretized Porous Medium and Thin Film Equations.” <i>SIAM Journal on Numerical Analysis</i>, vol. 59, no. 1, Society for Industrial and Applied Mathematics, 2021, pp. 60–87, doi:<a href=\"https://doi.org/10.1137/19M1300017\">10.1137/19M1300017</a>.","short":"J.L. Fischer, D. Matthes, SIAM Journal on Numerical Analysis 59 (2021) 60–87."},"main_file_link":[{"url":"https://arxiv.org/abs/1911.04185","open_access":"1"}],"publisher":"Society for Industrial and Applied Mathematics","department":[{"_id":"JuFi"}],"volume":59,"external_id":{"arxiv":["1911.04185"],"isi":["000625044600003"]},"date_created":"2021-04-18T22:01:42Z","publication_status":"published","scopus_import":"1","issue":"1","month":"01","_id":"9335","publication_identifier":{"issn":["0036-1429"]},"acknowledgement":"This research was supported by the DFG Collaborative Research Center TRR 109, “Discretization in Geometry and Dynamics”.","year":"2021","article_type":"original","intvolume":"        59","date_published":"2021-01-01T00:00:00Z","doi":"10.1137/19M1300017","day":"01","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","arxiv":1,"publication":"SIAM Journal on Numerical Analysis","isi":1,"oa_version":"Preprint","article_processing_charge":"No","status":"public","language":[{"iso":"eng"}],"page":"60-87","date_updated":"2023-08-08T13:10:40Z","title":"The waiting time phenomenon in spatially discretized porous medium and thin film equations","author":[{"last_name":"Fischer","full_name":"Fischer, Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0479-558X","first_name":"Julian L"},{"last_name":"Matthes","full_name":"Matthes, Daniel","first_name":"Daniel"}]},{"volume":281,"department":[{"_id":"RoSe"}],"publisher":"Elsevier","main_file_link":[{"url":"https://arxiv.org/abs/1911.03187","open_access":"1"}],"abstract":[{"text":"We consider the stochastic quantization of a quartic double-well energy functional in the semiclassical regime and derive optimal asymptotics for the exponentially small splitting of the ground state energy. Our result provides an infinite-dimensional version of some sharp tunneling estimates known in finite dimensions for semiclassical Witten Laplacians in degree zero. From a stochastic point of view it proves that the L2 spectral gap of the stochastic one-dimensional Allen-Cahn equation in finite volume satisfies a Kramers-type formula in the limit of vanishing noise. We work with finite-dimensional lattice approximations and establish semiclassical estimates which are uniform in the dimension. Our key estimate shows that the constant separating the two exponentially small eigenvalues from the rest of the spectrum can be taken independently of the dimension.","lang":"eng"}],"type":"journal_article","citation":{"ieee":"M. Brooks and G. Di Gesù, “Sharp tunneling estimates for a double-well model in infinite dimension,” <i>Journal of Functional Analysis</i>, vol. 281, no. 3. Elsevier, 2021.","ama":"Brooks M, Di Gesù G. Sharp tunneling estimates for a double-well model in infinite dimension. <i>Journal of Functional Analysis</i>. 2021;281(3). doi:<a href=\"https://doi.org/10.1016/j.jfa.2021.109029\">10.1016/j.jfa.2021.109029</a>","apa":"Brooks, M., &#38; Di Gesù, G. (2021). Sharp tunneling estimates for a double-well model in infinite dimension. <i>Journal of Functional Analysis</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jfa.2021.109029\">https://doi.org/10.1016/j.jfa.2021.109029</a>","chicago":"Brooks, Morris, and Giacomo Di Gesù. “Sharp Tunneling Estimates for a Double-Well Model in Infinite Dimension.” <i>Journal of Functional Analysis</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.jfa.2021.109029\">https://doi.org/10.1016/j.jfa.2021.109029</a>.","ista":"Brooks M, Di Gesù G. 2021. Sharp tunneling estimates for a double-well model in infinite dimension. Journal of Functional Analysis. 281(3), 109029.","mla":"Brooks, Morris, and Giacomo Di Gesù. “Sharp Tunneling Estimates for a Double-Well Model in Infinite Dimension.” <i>Journal of Functional Analysis</i>, vol. 281, no. 3, 109029, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.jfa.2021.109029\">10.1016/j.jfa.2021.109029</a>.","short":"M. Brooks, G. Di Gesù, Journal of Functional Analysis 281 (2021)."},"quality_controlled":"1","_id":"9348","month":"04","scopus_import":"1","issue":"3","publication_status":"published","date_created":"2021-04-25T22:01:29Z","external_id":{"arxiv":["1911.03187"],"isi":["000644702800005"]},"arxiv":1,"publication":"Journal of Functional Analysis","isi":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"07","doi":"10.1016/j.jfa.2021.109029","oa":1,"intvolume":"       281","date_published":"2021-04-07T00:00:00Z","article_number":"109029","publication_identifier":{"issn":["0022-1236"],"eissn":["1096-0783"]},"article_type":"original","year":"2021","acknowledgement":"GDG gratefully acknowledges the financial support of HIM Bonn in the framework of the 2019 Junior Trimester Programs “Kinetic Theory” and “Randomness, PDEs and Nonlinear Fluctuations” and the hospitality at the University of Rome La Sapienza during his frequent visits.","title":"Sharp tunneling estimates for a double-well model in infinite dimension","author":[{"last_name":"Brooks","full_name":"Brooks, Morris","id":"B7ECF9FC-AA38-11E9-AC9A-0930E6697425","orcid":"0000-0002-6249-0928","first_name":"Morris"},{"first_name":"Giacomo","full_name":"Di Gesù, Giacomo","last_name":"Di Gesù"}],"date_updated":"2023-08-08T13:15:11Z","language":[{"iso":"eng"}],"status":"public","article_processing_charge":"No","oa_version":"Preprint"},{"ddc":["530"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"publication":"Annales Henri Poincare","arxiv":1,"isi":1,"ec_funded":1,"year":"2021","acknowledgement":"The authors gratefully acknowledge Gérard Ben Arous for suggesting this kind of result. K.L.K. was partially supported by NSF CAREER Award DMS-125479 and a Simons Sabbatical Fellowship. S.R. acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. B. S. gratefully acknowledges partial support from the NCCR SwissMAP, from the Swiss National Science Foundation through the Grant “Dynamical and energetic properties of Bose–Einstein condensates” and from the European Research Council through the ERC-AdG CLaQS. Funding Open access funding provided by Institute of Science and Technology (IST Austria).","article_type":"original","publication_identifier":{"issn":["1424-0637"]},"intvolume":"        22","date_published":"2021-04-08T00:00:00Z","doi":"10.1007/s00023-021-01044-1","day":"08","oa":1,"file":[{"checksum":"1a0fb963f2f415ba470881a794f20eb6","content_type":"application/pdf","relation":"main_file","date_updated":"2021-10-15T11:15:40Z","file_id":"10143","access_level":"open_access","creator":"cchlebak","file_size":522669,"success":1,"file_name":"2021_Annales_Kirkpatrick.pdf","date_created":"2021-10-15T11:15:40Z"}],"file_date_updated":"2021-10-15T11:15:40Z","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","status":"public","language":[{"iso":"eng"}],"date_updated":"2025-06-12T06:39:59Z","page":"2595-2618","title":"A large deviation principle in many-body quantum dynamics","author":[{"last_name":"Kirkpatrick","full_name":"Kirkpatrick, Kay","first_name":"Kay"},{"first_name":"Simone Anna Elvira","id":"856966FE-A408-11E9-977E-802DE6697425","full_name":"Rademacher, Simone Anna Elvira","last_name":"Rademacher","orcid":"0000-0001-5059-4466"},{"last_name":"Schlein","full_name":"Schlein, Benjamin","first_name":"Benjamin"}],"oa_version":"Published Version","publisher":"Springer Nature","department":[{"_id":"RoSe"}],"volume":22,"quality_controlled":"1","abstract":[{"text":"We consider the many-body quantum evolution of a factorized initial data, in the mean-field regime. We show that fluctuations around the limiting Hartree dynamics satisfy large deviation estimates that are consistent with central limit theorems that have been established in the last years. ","lang":"eng"}],"pmid":1,"type":"journal_article","citation":{"short":"K. Kirkpatrick, S.A.E. Rademacher, B. Schlein, Annales Henri Poincare 22 (2021) 2595–2618.","apa":"Kirkpatrick, K., Rademacher, S. A. E., &#38; Schlein, B. (2021). A large deviation principle in many-body quantum dynamics. <i>Annales Henri Poincare</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00023-021-01044-1\">https://doi.org/10.1007/s00023-021-01044-1</a>","ieee":"K. Kirkpatrick, S. A. E. Rademacher, and B. Schlein, “A large deviation principle in many-body quantum dynamics,” <i>Annales Henri Poincare</i>, vol. 22. Springer Nature, pp. 2595–2618, 2021.","ama":"Kirkpatrick K, Rademacher SAE, Schlein B. A large deviation principle in many-body quantum dynamics. <i>Annales Henri Poincare</i>. 2021;22:2595-2618. doi:<a href=\"https://doi.org/10.1007/s00023-021-01044-1\">10.1007/s00023-021-01044-1</a>","mla":"Kirkpatrick, Kay, et al. “A Large Deviation Principle in Many-Body Quantum Dynamics.” <i>Annales Henri Poincare</i>, vol. 22, Springer Nature, 2021, pp. 2595–618, doi:<a href=\"https://doi.org/10.1007/s00023-021-01044-1\">10.1007/s00023-021-01044-1</a>.","chicago":"Kirkpatrick, Kay, Simone Anna Elvira Rademacher, and Benjamin Schlein. “A Large Deviation Principle in Many-Body Quantum Dynamics.” <i>Annales Henri Poincare</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s00023-021-01044-1\">https://doi.org/10.1007/s00023-021-01044-1</a>.","ista":"Kirkpatrick K, Rademacher SAE, Schlein B. 2021. A large deviation principle in many-body quantum dynamics. Annales Henri Poincare. 22, 2595–2618."},"scopus_import":"1","month":"04","_id":"9351","external_id":{"arxiv":["2010.13754"],"isi":["000638022600001"],"pmid":["34776771"]},"date_created":"2021-04-25T22:01:30Z","publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"}},{"quality_controlled":"1","citation":{"short":"J.L. Fischer, D. Gallistl, D. Peterseim, SIAM Journal on Numerical Analysis 59 (2021) 660–674.","chicago":"Fischer, Julian L, Dietmar Gallistl, and Dietmar Peterseim. “A Priori Error Analysis of a Numerical Stochastic Homogenization Method.” <i>SIAM Journal on Numerical Analysis</i>. Society for Industrial and Applied Mathematics, 2021. <a href=\"https://doi.org/10.1137/19M1308992\">https://doi.org/10.1137/19M1308992</a>.","ista":"Fischer JL, Gallistl D, Peterseim D. 2021. A priori error analysis of a numerical stochastic homogenization method. SIAM Journal on Numerical Analysis. 59(2), 660–674.","mla":"Fischer, Julian L., et al. “A Priori Error Analysis of a Numerical Stochastic Homogenization Method.” <i>SIAM Journal on Numerical Analysis</i>, vol. 59, no. 2, Society for Industrial and Applied Mathematics, 2021, pp. 660–74, doi:<a href=\"https://doi.org/10.1137/19M1308992\">10.1137/19M1308992</a>.","ama":"Fischer JL, Gallistl D, Peterseim D. A priori error analysis of a numerical stochastic homogenization method. <i>SIAM Journal on Numerical Analysis</i>. 2021;59(2):660-674. doi:<a href=\"https://doi.org/10.1137/19M1308992\">10.1137/19M1308992</a>","ieee":"J. L. Fischer, D. Gallistl, and D. Peterseim, “A priori error analysis of a numerical stochastic homogenization method,” <i>SIAM Journal on Numerical Analysis</i>, vol. 59, no. 2. Society for Industrial and Applied Mathematics, pp. 660–674, 2021.","apa":"Fischer, J. L., Gallistl, D., &#38; Peterseim, D. (2021). A priori error analysis of a numerical stochastic homogenization method. <i>SIAM Journal on Numerical Analysis</i>. Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/19M1308992\">https://doi.org/10.1137/19M1308992</a>"},"type":"journal_article","abstract":[{"lang":"eng","text":"This paper provides an a priori error analysis of a localized orthogonal decomposition method for the numerical stochastic homogenization of a model random diffusion problem. If the uniformly elliptic and bounded random coefficient field of the model problem is stationary and satisfies a quantitative decorrelation assumption in the form of the spectral gap inequality, then the expected $L^2$ error of the method can be estimated, up to logarithmic factors, by $H+(\\varepsilon/H)^{d/2}$, $\\varepsilon$ being the small correlation length of the random coefficient and $H$ the width of the coarse finite element mesh that determines the spatial resolution. The proof bridges recent results of numerical homogenization and quantitative stochastic homogenization."}],"main_file_link":[{"url":"https://arxiv.org/abs/1912.11646","open_access":"1"}],"publisher":"Society for Industrial and Applied Mathematics","department":[{"_id":"JuFi"}],"volume":59,"external_id":{"arxiv":["1912.11646"],"isi":["000646030400003"]},"date_created":"2021-04-25T22:01:31Z","publication_status":"published","issue":"2","scopus_import":"1","month":"03","_id":"9352","acknowledgement":"This work was initiated while the authors enjoyed the kind hospitality of the Hausdorff Institute for Mathematics in Bonn during the trimester program Multiscale Problems: Algorithms, Numerical Analysis, and Computation. D. Peterseim would like to acknowledge the kind hospitality of the Erwin Schrödinger International Institute  for  Mathematics and Physics  (ESI), where parts of this research were developed under the frame of the thematic program Numerical Analysis of Complex PDE Models in the Sciences.","article_type":"original","publication_identifier":{"issn":["0036-1429"]},"year":"2021","date_published":"2021-03-09T00:00:00Z","intvolume":"        59","oa":1,"doi":"10.1137/19M1308992","day":"09","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"publication":"SIAM Journal on Numerical Analysis","arxiv":1,"oa_version":"Preprint","article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","date_updated":"2023-08-08T13:13:37Z","page":"660-674","title":"A priori error analysis of a numerical stochastic homogenization method","author":[{"orcid":"0000-0002-0479-558X","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","full_name":"Fischer, Julian L","last_name":"Fischer","first_name":"Julian L"},{"full_name":"Gallistl, Dietmar","last_name":"Gallistl","first_name":"Dietmar"},{"last_name":"Peterseim","full_name":"Peterseim, Dietmar","first_name":"Dietmar"}]},{"author":[{"full_name":"Ho, Quoc P","last_name":"Ho","id":"3DD82E3C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6889-1418","first_name":"Quoc P"}],"title":"Homological stability and densities of generalized configuration spaces","date_updated":"2025-04-14T09:09:36Z","page":"813-912","status":"public","language":[{"iso":"eng"}],"has_accepted_license":"1","article_processing_charge":"No","file_date_updated":"2021-05-03T06:54:06Z","oa_version":"Submitted Version","keyword":["Generalized configuration spaces","homological stability","homological densities","chiral algebras","chiral homology","factorization algebras","Koszul duality","Ran space"],"isi":1,"publication":"Geometry & Topology","arxiv":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"_id":"25E549F4-B435-11E9-9278-68D0E5697425","name":"Arithmetic and physics of Higgs moduli spaces","grant_number":"320593","call_identifier":"FP7"},{"call_identifier":"FWF","name":"Algebro-Geometric Applications of Factorization Homology","_id":"26B96266-B435-11E9-9278-68D0E5697425","grant_number":"M02751"}],"ddc":["514","516","512"],"oa":1,"file":[{"relation":"main_file","content_type":"application/pdf","checksum":"643a8d2d6f06f0888dcd7503f55d0920","file_id":"9366","date_updated":"2021-05-03T06:54:06Z","access_level":"open_access","file_size":479268,"creator":"qho","file_name":"densities.pdf","date_created":"2021-05-03T06:54:06Z","success":1}],"doi":"10.2140/gt.2021.25.813","day":"27","date_published":"2021-04-27T00:00:00Z","intvolume":"        25","article_type":"original","publication_identifier":{"issn":["1364-0380"]},"acknowledgement":"This paper owes an obvious intellectual debt to the illuminating treatments of factorization homology by J.\r\nFrancis, D. Gaitsgory, and J. Lurie in [GL,G1, FG]. The author would like to thank B. Farb and J. Wolfson for\r\nbringing the question of explaining coincidences in homological densities to his attention. Moreover, the author\r\nthanks J. Wolfson for many helpful conversations on the subject, O. Randal-Williams for many comments which\r\ngreatly help improve the exposition, and G. C. Drummond-Cole for many useful conversations on L∞-algebras.\r\nFinally, the author is grateful to the anonymous referee for carefully reading the manuscript and for providing\r\nnumerous comments which greatly helped improve the clarity and precision of the exposition.\r\nThis work is supported by the Advanced Grant “Arithmetic and Physics of Higgs moduli spaces” No. 320593 of\r\nthe European Research Council and the Lise Meitner fellowship “Algebro-Geometric Applications of Factorization\r\nHomology,” Austrian Science Fund (FWF): M 2751.","year":"2021","ec_funded":1,"_id":"9359","month":"04","issue":"2","scopus_import":"1","publication_status":"published","date_created":"2021-05-02T06:59:33Z","external_id":{"arxiv":["1802.07948"],"isi":["000682738600005"]},"volume":25,"department":[{"_id":"TaHa"}],"publisher":"Mathematical Sciences Publishers","corr_author":"1","citation":{"apa":"Ho, Q. P. (2021). Homological stability and densities of generalized configuration spaces. <i>Geometry &#38; Topology</i>. Mathematical Sciences Publishers. <a href=\"https://doi.org/10.2140/gt.2021.25.813\">https://doi.org/10.2140/gt.2021.25.813</a>","ama":"Ho QP. Homological stability and densities of generalized configuration spaces. <i>Geometry &#38; Topology</i>. 2021;25(2):813-912. doi:<a href=\"https://doi.org/10.2140/gt.2021.25.813\">10.2140/gt.2021.25.813</a>","ieee":"Q. P. Ho, “Homological stability and densities of generalized configuration spaces,” <i>Geometry &#38; Topology</i>, vol. 25, no. 2. Mathematical Sciences Publishers, pp. 813–912, 2021.","chicago":"Ho, Quoc P. “Homological Stability and Densities of Generalized Configuration Spaces.” <i>Geometry &#38; Topology</i>. Mathematical Sciences Publishers, 2021. <a href=\"https://doi.org/10.2140/gt.2021.25.813\">https://doi.org/10.2140/gt.2021.25.813</a>.","ista":"Ho QP. 2021. Homological stability and densities of generalized configuration spaces. Geometry &#38; Topology. 25(2), 813–912.","mla":"Ho, Quoc P. “Homological Stability and Densities of Generalized Configuration Spaces.” <i>Geometry &#38; Topology</i>, vol. 25, no. 2, Mathematical Sciences Publishers, 2021, pp. 813–912, doi:<a href=\"https://doi.org/10.2140/gt.2021.25.813\">10.2140/gt.2021.25.813</a>.","short":"Q.P. Ho, Geometry &#38; Topology 25 (2021) 813–912."},"type":"journal_article","abstract":[{"text":"We prove that the factorization homologies of a scheme with coefficients in truncated polynomial algebras compute the cohomologies of its generalized configuration spaces. Using Koszul duality between commutative algebras and Lie algebras, we obtain new expressions for the cohomologies of the latter. As a consequence, we obtain a uniform and conceptual approach for treating homological stability, homological densities, and arithmetic densities of generalized configuration spaces. Our results categorify, generalize, and in fact provide a conceptual understanding of the coincidences appearing in the work of Farb--Wolfson--Wood. Our computation of the stable homological densities also yields rational homotopy types, answering a question posed by Vakil--Wood. Our approach hinges on the study of homological stability of cohomological Chevalley complexes, which is of independent interest.\r\n","lang":"eng"}],"quality_controlled":"1"},{"acknowledgement":"We gratefully acknowledge the Arabidopsis Biological Resource Centre (ABRC) for providing T-DNA insertional mutants, and Prof. Remko Offringa for sharing published seeds. We thank Yuchuan Liu (Shanghai OE Biotech Co., Ltd) for help with proteomics data analysis, Xixi Zhang (IST Austria) for providing the pDONR-P4P1r-mCherry plasmid, and Yao Xiao (Technical University of Munich), Alexander Johnson (IST Austria) and Hana Semeradova (IST Austria) for helpful discussions. The study was supported by National Natural Science Foundation of China (NSFC, 31721001, 91954206, to H.-W. X.), “Ten-Thousand Talent Program” (to H.-W. X.) and Collaborative Innovation Center of Crop Stress Biology, Henan Province, and Austrian Science Fund (FWF): I 3630-B25 (to J. F.). S.T. was funded by a European Molecular Biology Organization (EMBO) long-term postdoctoral fellowship (ALTF 723-2015).","publication_identifier":{"issn":["0032-0889"],"eissn":["1532-2548"]},"article_type":"original","year":"2021","date_published":"2021-04-30T00:00:00Z","intvolume":"       186","oa":1,"doi":"10.1093/plphys/kiab199","day":"30","project":[{"_id":"256FEF10-B435-11E9-9278-68D0E5697425","name":"Molecular Mechanism underlying Salicylic Acid Regulation of Endocytic Trafficking in Arabidopsis","grant_number":"723-2015"},{"_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630","call_identifier":"FWF"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","isi":1,"publication":"Plant Physiology","oa_version":"Published Version","article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","date_updated":"2024-11-04T12:32:08Z","page":"2003-2020","author":[{"first_name":"W","full_name":"Kong, W","last_name":"Kong"},{"orcid":"0000-0002-0471-8285","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","full_name":"Tan, Shutang","last_name":"Tan","first_name":"Shutang"},{"full_name":"Zhao, Q","last_name":"Zhao","first_name":"Q"},{"full_name":"Lin, DL","last_name":"Lin","first_name":"DL"},{"first_name":"ZH","full_name":"Xu, ZH","last_name":"Xu"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"},{"first_name":"HW","last_name":"Xue","full_name":"Xue, HW"}],"title":"mRNA surveillance complex PELOTA-HBS1 eegulates phosphoinositide-sependent protein kinase1 and plant growth","quality_controlled":"1","citation":{"short":"W. Kong, S. Tan, Q. Zhao, D. Lin, Z. Xu, J. Friml, H. Xue, Plant Physiology 186 (2021) 2003–2020.","chicago":"Kong, W, Shutang Tan, Q Zhao, DL Lin, ZH Xu, Jiří Friml, and HW Xue. “MRNA Surveillance Complex PELOTA-HBS1 Eegulates Phosphoinositide-Sependent Protein Kinase1 and Plant Growth.” <i>Plant Physiology</i>. American Society of Plant Biologists, 2021. <a href=\"https://doi.org/10.1093/plphys/kiab199\">https://doi.org/10.1093/plphys/kiab199</a>.","ista":"Kong W, Tan S, Zhao Q, Lin D, Xu Z, Friml J, Xue H. 2021. mRNA surveillance complex PELOTA-HBS1 eegulates phosphoinositide-sependent protein kinase1 and plant growth. Plant Physiology. 186(4), 2003–2020.","mla":"Kong, W., et al. “MRNA Surveillance Complex PELOTA-HBS1 Eegulates Phosphoinositide-Sependent Protein Kinase1 and Plant Growth.” <i>Plant Physiology</i>, vol. 186, no. 4, American Society of Plant Biologists, 2021, pp. 2003–20, doi:<a href=\"https://doi.org/10.1093/plphys/kiab199\">10.1093/plphys/kiab199</a>.","ieee":"W. Kong <i>et al.</i>, “mRNA surveillance complex PELOTA-HBS1 eegulates phosphoinositide-sependent protein kinase1 and plant growth,” <i>Plant Physiology</i>, vol. 186, no. 4. American Society of Plant Biologists, pp. 2003–2020, 2021.","ama":"Kong W, Tan S, Zhao Q, et al. mRNA surveillance complex PELOTA-HBS1 eegulates phosphoinositide-sependent protein kinase1 and plant growth. <i>Plant Physiology</i>. 2021;186(4):2003-2020. doi:<a href=\"https://doi.org/10.1093/plphys/kiab199\">10.1093/plphys/kiab199</a>","apa":"Kong, W., Tan, S., Zhao, Q., Lin, D., Xu, Z., Friml, J., &#38; Xue, H. (2021). mRNA surveillance complex PELOTA-HBS1 eegulates phosphoinositide-sependent protein kinase1 and plant growth. <i>Plant Physiology</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1093/plphys/kiab199\">https://doi.org/10.1093/plphys/kiab199</a>"},"abstract":[{"text":"The quality control system for messenger RNA (mRNA) is fundamental for cellular activities in eukaryotes. To elucidate the molecular mechanism of 3'-Phosphoinositide-Dependent Protein Kinase1 (PDK1), a master regulator that is essential throughout eukaryotic growth and development, we employed a forward genetic approach to screen for suppressors of the loss-of-function T-DNA insertion double mutant pdk1.1 pdk1.2 in Arabidopsis thaliana. Notably, the severe growth attenuation of pdk1.1 pdk1.2 was rescued by sop21 (suppressor of pdk1.1 pdk1.2), which harbours a loss-of-function mutation in PELOTA1 (PEL1). PEL1 is a homologue of mammalian PELOTA and yeast (Saccharomyces cerevisiae) DOM34p, which each form a heterodimeric complex with the GTPase HBS1 (HSP70 SUBFAMILY B SUPPRESSOR1, also called SUPERKILLER PROTEIN7, SKI7), a protein that is responsible for ribosomal rescue and thereby assures the quality and fidelity of mRNA molecules during translation. Genetic analysis further revealed that a dysfunctional PEL1-HBS1 complex failed to degrade the T-DNA-disrupted PDK1 transcripts, which were truncated but functional, and thus rescued the growth and developmental defects of pdk1.1 pdk1.2. Our studies demonstrated the functionality of a homologous PELOTA-HBS1 complex and identified its essential regulatory role in plants, providing insights into the mechanism of mRNA quality control.","lang":"eng"}],"pmid":1,"type":"journal_article","main_file_link":[{"url":"https://doi.org/10.1093/plphys/kiab199","open_access":"1"}],"publisher":"American Society of Plant Biologists","department":[{"_id":"JiFr"}],"volume":186,"external_id":{"pmid":["33930167"],"isi":["000703922000025"]},"date_created":"2021-05-03T13:28:20Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"publication_status":"published","scopus_import":"1","issue":"4","month":"04","_id":"9368"},{"article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","date_updated":"2024-10-21T06:02:11Z","page":"978-988","author":[{"first_name":"Roger K.","full_name":"Butlin, Roger K.","last_name":"Butlin"},{"full_name":"Servedio, Maria R.","last_name":"Servedio","first_name":"Maria R."},{"full_name":"Smadja, Carole M.","last_name":"Smadja","first_name":"Carole M."},{"first_name":"Claudia","full_name":"Bank, Claudia","last_name":"Bank"},{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"},{"full_name":"Flaxman, Samuel M.","last_name":"Flaxman","first_name":"Samuel M."},{"full_name":"Giraud, Tatiana","last_name":"Giraud","first_name":"Tatiana"},{"first_name":"Robin","last_name":"Hopkins","full_name":"Hopkins, Robin"},{"first_name":"Erica L.","full_name":"Larson, Erica L.","last_name":"Larson"},{"full_name":"Maan, Martine E.","last_name":"Maan","first_name":"Martine E."},{"last_name":"Meier","full_name":"Meier, Joana","first_name":"Joana"},{"last_name":"Merrill","full_name":"Merrill, Richard","first_name":"Richard"},{"last_name":"Noor","full_name":"Noor, Mohamed A. F.","first_name":"Mohamed A. F."},{"last_name":"Ortiz‐Barrientos","full_name":"Ortiz‐Barrientos, Daniel","first_name":"Daniel"},{"full_name":"Qvarnström, Anna","last_name":"Qvarnström","first_name":"Anna"}],"title":"Homage to Felsenstein 1981, or why are there so few/many species?","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics","General Agricultural and Biological Sciences"],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication":"Evolution","isi":1,"acknowledgement":"RKB was funded by the Natural Environment Research Council (NE/P012272/1 & NE/P001610/1), the European Research Council (693030 BARRIERS), and the Swedish Research Council (VR) (2018‐03695). MRS was funded by the National Science Foundation (Grant No. DEB1939290).","year":"2021","publication_identifier":{"eissn":["1558-5646"],"issn":["0014-3820"]},"article_type":"original","intvolume":"        75","date_published":"2021-04-19T00:00:00Z","day":"19","doi":"10.1111/evo.14235","oa":1,"issue":"5","scopus_import":"1","month":"04","_id":"9374","external_id":{"isi":["000647224000001"]},"date_created":"2021-05-06T04:34:47Z","publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"main_file_link":[{"open_access":"1","url":"https://onlinelibrary.wiley.com/doi/10.1111/evo.14235"}],"publisher":"Wiley","department":[{"_id":"NiBa"}],"volume":75,"quality_controlled":"1","type":"journal_article","abstract":[{"lang":"eng","text":"If there are no constraints on the process of speciation, then the number of species might be expected to match the number of available niches and this number might be indefinitely large. One possible constraint is the opportunity for allopatric divergence. In 1981, Felsenstein used a simple and elegant model to ask if there might also be genetic constraints. He showed that progress towards speciation could be described by the build‐up of linkage disequilibrium among divergently selected loci and between these loci and those contributing to other forms of reproductive isolation. Therefore, speciation is opposed by recombination, because it tends to break down linkage disequilibria. Felsenstein then introduced a crucial distinction between “two‐allele” models, which are subject to this effect, and “one‐allele” models, which are free from the recombination constraint. These fundamentally important insights have been the foundation for both empirical and theoretical studies of speciation ever since."}],"citation":{"short":"R.K. Butlin, M.R. Servedio, C.M. Smadja, C. Bank, N.H. Barton, S.M. Flaxman, T. Giraud, R. Hopkins, E.L. Larson, M.E. Maan, J. Meier, R. Merrill, M.A.F. Noor, D. Ortiz‐Barrientos, A. Qvarnström, Evolution 75 (2021) 978–988.","ama":"Butlin RK, Servedio MR, Smadja CM, et al. Homage to Felsenstein 1981, or why are there so few/many species? <i>Evolution</i>. 2021;75(5):978-988. doi:<a href=\"https://doi.org/10.1111/evo.14235\">10.1111/evo.14235</a>","ieee":"R. K. Butlin <i>et al.</i>, “Homage to Felsenstein 1981, or why are there so few/many species?,” <i>Evolution</i>, vol. 75, no. 5. Wiley, pp. 978–988, 2021.","apa":"Butlin, R. K., Servedio, M. R., Smadja, C. M., Bank, C., Barton, N. H., Flaxman, S. M., … Qvarnström, A. (2021). Homage to Felsenstein 1981, or why are there so few/many species? <i>Evolution</i>. Wiley. <a href=\"https://doi.org/10.1111/evo.14235\">https://doi.org/10.1111/evo.14235</a>","chicago":"Butlin, Roger K., Maria R. Servedio, Carole M. Smadja, Claudia Bank, Nicholas H Barton, Samuel M. Flaxman, Tatiana Giraud, et al. “Homage to Felsenstein 1981, or Why Are There so Few/Many Species?” <i>Evolution</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/evo.14235\">https://doi.org/10.1111/evo.14235</a>.","ista":"Butlin RK, Servedio MR, Smadja CM, Bank C, Barton NH, Flaxman SM, Giraud T, Hopkins R, Larson EL, Maan ME, Meier J, Merrill R, Noor MAF, Ortiz‐Barrientos D, Qvarnström A. 2021. Homage to Felsenstein 1981, or why are there so few/many species? Evolution. 75(5), 978–988.","mla":"Butlin, Roger K., et al. “Homage to Felsenstein 1981, or Why Are There so Few/Many Species?” <i>Evolution</i>, vol. 75, no. 5, Wiley, 2021, pp. 978–88, doi:<a href=\"https://doi.org/10.1111/evo.14235\">10.1111/evo.14235</a>."}},{"publisher":"National Academy of Sciences","volume":118,"department":[{"_id":"NiBa"}],"citation":{"ista":"Meier JI, Salazar PA, Kučka M, Davies RW, Dréau A, Aldás I, Power OB, Nadeau NJ, Bridle JR, Rolian C, Barton NH, McMillan WO, Jiggins CD, Chan YF. 2021. Haplotype tagging reveals parallel formation of hybrid races in two butterfly species. Proceedings of the National Academy of Sciences of the United States of America. 118(25), e2015005118.","chicago":"Meier, Joana I., Patricio A. Salazar, Marek Kučka, Robert William Davies, Andreea Dréau, Ismael Aldás, Olivia Box Power, et al. “Haplotype Tagging Reveals Parallel Formation of Hybrid Races in Two Butterfly Species.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2021. <a href=\"https://doi.org/10.1073/pnas.2015005118\">https://doi.org/10.1073/pnas.2015005118</a>.","mla":"Meier, Joana I., et al. “Haplotype Tagging Reveals Parallel Formation of Hybrid Races in Two Butterfly Species.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 118, no. 25, e2015005118, National Academy of Sciences, 2021, doi:<a href=\"https://doi.org/10.1073/pnas.2015005118\">10.1073/pnas.2015005118</a>.","ama":"Meier JI, Salazar PA, Kučka M, et al. Haplotype tagging reveals parallel formation of hybrid races in two butterfly species. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2021;118(25). doi:<a href=\"https://doi.org/10.1073/pnas.2015005118\">10.1073/pnas.2015005118</a>","apa":"Meier, J. I., Salazar, P. A., Kučka, M., Davies, R. W., Dréau, A., Aldás, I., … Chan, Y. F. (2021). Haplotype tagging reveals parallel formation of hybrid races in two butterfly species. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2015005118\">https://doi.org/10.1073/pnas.2015005118</a>","ieee":"J. I. Meier <i>et al.</i>, “Haplotype tagging reveals parallel formation of hybrid races in two butterfly species,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 118, no. 25. National Academy of Sciences, 2021.","short":"J.I. Meier, P.A. Salazar, M. Kučka, R.W. Davies, A. Dréau, I. Aldás, O.B. Power, N.J. Nadeau, J.R. Bridle, C. Rolian, N.H. Barton, W.O. McMillan, C.D. Jiggins, Y.F. Chan, Proceedings of the National Academy of Sciences of the United States of America 118 (2021)."},"type":"journal_article","abstract":[{"lang":"eng","text":"Genetic variation segregates as linked sets of variants, or haplotypes. Haplotypes and linkage are central to genetics and underpin virtually all genetic and selection analysis. And yet, genomic data often lack haplotype information, due to constraints in sequencing technologies. Here we present “haplotagging”, a simple, low-cost linked-read sequencing technique that allows sequencing of hundreds of individuals while retaining linkage information. We apply haplotagging to construct megabase-size haplotypes for over 600 individual butterflies (Heliconius erato and H. melpomene), which form overlapping hybrid zones across an elevational gradient in Ecuador. Haplotagging identifies loci controlling distinctive high- and lowland wing color patterns. Divergent haplotypes are found at the same major loci in both species, while chromosome rearrangements show no parallelism. Remarkably, in both species the geographic clines for the major wing pattern loci are displaced by 18 km, leading to the rise of a novel hybrid morph in the centre of the hybrid zone. We propose that shared warning signalling (Müllerian mimicry) may couple the cline shifts seen in both species, and facilitate the parallel co-emergence of a novel hybrid morph in both co-mimetic species. Our results show the power of efficient haplotyping methods when combined with large-scale sequencing data from natural populations."}],"pmid":1,"quality_controlled":"1","month":"06","scopus_import":"1","issue":"25","_id":"9375","external_id":{"isi":["000671755600001"],"pmid":["34155138"]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"publication_status":"published","date_created":"2021-05-07T17:10:21Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"isi":1,"publication":"Proceedings of the National Academy of Sciences of the United States of America","article_number":"e2015005118","publication_identifier":{"eissn":["0027-8424"]},"year":"2021","acknowledgement":"We thank Felicity Jones for input into experimental design, helpful discussion and improving the manuscript. We thank the Rolian, Jiggins, Chan and Jones Labs members for support, insightful scientific discussion and improving the manuscript. We thank the Rolian lab members, the Animal Resource Centre staff at the University of Calgary, and Caroline Schmid and Ann-Katrin Geysel at the Friedrich Miescher Laboratory for animal husbandry. We thank Christa Lanz, Rebecca Schwab and Ilja Bezrukov for assistance with high-throughput sequencing and associated data processing; Andre Noll and the MPI Tübingen IT team for computational support. We thank Ben Haller and Richard Durbin for helpful discussions. We thank David M. Kingsley for thoughtful input that has greatly improved our manuscript. J.I.M. is supported by a Research Fellowship from St. John’s College, Cambridge. A.D. was supported by a European Research Council Consolidator Grant (No. 617279 “EvolRecombAdapt”, P/I Felicity Jones). C.R. is supported by Discovery Grant #4181932 from the Natural Sciences and Engineering Research Council of Canada and by the Faculty of Veterinary Medicine at the University of Calgary. C.D.J. is supported by a BBSRC grant BB/R007500 and a European Research Council Advanced Grant (No. 339873 “SpeciationGenetics”). M.K. and Y.F.C. are supported by the Max Planck Society and a European Research Council Starting Grant (No. 639096 “HybridMiX”).","article_type":"original","file":[{"date_updated":"2022-03-08T08:18:16Z","file_id":"10835","content_type":"application/pdf","checksum":"cb30c6166b2132ee60d616b31a1a7c29","relation":"main_file","file_name":"2021_PNAS_Meier.pdf","success":1,"date_created":"2022-03-08T08:18:16Z","creator":"dernst","file_size":20592929,"access_level":"open_access"}],"oa":1,"doi":"10.1073/pnas.2015005118","day":"21","date_published":"2021-06-21T00:00:00Z","intvolume":"       118","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","has_accepted_license":"1","file_date_updated":"2022-03-08T08:18:16Z","title":"Haplotype tagging reveals parallel formation of hybrid races in two butterfly species","author":[{"first_name":"Joana I.","last_name":"Meier","full_name":"Meier, Joana I."},{"first_name":"Patricio A.","full_name":"Salazar, Patricio A.","last_name":"Salazar"},{"full_name":"Kučka, Marek","last_name":"Kučka","first_name":"Marek"},{"last_name":"Davies","full_name":"Davies, Robert William","first_name":"Robert William"},{"first_name":"Andreea","last_name":"Dréau","full_name":"Dréau, Andreea"},{"last_name":"Aldás","full_name":"Aldás, Ismael","first_name":"Ismael"},{"last_name":"Power","full_name":"Power, Olivia Box","first_name":"Olivia Box"},{"first_name":"Nicola J.","full_name":"Nadeau, Nicola J.","last_name":"Nadeau"},{"first_name":"Jon R.","full_name":"Bridle, Jon R.","last_name":"Bridle"},{"first_name":"Campbell","full_name":"Rolian, Campbell","last_name":"Rolian"},{"first_name":"Nicholas H","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"full_name":"McMillan, W. Owen","last_name":"McMillan","first_name":"W. Owen"},{"first_name":"Chris D.","full_name":"Jiggins, Chris D.","last_name":"Jiggins"},{"last_name":"Chan","full_name":"Chan, Yingguang Frank","first_name":"Yingguang Frank"}],"date_updated":"2025-05-14T10:58:04Z","oa_version":"Published Version"},{"quality_controlled":"1","citation":{"ama":"Zhang R, Auzinger T, Bickel B. Computational design of planar multistable compliant structures. <i>ACM Transactions on Graphics</i>. 2021;40(5). doi:<a href=\"https://doi.org/10.1145/3453477\">10.1145/3453477</a>","ieee":"R. Zhang, T. Auzinger, and B. Bickel, “Computational design of planar multistable compliant structures,” <i>ACM Transactions on Graphics</i>, vol. 40, no. 5. Association for Computing Machinery, 2021.","apa":"Zhang, R., Auzinger, T., &#38; Bickel, B. (2021). Computational design of planar multistable compliant structures. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3453477\">https://doi.org/10.1145/3453477</a>","mla":"Zhang, Ran, et al. “Computational Design of Planar Multistable Compliant Structures.” <i>ACM Transactions on Graphics</i>, vol. 40, no. 5, 186, Association for Computing Machinery, 2021, doi:<a href=\"https://doi.org/10.1145/3453477\">10.1145/3453477</a>.","chicago":"Zhang, Ran, Thomas Auzinger, and Bernd Bickel. “Computational Design of Planar Multistable Compliant Structures.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3453477\">https://doi.org/10.1145/3453477</a>.","ista":"Zhang R, Auzinger T, Bickel B. 2021. Computational design of planar multistable compliant structures. ACM Transactions on Graphics. 40(5), 186.","short":"R. Zhang, T. Auzinger, B. Bickel, ACM Transactions on Graphics 40 (2021)."},"type":"journal_article","abstract":[{"text":"This paper presents a method for designing planar multistable compliant structures. Given a sequence of desired stable states and the corresponding poses of the structure, we identify the topology and geometric realization of a mechanism—consisting of bars and joints—that is able to physically reproduce the desired multistable behavior. In order to solve this problem efficiently, we build on insights from minimally rigid graph theory to identify simple but effective topologies for the mechanism. We then optimize its geometric parameters, such as joint positions and bar lengths, to obtain correct transitions between the given poses. Simultaneously, we ensure adequate stability of each pose based on an effective approximate error metric related to the elastic energy Hessian of the bars in the mechanism. As demonstrated by our results, we obtain functional multistable mechanisms of manageable complexity that can be fabricated using 3D printing. Further, we evaluated the effectiveness of our method on a large number of examples in the simulation and fabricated several physical prototypes.","lang":"eng"}],"department":[{"_id":"BeBi"}],"volume":40,"publisher":"Association for Computing Machinery","date_created":"2021-05-08T17:37:08Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"published","external_id":{"isi":["000752079300003"]},"_id":"9376","scopus_import":"1","issue":"5","month":"10","date_published":"2021-10-08T00:00:00Z","intvolume":"        40","oa":1,"file":[{"access_level":"open_access","creator":"bbickel","file_size":18926557,"file_name":"Multistable-authorversion.pdf","date_created":"2021-05-08T17:36:59Z","checksum":"8564b3118457d4c8939a8ef2b1a2f16c","content_type":"application/pdf","relation":"main_file","date_updated":"2021-05-08T17:36:59Z","file_id":"9377"},{"relation":"main_file","checksum":"3b6e874e30bfa1bfc3ad3498710145a1","content_type":"video/mp4","file_id":"9378","date_updated":"2021-05-08T17:38:22Z","access_level":"open_access","success":1,"file_name":"multistable-video.mp4","date_created":"2021-05-08T17:38:22Z","file_size":76542901,"creator":"bbickel"},{"title":"Supplementary Material for “Computational Design of Planar Multistable Compliant Structures”","file_id":"10562","date_updated":"2021-12-17T08:13:51Z","relation":"supplementary_material","checksum":"20dc3bc42e1a912a5b0247c116772098","content_type":"application/pdf","file_size":3367072,"creator":"bbickel","file_name":"multistable-supplementary material.pdf","description":"This document provides additional results and analyzes the robustness and limitations of our approach.","date_created":"2021-12-17T08:13:51Z","access_level":"open_access"}],"day":"08","doi":"10.1145/3453477","publication_identifier":{"eissn":["1557-7368"],"issn":["0730-0301"]},"year":"2021","acknowledgement":"We would like to thank everyone who contributed to this paper, the authors of artworks for all the examples, including @macrovec-tor_official and Wikimedia for the FLAG semaphore, and @pikisuper-star for the FIGURINE. The photos of iconic poses in the teaser were supplied by (from left to right): Mike Hewitt/Olympics Day 8 - Athletics/Gettty Images, Oneinchpunch/Basketball player training on acourt in New york city/Shutterstock, and Andrew Redington/TigerWoods/Getty Images. We also want to express our gratitude to Christian Hafner for insightful discussions, the IST Austria machine shop SSU, all proof-readers, and anonymous reviewers. This project has received funding from the European Union’s Horizon 2020 research and innovation programme, under the Marie Skłodowska-Curie grant agreement No 642841 (DISTRO), and under the European Research Council grant agreement No 715767 (MATERIALIZABLE).","article_type":"original","ec_funded":1,"article_number":"186","acknowledged_ssus":[{"_id":"M-Shop"}],"isi":1,"publication":"ACM Transactions on Graphics","ddc":["000"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"grant_number":"642841","_id":"2508E324-B435-11E9-9278-68D0E5697425","name":"Distributed 3D Object Design","call_identifier":"H2020"},{"call_identifier":"H2020","grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","_id":"24F9549A-B435-11E9-9278-68D0E5697425"}],"oa_version":"Published Version","keyword":["multistability","mechanism","computational design","rigidity"],"date_updated":"2025-03-31T15:58:16Z","author":[{"first_name":"Ran","last_name":"Zhang","full_name":"Zhang, Ran","id":"4DDBCEB0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3808-281X"},{"first_name":"Thomas","orcid":"0000-0002-1546-3265","id":"4718F954-F248-11E8-B48F-1D18A9856A87","full_name":"Auzinger, Thomas","last_name":"Auzinger"},{"first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","full_name":"Bickel, Bernd","last_name":"Bickel","orcid":"0000-0001-6511-9385"}],"title":"Computational design of planar multistable compliant structures","article_processing_charge":"No","has_accepted_license":"1","file_date_updated":"2021-12-17T08:13:51Z","language":[{"iso":"eng"}],"status":"public"},{"quality_controlled":"1","type":"journal_article","abstract":[{"lang":"eng","text":"When B cells encounter membrane-bound antigens, the formation and coalescence of B cell antigen receptor (BCR) microclusters amplifies BCR signaling. The ability of B cells to probe the surface of antigen-presenting cells (APCs) and respond to APC-bound antigens requires remodeling of the actin cytoskeleton. Initial BCR signaling stimulates actin-related protein (Arp) 2/3 complex-dependent actin polymerization, which drives B cell spreading as well as the centripetal movement and coalescence of BCR microclusters at the B cell-APC synapse. Sustained actin polymerization depends on concomitant actin filament depolymerization, which enables the recycling of actin monomers and Arp2/3 complexes. Cofilin-mediated severing of actin filaments is a rate-limiting step in the morphological changes that occur during immune synapse formation. Hence, regulators of cofilin activity such as WD repeat-containing protein 1 (Wdr1), LIM domain kinase (LIMK), and coactosin-like 1 (Cotl1) may also be essential for actin-dependent processes in B cells. Wdr1 enhances cofilin-mediated actin disassembly. Conversely, Cotl1 competes with cofilin for binding to actin and LIMK phosphorylates cofilin and prevents it from binding to actin filaments. We now show that Wdr1 and LIMK have distinct roles in BCR-induced assembly of the peripheral actin structures that drive B cell spreading, and that cofilin, Wdr1, and LIMK all contribute to the actin-dependent amplification of BCR signaling at the immune synapse. Depleting Cotl1 had no effect on these processes. Thus, the Wdr1-LIMK-cofilin axis is critical for BCR-induced actin remodeling and for B cell responses to APC-bound antigens."}],"pmid":1,"citation":{"ama":"Bolger-Munro M, Choi K, Cheung F, et al. The Wdr1-LIMK-Cofilin axis controls B cell antigen receptor-induced actin remodeling and signaling at the immune synapse. <i>Frontiers in Cell and Developmental Biology</i>. 2021;9. doi:<a href=\"https://doi.org/10.3389/fcell.2021.649433\">10.3389/fcell.2021.649433</a>","ieee":"M. Bolger-Munro <i>et al.</i>, “The Wdr1-LIMK-Cofilin axis controls B cell antigen receptor-induced actin remodeling and signaling at the immune synapse,” <i>Frontiers in Cell and Developmental Biology</i>, vol. 9. Frontiers Media, 2021.","apa":"Bolger-Munro, M., Choi, K., Cheung, F., Liu, Y. T., Dang-Lawson, M., Deretic, N., … Gold, M. R. (2021). The Wdr1-LIMK-Cofilin axis controls B cell antigen receptor-induced actin remodeling and signaling at the immune synapse. <i>Frontiers in Cell and Developmental Biology</i>. Frontiers Media. <a href=\"https://doi.org/10.3389/fcell.2021.649433\">https://doi.org/10.3389/fcell.2021.649433</a>","mla":"Bolger-Munro, Madison, et al. “The Wdr1-LIMK-Cofilin Axis Controls B Cell Antigen Receptor-Induced Actin Remodeling and Signaling at the Immune Synapse.” <i>Frontiers in Cell and Developmental Biology</i>, vol. 9, 649433, Frontiers Media, 2021, doi:<a href=\"https://doi.org/10.3389/fcell.2021.649433\">10.3389/fcell.2021.649433</a>.","ista":"Bolger-Munro M, Choi K, Cheung F, Liu YT, Dang-Lawson M, Deretic N, Keane C, Gold MR. 2021. The Wdr1-LIMK-Cofilin axis controls B cell antigen receptor-induced actin remodeling and signaling at the immune synapse. Frontiers in Cell and Developmental Biology. 9, 649433.","chicago":"Bolger-Munro, Madison, Kate Choi, Faith Cheung, Yi Tian Liu, May Dang-Lawson, Nikola Deretic, Connor Keane, and Michael R. Gold. “The Wdr1-LIMK-Cofilin Axis Controls B Cell Antigen Receptor-Induced Actin Remodeling and Signaling at the Immune Synapse.” <i>Frontiers in Cell and Developmental Biology</i>. Frontiers Media, 2021. <a href=\"https://doi.org/10.3389/fcell.2021.649433\">https://doi.org/10.3389/fcell.2021.649433</a>.","short":"M. Bolger-Munro, K. Choi, F. Cheung, Y.T. Liu, M. Dang-Lawson, N. Deretic, C. Keane, M.R. Gold, Frontiers in Cell and Developmental Biology 9 (2021)."},"publisher":"Frontiers Media","department":[{"_id":"CaHe"}],"volume":9,"external_id":{"isi":["000644419500001"],"pmid":["33928084"]},"date_created":"2021-05-09T22:01:37Z","publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"scopus_import":"1","month":"04","_id":"9379","publication_identifier":{"eissn":["2296-634X"]},"acknowledgement":"We thank the UBC Life Sciences Institute Imaging Facility andthe UBC Flow Cytometry Facility.","article_type":"original","year":"2021","article_number":"649433","intvolume":"         9","date_published":"2021-04-13T00:00:00Z","doi":"10.3389/fcell.2021.649433","day":"13","oa":1,"file":[{"relation":"main_file","checksum":"8c8a03575d2f7583f88dc3b658b0976b","content_type":"application/pdf","file_id":"9386","date_updated":"2021-05-11T15:09:23Z","access_level":"open_access","date_created":"2021-05-11T15:09:23Z","success":1,"file_name":"2021_Frontiers_Cell_Bolger-Munro.pdf","file_size":4076024,"creator":"kschuh"}],"ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Frontiers in Cell and Developmental Biology","isi":1,"keyword":["B cell","actin","immune synapse","cell spreading","cofilin","WDR1 (AIP1)","LIM domain kinase","B cell receptor (BCR)"],"oa_version":"Published Version","file_date_updated":"2021-05-11T15:09:23Z","article_processing_charge":"No","has_accepted_license":"1","status":"public","language":[{"iso":"eng"}],"date_updated":"2023-10-18T08:19:49Z","author":[{"first_name":"Madison","orcid":"0000-0002-8176-4824","full_name":"Bolger-Munro, Madison","last_name":"Bolger-Munro","id":"516F03FA-93A3-11EA-A7C5-D6BE3DDC885E"},{"first_name":"Kate","full_name":"Choi, Kate","last_name":"Choi"},{"first_name":"Faith","full_name":"Cheung, Faith","last_name":"Cheung"},{"last_name":"Liu","full_name":"Liu, Yi Tian","first_name":"Yi Tian"},{"first_name":"May","last_name":"Dang-Lawson","full_name":"Dang-Lawson, May"},{"first_name":"Nikola","last_name":"Deretic","full_name":"Deretic, Nikola"},{"last_name":"Keane","full_name":"Keane, Connor","first_name":"Connor"},{"first_name":"Michael R.","full_name":"Gold, Michael R.","last_name":"Gold"}],"title":"The Wdr1-LIMK-Cofilin axis controls B cell antigen receptor-induced actin remodeling and signaling at the immune synapse"}]