[{"publication_status":"published","year":"2021","publication_identifier":{"isbn":["9783030678982"],"eissn":["1611-3349"],"issn":["0302-9743"]},"language":[{"iso":"eng"}],"publication":"Conference on Algorithms and Discrete Applied Mathematics","day":"28","page":"346-358","date_created":"2021-03-07T23:01:25Z","date_published":"2021-01-28T00:00:00Z","doi":"10.1007/978-3-030-67899-9_28","volume":12601,"abstract":[{"text":"In the multiway cut problem we are given a weighted undirected graph G=(V,E) and a set T⊆V of k terminals. The goal is to find a minimum weight set of edges E′⊆E with the property that by removing E′ from G all the terminals become disconnected. In this paper we present a simple local search approximation algorithm for the multiway cut problem with approximation ratio 2−2k . We present an experimental evaluation of the performance of our local search algorithm and show that it greatly outperforms the isolation heuristic of Dalhaus et al. and it has similar performance as the much more complex algorithms of Calinescu et al., Sharma and Vondrak, and Buchbinder et al. which have the currently best known approximation ratios for this problem.","lang":"eng"}],"oa_version":"None","scopus_import":"1","quality_controlled":"1","publisher":"Springer Nature","alternative_title":["LNCS"],"intvolume":" 12601","month":"01","citation":{"mla":"Bloch-Hansen, Andrew, et al. “Experimental Evaluation of a Local Search Approximation Algorithm for the Multiway Cut Problem.” Conference on Algorithms and Discrete Applied Mathematics, vol. 12601, Springer Nature, 2021, pp. 346–58, doi:10.1007/978-3-030-67899-9_28.","ieee":"A. Bloch-Hansen, N. Samei, and R. Solis-Oba, “Experimental evaluation of a local search approximation algorithm for the multiway cut problem,” in Conference on Algorithms and Discrete Applied Mathematics, Rupnagar, India, 2021, vol. 12601, pp. 346–358.","short":"A. Bloch-Hansen, N. Samei, R. Solis-Oba, in:, Conference on Algorithms and Discrete Applied Mathematics, Springer Nature, 2021, pp. 346–358.","apa":"Bloch-Hansen, A., Samei, N., & Solis-Oba, R. (2021). Experimental evaluation of a local search approximation algorithm for the multiway cut problem. In Conference on Algorithms and Discrete Applied Mathematics (Vol. 12601, pp. 346–358). Rupnagar, India: Springer Nature. https://doi.org/10.1007/978-3-030-67899-9_28","ama":"Bloch-Hansen A, Samei N, Solis-Oba R. Experimental evaluation of a local search approximation algorithm for the multiway cut problem. In: Conference on Algorithms and Discrete Applied Mathematics. Vol 12601. Springer Nature; 2021:346-358. doi:10.1007/978-3-030-67899-9_28","chicago":"Bloch-Hansen, Andrew, Nasim Samei, and Roberto Solis-Oba. “Experimental Evaluation of a Local Search Approximation Algorithm for the Multiway Cut Problem.” In Conference on Algorithms and Discrete Applied Mathematics, 12601:346–58. Springer Nature, 2021. https://doi.org/10.1007/978-3-030-67899-9_28.","ista":"Bloch-Hansen A, Samei N, Solis-Oba R. 2021. Experimental evaluation of a local search approximation algorithm for the multiway cut problem. Conference on Algorithms and Discrete Applied Mathematics. CALDAM: Conference on Algorithms and Discrete Applied Mathematics, LNCS, vol. 12601, 346–358."},"date_updated":"2023-10-10T09:29:08Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"first_name":"Andrew","full_name":"Bloch-Hansen, Andrew","last_name":"Bloch-Hansen"},{"full_name":"Samei, Nasim","last_name":"Samei","id":"C1531CAE-36E9-11EA-845F-33AA3DDC885E","first_name":"Nasim"},{"last_name":"Solis-Oba","full_name":"Solis-Oba, Roberto","first_name":"Roberto"}],"title":"Experimental evaluation of a local search approximation algorithm for the multiway cut problem","department":[{"_id":"VlKo"}],"_id":"9227","conference":{"location":"Rupnagar, India","end_date":"2021-02-13","start_date":"2021-02-11","name":"CALDAM: Conference on Algorithms and Discrete Applied Mathematics"},"type":"conference","status":"public"},{"_id":"8817","article_type":"original","type":"journal_article","status":"public","date_updated":"2023-10-10T09:30:23Z","department":[{"_id":"VlKo"}],"abstract":[{"text":"The paper introduces an inertial extragradient subgradient method with self-adaptive step sizes for solving equilibrium problems in real Hilbert spaces. Weak convergence of the proposed method is obtained under the condition that the bifunction is pseudomonotone and Lipchitz continuous. Linear convergence is also given when the bifunction is strongly pseudomonotone and Lipchitz continuous. Numerical implementations and comparisons with other related inertial methods are given using test problems including a real-world application to Nash–Cournot oligopolistic electricity market equilibrium model.","lang":"eng"}],"oa_version":"None","scopus_import":"1","intvolume":" 93","month":"04","publication_status":"published","publication_identifier":{"eissn":["1432-5217"],"issn":["1432-2994"]},"language":[{"iso":"eng"}],"ec_funded":1,"volume":93,"issue":"2","project":[{"_id":"25FBA906-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice","grant_number":"616160"}],"citation":{"chicago":"Shehu, Yekini, Olaniyi S. Iyiola, Duong Viet Thong, and Nguyen Thi Cam Van. “An Inertial Subgradient Extragradient Algorithm Extended to Pseudomonotone Equilibrium Problems.” Mathematical Methods of Operations Research. Springer Nature, 2021. https://doi.org/10.1007/s00186-020-00730-w.","ista":"Shehu Y, Iyiola OS, Thong DV, Van NTC. 2021. An inertial subgradient extragradient algorithm extended to pseudomonotone equilibrium problems. Mathematical Methods of Operations Research. 93(2), 213–242.","mla":"Shehu, Yekini, et al. “An Inertial Subgradient Extragradient Algorithm Extended to Pseudomonotone Equilibrium Problems.” Mathematical Methods of Operations Research, vol. 93, no. 2, Springer Nature, 2021, pp. 213–42, doi:10.1007/s00186-020-00730-w.","apa":"Shehu, Y., Iyiola, O. S., Thong, D. V., & Van, N. T. C. (2021). An inertial subgradient extragradient algorithm extended to pseudomonotone equilibrium problems. Mathematical Methods of Operations Research. Springer Nature. https://doi.org/10.1007/s00186-020-00730-w","ama":"Shehu Y, Iyiola OS, Thong DV, Van NTC. An inertial subgradient extragradient algorithm extended to pseudomonotone equilibrium problems. Mathematical Methods of Operations Research. 2021;93(2):213-242. doi:10.1007/s00186-020-00730-w","ieee":"Y. Shehu, O. S. Iyiola, D. V. Thong, and N. T. C. Van, “An inertial subgradient extragradient algorithm extended to pseudomonotone equilibrium problems,” Mathematical Methods of Operations Research, vol. 93, no. 2. Springer Nature, pp. 213–242, 2021.","short":"Y. Shehu, O.S. Iyiola, D.V. Thong, N.T.C. Van, Mathematical Methods of Operations Research 93 (2021) 213–242."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","external_id":{"isi":["000590497300001"]},"author":[{"last_name":"Shehu","full_name":"Shehu, Yekini","orcid":"0000-0001-9224-7139","id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87","first_name":"Yekini"},{"first_name":"Olaniyi S.","last_name":"Iyiola","full_name":"Iyiola, Olaniyi S."},{"full_name":"Thong, Duong Viet","last_name":"Thong","first_name":"Duong Viet"},{"full_name":"Van, Nguyen Thi Cam","last_name":"Van","first_name":"Nguyen Thi Cam"}],"title":"An inertial subgradient extragradient algorithm extended to pseudomonotone equilibrium problems","acknowledgement":"The authors are grateful to the two referees and the Associate Editor for their comments and suggestions which have improved the earlier version of the paper greatly. The project of Yekini Shehu has received funding from the European Research Council (ERC) under the European Union’s Seventh Framework Program (FP7 - 2007-2013) (Grant agreement No. 616160).","publisher":"Springer Nature","quality_controlled":"1","year":"2021","isi":1,"publication":"Mathematical Methods of Operations Research","day":"01","page":"213-242","date_created":"2020-11-29T23:01:18Z","date_published":"2021-04-01T00:00:00Z","doi":"10.1007/s00186-020-00730-w"},{"volume":76,"issue":"2","publication_status":"published","publication_identifier":{"issn":["1422-6383"],"eissn":["1420-9012"]},"language":[{"iso":"eng"}],"scopus_import":"1","intvolume":" 76","month":"03","abstract":[{"lang":"eng","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."}],"oa_version":"None","department":[{"_id":"VlKo"}],"date_updated":"2023-10-10T09:47:33Z","article_type":"original","type":"journal_article","status":"public","_id":"9315","date_created":"2021-04-11T22:01:14Z","date_published":"2021-03-25T00:00:00Z","doi":"10.1007/s00025-021-01381-x","year":"2021","isi":1,"publication":"Results in Mathematics","day":"25","publisher":"Springer Nature","quality_controlled":"1","acknowledgement":"The research of this author is supported by the Postdoctoral Fellowship from Institute of Science and Technology (IST), Austria.","article_processing_charge":"No","external_id":{"isi":["000632917700001"]},"author":[{"full_name":"Iyiola, Olaniyi S.","last_name":"Iyiola","first_name":"Olaniyi S."},{"full_name":"Shehu, Yekini","orcid":"0000-0001-9224-7139","last_name":"Shehu","id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87","first_name":"Yekini"}],"title":"New convergence results for inertial Krasnoselskii–Mann iterations in Hilbert spaces with applications","citation":{"ieee":"O. S. Iyiola and Y. Shehu, “New convergence results for inertial Krasnoselskii–Mann iterations in Hilbert spaces with applications,” Results in Mathematics, vol. 76, no. 2. Springer Nature, 2021.","short":"O.S. Iyiola, Y. Shehu, Results in Mathematics 76 (2021).","apa":"Iyiola, O. S., & Shehu, Y. (2021). New convergence results for inertial Krasnoselskii–Mann iterations in Hilbert spaces with applications. Results in Mathematics. Springer Nature. https://doi.org/10.1007/s00025-021-01381-x","ama":"Iyiola OS, Shehu Y. New convergence results for inertial Krasnoselskii–Mann iterations in Hilbert spaces with applications. Results in Mathematics. 2021;76(2). doi:10.1007/s00025-021-01381-x","mla":"Iyiola, Olaniyi S., and Yekini Shehu. “New Convergence Results for Inertial Krasnoselskii–Mann Iterations in Hilbert Spaces with Applications.” Results in Mathematics, vol. 76, no. 2, 75, Springer Nature, 2021, doi:10.1007/s00025-021-01381-x.","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.","chicago":"Iyiola, Olaniyi S., and Yekini Shehu. “New Convergence Results for Inertial Krasnoselskii–Mann Iterations in Hilbert Spaces with Applications.” Results in Mathematics. Springer Nature, 2021. https://doi.org/10.1007/s00025-021-01381-x."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"75"},{"_id":"9365","status":"public","type":"journal_article","article_type":"original","date_updated":"2023-10-10T09:48:41Z","department":[{"_id":"VlKo"}],"oa_version":"None","abstract":[{"lang":"eng","text":"In this paper, we propose a new iterative method with alternated inertial step for solving split common null point problem in real Hilbert spaces. We obtain weak convergence of the proposed iterative algorithm. Furthermore, we introduce the notion of bounded linear regularity property for the split common null point problem and obtain the linear convergence property for the new algorithm under some mild assumptions. Finally, we provide some numerical examples to demonstrate the performance and efficiency of the proposed method."}],"month":"04","scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1029-4945"],"issn":["0233-1934"]},"ec_funded":1,"project":[{"_id":"25FBA906-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"616160","name":"Discrete Optimization in Computer Vision: Theory and Practice"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Ogbuisi, Ferdinard U., et al. “Convergence Analysis of New Inertial Method for the Split Common Null Point Problem.” Optimization, Taylor and Francis, 2021, doi:10.1080/02331934.2021.1914035.","short":"F.U. Ogbuisi, Y. Shehu, J.C. Yao, Optimization (2021).","ieee":"F. U. Ogbuisi, Y. Shehu, and J. C. Yao, “Convergence analysis of new inertial method for the split common null point problem,” Optimization. Taylor and Francis, 2021.","apa":"Ogbuisi, F. U., Shehu, Y., & Yao, J. C. (2021). Convergence analysis of new inertial method for the split common null point problem. Optimization. Taylor and Francis. https://doi.org/10.1080/02331934.2021.1914035","ama":"Ogbuisi FU, Shehu Y, Yao JC. Convergence analysis of new inertial method for the split common null point problem. Optimization. 2021. doi:10.1080/02331934.2021.1914035","chicago":"Ogbuisi, Ferdinard U., Yekini Shehu, and Jen Chih Yao. “Convergence Analysis of New Inertial Method for the Split Common Null Point Problem.” Optimization. Taylor and Francis, 2021. https://doi.org/10.1080/02331934.2021.1914035.","ista":"Ogbuisi FU, Shehu Y, Yao JC. 2021. Convergence analysis of new inertial method for the split common null point problem. Optimization."},"title":"Convergence analysis of new inertial method for the split common null point problem","external_id":{"isi":["000640109300001"]},"article_processing_charge":"No","author":[{"full_name":"Ogbuisi, Ferdinard U.","last_name":"Ogbuisi","first_name":"Ferdinard U."},{"last_name":"Shehu","orcid":"0000-0001-9224-7139","full_name":"Shehu, Yekini","id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87","first_name":"Yekini"},{"first_name":"Jen Chih","last_name":"Yao","full_name":"Yao, Jen Chih"}],"acknowledgement":"The second author has received funding from the European Research Council (ERC) under the European Union's Seventh Framework Program (FP7-2007-2013) (Grant agreement No. 616160).","quality_controlled":"1","publisher":"Taylor and Francis","publication":"Optimization","day":"14","year":"2021","isi":1,"date_created":"2021-05-02T22:01:29Z","doi":"10.1080/02331934.2021.1914035","date_published":"2021-04-14T00:00:00Z"},{"project":[{"call_identifier":"H2020","_id":"05943252-7A3F-11EA-A408-12923DDC885E","grant_number":"851288","name":"Design Principles of Branching Morphogenesis"},{"grant_number":"P31639","name":"Active mechano-chemical description of the cell cytoskeleton","_id":"268294B6-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"title":"Cell monolayers sense curvature by exploiting active mechanics and nuclear mechanoadaptation","article_processing_charge":"No","external_id":{"isi":["000720204300004"]},"author":[{"full_name":"Luciano, Marine","last_name":"Luciano","first_name":"Marine"},{"first_name":"Shi-lei","id":"31D2C804-F248-11E8-B48F-1D18A9856A87","full_name":"Xue, Shi-lei","last_name":"Xue"},{"last_name":"De Vos","full_name":"De Vos, Winnok H.","first_name":"Winnok H."},{"full_name":"Redondo-Morata, Lorena","last_name":"Redondo-Morata","first_name":"Lorena"},{"last_name":"Surin","full_name":"Surin, Mathieu","first_name":"Mathieu"},{"first_name":"Frank","last_name":"Lafont","full_name":"Lafont, Frank"},{"first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561"},{"first_name":"Sylvain","last_name":"Gabriele","full_name":"Gabriele, Sylvain"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Luciano M, Xue S, De Vos WH, Redondo-Morata L, Surin M, Lafont F, Hannezo EB, Gabriele S. 2021. Cell monolayers sense curvature by exploiting active mechanics and nuclear mechanoadaptation. Nature Physics. 17(12), 1382–1390.","chicago":"Luciano, Marine, Shi-lei Xue, Winnok H. De Vos, Lorena Redondo-Morata, Mathieu Surin, Frank Lafont, Edouard B Hannezo, and Sylvain Gabriele. “Cell Monolayers Sense Curvature by Exploiting Active Mechanics and Nuclear Mechanoadaptation.” Nature Physics. Springer Nature, 2021. https://doi.org/10.1038/s41567-021-01374-1.","ama":"Luciano M, Xue S, De Vos WH, et al. Cell monolayers sense curvature by exploiting active mechanics and nuclear mechanoadaptation. Nature Physics. 2021;17(12):1382–1390. doi:10.1038/s41567-021-01374-1","apa":"Luciano, M., Xue, S., De Vos, W. H., Redondo-Morata, L., Surin, M., Lafont, F., … Gabriele, S. (2021). Cell monolayers sense curvature by exploiting active mechanics and nuclear mechanoadaptation. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-021-01374-1","ieee":"M. Luciano et al., “Cell monolayers sense curvature by exploiting active mechanics and nuclear mechanoadaptation,” Nature Physics, vol. 17, no. 12. Springer Nature, pp. 1382–1390, 2021.","short":"M. Luciano, S. Xue, W.H. De Vos, L. Redondo-Morata, M. Surin, F. Lafont, E.B. Hannezo, S. Gabriele, Nature Physics 17 (2021) 1382–1390.","mla":"Luciano, Marine, et al. “Cell Monolayers Sense Curvature by Exploiting Active Mechanics and Nuclear Mechanoadaptation.” Nature Physics, vol. 17, no. 12, Springer Nature, 2021, pp. 1382–1390, doi:10.1038/s41567-021-01374-1."},"oa":1,"quality_controlled":"1","publisher":"Springer Nature","acknowledgement":"S.G. acknowledges funding from FEDER Prostem Research Project no. 1510614 (Wallonia DG06), F.R.S.-FNRS Epiforce Research Project no. T.0092.21 and Interreg MAT(T)ISSE project, which is financially supported by Interreg France-Wallonie-Vlaanderen (Fonds Européen de Développement Régional, FEDER-ERDF). This project was supported by the European Research Council under the European Union’s Horizon 2020 Research and Innovation Programme grant agreement 851288 (to E.H.), and by the Austrian Science Fund (FWF) (P 31639; to E.H.). L.R.M. acknowledges funding from the Agence National de la Recherche (ANR), as part of the ‘Investments d’Avenir’ Programme (I-SITE ULNE/ANR-16-IDEX-0004 ULNE). This work benefited from ANR-10-EQPX-04-01 and FEDER 12001407 grants to F.L. W.D.V. is supported by the Research Foundation Flanders (FWO 1516619N, FWO GOO5819N, FWO I003420N, FWO IRI I000321N) and is member of the Research Excellence Consortium µNEURO at the University of Antwerp. M.L. is financially supported by FRIA (F.R.S.-FNRS). M.S. is a Senior Research Associate of the Fund for Scientific Research (F.R.S.-FNRS) and acknowledges EOS grant no. 30650939 (PRECISION). Sketches in Figs. 1a and 5e and Extended Data Fig. 9 were drawn by C. Levicek.","date_created":"2021-11-28T23:01:29Z","date_published":"2021-11-18T00:00:00Z","doi":"10.1038/s41567-021-01374-1","page":"1382–1390","publication":"Nature Physics","day":"18","year":"2021","has_accepted_license":"1","isi":1,"status":"public","article_type":"original","type":"journal_article","_id":"10365","department":[{"_id":"EdHa"}],"file_date_updated":"2023-10-11T09:31:43Z","ddc":["530"],"date_updated":"2023-10-16T06:31:54Z","intvolume":" 17","month":"11","scopus_import":"1","oa_version":"Submitted Version","abstract":[{"text":"The early development of many organisms involves the folding of cell monolayers, but this behaviour is difficult to reproduce in vitro; therefore, both mechanistic causes and effects of local curvature remain unclear. Here we study epithelial cell monolayers on corrugated hydrogels engineered into wavy patterns, examining how concave and convex curvatures affect cellular and nuclear shape. We find that substrate curvature affects monolayer thickness, which is larger in valleys than crests. We show that this feature generically arises in a vertex model, leading to the hypothesis that cells may sense curvature by modifying the thickness of the tissue. We find that local curvature also affects nuclear morphology and positioning, which we explain by extending the vertex model to take into account membrane–nucleus interactions, encoding thickness modulation in changes to nuclear deformation and position. We propose that curvature governs the spatial distribution of yes-associated proteins via nuclear shape and density changes. We show that curvature also induces significant variations in lamins, chromatin condensation and cell proliferation rate in folded epithelial tissues. Together, this work identifies active cell mechanics and nuclear mechanoadaptation as the key players of the mechanistic regulation of epithelia to substrate curvature.","lang":"eng"}],"ec_funded":1,"related_material":{"link":[{"url":"https://ist.ac.at/en/news/how-cells-feel-curvature/","relation":"press_release","description":"News on IST Webpage"}]},"issue":"12","volume":17,"language":[{"iso":"eng"}],"file":[{"date_created":"2023-10-11T09:31:43Z","file_name":"50145_4_merged_1630498627.pdf","creator":"channezo","date_updated":"2023-10-11T09:31:43Z","file_size":40285498,"file_id":"14420","checksum":"5d6d76750a71d7cb632bb15417c38ef7","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]}},{"author":[{"full_name":"Klionsky, Daniel J.","last_name":"Klionsky","first_name":"Daniel J."},{"first_name":"Amal Kamal","last_name":"Abdel-Aziz","full_name":"Abdel-Aziz, Amal Kamal"},{"full_name":"Abdelfatah, Sara","last_name":"Abdelfatah","first_name":"Sara"},{"last_name":"Abdellatif","full_name":"Abdellatif, Mahmoud","first_name":"Mahmoud"},{"full_name":"Abdoli, Asghar","last_name":"Abdoli","first_name":"Asghar"},{"first_name":"Steffen","last_name":"Abel","full_name":"Abel, Steffen"},{"last_name":"Abeliovich","full_name":"Abeliovich, Hagai","first_name":"Hagai"},{"last_name":"Abildgaard","full_name":"Abildgaard, Marie H.","first_name":"Marie H."},{"last_name":"Abudu","full_name":"Abudu, Yakubu Princely","first_name":"Yakubu Princely"},{"first_name":"Abraham","full_name":"Acevedo-Arozena, Abraham","last_name":"Acevedo-Arozena"},{"first_name":"Iannis E.","full_name":"Adamopoulos, Iannis E.","last_name":"Adamopoulos"},{"first_name":"Khosrow","last_name":"Adeli","full_name":"Adeli, Khosrow"},{"first_name":"Timon E.","full_name":"Adolph, Timon E.","last_name":"Adolph"},{"first_name":"Annagrazia","last_name":"Adornetto","full_name":"Adornetto, Annagrazia"},{"first_name":"Elma","last_name":"Aflaki","full_name":"Aflaki, Elma"},{"first_name":"Galila","last_name":"Agam","full_name":"Agam, Galila"},{"full_name":"Agarwal, Anupam","last_name":"Agarwal","first_name":"Anupam"},{"first_name":"Bharat B.","full_name":"Aggarwal, Bharat B.","last_name":"Aggarwal"},{"last_name":"Agnello","full_name":"Agnello, Maria","first_name":"Maria"},{"first_name":"Patrizia","last_name":"Agostinis","full_name":"Agostinis, Patrizia"},{"full_name":"Agrewala, Javed N.","last_name":"Agrewala","first_name":"Javed N."},{"first_name":"Alexander","full_name":"Agrotis, Alexander","last_name":"Agrotis"},{"last_name":"Aguilar","full_name":"Aguilar, Patricia V.","first_name":"Patricia V."},{"full_name":"Ahmad, S. Tariq","last_name":"Ahmad","first_name":"S. Tariq"},{"first_name":"Zubair M.","last_name":"Ahmed","full_name":"Ahmed, Zubair M."},{"first_name":"Ulises","last_name":"Ahumada-Castro","full_name":"Ahumada-Castro, Ulises"},{"last_name":"Aits","full_name":"Aits, Sonja","first_name":"Sonja"},{"first_name":"Shu","full_name":"Aizawa, Shu","last_name":"Aizawa"},{"first_name":"Yunus","full_name":"Akkoc, Yunus","last_name":"Akkoc"},{"last_name":"Akoumianaki","full_name":"Akoumianaki, Tonia","first_name":"Tonia"},{"full_name":"Akpinar, Hafize Aysin","last_name":"Akpinar","first_name":"Hafize Aysin"},{"first_name":"Ahmed M.","full_name":"Al-Abd, Ahmed M.","last_name":"Al-Abd"},{"first_name":"Lina","full_name":"Al-Akra, Lina","last_name":"Al-Akra"},{"full_name":"Al-Gharaibeh, Abeer","last_name":"Al-Gharaibeh","first_name":"Abeer"},{"full_name":"Alaoui-Jamali, Moulay A.","last_name":"Alaoui-Jamali","first_name":"Moulay A."},{"full_name":"Alberti, Simon","last_name":"Alberti","first_name":"Simon"},{"last_name":"Alcocer-Gómez","full_name":"Alcocer-Gómez, Elísabet","first_name":"Elísabet"},{"last_name":"Alessandri","full_name":"Alessandri, Cristiano","first_name":"Cristiano"},{"first_name":"Muhammad","last_name":"Ali","full_name":"Ali, Muhammad"},{"first_name":"M. 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Reipert, R.S. Rekha, H. Ren, J. Ren, W. Ren, T. Renault, G. Renga, K. Reue, K. Rewitz, B. Ribeiro De Andrade Ramos, S.A. Riazuddin, T.M. Ribeiro-Rodrigues, J.E. Ricci, R. Ricci, V. Riccio, D.R. Richardson, Y. Rikihisa, M.V. Risbud, R.M. Risueño, K. Ritis, S. Rizza, R. Rizzuto, H.C. Roberts, L.D. Roberts, K.J. Robinson, M.C. Roccheri, S. Rocchi, G.G. Rodney, T. Rodrigues, V.R. Rodrigues Silva, A. Rodriguez, R. Rodriguez-Barrueco, N. Rodriguez-Henche, H. Rodriguez-Rocha, J. Roelofs, R.S. Rogers, V.V. Rogov, A.I. Rojo, K. Rolka, V. Romanello, L. Romani, A. Romano, P.S. Romano, D. Romeo-Guitart, L.C. Romero, M. Romero, J.C. Roney, C. Rongo, S. Roperto, M.T. Rosenfeldt, P. Rosenstiel, A.G. Rosenwald, K.A. Roth, L. Roth, S. Roth, K.M.A. Rouschop, B.D. Roussel, S. Roux, P. Rovere-Querini, A. Roy, A. Rozieres, D. Ruano, D.C. Rubinsztein, M.P. Rubtsova, K. Ruckdeschel, C. Ruckenstuhl, E. Rudolf, R. Rudolf, A. Ruggieri, A.A. Ruparelia, P. Rusmini, R.R. Russell, G.L. Russo, M. Russo, R. 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Yung, D.N. Zacks, G. Zaffagnini, V.O. Zambelli, I. Zanella, Q.S. Zang, S. Zanivan, S. Zappavigna, P. Zaragoza, K.S. Zarbalis, A. Zarebkohan, A. Zarrouk, S.O. Zeitlin, J. Zeng, J.D. Zeng, E. Žerovnik, L. Zhan, B. Zhang, D.D. Zhang, H. Zhang, H. Zhang, H. Zhang, H. Zhang, H. Zhang, H. Zhang, H. Zhang, H.L. Zhang, J. Zhang, J. Zhang, J.P. Zhang, K.Y.B. Zhang, L.W. Zhang, L. Zhang, L. Zhang, L. Zhang, L. Zhang, M. Zhang, P. Zhang, S. Zhang, W. Zhang, X. Zhang, X.W. Zhang, X. Zhang, X. Zhang, X. Zhang, X. Zhang, X.D. Zhang, Y. Zhang, Y. Zhang, Y. Zhang, Y.D. Zhang, Y. Zhang, Y.Y. Zhang, Y. Zhang, Z. Zhang, Z. Zhang, Z. Zhang, Z. Zhang, Z. Zhang, Z. Zhang, H. Zhao, L. Zhao, S. Zhao, T. Zhao, X.F. Zhao, Y. Zhao, Y. Zhao, Y. Zhao, Y. Zhao, G. Zheng, K. Zheng, L. Zheng, S. Zheng, X.L. Zheng, Y. Zheng, Z.G. Zheng, B. Zhivotovsky, Q. Zhong, A. Zhou, B. Zhou, C. Zhou, G. Zhou, H. Zhou, H. Zhou, H. Zhou, J. Zhou, J. Zhou, J. Zhou, J. Zhou, K. Zhou, R. Zhou, X.J. Zhou, Y. Zhou, Y. Zhou, Y. Zhou, Z.Y. Zhou, Z. Zhou, B. Zhu, C. Zhu, G.Q. Zhu, H. Zhu, H. Zhu, H. Zhu, W.G. Zhu, Y. Zhu, Y. Zhu, H. Zhuang, X. Zhuang, K. Zientara-Rytter, C.M. Zimmermann, E. Ziviani, T. Zoladek, W.X. Zong, D.B. Zorov, A. Zorzano, W. Zou, Z. Zou, Z. Zou, S. Zuryn, W. Zwerschke, B. Brand-Saberi, X.C. Dong, C.S. Kenchappa, Z. Li, Y. Lin, S. Oshima, Y. Rong, J.C. Sluimer, C.L. Stallings, C.K. Tong, Autophagy 17 (2021) 1–382.","apa":"Klionsky, D. J., Abdel-Aziz, A. K., Abdelfatah, S., Abdellatif, M., Abdoli, A., Abel, S., … Tong, C. K. (2021). Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition). Autophagy. Taylor & Francis. https://doi.org/10.1080/15548627.2020.1797280","ama":"Klionsky DJ, Abdel-Aziz AK, Abdelfatah S, et al. Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition). Autophagy. 2021;17(1):1-382. doi:10.1080/15548627.2020.1797280","chicago":"Klionsky, Daniel J., Amal Kamal Abdel-Aziz, Sara Abdelfatah, Mahmoud Abdellatif, Asghar Abdoli, Steffen Abel, Hagai Abeliovich, et al. “Guidelines for the Use and Interpretation of Assays for Monitoring Autophagy (4th Edition).” Autophagy. Taylor & Francis, 2021. https://doi.org/10.1080/15548627.2020.1797280.","ista":"Klionsky DJ et al. 2021. Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition). Autophagy. 17(1), 1–382."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"1-382","doi":"10.1080/15548627.2020.1797280","date_published":"2021-02-08T00:00:00Z","date_created":"2021-03-28T22:01:44Z","isi":1,"year":"2021","day":"08","publication":"Autophagy","publisher":"Taylor & Francis","quality_controlled":"1","oa":1,"acknowledgement":"This work was supported by the National Institute of General Medical Sciences [GM131919]. Due to space and other limitations, it is not possible to include all other sources of financial support.","department":[{"_id":"JiFr"},{"_id":"CaHe"}],"date_updated":"2023-10-16T09:43:56Z","article_type":"review","type":"journal_article","status":"public","_id":"9298","volume":17,"issue":"1","publication_identifier":{"issn":["1554-8627"],"eissn":["1554-8635"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1080/15548627.2020.1797280","open_access":"1"}],"month":"02","intvolume":" 17","abstract":[{"text":"In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field. ","lang":"eng"}],"oa_version":"Published Version","pmid":1},{"status":"public","article_type":"original","type":"journal_article","_id":"8742","department":[{"_id":"TiBr"}],"date_updated":"2023-10-17T07:39:01Z","month":"01","intvolume":" 33","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/2003.09593","open_access":"1"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We develop a version of Ekedahl’s geometric sieve for integral quadratic forms of rank at least five. As one ranges over the zeros of such quadratic forms, we use the sieve to compute the density of coprime values of polynomials, and furthermore, to address a question about local solubility in families of varieties parameterised by the zeros."}],"volume":33,"issue":"1","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0933-7741"],"eissn":["1435-5337"]},"publication_status":"published","project":[{"_id":"26AEDAB2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P32428","name":"New frontiers of the Manin conjecture"}],"title":"The geometric sieve for quadrics","author":[{"first_name":"Timothy D","id":"35827D50-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8314-0177","full_name":"Browning, Timothy D","last_name":"Browning"},{"full_name":"Heath-Brown, Roger","last_name":"Heath-Brown","first_name":"Roger"}],"article_processing_charge":"No","external_id":{"isi":["000604750900008"],"arxiv":["2003.09593"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Browning TD, Heath-Brown R. 2021. The geometric sieve for quadrics. Forum Mathematicum. 33(1), 147–165.","chicago":"Browning, Timothy D, and Roger Heath-Brown. “The Geometric Sieve for Quadrics.” Forum Mathematicum. De Gruyter, 2021. https://doi.org/10.1515/forum-2020-0074.","short":"T.D. Browning, R. Heath-Brown, Forum Mathematicum 33 (2021) 147–165.","ieee":"T. D. Browning and R. Heath-Brown, “The geometric sieve for quadrics,” Forum Mathematicum, vol. 33, no. 1. De Gruyter, pp. 147–165, 2021.","ama":"Browning TD, Heath-Brown R. The geometric sieve for quadrics. Forum Mathematicum. 2021;33(1):147-165. doi:10.1515/forum-2020-0074","apa":"Browning, T. D., & Heath-Brown, R. (2021). The geometric sieve for quadrics. Forum Mathematicum. De Gruyter. https://doi.org/10.1515/forum-2020-0074","mla":"Browning, Timothy D., and Roger Heath-Brown. “The Geometric Sieve for Quadrics.” Forum Mathematicum, vol. 33, no. 1, De Gruyter, 2021, pp. 147–65, doi:10.1515/forum-2020-0074."},"quality_controlled":"1","publisher":"De Gruyter","oa":1,"doi":"10.1515/forum-2020-0074","date_published":"2021-01-01T00:00:00Z","date_created":"2020-11-08T23:01:25Z","page":"147-165","day":"01","publication":"Forum Mathematicum","isi":1,"year":"2021"},{"day":"23","year":"2021","has_accepted_license":"1","date_created":"2021-09-23T07:31:44Z","date_published":"2021-09-23T00:00:00Z","doi":"10.15479/at:ista:10035","page":"276","acknowledgement":"I want to acknowledge the funding by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (682815 - TOCNeT).\r\n","oa":1,"publisher":"Institute of Science and Technology Austria","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"short":"K. Klein, On the Adaptive Security of Graph-Based Games, Institute of Science and Technology Austria, 2021.","ieee":"K. Klein, “On the adaptive security of graph-based games,” Institute of Science and Technology Austria, 2021.","ama":"Klein K. On the adaptive security of graph-based games. 2021. doi:10.15479/at:ista:10035","apa":"Klein, K. (2021). On the adaptive security of graph-based games. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10035","mla":"Klein, Karen. On the Adaptive Security of Graph-Based Games. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10035.","ista":"Klein K. 2021. On the adaptive security of graph-based games. Institute of Science and Technology Austria.","chicago":"Klein, Karen. “On the Adaptive Security of Graph-Based Games.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10035."},"title":"On the adaptive security of graph-based games","article_processing_charge":"No","author":[{"last_name":"Klein","full_name":"Klein, Karen","first_name":"Karen","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87"}],"project":[{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Teaching Old Crypto New Tricks","grant_number":"682815"}],"language":[{"iso":"eng"}],"file":[{"creator":"cchlebak","file_size":2104726,"date_updated":"2021-10-04T12:22:33Z","file_name":"thesis_pdfa.pdf","date_created":"2021-10-04T12:22:33Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"10082","checksum":"73a44345c683e81f3e765efbf86fdcc5"},{"checksum":"7b80df30a0e686c3ef6a56d4e1c59e29","file_id":"10085","content_type":"application/x-zip-compressed","relation":"source_file","access_level":"closed","file_name":"thesis_final (1).zip","date_created":"2021-10-05T07:04:37Z","file_size":9538359,"date_updated":"2022-03-10T12:15:18Z","creator":"cchlebak"}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"ec_funded":1,"related_material":{"record":[{"status":"public","id":"10044","relation":"part_of_dissertation"},{"id":"10049","status":"public","relation":"part_of_dissertation"},{"id":"637","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"10041","relation":"part_of_dissertation"},{"status":"public","id":"6430","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"10048"}]},"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Many security definitions come in two flavors: a stronger “adaptive” flavor, where the adversary can arbitrarily make various choices during the course of the attack, and a weaker “selective” flavor where the adversary must commit to some or all of their choices a-priori. For example, in the context of identity-based encryption, selective security requires the adversary to decide on the identity of the attacked party at the very beginning of the game whereas adaptive security allows the attacker to first see the master public key and some secret keys before making this choice. Often, it appears to be much easier to achieve selective security than it is to achieve adaptive security. A series of several recent works shows how to cleverly achieve adaptive security in several such scenarios including generalized selective decryption [Pan07][FJP15], constrained PRFs [FKPR14], and Yao’s garbled circuits [JW16]. Although the above works expressed vague intuition that they share a common technique, the connection was never made precise. In this work we present a new framework (published at Crypto ’17 [JKK+17a]) that connects all of these works and allows us to present them in a unified and simplified fashion. Having the framework in place, we show how to achieve adaptive security for proxy re-encryption schemes (published at PKC ’19 [FKKP19]) and provide the first adaptive security proofs for continuous group key agreement protocols (published at S&P ’21 [KPW+21]). Questioning optimality of our framework, we then show that currently used proof techniques cannot lead to significantly better security guarantees for \"graph-building\" games (published at TCC ’21 [KKPW21a]). These games cover generalized selective decryption, as well as the security of prominent constructions for constrained PRFs, continuous group key agreement, and proxy re-encryption. Finally, we revisit the adaptive security of Yao’s garbled circuits and extend the analysis of Jafargholi and Wichs in two directions: While they prove adaptive security only for a modified construction with increased online complexity, we provide the first positive results for the original construction by Yao (published at TCC ’21 [KKP21a]). On the negative side, we prove that the results of Jafargholi and Wichs are essentially optimal by showing that no black-box reduction can provide a significantly better security bound (published at Crypto ’21 [KKPW21c])."}],"month":"09","alternative_title":["ISTA Thesis"],"ddc":["519"],"date_updated":"2023-10-17T09:24:07Z","supervisor":[{"orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z"}],"department":[{"_id":"GradSch"},{"_id":"KrPi"}],"file_date_updated":"2022-03-10T12:15:18Z","_id":"10035","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"dissertation"},{"oa_version":"Preprint","abstract":[{"lang":"eng","text":"The security of cryptographic primitives and protocols against adversaries that are allowed to make adaptive choices (e.g., which parties to corrupt or which queries to make) is notoriously difficult to establish. A broad theoretical framework was introduced by Jafargholi et al. [Crypto’17] for this purpose. In this paper we initiate the study of lower bounds on loss in adaptive security for certain cryptographic protocols considered in the framework. We prove lower bounds that almost match the upper bounds (proven using the framework) for proxy re-encryption, prefix-constrained PRFs and generalized selective decryption, a security game that captures the security of certain group messaging and broadcast encryption schemes. Those primitives have in common that their security game involves an underlying graph that can be adaptively built by the adversary. Some of our lower bounds only apply to a restricted class of black-box reductions which we term “oblivious” (the existing upper bounds are of this restricted type), some apply to the broader but still restricted class of non-rewinding reductions, while our lower bound for proxy re-encryption applies to all black-box reductions. The fact that some of our lower bounds seem to crucially rely on obliviousness or at least a non-rewinding reduction hints to the exciting possibility that the existing upper bounds can be improved by using more sophisticated reductions. Our main conceptual contribution is a two-player multi-stage game called the Builder-Pebbler Game. We can translate bounds on the winning probabilities for various instantiations of this game into cryptographic lower bounds for the above-mentioned primitives using oracle separation techniques."}],"month":"11","intvolume":" 13043","alternative_title":["LNCS"],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://ia.cr/2021/059"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9-783-0309-0452-4"],"eissn":["1611-3349"],"issn":["0302-9743"]},"publication_status":"published","related_material":{"record":[{"relation":"earlier_version","id":"10048","status":"public"}]},"volume":13043,"ec_funded":1,"_id":"10410","status":"public","type":"conference","conference":{"name":"TCC: Theory of Cryptography","start_date":"2021-11-08","location":"Raleigh, NC, United States","end_date":"2021-11-11"},"date_updated":"2023-10-17T09:24:07Z","department":[{"_id":"KrPi"}],"acknowledgement":"C. Kamath—Supported by Azrieli International Postdoctoral Fellowship. Most of the work was done while the author was at Northeastern University and Charles University, funded by the IARPA grant IARPA/2019-19-020700009 and project PRIMUS/17/SCI/9, respectively. K. Klein—Supported in part by ERC CoG grant 724307. Most of the work was done while the author was at IST Austria funded by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (682815 - TOCNeT). K. Pietrzak—Funded by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (682815 - TOCNeT).","quality_controlled":"1","publisher":"Springer Nature","oa":1,"day":"04","publication":"19th International Conference","isi":1,"year":"2021","date_published":"2021-11-04T00:00:00Z","doi":"10.1007/978-3-030-90453-1_19","date_created":"2021-12-05T23:01:43Z","page":"550-581","project":[{"grant_number":"682815","name":"Teaching Old Crypto New Tricks","call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"apa":"Kamath Hosdurg, C., Klein, K., Pietrzak, K. Z., & Walter, M. (2021). The cost of adaptivity in security games on graphs. In 19th International Conference (Vol. 13043, pp. 550–581). Raleigh, NC, United States: Springer Nature. https://doi.org/10.1007/978-3-030-90453-1_19","ama":"Kamath Hosdurg C, Klein K, Pietrzak KZ, Walter M. The cost of adaptivity in security games on graphs. In: 19th International Conference. Vol 13043. Springer Nature; 2021:550-581. doi:10.1007/978-3-030-90453-1_19","short":"C. Kamath Hosdurg, K. Klein, K.Z. Pietrzak, M. Walter, in:, 19th International Conference, Springer Nature, 2021, pp. 550–581.","ieee":"C. Kamath Hosdurg, K. Klein, K. Z. Pietrzak, and M. Walter, “The cost of adaptivity in security games on graphs,” in 19th International Conference, Raleigh, NC, United States, 2021, vol. 13043, pp. 550–581.","mla":"Kamath Hosdurg, Chethan, et al. “The Cost of Adaptivity in Security Games on Graphs.” 19th International Conference, vol. 13043, Springer Nature, 2021, pp. 550–81, doi:10.1007/978-3-030-90453-1_19.","ista":"Kamath Hosdurg C, Klein K, Pietrzak KZ, Walter M. 2021. The cost of adaptivity in security games on graphs. 19th International Conference. TCC: Theory of Cryptography, LNCS, vol. 13043, 550–581.","chicago":"Kamath Hosdurg, Chethan, Karen Klein, Krzysztof Z Pietrzak, and Michael Walter. “The Cost of Adaptivity in Security Games on Graphs.” In 19th International Conference, 13043:550–81. Springer Nature, 2021. https://doi.org/10.1007/978-3-030-90453-1_19."},"title":"The cost of adaptivity in security games on graphs","author":[{"last_name":"Kamath Hosdurg","full_name":"Kamath Hosdurg, Chethan","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","first_name":"Chethan"},{"first_name":"Karen","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87","full_name":"Klein, Karen","last_name":"Klein"},{"last_name":"Pietrzak","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z","first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Walter, Michael","orcid":"0000-0003-3186-2482","last_name":"Walter","first_name":"Michael","id":"488F98B0-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["000728364000019"]},"article_processing_charge":"No"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-10-17T09:24:08Z","citation":{"ista":"Kamath Hosdurg C, Klein K, Pietrzak KZ, Walter M. 2021. The cost of adaptivity in security games on graphs. 19th Theory of Cryptography Conference 2021. TCC: Theory of Cryptography Conference.","chicago":"Kamath Hosdurg, Chethan, Karen Klein, Krzysztof Z Pietrzak, and Michael Walter. “The Cost of Adaptivity in Security Games on Graphs.” In 19th Theory of Cryptography Conference 2021. International Association for Cryptologic Research, 2021.","ama":"Kamath Hosdurg C, Klein K, Pietrzak KZ, Walter M. The cost of adaptivity in security games on graphs. In: 19th Theory of Cryptography Conference 2021. International Association for Cryptologic Research; 2021.","apa":"Kamath Hosdurg, C., Klein, K., Pietrzak, K. Z., & Walter, M. (2021). The cost of adaptivity in security games on graphs. In 19th Theory of Cryptography Conference 2021. Raleigh, NC, United States: International Association for Cryptologic Research.","short":"C. Kamath Hosdurg, K. Klein, K.Z. Pietrzak, M. Walter, in:, 19th Theory of Cryptography Conference 2021, International Association for Cryptologic Research, 2021.","ieee":"C. Kamath Hosdurg, K. Klein, K. Z. Pietrzak, and M. Walter, “The cost of adaptivity in security games on graphs,” in 19th Theory of Cryptography Conference 2021, Raleigh, NC, United States, 2021.","mla":"Kamath Hosdurg, Chethan, et al. “The Cost of Adaptivity in Security Games on Graphs.” 19th Theory of Cryptography Conference 2021, International Association for Cryptologic Research, 2021."},"title":"The cost of adaptivity in security games on graphs","department":[{"_id":"KrPi"}],"article_processing_charge":"No","author":[{"last_name":"Kamath Hosdurg","full_name":"Kamath Hosdurg, Chethan","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","first_name":"Chethan"},{"last_name":"Klein","full_name":"Klein, Karen","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87","first_name":"Karen"},{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z","full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654","last_name":"Pietrzak"},{"first_name":"Michael","id":"488F98B0-F248-11E8-B48F-1D18A9856A87","last_name":"Walter","full_name":"Walter, Michael","orcid":"0000-0003-3186-2482"}],"_id":"10048","status":"public","conference":{"name":"TCC: Theory of Cryptography Conference","location":"Raleigh, NC, United States","end_date":"2021-11-11","start_date":"2021-11-08"},"type":"conference","language":[{"iso":"eng"}],"publication":"19th Theory of Cryptography Conference 2021","day":"08","publication_status":"published","year":"2021","date_created":"2021-09-27T12:52:05Z","date_published":"2021-07-08T00:00:00Z","related_material":{"record":[{"relation":"later_version","status":"public","id":"10410"},{"id":"10035","status":"public","relation":"dissertation_contains"}]},"oa_version":"Preprint","abstract":[{"text":"The security of cryptographic primitives and protocols against adversaries that are allowed to make adaptive choices (e.g., which parties to corrupt or which queries to make) is notoriously difficult to establish. A broad theoretical\r\nframework was introduced by Jafargholi et al. [Crypto’17] for this purpose. In this paper we initiate the study of lower bounds on loss in adaptive security for certain cryptographic protocols considered in the framework. We prove lower\r\nbounds that almost match the upper bounds (proven using the framework) for proxy re-encryption, prefix-constrained PRFs and generalized selective decryption, a security game that captures the security of certain group messaging and\r\nbroadcast encryption schemes. Those primitives have in common that their security game involves an underlying graph that can be adaptively built by the adversary. Some of our lower bounds only apply to a restricted class of black-box reductions which we term “oblivious” (the existing upper bounds are of this restricted type), some apply to the broader but still restricted class of non-rewinding reductions, while our lower bound for proxy re-encryption applies to all black-box reductions. The fact that some of our lower bounds seem to crucially rely on obliviousness or at least a non-rewinding reduction hints to the exciting possibility that the existing upper bounds can be improved by using more sophisticated reductions. Our main conceptual contribution is a two-player multi-stage game called the Builder-Pebbler Game. We can translate bounds on the winning probabilities for various instantiations of this game into cryptographic lower bounds for the above-mentioned primitives using oracle separation techniques.\r\n","lang":"eng"}],"month":"07","oa":1,"main_file_link":[{"open_access":"1","url":"https://ia.cr/2021/059"}],"quality_controlled":"1","publisher":"International Association for Cryptologic Research"},{"publication_status":"published","publication_identifier":{"eissn":["1948-206X"],"issn":["2157-5045"]},"language":[{"iso":"eng"}],"ec_funded":1,"issue":"7","volume":14,"abstract":[{"text":"We prove an adiabatic theorem for the Landau–Pekar equations. This allows us to derive new results on the accuracy of their use as effective equations for the time evolution generated by the Fröhlich Hamiltonian with large coupling constant α. In particular, we show that the time evolution of Pekar product states with coherent phonon field and the electron being trapped by the phonons is well approximated by the Landau–Pekar equations until times short compared to α2.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1904.12532"}],"scopus_import":"1","intvolume":" 14","month":"11","date_updated":"2023-10-17T11:26:45Z","department":[{"_id":"RoSe"}],"_id":"10738","type":"journal_article","article_type":"original","status":"public","year":"2021","isi":1,"publication":"Analysis and PDE","day":"10","page":"2079-2100","date_created":"2022-02-06T23:01:33Z","doi":"10.2140/APDE.2021.14.2079","date_published":"2021-11-10T00:00:00Z","acknowledgement":"N. L. and R. S. gratefully acknowledge financial support by the European Research Council\r\n(ERC) under the European Union’s Horizon 2020 research and innovation programme (grant\r\nagreement No 694227). B. S. acknowledges support from the Swiss National Science Foundation (grant 200020_172623) and from the NCCR SwissMAP. N. L. would like to thank\r\nAndreas Deuchert and David Mitrouskas for interesting discussions. B. S. and R. S. would\r\nlike to thank Rupert Frank for stimulating discussions about the time-evolution of a polaron.\r\n","oa":1,"publisher":"Mathematical Sciences Publishers","quality_controlled":"1","citation":{"ista":"Leopold NK, Rademacher SAE, Schlein B, Seiringer R. 2021. The Landau–Pekar equations: Adiabatic theorem and accuracy. Analysis and PDE. 14(7), 2079–2100.","chicago":"Leopold, Nikolai K, Simone Anna Elvira Rademacher, Benjamin Schlein, and Robert Seiringer. “ The Landau–Pekar Equations: Adiabatic Theorem and Accuracy.” Analysis and PDE. Mathematical Sciences Publishers, 2021. https://doi.org/10.2140/APDE.2021.14.2079.","apa":"Leopold, N. K., Rademacher, S. A. E., Schlein, B., & Seiringer, R. (2021). The Landau–Pekar equations: Adiabatic theorem and accuracy. Analysis and PDE. Mathematical Sciences Publishers. https://doi.org/10.2140/APDE.2021.14.2079","ama":"Leopold NK, Rademacher SAE, Schlein B, Seiringer R. The Landau–Pekar equations: Adiabatic theorem and accuracy. Analysis and PDE. 2021;14(7):2079-2100. doi:10.2140/APDE.2021.14.2079","ieee":"N. K. Leopold, S. A. E. Rademacher, B. Schlein, and R. Seiringer, “ The Landau–Pekar equations: Adiabatic theorem and accuracy,” Analysis and PDE, vol. 14, no. 7. Mathematical Sciences Publishers, pp. 2079–2100, 2021.","short":"N.K. Leopold, S.A.E. Rademacher, B. Schlein, R. Seiringer, Analysis and PDE 14 (2021) 2079–2100.","mla":"Leopold, Nikolai K., et al. “ The Landau–Pekar Equations: Adiabatic Theorem and Accuracy.” Analysis and PDE, vol. 14, no. 7, Mathematical Sciences Publishers, 2021, pp. 2079–100, doi:10.2140/APDE.2021.14.2079."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","external_id":{"arxiv":["1904.12532"],"isi":["000733976600004"]},"author":[{"first_name":"Nikolai K","id":"4BC40BEC-F248-11E8-B48F-1D18A9856A87","last_name":"Leopold","full_name":"Leopold, Nikolai K","orcid":"0000-0002-0495-6822"},{"id":"856966FE-A408-11E9-977E-802DE6697425","first_name":"Simone Anna Elvira","last_name":"Rademacher","orcid":"0000-0001-5059-4466","full_name":"Rademacher, Simone Anna Elvira"},{"last_name":"Schlein","full_name":"Schlein, Benjamin","first_name":"Benjamin"},{"last_name":"Seiringer","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"}],"title":" The Landau–Pekar equations: Adiabatic theorem and accuracy","project":[{"grant_number":"694227","name":"Analysis of quantum many-body systems","call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}]},{"oa":1,"publisher":"Institute of Science and Technology Austria","page":"132","date_created":"2021-12-08T21:52:28Z","date_published":"2021-12-09T00:00:00Z","doi":"10.15479/at:ista:10429","year":"2021","has_accepted_license":"1","day":"09","project":[{"call_identifier":"H2020","_id":"268A44D6-B435-11E9-9278-68D0E5697425","name":"Elastic Coordination for Scalable Machine Learning","grant_number":"805223"}],"article_processing_charge":"No","author":[{"id":"3279A00C-F248-11E8-B48F-1D18A9856A87","first_name":"Giorgi","last_name":"Nadiradze","orcid":"0000-0001-5634-0731","full_name":"Nadiradze, Giorgi"}],"title":"On achieving scalability through relaxation","citation":{"chicago":"Nadiradze, Giorgi. “On Achieving Scalability through Relaxation.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10429.","ista":"Nadiradze G. 2021. On achieving scalability through relaxation. Institute of Science and Technology Austria.","mla":"Nadiradze, Giorgi. On Achieving Scalability through Relaxation. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10429.","ama":"Nadiradze G. On achieving scalability through relaxation. 2021. doi:10.15479/at:ista:10429","apa":"Nadiradze, G. (2021). On achieving scalability through relaxation. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10429","short":"G. Nadiradze, On Achieving Scalability through Relaxation, Institute of Science and Technology Austria, 2021.","ieee":"G. Nadiradze, “On achieving scalability through relaxation,” Institute of Science and Technology Austria, 2021."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","alternative_title":["ISTA Thesis"],"month":"12","abstract":[{"text":"The scalability of concurrent data structures and distributed algorithms strongly depends on\r\nreducing the contention for shared resources and the costs of synchronization and communication. We show how such cost reductions can be attained by relaxing the strict consistency conditions required by sequential implementations. In the first part of the thesis, we consider relaxation in the context of concurrent data structures. Specifically, in data structures \r\nsuch as priority queues, imposing strong semantics renders scalability impossible, since a correct implementation of the remove operation should return only the element with highest priority. Intuitively, attempting to invoke remove operations concurrently creates a race condition. This bottleneck can be circumvented by relaxing semantics of the affected data structure, thus allowing removal of the elements which are no longer required to have the highest priority. We prove that the randomized implementations of relaxed data structures provide provable guarantees on the priority of the removed elements even under concurrency. Additionally, we show that in some cases the relaxed data structures can be used to scale the classical algorithms which are usually implemented with the exact ones. In the second part, we study parallel variants of the stochastic gradient descent (SGD) algorithm, which distribute computation among the multiple processors, thus reducing the running time. Unfortunately, in order for standard parallel SGD to succeed, each processor has to maintain a local copy of the necessary model parameter, which is identical to the local copies of other processors; the overheads from this perfect consistency in terms of communication and synchronization can negate the speedup gained by distributing the computation. We show that the consistency conditions required by SGD can be relaxed, allowing the algorithm to be more flexible in terms of tolerating quantized communication, asynchrony, or even crash faults, while its convergence remains asymptotically the same.","lang":"eng"}],"oa_version":"Published Version","ec_funded":1,"related_material":{"record":[{"relation":"part_of_dissertation","id":"10432","status":"public"},{"status":"public","id":"6673","relation":"part_of_dissertation"},{"id":"5965","status":"public","relation":"part_of_dissertation"},{"id":"10435","status":"public","relation":"part_of_dissertation"}]},"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"6bf14e9a523387328f016c0689f5e10e","file_id":"10436","success":1,"creator":"gnadirad","date_updated":"2021-12-09T17:47:49Z","file_size":2370859,"date_created":"2021-12-09T17:47:49Z","file_name":"Thesis_Final_09_12_2021.pdf"},{"checksum":"914d6c5ca86bd0add471971a8f4c4341","file_id":"10437","content_type":"application/zip","relation":"source_file","access_level":"closed","file_name":"Thesis_Final_09_12_2021.zip","date_created":"2021-12-09T17:47:49Z","file_size":2596924,"date_updated":"2022-03-28T12:55:12Z","creator":"gnadirad"}],"type":"dissertation","status":"public","_id":"10429","file_date_updated":"2022-03-28T12:55:12Z","department":[{"_id":"GradSch"},{"_id":"DaAl"}],"date_updated":"2023-10-17T11:48:55Z","supervisor":[{"first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian"}],"ddc":["000"]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-10-17T11:48:56Z","citation":{"ista":"Nadiradze G, Sabour A, Davies P, Li S, Alistarh D-A. 2021. Asynchronous decentralized SGD with quantized and local updates. 35th Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems.","chicago":"Nadiradze, Giorgi, Amirmojtaba Sabour, Peter Davies, Shigang Li, and Dan-Adrian Alistarh. “Asynchronous Decentralized SGD with Quantized and Local Updates.” In 35th Conference on Neural Information Processing Systems. Neural Information Processing Systems Foundation, 2021.","short":"G. Nadiradze, A. Sabour, P. Davies, S. Li, D.-A. Alistarh, in:, 35th Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2021.","ieee":"G. Nadiradze, A. Sabour, P. Davies, S. Li, and D.-A. Alistarh, “Asynchronous decentralized SGD with quantized and local updates,” in 35th Conference on Neural Information Processing Systems, Sydney, Australia, 2021.","ama":"Nadiradze G, Sabour A, Davies P, Li S, Alistarh D-A. Asynchronous decentralized SGD with quantized and local updates. In: 35th Conference on Neural Information Processing Systems. Neural Information Processing Systems Foundation; 2021.","apa":"Nadiradze, G., Sabour, A., Davies, P., Li, S., & Alistarh, D.-A. (2021). Asynchronous decentralized SGD with quantized and local updates. In 35th Conference on Neural Information Processing Systems. Sydney, Australia: Neural Information Processing Systems Foundation.","mla":"Nadiradze, Giorgi, et al. “Asynchronous Decentralized SGD with Quantized and Local Updates.” 35th Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2021."},"title":"Asynchronous decentralized SGD with quantized and local updates","department":[{"_id":"DaAl"}],"external_id":{"arxiv":["1910.12308"]},"article_processing_charge":"No","author":[{"orcid":"0000-0001-5634-0731","full_name":"Nadiradze, Giorgi","last_name":"Nadiradze","id":"3279A00C-F248-11E8-B48F-1D18A9856A87","first_name":"Giorgi"},{"full_name":"Sabour, Amirmojtaba","last_name":"Sabour","id":"bcc145fd-e77f-11ea-ae8b-80d661dbff67","first_name":"Amirmojtaba"},{"id":"11396234-BB50-11E9-B24C-90FCE5697425","first_name":"Peter","orcid":"0000-0002-5646-9524","full_name":"Davies, Peter","last_name":"Davies"},{"full_name":"Li, Shigang","last_name":"Li","first_name":"Shigang"},{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian"}],"_id":"10435","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"},{"name":"Elastic Coordination for Scalable Machine Learning","grant_number":"805223","call_identifier":"H2020","_id":"268A44D6-B435-11E9-9278-68D0E5697425"}],"status":"public","conference":{"end_date":"2021-12-14","location":"Sydney, Australia","start_date":"2021-12-06","name":"NeurIPS: Neural Information Processing Systems"},"type":"conference","language":[{"iso":"eng"}],"publication":"35th Conference on Neural Information Processing Systems","day":"01","publication_status":"published","year":"2021","date_created":"2021-12-09T10:59:12Z","ec_funded":1,"date_published":"2021-12-01T00:00:00Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10429"}]},"acknowledgement":"We gratefully acknowledge funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 805223 ScaleML). PD partly conducted this work while at IST Austria and was supported by the European Union’s Horizon 2020 programme under the Marie Skłodowska-Curie grant agreement No. 754411. SL was funded in part by European Research Council (ERC) under the European Union’s Horizon 2020 programme (grant agreement DAPP, No. 678880, and EPiGRAM-HS, No. 801039).\r\n","oa_version":"Published Version","abstract":[{"text":"Decentralized optimization is emerging as a viable alternative for scalable distributed machine learning, but also introduces new challenges in terms of synchronization costs. To this end, several communication-reduction techniques, such as non-blocking communication, quantization, and local steps, have been explored in the decentralized setting. Due to the complexity of analyzing optimization in such a relaxed setting, this line of work often assumes \\emph{global} communication rounds, which require additional synchronization. In this paper, we consider decentralized optimization in the simpler, but harder to analyze, \\emph{asynchronous gossip} model, in which communication occurs in discrete, randomly chosen pairings among nodes. Perhaps surprisingly, we show that a variant of SGD called \\emph{SwarmSGD} still converges in this setting, even if \\emph{non-blocking communication}, \\emph{quantization}, and \\emph{local steps} are all applied \\emph{in conjunction}, and even if the node data distributions and underlying graph topology are both \\emph{heterogenous}. Our analysis is based on a new connection with multi-dimensional load-balancing processes. We implement this algorithm and deploy it in a super-computing environment, showing that it can outperform previous decentralized methods in terms of end-to-end training time, and that it can even rival carefully-tuned large-batch SGD for certain tasks.","lang":"eng"}],"month":"12","oa":1,"main_file_link":[{"open_access":"1","url":"https://papers.nips.cc/paper/2021/hash/362c99307cdc3f2d8b410652386a9dd1-Abstract.html"}],"publisher":"Neural Information Processing Systems Foundation","quality_controlled":"1"},{"acknowledgement":"M. Mondelli would like to thank László Erdős for helpful discussions. M. Mondelli was partially supported by the 2019 Lopez-Loreta Prize. R. Venkataramanan was partially supported by the Alan Turing Institute under the EPSRC grant EP/N510129/1.\r\n","oa":1,"quality_controlled":"1","publisher":"Neural Information Processing Systems Foundation","year":"2021","publication":"35th Conference on Neural Information Processing Systems","day":"01","page":"29616-29629","date_created":"2022-01-03T10:50:02Z","date_published":"2021-12-01T00:00:00Z","project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"citation":{"chicago":"Mondelli, Marco, and Ramji Venkataramanan. “PCA Initialization for Approximate Message Passing in Rotationally Invariant Models.” In 35th Conference on Neural Information Processing Systems, 35:29616–29. Neural Information Processing Systems Foundation, 2021.","ista":"Mondelli M, Venkataramanan R. 2021. PCA initialization for approximate message passing in rotationally invariant models. 35th Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 35, 29616–29629.","mla":"Mondelli, Marco, and Ramji Venkataramanan. “PCA Initialization for Approximate Message Passing in Rotationally Invariant Models.” 35th Conference on Neural Information Processing Systems, vol. 35, Neural Information Processing Systems Foundation, 2021, pp. 29616–29.","ieee":"M. Mondelli and R. Venkataramanan, “PCA initialization for approximate message passing in rotationally invariant models,” in 35th Conference on Neural Information Processing Systems, Virtual, 2021, vol. 35, pp. 29616–29629.","short":"M. Mondelli, R. Venkataramanan, in:, 35th Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2021, pp. 29616–29629.","apa":"Mondelli, M., & Venkataramanan, R. (2021). PCA initialization for approximate message passing in rotationally invariant models. In 35th Conference on Neural Information Processing Systems (Vol. 35, pp. 29616–29629). Virtual: Neural Information Processing Systems Foundation.","ama":"Mondelli M, Venkataramanan R. PCA initialization for approximate message passing in rotationally invariant models. In: 35th Conference on Neural Information Processing Systems. Vol 35. Neural Information Processing Systems Foundation; 2021:29616-29629."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["2106.02356"]},"article_processing_charge":"No","author":[{"id":"27EB676C-8706-11E9-9510-7717E6697425","first_name":"Marco","last_name":"Mondelli","orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco"},{"first_name":"Ramji","last_name":"Venkataramanan","full_name":"Venkataramanan, Ramji"}],"title":"PCA initialization for approximate message passing in rotationally invariant models","abstract":[{"lang":"eng","text":"We study the problem of estimating a rank-$1$ signal in the presence of rotationally invariant noise-a class of perturbations more general than Gaussian noise. Principal Component Analysis (PCA) provides a natural estimator, and sharp results on its performance have been obtained in the high-dimensional regime. Recently, an Approximate Message Passing (AMP) algorithm has been proposed as an alternative estimator with the potential to improve the accuracy of PCA. However, the existing analysis of AMP requires an initialization that is both correlated with the signal and independent of the noise, which is often unrealistic in practice. In this work, we combine the two methods, and propose to initialize AMP with PCA. Our main result is a rigorous asymptotic characterization of the performance of this estimator. Both the AMP algorithm and its analysis differ from those previously derived in the Gaussian setting: at every iteration, our AMP algorithm requires a specific term to account for PCA initialization, while in the Gaussian case, PCA initialization affects only the first iteration of AMP. The proof is based on a two-phase artificial AMP that first approximates the PCA estimator and then mimics the true AMP. Our numerical simulations show an excellent agreement between AMP results and theoretical predictions, and suggest an interesting open direction on achieving Bayes-optimal performance."}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2106.02356"}],"scopus_import":"1","intvolume":" 35","month":"12","publication_status":"published","publication_identifier":{"isbn":["9781713845393"],"issn":["1049-5258"]},"language":[{"iso":"eng"}],"volume":35,"_id":"10593","conference":{"start_date":"2021-12-06","location":"Virtual","end_date":"2021-12-14","name":"NeurIPS: Neural Information Processing Systems"},"type":"conference","status":"public","date_updated":"2023-10-17T11:48:23Z","department":[{"_id":"MaMo"}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Nguyen, Quynh, Pierre Bréchet, and Marco Mondelli. “When Are Solutions Connected in Deep Networks?” In 35th Conference on Neural Information Processing Systems, Vol. 35. Neural Information Processing Systems Foundation, 2021.","ista":"Nguyen Q, Bréchet P, Mondelli M. 2021. When are solutions connected in deep networks? 35th Conference on Neural Information Processing Systems. 35th Conference on Neural Information Processing Systems vol. 35.","mla":"Nguyen, Quynh, et al. “When Are Solutions Connected in Deep Networks?” 35th Conference on Neural Information Processing Systems, vol. 35, Neural Information Processing Systems Foundation, 2021.","ieee":"Q. Nguyen, P. Bréchet, and M. Mondelli, “When are solutions connected in deep networks?,” in 35th Conference on Neural Information Processing Systems, Virtual, 2021, vol. 35.","short":"Q. Nguyen, P. Bréchet, M. Mondelli, in:, 35th Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2021.","ama":"Nguyen Q, Bréchet P, Mondelli M. When are solutions connected in deep networks? In: 35th Conference on Neural Information Processing Systems. Vol 35. Neural Information Processing Systems Foundation; 2021.","apa":"Nguyen, Q., Bréchet, P., & Mondelli, M. (2021). When are solutions connected in deep networks? In 35th Conference on Neural Information Processing Systems (Vol. 35). Virtual: Neural Information Processing Systems Foundation."},"title":"When are solutions connected in deep networks?","author":[{"first_name":"Quynh","full_name":"Nguyen, Quynh","last_name":"Nguyen"},{"first_name":"Pierre","full_name":"Bréchet, Pierre","last_name":"Bréchet"},{"id":"27EB676C-8706-11E9-9510-7717E6697425","first_name":"Marco","last_name":"Mondelli","full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020"}],"article_processing_charge":"No","external_id":{"arxiv":["2102.09671"]},"project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"day":"01","publication":"35th Conference on Neural Information Processing Systems","year":"2021","date_published":"2021-12-01T00:00:00Z","date_created":"2022-01-03T10:56:20Z","acknowledgement":"MM was partially supported by the 2019 Lopez-Loreta Prize. QN and PB acknowledge support from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no 757983).","quality_controlled":"1","publisher":"Neural Information Processing Systems Foundation","oa":1,"date_updated":"2023-10-17T11:48:40Z","department":[{"_id":"MaMo"}],"_id":"10594","status":"public","type":"conference","conference":{"name":"35th Conference on Neural Information Processing Systems","location":"Virtual","end_date":"2021-12-14","start_date":"2021-12-06"},"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9781713845393"],"issn":["1049-5258"]},"publication_status":"published","volume":35,"oa_version":"Preprint","abstract":[{"text":"The question of how and why the phenomenon of mode connectivity occurs in training deep neural networks has gained remarkable attention in the research community. From a theoretical perspective, two possible explanations have been proposed: (i) the loss function has connected sublevel sets, and (ii) the solutions found by stochastic gradient descent are dropout stable. While these explanations provide insights into the phenomenon, their assumptions are not always satisfied in practice. In particular, the first approach requires the network to have one layer with order of N neurons (N being the number of training samples), while the second one requires the loss to be almost invariant after removing half of the neurons at each layer (up to some rescaling of the remaining ones). In this work, we improve both conditions by exploiting the quality of the features at every intermediate layer together with a milder over-parameterization condition. More specifically, we show that: (i) under generic assumptions on the features of intermediate layers, it suffices that the last two hidden layers have order of N−−√ neurons, and (ii) if subsets of features at each layer are linearly separable, then no over-parameterization is needed to show the connectivity. Our experiments confirm that the proposed condition ensures the connectivity of solutions found by stochastic gradient descent, even in settings where the previous requirements do not hold.","lang":"eng"}],"month":"12","intvolume":" 35","main_file_link":[{"url":"https://arxiv.org/abs/2102.09671","open_access":"1"}]},{"acknowledgement":"NJL is supported by the MBIE Endeavour Fund (UOOX1805) and GL is by the Julius von Haast Fellowship of New Zealand. SM acknowledges stimulating discussions with T M Jensen.","publisher":"IOP Publishing","quality_controlled":"1","oa":1,"has_accepted_license":"1","isi":1,"year":"2021","day":"15","publication":"Quantum Science and Technology","date_published":"2021-07-15T00:00:00Z","doi":"10.1088/2058-9565/ac0f36","date_created":"2021-08-08T22:01:25Z","article_number":"045005","citation":{"mla":"Mobassem, Sonia, et al. “Thermal Noise in Electro-Optic Devices at Cryogenic Temperatures.” Quantum Science and Technology, vol. 6, no. 4, 045005, IOP Publishing, 2021, doi:10.1088/2058-9565/ac0f36.","ieee":"S. Mobassem, N. J. Lambert, A. R. Rueda Sanchez, J. M. Fink, G. Leuchs, and H. G. L. Schwefel, “Thermal noise in electro-optic devices at cryogenic temperatures,” Quantum Science and Technology, vol. 6, no. 4. IOP Publishing, 2021.","short":"S. Mobassem, N.J. Lambert, A.R. Rueda Sanchez, J.M. Fink, G. Leuchs, H.G.L. Schwefel, Quantum Science and Technology 6 (2021).","apa":"Mobassem, S., Lambert, N. J., Rueda Sanchez, A. R., Fink, J. M., Leuchs, G., & Schwefel, H. G. L. (2021). Thermal noise in electro-optic devices at cryogenic temperatures. Quantum Science and Technology. IOP Publishing. https://doi.org/10.1088/2058-9565/ac0f36","ama":"Mobassem S, Lambert NJ, Rueda Sanchez AR, Fink JM, Leuchs G, Schwefel HGL. Thermal noise in electro-optic devices at cryogenic temperatures. Quantum Science and Technology. 2021;6(4). doi:10.1088/2058-9565/ac0f36","chicago":"Mobassem, Sonia, Nicholas J. Lambert, Alfredo R Rueda Sanchez, Johannes M Fink, Gerd Leuchs, and Harald G.L. Schwefel. “Thermal Noise in Electro-Optic Devices at Cryogenic Temperatures.” Quantum Science and Technology. IOP Publishing, 2021. https://doi.org/10.1088/2058-9565/ac0f36.","ista":"Mobassem S, Lambert NJ, Rueda Sanchez AR, Fink JM, Leuchs G, Schwefel HGL. 2021. Thermal noise in electro-optic devices at cryogenic temperatures. Quantum Science and Technology. 6(4), 045005."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Sonia","full_name":"Mobassem, Sonia","last_name":"Mobassem"},{"last_name":"Lambert","full_name":"Lambert, Nicholas J.","first_name":"Nicholas J."},{"orcid":"0000-0001-6249-5860","full_name":"Rueda Sanchez, Alfredo R","last_name":"Rueda Sanchez","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","first_name":"Alfredo R"},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","last_name":"Fink"},{"full_name":"Leuchs, Gerd","last_name":"Leuchs","first_name":"Gerd"},{"first_name":"Harald G.L.","full_name":"Schwefel, Harald G.L.","last_name":"Schwefel"}],"external_id":{"isi":["000673081500001"],"arxiv":["2008.08764"]},"article_processing_charge":"Yes","title":"Thermal noise in electro-optic devices at cryogenic temperatures","abstract":[{"text":"The quantum bits (qubits) on which superconducting quantum computers are based have energy scales corresponding to photons with GHz frequencies. The energy of photons in the gigahertz domain is too low to allow transmission through the noisy room-temperature environment, where the signal would be lost in thermal noise. Optical photons, on the other hand, have much higher energies, and signals can be detected using highly efficient single-photon detectors. Transduction from microwave to optical frequencies is therefore a potential enabling technology for quantum devices. However, in such a device the optical pump can be a source of thermal noise and thus degrade the fidelity; the similarity of input microwave state to the output optical state. In order to investigate the magnitude of this effect we model the sub-Kelvin thermal behavior of an electro-optic transducer based on a lithium niobate whispering gallery mode resonator. We find that there is an optimum power level for a continuous pump, whilst pulsed operation of the pump increases the fidelity of the conversion.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"07","intvolume":" 6","publication_identifier":{"eissn":["2058-9565"]},"publication_status":"published","file":[{"creator":"cchlebak","date_updated":"2021-08-09T12:23:13Z","file_size":2366118,"date_created":"2021-08-09T12:23:13Z","file_name":"2021_QuantumScienceTechnology_Mobassem.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"9836","checksum":"b15c2c228487a75002c3b52d56f23d5c"}],"language":[{"iso":"eng"}],"volume":6,"issue":"4","_id":"9815","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","date_updated":"2023-10-17T12:54:54Z","ddc":["530"],"file_date_updated":"2021-08-09T12:23:13Z","department":[{"_id":"JoFi"}]},{"citation":{"mla":"Cao, Deqing, et al. “Sharp Kinetic Acceleration Potentials during Mediated Redox Catalysis of Insulators.” Research Square, Research Square, doi:10.21203/rs.3.rs-750965/v1.","ieee":"D. Cao et al., “Sharp kinetic acceleration potentials during mediated redox catalysis of insulators,” Research Square. Research Square.","short":"D. Cao, X. Shen, A. Wang, F. Yu, Y. Wu, S. Shi, S.A. Freunberger, Y. Chen, Research Square (n.d.).","ama":"Cao D, Shen X, Wang A, et al. Sharp kinetic acceleration potentials during mediated redox catalysis of insulators. Research Square. doi:10.21203/rs.3.rs-750965/v1","apa":"Cao, D., Shen, X., Wang, A., Yu, F., Wu, Y., Shi, S., … Chen, Y. (n.d.). Sharp kinetic acceleration potentials during mediated redox catalysis of insulators. Research Square. Research Square. https://doi.org/10.21203/rs.3.rs-750965/v1","chicago":"Cao, Deqing, Xiaoxiao Shen, Aiping Wang, Fengjiao Yu, Yuping Wu, Siqi Shi, Stefan Alexander Freunberger, and Yuhui Chen. “Sharp Kinetic Acceleration Potentials during Mediated Redox Catalysis of Insulators.” Research Square. Research Square, n.d. https://doi.org/10.21203/rs.3.rs-750965/v1.","ista":"Cao D, Shen X, Wang A, Yu F, Wu Y, Shi S, Freunberger SA, Chen Y. Sharp kinetic acceleration potentials during mediated redox catalysis of insulators. Research Square, 10.21203/rs.3.rs-750965/v1."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Cao, Deqing","last_name":"Cao","first_name":"Deqing"},{"first_name":"Xiaoxiao","last_name":"Shen","full_name":"Shen, Xiaoxiao"},{"first_name":"Aiping","full_name":"Wang, Aiping","last_name":"Wang"},{"first_name":"Fengjiao","full_name":"Yu, Fengjiao","last_name":"Yu"},{"full_name":"Wu, Yuping","last_name":"Wu","first_name":"Yuping"},{"full_name":"Shi, Siqi","last_name":"Shi","first_name":"Siqi"},{"orcid":"0000-0003-2902-5319","full_name":"Freunberger, Stefan Alexander","last_name":"Freunberger","first_name":"Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425"},{"last_name":"Chen","full_name":"Chen, Yuhui","first_name":"Yuhui"}],"article_processing_charge":"No","title":"Sharp kinetic acceleration potentials during mediated redox catalysis of insulators","has_accepted_license":"1","year":"2021","day":"18","publication":"Research Square","page":"21","doi":"10.21203/rs.3.rs-750965/v1","date_published":"2021-08-18T00:00:00Z","date_created":"2021-08-31T12:54:16Z","acknowledgement":"This work was financially supported by the National Natural Science Foundation of China (51773092, 21975124, 11874254, 51802187, U2030206). S.A.F. is indebted to IST Austria for support. ","publisher":"Research Square","oa":1,"date_updated":"2023-10-17T13:06:29Z","ddc":["541"],"department":[{"_id":"StFr"}],"file_date_updated":"2021-08-31T14:02:19Z","_id":"9978","type":"preprint","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","keyword":["Catalysis","Energy engineering","Materials theory and modeling"],"publication_identifier":{"eissn":["2693-5015"]},"publication_status":"submitted","file":[{"creator":"cchlebak","file_size":1019662,"date_updated":"2021-08-31T14:02:19Z","file_name":"2021_ResearchSquare_Cao.pdf","date_created":"2021-08-31T14:02:19Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"1878e91c29d5769ed5a827b0b7addf00","file_id":"9979"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"later_version","status":"public","id":"10813"}]},"abstract":[{"text":"Redox mediators could catalyse otherwise slow and energy-inefficient cycling of Li-S and Li-O 2 batteries by shuttling electrons/holes between the electrode and the solid insulating storage materials. For mediators to work efficiently they need to oxidize the solid with fast kinetics yet the lowest possible overpotential. Here, we found that when the redox potentials of mediators are tuned via, e.g., Li + concentration in the electrolyte, they exhibit distinct threshold potentials, where the kinetics accelerate several-fold within a range as small as 10 mV. This phenomenon is independent of types of mediators and electrolyte. The acceleration originates from the overpotentials required to activate fast Li + /e – extraction and the following chemical step at specific abundant surface facets. Efficient redox catalysis at insulating solids requires therefore carefully considering the surface conditions of the storage materials and electrolyte-dependent redox potentials, which may be tuned by salt concentrations or solvents.","lang":"eng"}],"oa_version":"Preprint","month":"08"},{"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1559-7016"],"issn":["0271-678x"]},"publication_status":"published","issue":"7","volume":41,"pmid":1,"oa_version":"Published Version","abstract":[{"text":"P-glycoprotein (ABCB1) and breast cancer resistance protein (ABCG2) restrict at the blood–brain barrier (BBB) the brain distribution of the majority of currently known molecularly targeted anticancer drugs. To improve brain delivery of dual ABCB1/ABCG2 substrates, both ABCB1 and ABCG2 need to be inhibited simultaneously at the BBB. We examined the feasibility of simultaneous ABCB1/ABCG2 inhibition with i.v. co-infusion of erlotinib and tariquidar by studying brain distribution of the model ABCB1/ABCG2 substrate [11C]erlotinib in mice and rhesus macaques with PET. Tolerability of the erlotinib/tariquidar combination was assessed in human embryonic stem cell-derived cerebral organoids. In mice and macaques, baseline brain distribution of [11C]erlotinib was low (brain distribution volume, VT,brain < 0.3 mL/cm3). Co-infusion of erlotinib and tariquidar increased VT,brain in mice by 3.0-fold and in macaques by 3.4- to 5.0-fold, while infusion of erlotinib alone or tariquidar alone led to less pronounced VT,brain increases in both species. Treatment of cerebral organoids with erlotinib/tariquidar led to an induction of Caspase-3-dependent apoptosis. Co-infusion of erlotinib/tariquidar may potentially allow for complete ABCB1/ABCG2 inhibition at the BBB, while simultaneously achieving brain-targeted EGFR inhibition. Our protocol may be applicable to enhance brain delivery of molecularly targeted anticancer drugs for a more effective treatment of brain tumors.","lang":"eng"}],"month":"07","intvolume":" 41","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8221757/"}],"date_updated":"2023-10-18T06:45:30Z","department":[{"_id":"GaNo"}],"_id":"8730","status":"public","article_type":"original","type":"journal_article","day":"01","publication":"Journal of Cerebral Blood Flow and Metabolism","isi":1,"year":"2021","doi":"10.1177/0271678X20965500","date_published":"2021-07-01T00:00:00Z","date_created":"2020-11-06T08:39:01Z","page":"1634-1646","quality_controlled":"1","publisher":"SAGE Publications","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Tournier, N., Goutal, S., Mairinger, S., Lozano, I., Filip, T., Sauberer, M., … Langer, O. (2021). Complete inhibition of ABCB1 and ABCG2 at the blood-brain barrier by co-infusion of erlotinib and tariquidar to improve brain delivery of the model ABCB1/ABCG2 substrate [11C]erlotinib. Journal of Cerebral Blood Flow and Metabolism. SAGE Publications. https://doi.org/10.1177/0271678X20965500","ama":"Tournier N, Goutal S, Mairinger S, et al. Complete inhibition of ABCB1 and ABCG2 at the blood-brain barrier by co-infusion of erlotinib and tariquidar to improve brain delivery of the model ABCB1/ABCG2 substrate [11C]erlotinib. Journal of Cerebral Blood Flow and Metabolism. 2021;41(7):1634-1646. doi:10.1177/0271678X20965500","ieee":"N. Tournier et al., “Complete inhibition of ABCB1 and ABCG2 at the blood-brain barrier by co-infusion of erlotinib and tariquidar to improve brain delivery of the model ABCB1/ABCG2 substrate [11C]erlotinib,” Journal of Cerebral Blood Flow and Metabolism, vol. 41, no. 7. SAGE Publications, pp. 1634–1646, 2021.","short":"N. Tournier, S. Goutal, S. Mairinger, I. Lozano, T. Filip, M. Sauberer, F. Caillé, L. Breuil, J. Stanek, A. Freeman, G. Novarino, C. Truillet, T. Wanek, O. Langer, Journal of Cerebral Blood Flow and Metabolism 41 (2021) 1634–1646.","mla":"Tournier, N., et al. “Complete Inhibition of ABCB1 and ABCG2 at the Blood-Brain Barrier by Co-Infusion of Erlotinib and Tariquidar to Improve Brain Delivery of the Model ABCB1/ABCG2 Substrate [11C]Erlotinib.” Journal of Cerebral Blood Flow and Metabolism, vol. 41, no. 7, SAGE Publications, 2021, pp. 1634–46, doi:10.1177/0271678X20965500.","ista":"Tournier N, Goutal S, Mairinger S, Lozano I, Filip T, Sauberer M, Caillé F, Breuil L, Stanek J, Freeman A, Novarino G, Truillet C, Wanek T, Langer O. 2021. Complete inhibition of ABCB1 and ABCG2 at the blood-brain barrier by co-infusion of erlotinib and tariquidar to improve brain delivery of the model ABCB1/ABCG2 substrate [11C]erlotinib. Journal of Cerebral Blood Flow and Metabolism. 41(7), 1634–1646.","chicago":"Tournier, N, S Goutal, S Mairinger, IH Lozano, T Filip, M Sauberer, F Caillé, et al. “Complete Inhibition of ABCB1 and ABCG2 at the Blood-Brain Barrier by Co-Infusion of Erlotinib and Tariquidar to Improve Brain Delivery of the Model ABCB1/ABCG2 Substrate [11C]Erlotinib.” Journal of Cerebral Blood Flow and Metabolism. SAGE Publications, 2021. https://doi.org/10.1177/0271678X20965500."},"title":"Complete inhibition of ABCB1 and ABCG2 at the blood-brain barrier by co-infusion of erlotinib and tariquidar to improve brain delivery of the model ABCB1/ABCG2 substrate [11C]erlotinib","author":[{"first_name":"N","full_name":"Tournier, N","last_name":"Tournier"},{"first_name":"S","last_name":"Goutal","full_name":"Goutal, S"},{"full_name":"Mairinger, S","last_name":"Mairinger","first_name":"S"},{"first_name":"IH","last_name":"Lozano","full_name":"Lozano, IH"},{"last_name":"Filip","full_name":"Filip, T","first_name":"T"},{"first_name":"M","last_name":"Sauberer","full_name":"Sauberer, M"},{"full_name":"Caillé, F","last_name":"Caillé","first_name":"F"},{"last_name":"Breuil","full_name":"Breuil, L","first_name":"L"},{"last_name":"Stanek","full_name":"Stanek, J","first_name":"J"},{"first_name":"AF","last_name":"Freeman","full_name":"Freeman, AF"},{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","last_name":"Novarino"},{"full_name":"Truillet, C","last_name":"Truillet","first_name":"C"},{"first_name":"T","last_name":"Wanek","full_name":"Wanek, T"},{"full_name":"Langer, O","last_name":"Langer","first_name":"O"}],"article_processing_charge":"No","external_id":{"pmid":["33081568"],"isi":["000664214100012"]}},{"citation":{"chicago":"Stankowski, Sean, and Mark Ravinet. “Defining the Speciation Continuum.” Evolution. Oxford University Press, 2021. https://doi.org/10.1111/evo.14215.","ista":"Stankowski S, Ravinet M. 2021. Defining the speciation continuum. Evolution. 75(6), 1256–1273.","mla":"Stankowski, Sean, and Mark Ravinet. “Defining the Speciation Continuum.” Evolution, vol. 75, no. 6, Oxford University Press, 2021, pp. 1256–73, doi:10.1111/evo.14215.","ieee":"S. Stankowski and M. Ravinet, “Defining the speciation continuum,” Evolution, vol. 75, no. 6. Oxford University Press, pp. 1256–1273, 2021.","short":"S. Stankowski, M. Ravinet, Evolution 75 (2021) 1256–1273.","apa":"Stankowski, S., & Ravinet, M. (2021). Defining the speciation continuum. Evolution. Oxford University Press. https://doi.org/10.1111/evo.14215","ama":"Stankowski S, Ravinet M. Defining the speciation continuum. Evolution. 2021;75(6):1256-1273. doi:10.1111/evo.14215"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Stankowski","full_name":"Stankowski, Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean"},{"full_name":"Ravinet, Mark","last_name":"Ravinet","first_name":"Mark"}],"article_processing_charge":"No","external_id":{"isi":["000647226400001"]},"title":"Defining the speciation continuum","acknowledgement":"We thank M. Garlovsky, S. Martin, C. Cooney, C. Roux, J. Larson, and J. Mallet for critical feedback and for discussion. K. Lohse, M. de la Cámara, J. Cerca, M. A. Chase, C. Baskett, A. M. Westram, and N. H. Barton gave feedback on a draft of the manuscript. O. Seehausen, two anonymous reviewers, and the AE (Michael Kopp) provided comments that greatly improved the manuscript. V. Holzmann made many corrections to the proofs. G. Bisschop and K. Lohse kindly contributed the simulations and analyses presented in Box 3. We would also like to extend our thanks to everyone who took part in the speciation survey, which received ethical approval through the University of Sheffield Ethics Review Procedure (Application 029768). We are especially grateful to R. K. Butlin for stimulating discussion throughout the writing of the manuscript and for feedback on an earlier draft.","quality_controlled":"1","publisher":"Oxford University Press","oa":1,"isi":1,"has_accepted_license":"1","year":"2021","day":"22","publication":"Evolution","page":"1256-1273","doi":"10.1111/evo.14215","date_published":"2021-03-22T00:00:00Z","date_created":"2021-05-09T22:01:39Z","_id":"9383","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"status":"public","date_updated":"2023-10-18T08:16:01Z","ddc":["570"],"file_date_updated":"2022-03-25T12:02:04Z","department":[{"_id":"NiBa"}],"abstract":[{"text":"A primary roadblock to our understanding of speciation is that it usually occurs over a timeframe that is too long to study from start to finish. The idea of a speciation continuum provides something of a solution to this problem; rather than observing the entire process, we can simply reconstruct it from the multitude of speciation events that surround us. But what do we really mean when we talk about the speciation continuum, and can it really help us understand speciation? We explored these questions using a literature review and online survey of speciation researchers. Although most researchers were familiar with the concept and thought it was useful, our survey revealed extensive disagreement about what the speciation continuum actually tells us. This is due partly to the lack of a clear definition. Here, we provide an explicit definition that is compatible with the Biological Species Concept. That is, the speciation continuum is a continuum of reproductive isolation. After outlining the logic of the definition in light of alternatives, we explain why attempts to reconstruct the speciation process from present‐day populations will ultimately fail. We then outline how we think the speciation continuum concept can continue to act as a foundation for understanding the continuum of reproductive isolation that surrounds us.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"03","intvolume":" 75","publication_identifier":{"eissn":["1558-5646"],"issn":["0014-3820"]},"publication_status":"published","file":[{"success":1,"checksum":"96f6ccf15d95a4e9f7c0b27eee570fa6","file_id":"10921","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2021_Evolution_Stankowski.pdf","date_created":"2022-03-25T12:02:04Z","creator":"kschuh","file_size":719991,"date_updated":"2022-03-25T12:02:04Z"}],"language":[{"iso":"eng"}],"volume":75,"issue":"6","license":"https://creativecommons.org/licenses/by-nc/4.0/"},{"publisher":"Springer Nature","quality_controlled":"1","oa":1,"acknowledgement":"We thank N. Gnyliukh and L. Hörmayer for technical assistance and N. Paris for sharing PM-Cyto seeds. We gratefully acknowledge the Life Science, Machine Shop and Bioimaging Facilities of IST Austria. This project has received funding from the European Research Council Advanced Grant (ETAP-742985) and the Austrian Science Fund (FWF) under I 3630-B25 to J.F., the National Institutes of Health (GM067203) to W.M.G., the Netherlands Organization for Scientific Research (NWO; VIDI-864.13.001), Research Foundation-Flanders (FWO; Odysseus II G0D0515N) and a European Research Council Starting Grant (TORPEDO-714055) to W.S. and B.D.R., the VICI grant (865.14.001) from the Netherlands Organization for Scientific Research to M.R. and D.W., the Australian Research Council and China National Distinguished Expert Project (WQ20174400441) to S.S., the MEXT/JSPS KAKENHI to K.T. (20K06685) and T.K. (20H05687 and 20H05910), the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie grant agreement no. 665385 and the DOC Fellowship of the Austrian Academy of Sciences to L.L., and the China Scholarship Council to J.C.","page":"273-277","doi":"10.1038/s41586-021-04037-6","date_published":"2021-11-11T00:00:00Z","date_created":"2021-11-07T23:01:25Z","isi":1,"year":"2021","day":"11","publication":"Nature","project":[{"grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"_id":"26B4D67E-B435-11E9-9278-68D0E5697425","grant_number":"25351","name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root"}],"author":[{"full_name":"Li, Lanxin","orcid":"0000-0002-5607-272X","last_name":"Li","first_name":"Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","last_name":"Verstraeten","full_name":"Verstraeten, Inge","orcid":"0000-0001-7241-2328"},{"full_name":"Roosjen, Mark","last_name":"Roosjen","first_name":"Mark"},{"last_name":"Takahashi","full_name":"Takahashi, Koji","first_name":"Koji"},{"first_name":"Lesia","id":"3922B506-F248-11E8-B48F-1D18A9856A87","last_name":"Rodriguez Solovey","full_name":"Rodriguez Solovey, Lesia","orcid":"0000-0002-7244-7237"},{"orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack","last_name":"Merrin","first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Chen","full_name":"Chen, Jian","first_name":"Jian"},{"full_name":"Shabala, Lana","last_name":"Shabala","first_name":"Lana"},{"last_name":"Smet","full_name":"Smet, Wouter","first_name":"Wouter"},{"full_name":"Ren, Hong","last_name":"Ren","first_name":"Hong"},{"first_name":"Steffen","last_name":"Vanneste","full_name":"Vanneste, Steffen"},{"full_name":"Shabala, Sergey","last_name":"Shabala","first_name":"Sergey"},{"last_name":"De Rybel","full_name":"De Rybel, Bert","first_name":"Bert"},{"last_name":"Weijers","full_name":"Weijers, Dolf","first_name":"Dolf"},{"full_name":"Kinoshita, Toshinori","last_name":"Kinoshita","first_name":"Toshinori"},{"last_name":"Gray","full_name":"Gray, William M.","first_name":"William M."},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml"}],"article_processing_charge":"No","external_id":{"pmid":["34707283"],"isi":["000713338100006"]},"title":"Cell surface and intracellular auxin signalling for H+ fluxes in root growth","citation":{"mla":"Li, Lanxin, et al. “Cell Surface and Intracellular Auxin Signalling for H+ Fluxes in Root Growth.” Nature, vol. 599, no. 7884, Springer Nature, 2021, pp. 273–77, doi:10.1038/s41586-021-04037-6.","apa":"Li, L., Verstraeten, I., Roosjen, M., Takahashi, K., Rodriguez Solovey, L., Merrin, J., … Friml, J. (2021). Cell surface and intracellular auxin signalling for H+ fluxes in root growth. Nature. Springer Nature. https://doi.org/10.1038/s41586-021-04037-6","ama":"Li L, Verstraeten I, Roosjen M, et al. Cell surface and intracellular auxin signalling for H+ fluxes in root growth. Nature. 2021;599(7884):273-277. doi:10.1038/s41586-021-04037-6","short":"L. Li, I. Verstraeten, M. Roosjen, K. Takahashi, L. Rodriguez Solovey, J. Merrin, J. Chen, L. Shabala, W. Smet, H. Ren, S. Vanneste, S. Shabala, B. De Rybel, D. Weijers, T. Kinoshita, W.M. Gray, J. Friml, Nature 599 (2021) 273–277.","ieee":"L. Li et al., “Cell surface and intracellular auxin signalling for H+ fluxes in root growth,” Nature, vol. 599, no. 7884. Springer Nature, pp. 273–277, 2021.","chicago":"Li, Lanxin, Inge Verstraeten, Mark Roosjen, Koji Takahashi, Lesia Rodriguez Solovey, Jack Merrin, Jian Chen, et al. “Cell Surface and Intracellular Auxin Signalling for H+ Fluxes in Root Growth.” Nature. Springer Nature, 2021. https://doi.org/10.1038/s41586-021-04037-6.","ista":"Li L, Verstraeten I, Roosjen M, Takahashi K, Rodriguez Solovey L, Merrin J, Chen J, Shabala L, Smet W, Ren H, Vanneste S, Shabala S, De Rybel B, Weijers D, Kinoshita T, Gray WM, Friml J. 2021. Cell surface and intracellular auxin signalling for H+ fluxes in root growth. Nature. 599(7884), 273–277."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","main_file_link":[{"url":"https://www.doi.org/10.21203/rs.3.rs-266395/v3","open_access":"1"}],"month":"11","intvolume":" 599","abstract":[{"lang":"eng","text":"Growth regulation tailors development in plants to their environment. A prominent example of this is the response to gravity, in which shoots bend up and roots bend down1. This paradox is based on opposite effects of the phytohormone auxin, which promotes cell expansion in shoots while inhibiting it in roots via a yet unknown cellular mechanism2. Here, by combining microfluidics, live imaging, genetic engineering and phosphoproteomics in Arabidopsis thaliana, we advance understanding of how auxin inhibits root growth. We show that auxin activates two distinct, antagonistically acting signalling pathways that converge on rapid regulation of apoplastic pH, a causative determinant of growth. Cell surface-based TRANSMEMBRANE KINASE1 (TMK1) interacts with and mediates phosphorylation and activation of plasma membrane H+-ATPases for apoplast acidification, while intracellular canonical auxin signalling promotes net cellular H+ influx, causing apoplast alkalinization. Simultaneous activation of these two counteracting mechanisms poises roots for rapid, fine-tuned growth modulation in navigating complex soil environments."}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"Bio"}],"oa_version":"Preprint","pmid":1,"issue":"7884","related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/stop-and-grow/","description":"News on IST Webpage"}],"record":[{"status":"public","id":"10095","relation":"earlier_version"}]},"volume":599,"ec_funded":1,"publication_identifier":{"eissn":["14764687"],"issn":["00280836"]},"publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","status":"public","keyword":["Multidisciplinary"],"_id":"10223","department":[{"_id":"JiFr"},{"_id":"NanoFab"}],"date_updated":"2023-10-18T08:30:53Z"},{"_id":"9379","keyword":["B cell","actin","immune synapse","cell spreading","cofilin","WDR1 (AIP1)","LIM domain kinase","B cell receptor (BCR)"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","ddc":["570"],"date_updated":"2023-10-18T08:19:49Z","department":[{"_id":"CaHe"}],"file_date_updated":"2021-05-11T15:09:23Z","oa_version":"Published Version","pmid":1,"abstract":[{"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.","lang":"eng"}],"intvolume":" 9","month":"04","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"8c8a03575d2f7583f88dc3b658b0976b","file_id":"9386","creator":"kschuh","file_size":4076024,"date_updated":"2021-05-11T15:09:23Z","file_name":"2021_Frontiers_Cell_Bolger-Munro.pdf","date_created":"2021-05-11T15:09:23Z"}],"publication_status":"published","publication_identifier":{"eissn":["2296-634X"]},"volume":9,"article_number":"649433","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.” Frontiers in Cell and Developmental Biology. Frontiers Media, 2021. https://doi.org/10.3389/fcell.2021.649433.","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.","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.” Frontiers in Cell and Developmental Biology, vol. 9, 649433, Frontiers Media, 2021, doi:10.3389/fcell.2021.649433.","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).","ieee":"M. Bolger-Munro et al., “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, vol. 9. Frontiers Media, 2021.","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. Frontiers in Cell and Developmental Biology. 2021;9. doi:10.3389/fcell.2021.649433","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. Frontiers in Cell and Developmental Biology. Frontiers Media. https://doi.org/10.3389/fcell.2021.649433"},"title":"The Wdr1-LIMK-Cofilin axis controls B cell antigen receptor-induced actin remodeling and signaling at the immune synapse","article_processing_charge":"No","external_id":{"pmid":["33928084"],"isi":["000644419500001"]},"author":[{"orcid":"0000-0002-8176-4824","full_name":"Bolger-Munro, Madison","last_name":"Bolger-Munro","id":"516F03FA-93A3-11EA-A7C5-D6BE3DDC885E","first_name":"Madison"},{"last_name":"Choi","full_name":"Choi, Kate","first_name":"Kate"},{"full_name":"Cheung, Faith","last_name":"Cheung","first_name":"Faith"},{"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","full_name":"Deretic, Nikola","last_name":"Deretic"},{"first_name":"Connor","full_name":"Keane, Connor","last_name":"Keane"},{"first_name":"Michael R.","last_name":"Gold","full_name":"Gold, Michael R."}],"acknowledgement":"We thank the UBC Life Sciences Institute Imaging Facility andthe UBC Flow Cytometry Facility.","oa":1,"quality_controlled":"1","publisher":"Frontiers Media","publication":"Frontiers in Cell and Developmental Biology","day":"13","year":"2021","isi":1,"has_accepted_license":"1","date_created":"2021-05-09T22:01:37Z","date_published":"2021-04-13T00:00:00Z","doi":"10.3389/fcell.2021.649433"},{"publication_identifier":{"eissn":["19326203"]},"publication_status":"published","file":[{"date_updated":"2021-05-04T13:22:19Z","file_size":2768282,"creator":"kschuh","date_created":"2021-05-04T13:22:19Z","file_name":"2021_pone_Chalk.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"9371","checksum":"c52da133850307d2031f552d998f00e8","success":1}],"language":[{"iso":"eng"}],"volume":16,"issue":"4","abstract":[{"text":"A central goal in systems neuroscience is to understand the functions performed by neural circuits. Previous top-down models addressed this question by comparing the behaviour of an ideal model circuit, optimised to perform a given function, with neural recordings. However, this requires guessing in advance what function is being performed, which may not be possible for many neural systems. To address this, we propose an inverse reinforcement learning (RL) framework for inferring the function performed by a neural network from data. We assume that the responses of each neuron in a network are optimised so as to drive the network towards ‘rewarded’ states, that are desirable for performing a given function. We then show how one can use inverse RL to infer the reward function optimised by the network from observing its responses. This inferred reward function can be used to predict how the neural network should adapt its dynamics to perform the same function when the external environment or network structure changes. This could lead to theoretical predictions about how neural network dynamics adapt to deal with cell death and/or varying sensory stimulus statistics.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","month":"04","intvolume":" 16","date_updated":"2023-10-18T08:17:42Z","ddc":["570"],"file_date_updated":"2021-05-04T13:22:19Z","department":[{"_id":"GaTk"}],"_id":"9362","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","isi":1,"has_accepted_license":"1","year":"2021","day":"15","publication":"PLoS ONE","doi":"10.1371/journal.pone.0248940","date_published":"2021-04-15T00:00:00Z","date_created":"2021-05-02T22:01:28Z","acknowledgement":"The authors would like to thank Ulisse Ferrari for useful discussions and feedback.","publisher":"Public Library of Science","quality_controlled":"1","oa":1,"citation":{"apa":"Chalk, M. J., Tkačik, G., & Marre, O. (2021). Inferring the function performed by a recurrent neural network. PLoS ONE. Public Library of Science. https://doi.org/10.1371/journal.pone.0248940","ama":"Chalk MJ, Tkačik G, Marre O. Inferring the function performed by a recurrent neural network. PLoS ONE. 2021;16(4). doi:10.1371/journal.pone.0248940","short":"M.J. Chalk, G. Tkačik, O. Marre, PLoS ONE 16 (2021).","ieee":"M. J. Chalk, G. Tkačik, and O. Marre, “Inferring the function performed by a recurrent neural network,” PLoS ONE, vol. 16, no. 4. Public Library of Science, 2021.","mla":"Chalk, Matthew J., et al. “Inferring the Function Performed by a Recurrent Neural Network.” PLoS ONE, vol. 16, no. 4, e0248940, Public Library of Science, 2021, doi:10.1371/journal.pone.0248940.","ista":"Chalk MJ, Tkačik G, Marre O. 2021. Inferring the function performed by a recurrent neural network. PLoS ONE. 16(4), e0248940.","chicago":"Chalk, Matthew J, Gašper Tkačik, and Olivier Marre. “Inferring the Function Performed by a Recurrent Neural Network.” PLoS ONE. Public Library of Science, 2021. https://doi.org/10.1371/journal.pone.0248940."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Matthew J","id":"2BAAC544-F248-11E8-B48F-1D18A9856A87","last_name":"Chalk","full_name":"Chalk, Matthew J","orcid":"0000-0001-7782-4436"},{"last_name":"Tkačik","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Marre","full_name":"Marre, Olivier","first_name":"Olivier"}],"external_id":{"pmid":["33857170"],"isi":["000641474900072"]},"article_processing_charge":"No","title":"Inferring the function performed by a recurrent neural network","article_number":"e0248940"},{"file":[{"file_name":"2021_IntJMolecularSciences_Velasquez.pdf","date_created":"2021-09-06T12:50:19Z","creator":"cchlebak","file_size":2162247,"date_updated":"2021-09-07T09:04:53Z","checksum":"6b7055cf89f1b7ed8594c3fdf56f000b","file_id":"9988","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1422-0067"],"issn":["1661-6596"]},"publication_status":"published","issue":"17","volume":22,"oa_version":"Published Version","pmid":1,"abstract":[{"text":"Size control is a fundamental question in biology, showing incremental complexity in plants, whose cells possess a rigid cell wall. The phytohormone auxin is a vital growth regulator with central importance for differential growth control. Our results indicate that auxin-reliant growth programs affect the molecular complexity of xyloglucans, the major type of cell wall hemicellulose in eudicots. Auxin-dependent induction and repression of growth coincide with reduced and enhanced molecular complexity of xyloglucans, respectively. In agreement with a proposed function in growth control, genetic interference with xyloglucan side decorations distinctly modulates auxin-dependent differential growth rates. Our work proposes that auxin-dependent growth programs have a spatially defined effect on xyloglucan’s molecular structure, which in turn affects cell wall mechanics and specifies differential, gravitropic hypocotyl growth.","lang":"eng"}],"month":"08","intvolume":" 22","scopus_import":"1","ddc":["575"],"date_updated":"2023-10-31T19:29:38Z","department":[{"_id":"EvBe"}],"file_date_updated":"2021-09-07T09:04:53Z","_id":"9986","status":"public","keyword":["auxin","growth","cell wall","xyloglucans","hypocotyls","gravitropism"],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"day":"26","publication":"International Journal of Molecular Sciences","has_accepted_license":"1","isi":1,"year":"2021","doi":"10.3390/ijms22179222","date_published":"2021-08-26T00:00:00Z","date_created":"2021-09-05T22:01:24Z","acknowledgement":"We are grateful to Paul Knox, Markus Pauly, Malcom O’Neill, and Ignacio Zarra for providing published material; the BOKU-VIBT Imaging Center for access and M. Debreczeny for expertise; J.I. Thaker and Georg Seifert for critical reading.\r\n","quality_controlled":"1","publisher":"MDPI","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"S.M. Velasquez, X. Guo, M. Gallemi, B. Aryal, P. Venhuizen, E. Barbez, K.A. Dünser, M. Darino, A. Pӗnčík, O. Novák, M. Kalyna, G. Mouille, E. Benková, R.P. Bhalerao, J. Mravec, J. Kleine-Vehn, International Journal of Molecular Sciences 22 (2021).","ieee":"S. M. Velasquez et al., “Xyloglucan remodeling defines auxin-dependent differential tissue expansion in plants,” International Journal of Molecular Sciences, vol. 22, no. 17. MDPI, 2021.","ama":"Velasquez SM, Guo X, Gallemi M, et al. Xyloglucan remodeling defines auxin-dependent differential tissue expansion in plants. International Journal of Molecular Sciences. 2021;22(17). doi:10.3390/ijms22179222","apa":"Velasquez, S. M., Guo, X., Gallemi, M., Aryal, B., Venhuizen, P., Barbez, E., … Kleine-Vehn, J. (2021). Xyloglucan remodeling defines auxin-dependent differential tissue expansion in plants. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms22179222","mla":"Velasquez, Silvia Melina, et al. “Xyloglucan Remodeling Defines Auxin-Dependent Differential Tissue Expansion in Plants.” International Journal of Molecular Sciences, vol. 22, no. 17, 9222, MDPI, 2021, doi:10.3390/ijms22179222.","ista":"Velasquez SM, Guo X, Gallemi M, Aryal B, Venhuizen P, Barbez E, Dünser KA, Darino M, Pӗnčík A, Novák O, Kalyna M, Mouille G, Benková E, Bhalerao RP, Mravec J, Kleine-Vehn J. 2021. Xyloglucan remodeling defines auxin-dependent differential tissue expansion in plants. International Journal of Molecular Sciences. 22(17), 9222.","chicago":"Velasquez, Silvia Melina, Xiaoyuan Guo, Marçal Gallemi, Bibek Aryal, Peter Venhuizen, Elke Barbez, Kai Alexander Dünser, et al. “Xyloglucan Remodeling Defines Auxin-Dependent Differential Tissue Expansion in Plants.” International Journal of Molecular Sciences. MDPI, 2021. https://doi.org/10.3390/ijms22179222."},"title":"Xyloglucan remodeling defines auxin-dependent differential tissue expansion in plants","author":[{"full_name":"Velasquez, Silvia Melina","last_name":"Velasquez","first_name":"Silvia Melina"},{"first_name":"Xiaoyuan","last_name":"Guo","full_name":"Guo, Xiaoyuan"},{"last_name":"Gallemi","orcid":"0000-0003-4675-6893","full_name":"Gallemi, Marçal","id":"460C6802-F248-11E8-B48F-1D18A9856A87","first_name":"Marçal"},{"full_name":"Aryal, Bibek","last_name":"Aryal","first_name":"Bibek"},{"last_name":"Venhuizen","full_name":"Venhuizen, Peter","first_name":"Peter"},{"first_name":"Elke","last_name":"Barbez","full_name":"Barbez, Elke"},{"first_name":"Kai Alexander","full_name":"Dünser, Kai Alexander","last_name":"Dünser"},{"full_name":"Darino, Martin","last_name":"Darino","first_name":"Martin"},{"last_name":"Pӗnčík","full_name":"Pӗnčík, Aleš","first_name":"Aleš"},{"first_name":"Ondřej","last_name":"Novák","full_name":"Novák, Ondřej"},{"full_name":"Kalyna, Maria","last_name":"Kalyna","first_name":"Maria"},{"full_name":"Mouille, Gregory","last_name":"Mouille","first_name":"Gregory"},{"first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva"},{"last_name":"Bhalerao","full_name":"Bhalerao, Rishikesh P.","first_name":"Rishikesh P."},{"first_name":"Jozef","last_name":"Mravec","full_name":"Mravec, Jozef"},{"last_name":"Kleine-Vehn","full_name":"Kleine-Vehn, Jürgen","first_name":"Jürgen"}],"article_processing_charge":"Yes","external_id":{"isi":["000694347100001"],"pmid":["34502129"]},"article_number":"9222"},{"pmid":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Transposable elements exist widely throughout plant genomes and play important roles in plant evolution. Auxin is an important regulator that is traditionally associated with root development and drought stress adaptation. The DEEPER ROOTING 1 (DRO1) gene is a key component of rice drought avoidance. Here, we identified a transposon that acts as an autonomous auxin‐responsive promoter and its presence at specific genome positions conveys physiological adaptations related to drought avoidance. Rice varieties with high and auxin‐mediated transcription of DRO1 in the root tip show deeper and longer root phenotypes and are thus better adapted to drought. The INDITTO2 transposon contains an auxin response element and displays auxin‐responsive promoter activity; it is thus able to convey auxin regulation of transcription to genes in its proximity. In the rice Acuce, which displays DRO1‐mediated drought adaptation, the INDITTO2 transposon was found to be inserted at the promoter region of the DRO1 locus. Transgenesis‐based insertion of the INDITTO2 transposon into the DRO1 promoter of the non‐adapted rice variety Nipponbare was sufficient to promote its drought avoidance. Our data identify an example of how transposons can act as promoters and convey hormonal regulation to nearby loci, improving plant fitness in response to different abiotic stresses."}],"intvolume":" 44","month":"06","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"checksum":"a812418fede076741c9c4dc07f317068","file_id":"14481","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2023-11-02T17:02:11Z","file_name":"Zhao PlantCellEnv 2021_accepted.pdf","date_updated":"2023-11-02T17:02:11Z","file_size":8437528,"creator":"amally"}],"publication_status":"published","publication_identifier":{"issn":["0140-7791"],"eissn":["1365-3040"]},"issue":"6","volume":44,"_id":"9189","status":"public","type":"journal_article","article_type":"original","ddc":["580"],"date_updated":"2023-11-07T08:18:36Z","file_date_updated":"2023-11-02T17:02:11Z","department":[{"_id":"JiFr"}],"oa":1,"quality_controlled":"1","publisher":"Wiley","publication":"Plant, Cell & Environment","day":"01","year":"2021","isi":1,"has_accepted_license":"1","date_created":"2021-02-24T10:07:21Z","date_published":"2021-06-01T00:00:00Z","doi":"10.1111/pce.14029","page":"1846-1857","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"Y. Zhao et al., “INDITTO2 transposon conveys auxin-mediated DRO1 transcription for rice drought avoidance,” Plant, Cell & Environment, vol. 44, no. 6. Wiley, pp. 1846–1857, 2021.","short":"Y. Zhao, L. Wu, Q. Fu, D. Wang, J. Li, B. Yao, S. Yu, L. Jiang, J. Qian, X. Zhou, L. Han, S. Zhao, C. Ma, Y. Zhang, C. Luo, Q. Dong, S. Li, L. Zhang, X. Jiang, Y. Li, H. Luo, K. Li, J. Yang, Q. Luo, L. Li, S. Peng, H. Huang, Z. Zuo, C. Liu, L. Wang, C. Li, X. He, J. Friml, Y. Du, Plant, Cell & Environment 44 (2021) 1846–1857.","ama":"Zhao Y, Wu L, Fu Q, et al. INDITTO2 transposon conveys auxin-mediated DRO1 transcription for rice drought avoidance. Plant, Cell & Environment. 2021;44(6):1846-1857. doi:10.1111/pce.14029","apa":"Zhao, Y., Wu, L., Fu, Q., Wang, D., Li, J., Yao, B., … Du, Y. (2021). INDITTO2 transposon conveys auxin-mediated DRO1 transcription for rice drought avoidance. Plant, Cell & Environment. Wiley. https://doi.org/10.1111/pce.14029","mla":"Zhao, Y., et al. “INDITTO2 Transposon Conveys Auxin-Mediated DRO1 Transcription for Rice Drought Avoidance.” Plant, Cell & Environment, vol. 44, no. 6, Wiley, 2021, pp. 1846–57, doi:10.1111/pce.14029.","ista":"Zhao Y, Wu L, Fu Q, Wang D, Li J, Yao B, Yu S, Jiang L, Qian J, Zhou X, Han L, Zhao S, Ma C, Zhang Y, Luo C, Dong Q, Li S, Zhang L, Jiang X, Li Y, Luo H, Li K, Yang J, Luo Q, Li L, Peng S, Huang H, Zuo Z, Liu C, Wang L, Li C, He X, Friml J, Du Y. 2021. INDITTO2 transposon conveys auxin-mediated DRO1 transcription for rice drought avoidance. Plant, Cell & Environment. 44(6), 1846–1857.","chicago":"Zhao, Y, L Wu, Q Fu, D Wang, J Li, B Yao, S Yu, et al. “INDITTO2 Transposon Conveys Auxin-Mediated DRO1 Transcription for Rice Drought Avoidance.” Plant, Cell & Environment. Wiley, 2021. https://doi.org/10.1111/pce.14029."},"title":"INDITTO2 transposon conveys auxin-mediated DRO1 transcription for rice drought avoidance","external_id":{"isi":["000625398600001"],"pmid":["33576018"]},"article_processing_charge":"No","author":[{"first_name":"Y","full_name":"Zhao, Y","last_name":"Zhao"},{"first_name":"L","last_name":"Wu","full_name":"Wu, L"},{"last_name":"Fu","full_name":"Fu, Q","first_name":"Q"},{"first_name":"D","full_name":"Wang, D","last_name":"Wang"},{"first_name":"J","full_name":"Li, J","last_name":"Li"},{"first_name":"B","full_name":"Yao, B","last_name":"Yao"},{"first_name":"S","last_name":"Yu","full_name":"Yu, S"},{"first_name":"L","full_name":"Jiang, L","last_name":"Jiang"},{"first_name":"J","full_name":"Qian, J","last_name":"Qian"},{"first_name":"X","full_name":"Zhou, X","last_name":"Zhou"},{"first_name":"L","last_name":"Han","full_name":"Han, L"},{"first_name":"S","last_name":"Zhao","full_name":"Zhao, S"},{"last_name":"Ma","full_name":"Ma, C","first_name":"C"},{"first_name":"Y","full_name":"Zhang, Y","last_name":"Zhang"},{"last_name":"Luo","full_name":"Luo, C","first_name":"C"},{"first_name":"Q","last_name":"Dong","full_name":"Dong, Q"},{"first_name":"S","full_name":"Li, S","last_name":"Li"},{"first_name":"L","full_name":"Zhang, L","last_name":"Zhang"},{"first_name":"X","last_name":"Jiang","full_name":"Jiang, X"},{"last_name":"Li","full_name":"Li, Y","first_name":"Y"},{"full_name":"Luo, H","last_name":"Luo","first_name":"H"},{"last_name":"Li","full_name":"Li, K","first_name":"K"},{"last_name":"Yang","full_name":"Yang, J","first_name":"J"},{"last_name":"Luo","full_name":"Luo, Q","first_name":"Q"},{"first_name":"L","last_name":"Li","full_name":"Li, L"},{"first_name":"S","last_name":"Peng","full_name":"Peng, S"},{"first_name":"H","last_name":"Huang","full_name":"Huang, H"},{"first_name":"Z","full_name":"Zuo, Z","last_name":"Zuo"},{"first_name":"C","last_name":"Liu","full_name":"Liu, C"},{"first_name":"L","full_name":"Wang, L","last_name":"Wang"},{"last_name":"Li","full_name":"Li, C","first_name":"C"},{"last_name":"He","full_name":"He, X","first_name":"X"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml"},{"first_name":"Y","last_name":"Du","full_name":"Du, Y"}]},{"acknowledgement":"This work started when A.G. was visiting the Erwin Schrödinger Institute and then continued when D.F. and L.P visited the Theoretical Chemistry Department of the Vrije Universiteit Amsterdam. The authors thanks the hospitality of both places and, especially, P. Gori-Giorgi and K. Giesbertz for fruitful discussions and literature suggestions in the early state of the project. Finally, the authors also thanks J. Maas and R. Seiringer for their feedback and useful comments to a first draft of the article. L.P. acknowledges support by the Austrian Science Fund (FWF), grants No W1245 and NoF65. D.F acknowledges support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreements No 716117 and No 694227). A.G. acknowledges funding by the European Research Council under H2020/MSCA-IF “OTmeetsDFT” [grant ID: 795942].","oa":1,"publication":"arXiv","day":"21","year":"2021","has_accepted_license":"1","date_created":"2021-08-06T09:07:12Z","date_published":"2021-07-21T00:00:00Z","doi":"10.48550/arXiv.2106.11217","article_number":"2106.11217","project":[{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Analysis of quantum many-body systems","grant_number":"694227"},{"call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics"},{"name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Feliciangeli D, Gerolin A, Portinale L. A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature. arXiv. doi:10.48550/arXiv.2106.11217","apa":"Feliciangeli, D., Gerolin, A., & Portinale, L. (n.d.). A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature. arXiv. https://doi.org/10.48550/arXiv.2106.11217","short":"D. Feliciangeli, A. Gerolin, L. Portinale, ArXiv (n.d.).","ieee":"D. Feliciangeli, A. Gerolin, and L. Portinale, “A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature,” arXiv. .","mla":"Feliciangeli, Dario, et al. “A Non-Commutative Entropic Optimal Transport Approach to Quantum Composite Systems at Positive Temperature.” ArXiv, 2106.11217, doi:10.48550/arXiv.2106.11217.","ista":"Feliciangeli D, Gerolin A, Portinale L. A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature. arXiv, 2106.11217.","chicago":"Feliciangeli, Dario, Augusto Gerolin, and Lorenzo Portinale. “A Non-Commutative Entropic Optimal Transport Approach to Quantum Composite Systems at Positive Temperature.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2106.11217."},"title":"A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature","article_processing_charge":"No","external_id":{"arxiv":["2106.11217"]},"author":[{"id":"41A639AA-F248-11E8-B48F-1D18A9856A87","first_name":"Dario","full_name":"Feliciangeli, Dario","orcid":"0000-0003-0754-8530","last_name":"Feliciangeli"},{"full_name":"Gerolin, Augusto","last_name":"Gerolin","first_name":"Augusto"},{"full_name":"Portinale, Lorenzo","last_name":"Portinale","first_name":"Lorenzo","id":"30AD2CBC-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Preprint","abstract":[{"text":"This paper establishes new connections between many-body quantum systems, One-body Reduced Density Matrices Functional Theory (1RDMFT) and Optimal Transport (OT), by interpreting the problem of computing the ground-state energy of a finite dimensional composite quantum system at positive temperature as a non-commutative entropy regularized Optimal Transport problem. We develop a new approach to fully characterize the dual-primal solutions in such non-commutative setting. The mathematical formalism is particularly relevant in quantum chemistry: numerical realizations of the many-electron ground state energy can be computed via a non-commutative version of Sinkhorn algorithm. Our approach allows to prove convergence and robustness of this algorithm, which, to our best knowledge, were unknown even in the two marginal case. Our methods are based on careful a priori estimates in the dual problem, which we believe to be of independent interest. Finally, the above results are extended in 1RDMFT setting, where bosonic or fermionic symmetry conditions are enforced on the problem.","lang":"eng"}],"month":"07","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2106.11217"}],"language":[{"iso":"eng"}],"publication_status":"submitted","ec_funded":1,"related_material":{"record":[{"id":"9733","status":"public","relation":"dissertation_contains"},{"status":"public","id":"10030","relation":"dissertation_contains"},{"status":"public","id":"12911","relation":"later_version"}]},"_id":"9792","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"preprint","ddc":["510"],"date_updated":"2023-11-14T13:21:01Z","department":[{"_id":"RoSe"},{"_id":"JaMa"}]},{"project":[{"grant_number":"715571","name":"Microglia action towards neuronal circuit formation and function in health and disease","call_identifier":"H2020","_id":"25D4A630-B435-11E9-9278-68D0E5697425"}],"citation":{"mla":"Maes, Margaret E., et al. “Optimizing AAV2/6 Microglial Targeting Identified Enhanced Efficiency in the Photoreceptor Degenerative Environment.” Molecular Therapy - Methods and Clinical Development, vol. 23, Elsevier, 2021, pp. 210–24, doi:10.1016/j.omtm.2021.09.006.","apa":"Maes, M. E., Wögenstein, G. M., Colombo, G., Casado Polanco, R., & Siegert, S. (2021). Optimizing AAV2/6 microglial targeting identified enhanced efficiency in the photoreceptor degenerative environment. Molecular Therapy - Methods and Clinical Development. Elsevier. https://doi.org/10.1016/j.omtm.2021.09.006","ama":"Maes ME, Wögenstein GM, Colombo G, Casado Polanco R, Siegert S. Optimizing AAV2/6 microglial targeting identified enhanced efficiency in the photoreceptor degenerative environment. Molecular Therapy - Methods and Clinical Development. 2021;23:210-224. doi:10.1016/j.omtm.2021.09.006","ieee":"M. E. Maes, G. M. Wögenstein, G. Colombo, R. Casado Polanco, and S. Siegert, “Optimizing AAV2/6 microglial targeting identified enhanced efficiency in the photoreceptor degenerative environment,” Molecular Therapy - Methods and Clinical Development, vol. 23. Elsevier, pp. 210–224, 2021.","short":"M.E. Maes, G.M. Wögenstein, G. Colombo, R. Casado Polanco, S. Siegert, Molecular Therapy - Methods and Clinical Development 23 (2021) 210–224.","chicago":"Maes, Margaret E, Gabriele M. Wögenstein, Gloria Colombo, Raquel Casado Polanco, and Sandra Siegert. “Optimizing AAV2/6 Microglial Targeting Identified Enhanced Efficiency in the Photoreceptor Degenerative Environment.” Molecular Therapy - Methods and Clinical Development. Elsevier, 2021. https://doi.org/10.1016/j.omtm.2021.09.006.","ista":"Maes ME, Wögenstein GM, Colombo G, Casado Polanco R, Siegert S. 2021. Optimizing AAV2/6 microglial targeting identified enhanced efficiency in the photoreceptor degenerative environment. Molecular Therapy - Methods and Clinical Development. 23, 210–224."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","external_id":{"isi":["000748748500019"]},"article_processing_charge":"Yes","author":[{"last_name":"Maes","full_name":"Maes, Margaret E","orcid":"0000-0001-9642-1085","id":"3838F452-F248-11E8-B48F-1D18A9856A87","first_name":"Margaret E"},{"full_name":"Wögenstein, Gabriele M.","last_name":"Wögenstein","first_name":"Gabriele M."},{"first_name":"Gloria","id":"3483CF6C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9434-8902","full_name":"Colombo, Gloria","last_name":"Colombo"},{"last_name":"Casado Polanco","orcid":"0000-0001-8293-4568","full_name":"Casado Polanco, Raquel","first_name":"Raquel","id":"15240fc1-dbcd-11ea-9d1d-ac5a786425fd"},{"first_name":"Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","last_name":"Siegert","orcid":"0000-0001-8635-0877","full_name":"Siegert, Sandra"}],"title":"Optimizing AAV2/6 microglial targeting identified enhanced efficiency in the photoreceptor degenerative environment","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. 715571). The research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Bioimaging Facility, the Life Science Facility, and the Pre-Clinical Facility, namely Sonja Haslinger and Michael Schunn for their animal colony management and support. We would also like to thank Chakrabarty Lab for sharing the plasmids for AAV2/6 production. Finally, we would like to thank the Siegert team members for discussion about the manuscript.","oa":1,"quality_controlled":"1","publisher":"Elsevier","year":"2021","isi":1,"has_accepted_license":"1","publication":"Molecular Therapy - Methods and Clinical Development","day":"10","page":"210-224","date_created":"2022-01-23T23:01:28Z","date_published":"2021-12-10T00:00:00Z","doi":"10.1016/j.omtm.2021.09.006","_id":"10655","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","date_updated":"2023-11-16T13:12:03Z","ddc":["570"],"department":[{"_id":"SaSi"},{"_id":"SiHi"}],"file_date_updated":"2022-01-24T07:43:09Z","abstract":[{"lang":"eng","text":"Adeno-associated viruses (AAVs) are widely used to deliver genetic material in vivo to distinct cell types such as neurons or glial cells, allowing for targeted manipulation. Transduction of microglia is mostly excluded from this strategy, likely due to the cells’ heterogeneous state upon environmental changes, which makes AAV design challenging. Here, we established the retina as a model system for microglial AAV validation and optimization. First, we show that AAV2/6 transduced microglia in both synaptic layers, where layer preference corresponds to the intravitreal or subretinal delivery method. Surprisingly, we observed significantly enhanced microglial transduction during photoreceptor degeneration. Thus, we modified the AAV6 capsid to reduce heparin binding by introducing four point mutations (K531E, R576Q, K493S, and K459S), resulting in increased microglial transduction in the outer plexiform layer. Finally, to improve microglial-specific transduction, we validated a Cre-dependent transgene delivery cassette for use in combination with the Cx3cr1CreERT2 mouse line. Together, our results provide a foundation for future studies optimizing AAV-mediated microglia transduction and highlight that environmental conditions influence microglial transduction efficiency.\r\n"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 23","month":"12","publication_status":"published","publication_identifier":{"eissn":["2329-0501"]},"language":[{"iso":"eng"}],"file":[{"creator":"cchlebak","file_size":4794147,"date_updated":"2022-01-24T07:43:09Z","file_name":"2021_MolTherMethodsClinDev_Maes.pdf","date_created":"2022-01-24T07:43:09Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"10657","checksum":"77dc540e8011c5475031bdf6ccef20a6"}],"ec_funded":1,"volume":23},{"oa":1,"publisher":"Elsevier ; Cell Press","quality_controlled":"1","acknowledgement":"This research was supported by the European Research Council (grant 715571 to S.S.). We thank Rouven Schulz, Michael Schunn, Claudia Gold, Gabriel Krens, Sarah Gorkiewicz, Margaret Maes, Jürgen Siegert, Marco Benevento, and Sara Oakeley for comments on the manuscript and the IST Austria Bioimaging Facility for the technical support.","date_created":"2021-12-19T23:01:32Z","doi":"10.1016/j.xpro.2021.101012","date_published":"2021-12-17T00:00:00Z","year":"2021","has_accepted_license":"1","publication":"STAR Protocols","day":"17","project":[{"call_identifier":"H2020","_id":"25D4A630-B435-11E9-9278-68D0E5697425","name":"Microglia action towards neuronal circuit formation and function in health and disease","grant_number":"715571"}],"article_number":"101012","article_processing_charge":"Yes","author":[{"full_name":"Venturino, Alessandro","orcid":"0000-0003-2356-9403","last_name":"Venturino","id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","first_name":"Alessandro"},{"full_name":"Siegert, Sandra","orcid":"0000-0001-8635-0877","last_name":"Siegert","first_name":"Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87"}],"title":"Minimally invasive protocols and quantification for microglia-mediated perineuronal net disassembly in mouse brain","citation":{"ista":"Venturino A, Siegert S. 2021. Minimally invasive protocols and quantification for microglia-mediated perineuronal net disassembly in mouse brain. STAR Protocols. 2(4), 101012.","chicago":"Venturino, Alessandro, and Sandra Siegert. “Minimally Invasive Protocols and Quantification for Microglia-Mediated Perineuronal Net Disassembly in Mouse Brain.” STAR Protocols. Elsevier ; Cell Press, 2021. https://doi.org/10.1016/j.xpro.2021.101012.","apa":"Venturino, A., & Siegert, S. (2021). Minimally invasive protocols and quantification for microglia-mediated perineuronal net disassembly in mouse brain. STAR Protocols. Elsevier ; Cell Press. https://doi.org/10.1016/j.xpro.2021.101012","ama":"Venturino A, Siegert S. Minimally invasive protocols and quantification for microglia-mediated perineuronal net disassembly in mouse brain. STAR Protocols. 2021;2(4). doi:10.1016/j.xpro.2021.101012","ieee":"A. Venturino and S. Siegert, “Minimally invasive protocols and quantification for microglia-mediated perineuronal net disassembly in mouse brain,” STAR Protocols, vol. 2, no. 4. Elsevier ; Cell Press, 2021.","short":"A. Venturino, S. Siegert, STAR Protocols 2 (2021).","mla":"Venturino, Alessandro, and Sandra Siegert. “Minimally Invasive Protocols and Quantification for Microglia-Mediated Perineuronal Net Disassembly in Mouse Brain.” STAR Protocols, vol. 2, no. 4, 101012, Elsevier ; Cell Press, 2021, doi:10.1016/j.xpro.2021.101012."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","intvolume":" 2","month":"12","acknowledged_ssus":[{"_id":"Bio"}],"abstract":[{"text":"Enzymatic digestion of the extracellular matrix with chondroitinase-ABC reinstates juvenile-like plasticity in the adult cortex as it also disassembles the perineuronal nets (PNNs). The disadvantage of the enzyme is that it must be applied intracerebrally and it degrades the ECM for several weeks. Here, we provide two minimally invasive and transient protocols for microglia-enabled PNN disassembly in mouse cortex: repeated treatment with ketamine-xylazine-acepromazine (KXA) anesthesia and 60-Hz light entrainment. We also discuss how to analyze PNNs within microglial endosomes-lysosomes. For complete details on the use and execution of this protocol, please refer to Venturino et al. (2021).","lang":"eng"}],"oa_version":"Published Version","ec_funded":1,"issue":"4","volume":2,"publication_status":"published","publication_identifier":{"eissn":["2666-1667"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2021-12-20T08:58:40Z","file_name":"2021_STARProt_Venturino.pdf","date_updated":"2021-12-20T08:58:40Z","file_size":6207060,"creator":"cchlebak","checksum":"9ea2501056c5df99e84726b845e9b976","file_id":"10570","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","_id":"10565","department":[{"_id":"SaSi"}],"file_date_updated":"2021-12-20T08:58:40Z","date_updated":"2023-11-16T13:11:04Z","ddc":["573"]},{"abstract":[{"text":"Mosaic analysis with double markers (MADM) technology enables the generation of genetic mosaic tissue in mice. MADM enables concomitant fluorescent cell labeling and introduction of a mutation of a gene of interest with single-cell resolution. This protocol highlights major steps for the generation of genetic mosaic tissue and the isolation and processing of respective tissues for downstream histological analysis. For complete details on the use and execution of this protocol, please refer to Contreras et al. (2021).","lang":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 2","month":"11","publication_status":"published","publication_identifier":{"eissn":["2666-1667"]},"language":[{"iso":"eng"}],"file":[{"file_name":"2021_STARProtocols_Amberg.pdf","date_created":"2021-11-22T08:23:58Z","file_size":7309464,"date_updated":"2021-11-22T08:23:58Z","creator":"cchlebak","success":1,"checksum":"9e3f6d06bf583e7a8b6a9e9a60500a28","file_id":"10329","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"ec_funded":1,"issue":"4","volume":2,"_id":"10321","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","date_updated":"2023-11-16T13:08:03Z","ddc":["573"],"department":[{"_id":"SiHi"}],"file_date_updated":"2021-11-22T08:23:58Z","acknowledgement":"This research was supported by the Scientific Service Units (SSU) at IST Austria through resources provided by the Bioimaging (BIF) and Preclinical Facilities (PCF). We particularly thank Mohammad Goudarzi for assistance with photography of mouse perfusion and dissection. N.A. received support from FWF Firnberg-Programm (T 1031). This work was also supported by IST Austria institutional funds; FWF SFB F78 to S.H.; and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 725780 LinPro) to S.H.","oa":1,"publisher":"Cell Press","quality_controlled":"1","year":"2021","has_accepted_license":"1","publication":"STAR Protocols","day":"10","date_created":"2021-11-21T23:01:28Z","date_published":"2021-11-10T00:00:00Z","doi":"10.1016/j.xpro.2021.100939","article_number":"100939","project":[{"grant_number":"725780","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Role of Eed in neural stem cell lineage progression","grant_number":"T0101031","call_identifier":"FWF","_id":"268F8446-B435-11E9-9278-68D0E5697425"},{"_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","grant_number":"F07805","name":"Molecular Mechanisms of Neural Stem Cell Lineage Progression"}],"citation":{"mla":"Amberg, Nicole, and Simon Hippenmeyer. “Genetic Mosaic Dissection of Candidate Genes in Mice Using Mosaic Analysis with Double Markers.” STAR Protocols, vol. 2, no. 4, 100939, Cell Press, 2021, doi:10.1016/j.xpro.2021.100939.","ieee":"N. Amberg and S. Hippenmeyer, “Genetic mosaic dissection of candidate genes in mice using mosaic analysis with double markers,” STAR Protocols, vol. 2, no. 4. Cell Press, 2021.","short":"N. Amberg, S. Hippenmeyer, STAR Protocols 2 (2021).","ama":"Amberg N, Hippenmeyer S. Genetic mosaic dissection of candidate genes in mice using mosaic analysis with double markers. STAR Protocols. 2021;2(4). doi:10.1016/j.xpro.2021.100939","apa":"Amberg, N., & Hippenmeyer, S. (2021). Genetic mosaic dissection of candidate genes in mice using mosaic analysis with double markers. STAR Protocols. Cell Press. https://doi.org/10.1016/j.xpro.2021.100939","chicago":"Amberg, Nicole, and Simon Hippenmeyer. “Genetic Mosaic Dissection of Candidate Genes in Mice Using Mosaic Analysis with Double Markers.” STAR Protocols. Cell Press, 2021. https://doi.org/10.1016/j.xpro.2021.100939.","ista":"Amberg N, Hippenmeyer S. 2021. Genetic mosaic dissection of candidate genes in mice using mosaic analysis with double markers. STAR Protocols. 2(4), 100939."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes","author":[{"last_name":"Amberg","orcid":"0000-0002-3183-8207","full_name":"Amberg, Nicole","first_name":"Nicole","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon"}],"title":"Genetic mosaic dissection of candidate genes in mice using mosaic analysis with double markers"},{"publisher":"Elsevier ","quality_controlled":"1","oa":1,"acknowledgement":"This research was supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the BioImaging Facility (BIF), and the Electron Microscopy Facility (EMF). We also thank Victor-Valentin Hodirnau for help with cryo-ET data acquisition. The authors acknowledge support from IST Austria and from the Austrian Science Fund (FWF): M02495 to G.D. and Austrian Science Fund (FWF): P33367 to F.K.M.S.","date_published":"2021-11-03T00:00:00Z","doi":"10.1016/j.jsb.2021.107808","date_created":"2021-11-15T12:21:42Z","isi":1,"has_accepted_license":"1","year":"2021","day":"03","publication":"Journal of Structural Biology","project":[{"_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367"},{"name":"Protein structure and function in filopodia across scales","grant_number":"M02495","_id":"2674F658-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"article_number":"107808","author":[{"id":"38C393BE-F248-11E8-B48F-1D18A9856A87","first_name":"Georgi A","orcid":"0000-0001-8370-6161","full_name":"Dimchev, Georgi A","last_name":"Dimchev"},{"first_name":"Behnam","full_name":"Amiri, Behnam","last_name":"Amiri"},{"id":"404F5528-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","last_name":"Fäßler","orcid":"0000-0001-7149-769X","full_name":"Fäßler, Florian"},{"first_name":"Martin","full_name":"Falcke, Martin","last_name":"Falcke"},{"last_name":"Schur","full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000720259500002"]},"title":"Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data","citation":{"chicago":"Dimchev, Georgi A, Behnam Amiri, Florian Fäßler, Martin Falcke, and Florian KM Schur. “Computational Toolbox for Ultrastructural Quantitative Analysis of Filament Networks in Cryo-ET Data.” Journal of Structural Biology. Elsevier , 2021. https://doi.org/10.1016/j.jsb.2021.107808.","ista":"Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. 2021. Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. Journal of Structural Biology. 213(4), 107808.","mla":"Dimchev, Georgi A., et al. “Computational Toolbox for Ultrastructural Quantitative Analysis of Filament Networks in Cryo-ET Data.” Journal of Structural Biology, vol. 213, no. 4, 107808, Elsevier , 2021, doi:10.1016/j.jsb.2021.107808.","ama":"Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. Journal of Structural Biology. 2021;213(4). doi:10.1016/j.jsb.2021.107808","apa":"Dimchev, G. A., Amiri, B., Fäßler, F., Falcke, M., & Schur, F. K. (2021). Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. Journal of Structural Biology. Elsevier . https://doi.org/10.1016/j.jsb.2021.107808","short":"G.A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, F.K. Schur, Journal of Structural Biology 213 (2021).","ieee":"G. A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, and F. K. Schur, “Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data,” Journal of Structural Biology, vol. 213, no. 4. Elsevier , 2021."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","month":"11","intvolume":" 213","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"abstract":[{"lang":"eng","text":"A precise quantitative description of the ultrastructural characteristics underlying biological mechanisms is often key to their understanding. This is particularly true for dynamic extra- and intracellular filamentous assemblies, playing a role in cell motility, cell integrity, cytokinesis, tissue formation and maintenance. For example, genetic manipulation or modulation of actin regulatory proteins frequently manifests in changes of the morphology, dynamics, and ultrastructural architecture of actin filament-rich cell peripheral structures, such as lamellipodia or filopodia. However, the observed ultrastructural effects often remain subtle and require sufficiently large datasets for appropriate quantitative analysis. The acquisition of such large datasets has been enabled by recent advances in high-throughput cryo-electron tomography (cryo-ET) methods. This also necessitates the development of complementary approaches to maximize the extraction of relevant biological information. We have developed a computational toolbox for the semi-automatic quantification of segmented and vectorized filamentous networks from pre-processed cryo-electron tomograms, facilitating the analysis and cross-comparison of multiple experimental conditions. GUI-based components simplify the processing of data and allow users to obtain a large number of ultrastructural parameters describing filamentous assemblies. We demonstrate the feasibility of this workflow by analyzing cryo-ET data of untreated and chemically perturbed branched actin filament networks and that of parallel actin filament arrays. In principle, the computational toolbox presented here is applicable for data analysis comprising any type of filaments in regular (i.e. parallel) or random arrangement. We show that it can ease the identification of key differences between experimental groups and facilitate the in-depth analysis of ultrastructural data in a time-efficient manner."}],"oa_version":"Published Version","related_material":{"record":[{"relation":"software","id":"14502","status":"public"}]},"issue":"4","volume":213,"publication_identifier":{"issn":["1047-8477"]},"publication_status":"published","file":[{"creator":"cchlebak","date_updated":"2021-11-15T13:11:27Z","file_size":16818304,"date_created":"2021-11-15T13:11:27Z","file_name":"2021_JournalStructBiol_Dimchev.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"6b209e4d44775d4e02b50f78982c15fa","file_id":"10291","success":1}],"language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","keyword":["Structural Biology"],"_id":"10290","file_date_updated":"2021-11-15T13:11:27Z","department":[{"_id":"FlSc"}],"date_updated":"2023-11-21T08:36:02Z","ddc":["572"]},{"oa":1,"quality_controlled":"1","publisher":"IEEE","date_created":"2021-08-29T22:01:16Z","date_published":"2021-06-21T00:00:00Z","doi":"10.23919/IFIPNetworking52078.2021.9472205","day":"21","year":"2021","isi":1,"project":[{"name":"Teaching Old Crypto New Tricks","grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"title":"LightPIR: Privacy-preserving route discovery for payment channel networks","article_processing_charge":"No","external_id":{"arxiv":["2104.04293"],"isi":["000853016800008"]},"author":[{"first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654"},{"last_name":"Salem","full_name":"Salem, Iosif","first_name":"Iosif"},{"full_name":"Schmid, Stefan","last_name":"Schmid","first_name":"Stefan"},{"last_name":"Yeo","full_name":"Yeo, Michelle X","id":"2D82B818-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle X"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Pietrzak, Krzysztof Z, Iosif Salem, Stefan Schmid, and Michelle X Yeo. “LightPIR: Privacy-Preserving Route Discovery for Payment Channel Networks.” IEEE, 2021. https://doi.org/10.23919/IFIPNetworking52078.2021.9472205.","ista":"Pietrzak KZ, Salem I, Schmid S, Yeo MX. 2021. LightPIR: Privacy-preserving route discovery for payment channel networks. 2021 IFIP Networking Conference (IFIP Networking).","mla":"Pietrzak, Krzysztof Z., et al. LightPIR: Privacy-Preserving Route Discovery for Payment Channel Networks. IEEE, 2021, doi:10.23919/IFIPNetworking52078.2021.9472205.","ieee":"K. Z. Pietrzak, I. Salem, S. Schmid, and M. X. Yeo, “LightPIR: Privacy-preserving route discovery for payment channel networks,” presented at the 2021 IFIP Networking Conference (IFIP Networking), Espoo and Helsinki, Finland, 2021.","short":"K.Z. Pietrzak, I. Salem, S. Schmid, M.X. Yeo, in:, IEEE, 2021.","ama":"Pietrzak KZ, Salem I, Schmid S, Yeo MX. LightPIR: Privacy-preserving route discovery for payment channel networks. In: IEEE; 2021. doi:10.23919/IFIPNetworking52078.2021.9472205","apa":"Pietrzak, K. Z., Salem, I., Schmid, S., & Yeo, M. X. (2021). LightPIR: Privacy-preserving route discovery for payment channel networks. Presented at the 2021 IFIP Networking Conference (IFIP Networking), Espoo and Helsinki, Finland: IEEE. https://doi.org/10.23919/IFIPNetworking52078.2021.9472205"},"month":"06","main_file_link":[{"url":"https://arxiv.org/abs/2104.04293","open_access":"1"}],"scopus_import":"1","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Payment channel networks are a promising approach to improve the scalability of cryptocurrencies: they allow to perform transactions in a peer-to-peer fashion, along multihop routes in the network, without requiring consensus on the blockchain. However, during the discovery of cost-efficient routes for the transaction, critical information may be revealed about the transacting entities. This paper initiates the study of privacy-preserving route discovery mechanisms for payment channel networks. In particular, we present LightPIR, an approach which allows a client to learn the shortest (or cheapest in terms of fees) path between two nodes without revealing any information about the endpoints of the transaction to the servers. The two main observations which allow for an efficient solution in LightPIR are that: (1) surprisingly, hub labelling algorithms – which were developed to preprocess “street network like” graphs so one can later efficiently compute shortest paths – also perform well for the graphs underlying payment channel networks, and that (2) hub labelling algorithms can be conveniently combined with private information retrieval. LightPIR relies on a simple hub labeling heuristic on top of existing hub labeling algorithms which leverages the specific topological features of cryptocurrency networks to further minimize storage and bandwidth overheads. In a case study considering the Lightning network, we show that our approach is an order of magnitude more efficient compared to a privacy-preserving baseline based on using private information retrieval on a database that stores all pairs shortest paths."}],"ec_funded":1,"related_material":{"record":[{"id":"14506","status":"public","relation":"dissertation_contains"}]},"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1861-2288"],"isbn":["978-1-6654-4501-6"],"eisbn":["978-3-9031-7639-3"]},"status":"public","conference":{"name":"2021 IFIP Networking Conference (IFIP Networking)","end_date":"2021-06-24","location":"Espoo and Helsinki, Finland","start_date":"2021-06-21"},"type":"conference","_id":"9969","department":[{"_id":"KrPi"}],"date_updated":"2023-11-30T10:54:50Z"},{"citation":{"chicago":"Chatterjee, Krishnendu, Ehsan Kafshdar Goharshady, Petr Novotný, and Dorde Zikelic. “Proving Non-Termination by Program Reversal.” In Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, 1033–48. Association for Computing Machinery, 2021. https://doi.org/10.1145/3453483.3454093.","ista":"Chatterjee K, Goharshady EK, Novotný P, Zikelic D. 2021. Proving non-termination by program reversal. Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation. PLDI: Programming Language Design and Implementation, 1033–1048.","mla":"Chatterjee, Krishnendu, et al. “Proving Non-Termination by Program Reversal.” Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2021, pp. 1033–48, doi:10.1145/3453483.3454093.","ama":"Chatterjee K, Goharshady EK, Novotný P, Zikelic D. Proving non-termination by program reversal. In: Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation. Association for Computing Machinery; 2021:1033-1048. doi:10.1145/3453483.3454093","apa":"Chatterjee, K., Goharshady, E. K., Novotný, P., & Zikelic, D. (2021). Proving non-termination by program reversal. In Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation (pp. 1033–1048). Online: Association for Computing Machinery. https://doi.org/10.1145/3453483.3454093","ieee":"K. Chatterjee, E. K. Goharshady, P. Novotný, and D. Zikelic, “Proving non-termination by program reversal,” in Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Online, 2021, pp. 1033–1048.","short":"K. Chatterjee, E.K. Goharshady, P. Novotný, D. Zikelic, in:, Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2021, pp. 1033–1048."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"isi":["000723661700067"],"arxiv":["2104.01189"]},"author":[{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"first_name":"Ehsan Kafshdar","full_name":"Goharshady, Ehsan Kafshdar","last_name":"Goharshady"},{"first_name":"Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","last_name":"Novotný","full_name":"Novotný, Petr"},{"first_name":"Dorde","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","last_name":"Zikelic","orcid":"0000-0002-4681-1699","full_name":"Zikelic, Dorde"}],"title":"Proving non-termination by program reversal","project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications"}],"year":"2021","isi":1,"publication":"Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation","day":"01","page":"1033-1048","date_created":"2021-07-11T22:01:17Z","date_published":"2021-06-01T00:00:00Z","doi":"10.1145/3453483.3454093","acknowledgement":"We thank the anonymous reviewers for their helpful comments. This research was partially supported by the ERCCoG 863818 (ForM-SMArt) and the Czech Science Foundation grant No. GJ19-15134Y.","oa":1,"publisher":"Association for Computing Machinery","quality_controlled":"1","date_updated":"2023-11-30T10:55:37Z","department":[{"_id":"KrCh"}],"_id":"9644","conference":{"location":"Online","end_date":"2021-06-26","start_date":"2021-06-20","name":"PLDI: Programming Language Design and Implementation"},"type":"conference","status":"public","publication_status":"published","publication_identifier":{"isbn":["9781450383912"]},"language":[{"iso":"eng"}],"ec_funded":1,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"14539"}]},"abstract":[{"lang":"eng","text":"We present a new approach to proving non-termination of non-deterministic integer programs. Our technique is rather simple but efficient. It relies on a purely syntactic reversal of the program's transition system followed by a constraint-based invariant synthesis with constraints coming from both the original and the reversed transition system. The latter task is performed by a simple call to an off-the-shelf SMT-solver, which allows us to leverage the latest advances in SMT-solving. Moreover, our method offers a combination of features not present (as a whole) in previous approaches: it handles programs with non-determinism, provides relative completeness guarantees and supports programs with polynomial arithmetic. The experiments performed with our prototype tool RevTerm show that our approach, despite its simplicity and stronger theoretical guarantees, is at least on par with the state-of-the-art tools, often achieving a non-trivial improvement under a proper configuration of its parameters."}],"oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/2104.01189","open_access":"1"}],"scopus_import":"1","month":"06"},{"_id":"9760","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","ddc":["530"],"date_updated":"2023-12-13T14:47:25Z","department":[{"_id":"GradSch"},{"_id":"MaSe"}],"file_date_updated":"2021-08-06T06:44:31Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"The quantum approximate optimization algorithm (QAOA) is a prospective near-term quantum algorithm due to its modest circuit depth and promising benchmarks. However, an external parameter optimization required in the QAOA could become a performance bottleneck. This motivates studies of the optimization landscape and search for heuristic ways of parameter initialization. In this work we visualize the optimization landscape of the QAOA applied to the MaxCut problem on random graphs, demonstrating that random initialization of the QAOA is prone to converging to local minima with suboptimal performance. We introduce the initialization of QAOA parameters based on the Trotterized quantum annealing (TQA) protocol, parameterized by the Trotter time step. We find that the TQA initialization allows to circumvent\r\nthe issue of false minima for a broad range of time steps, yielding the same performance as the best result out of an exponentially scaling number of random initializations. Moreover, we demonstrate that the optimal value of the time step coincides with the point of proliferation of Trotter errors in quantum annealing. Our results suggest practical ways of initializing QAOA protocols on near-term quantum devices and reveal new connections between QAOA and quantum annealing."}],"intvolume":" 5","month":"07","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"creator":"cchlebak","file_size":2312482,"date_updated":"2021-08-06T06:44:31Z","file_name":"2021_Quantum_Sack.pdf","date_created":"2021-08-06T06:44:31Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"9706c2bb8e748e9b5b138381995a7f6f","file_id":"9774"}],"publication_status":"published","publication_identifier":{"eissn":["2521-327X"]},"ec_funded":1,"volume":5,"related_material":{"record":[{"id":"14622","status":"public","relation":"dissertation_contains"}]},"article_number":"491","project":[{"_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020","grant_number":"850899","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Sack S, Serbyn M. 2021. Quantum annealing initialization of the quantum approximate optimization algorithm. Quantum. 5, 491.","chicago":"Sack, Stefan, and Maksym Serbyn. “Quantum Annealing Initialization of the Quantum Approximate Optimization Algorithm.” Quantum. Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften, 2021. https://doi.org/10.22331/Q-2021-07-01-491.","apa":"Sack, S., & Serbyn, M. (2021). Quantum annealing initialization of the quantum approximate optimization algorithm. Quantum. Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften. https://doi.org/10.22331/Q-2021-07-01-491","ama":"Sack S, Serbyn M. Quantum annealing initialization of the quantum approximate optimization algorithm. Quantum. 2021;5. doi:10.22331/Q-2021-07-01-491","short":"S. Sack, M. Serbyn, Quantum 5 (2021).","ieee":"S. Sack and M. Serbyn, “Quantum annealing initialization of the quantum approximate optimization algorithm,” Quantum, vol. 5. Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften, 2021.","mla":"Sack, Stefan, and Maksym Serbyn. “Quantum Annealing Initialization of the Quantum Approximate Optimization Algorithm.” Quantum, vol. 5, 491, Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften, 2021, doi:10.22331/Q-2021-07-01-491."},"title":"Quantum annealing initialization of the quantum approximate optimization algorithm","external_id":{"isi":["000669830600001"],"arxiv":["2101.05742"]},"article_processing_charge":"Yes","author":[{"first_name":"Stefan","id":"dd622248-f6e0-11ea-865d-ce382a1c81a5","full_name":"Sack, Stefan","orcid":"0000-0001-5400-8508","last_name":"Sack"},{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym","full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","last_name":"Serbyn"}],"acknowledgement":"We would like to thank D. Abanin and R. Medina for fruitful discussions and A. Smith and I. Kim for valuable feedback on the manuscript. We acknowledge support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899).","oa":1,"quality_controlled":"1","publisher":"Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften","publication":"Quantum","day":"01","year":"2021","isi":1,"has_accepted_license":"1","date_created":"2021-08-01T22:01:21Z","doi":"10.22331/Q-2021-07-01-491","date_published":"2021-07-01T00:00:00Z"},{"page":"619-639","date_created":"2021-12-05T23:01:45Z","doi":"10.1007/978-3-030-90870-6_33","date_published":"2021-11-10T00:00:00Z","year":"2021","isi":1,"publication":"24th International Symposium on Formal Methods","day":"10","oa":1,"publisher":"Springer Nature","quality_controlled":"1","acknowledgement":"This research was partially supported by the ERC CoG 863818 (ForM-SMArt), the Czech Science Foundation grant No. GJ19-15134Y, and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.","article_processing_charge":"No","external_id":{"isi":["000758218600033"],"arxiv":["2108.02188"]},"author":[{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"last_name":"Goharshady","full_name":"Goharshady, Ehsan Kafshdar","first_name":"Ehsan Kafshdar"},{"id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","first_name":"Petr","last_name":"Novotný","full_name":"Novotný, Petr"},{"last_name":"Zárevúcky","full_name":"Zárevúcky, Jiří","first_name":"Jiří"},{"full_name":"Zikelic, Dorde","orcid":"0000-0002-4681-1699","last_name":"Zikelic","first_name":"Dorde","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87"}],"title":"On lexicographic proof rules for probabilistic termination","citation":{"mla":"Chatterjee, Krishnendu, et al. “On Lexicographic Proof Rules for Probabilistic Termination.” 24th International Symposium on Formal Methods, vol. 13047, Springer Nature, 2021, pp. 619–39, doi:10.1007/978-3-030-90870-6_33.","apa":"Chatterjee, K., Goharshady, E. K., Novotný, P., Zárevúcky, J., & Zikelic, D. (2021). On lexicographic proof rules for probabilistic termination. In 24th International Symposium on Formal Methods (Vol. 13047, pp. 619–639). Virtual: Springer Nature. https://doi.org/10.1007/978-3-030-90870-6_33","ama":"Chatterjee K, Goharshady EK, Novotný P, Zárevúcky J, Zikelic D. On lexicographic proof rules for probabilistic termination. In: 24th International Symposium on Formal Methods. Vol 13047. Springer Nature; 2021:619-639. doi:10.1007/978-3-030-90870-6_33","short":"K. Chatterjee, E.K. Goharshady, P. Novotný, J. Zárevúcky, D. Zikelic, in:, 24th International Symposium on Formal Methods, Springer Nature, 2021, pp. 619–639.","ieee":"K. Chatterjee, E. K. Goharshady, P. Novotný, J. Zárevúcky, and D. Zikelic, “On lexicographic proof rules for probabilistic termination,” in 24th International Symposium on Formal Methods, Virtual, 2021, vol. 13047, pp. 619–639.","chicago":"Chatterjee, Krishnendu, Ehsan Kafshdar Goharshady, Petr Novotný, Jiří Zárevúcky, and Dorde Zikelic. “On Lexicographic Proof Rules for Probabilistic Termination.” In 24th International Symposium on Formal Methods, 13047:619–39. Springer Nature, 2021. https://doi.org/10.1007/978-3-030-90870-6_33.","ista":"Chatterjee K, Goharshady EK, Novotný P, Zárevúcky J, Zikelic D. 2021. On lexicographic proof rules for probabilistic termination. 24th International Symposium on Formal Methods. FM: Formal Methods, LNCS, vol. 13047, 619–639."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"},{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"ec_funded":1,"volume":13047,"related_material":{"record":[{"relation":"dissertation_contains","id":"14539","status":"public"},{"status":"public","id":"14778","relation":"later_version"}]},"publication_status":"published","publication_identifier":{"eisbn":["978-3-030-90870-6"],"isbn":["9-783-0309-0869-0"],"eissn":["1611-3349"],"issn":["0302-9743"]},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/2108.02188","open_access":"1"}],"scopus_import":"1","alternative_title":["LNCS"],"intvolume":" 13047","month":"11","abstract":[{"lang":"eng","text":"We consider the almost-sure (a.s.) termination problem for probabilistic programs, which are a stochastic extension of classical imperative programs. Lexicographic ranking functions provide a sound and practical approach for termination of non-probabilistic programs, and their extension to probabilistic programs is achieved via lexicographic ranking supermartingales (LexRSMs). However, LexRSMs introduced in the previous work have a limitation that impedes their automation: all of their components have to be non-negative in all reachable states. This might result in LexRSM not existing even for simple terminating programs. Our contributions are twofold: First, we introduce a generalization of LexRSMs which allows for some components to be negative. This standard feature of non-probabilistic termination proofs was hitherto not known to be sound in the probabilistic setting, as the soundness proof requires a careful analysis of the underlying stochastic process. Second, we present polynomial-time algorithms using our generalized LexRSMs for proving a.s. termination in broad classes of linear-arithmetic programs."}],"oa_version":"Preprint","department":[{"_id":"KrCh"}],"date_updated":"2024-01-17T08:19:41Z","conference":{"start_date":"2021-11-20","location":"Virtual","end_date":"2021-11-26","name":"FM: Formal Methods"},"type":"conference","status":"public","_id":"10414"},{"article_number":"2108017","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Chang, Cheng, et al. “Recent Progress on Two-Dimensional Materials.” Acta Physico-Chimica Sinica, vol. 37, no. 12, 2108017, Peking University, 2021, doi:10.3866/PKU.WHXB202108017.","ieee":"C. Chang et al., “Recent progress on two-dimensional materials,” Acta Physico-Chimica Sinica, vol. 37, no. 12. Peking University, 2021.","short":"C. Chang, W. Chen, Y. Chen, Y. Chen, Y. Chen, F. Ding, C. Fan, H.J. Fan, Z. Fan, C. Gong, Y. Gong, Q. He, X. Hong, S. Hu, W. Hu, W. Huang, Y. Huang, W. Ji, D. Li, L.J. Li, Q. Li, L. Lin, C. Ling, M. Liu, N. Liu, Z. Liu, K.P. Loh, J. Ma, F. Miao, H. Peng, M. Shao, L. Song, S. Su, S. Sun, C. Tan, Z. Tang, D. Wang, H. Wang, J. Wang, X. Wang, X. Wang, A.T.S. Wee, Z. Wei, Y. Wu, Z.S. Wu, J. Xiong, Q. Xiong, W. Xu, P. Yin, H. Zeng, Z. Zeng, T. Zhai, H. Zhang, H. Zhang, Q. Zhang, T. Zhang, X. Zhang, L.D. Zhao, M. Zhao, W. Zhao, Y. Zhao, K.G. Zhou, X. Zhou, Y. Zhou, H. Zhu, H. Zhang, Z. Liu, Acta Physico-Chimica Sinica 37 (2021).","apa":"Chang, C., Chen, W., Chen, Y., Chen, Y., Chen, Y., Ding, F., … Liu, Z. (2021). Recent progress on two-dimensional materials. Acta Physico-Chimica Sinica. Peking University. https://doi.org/10.3866/PKU.WHXB202108017","ama":"Chang C, Chen W, Chen Y, et al. Recent progress on two-dimensional materials. Acta Physico-Chimica Sinica. 2021;37(12). doi:10.3866/PKU.WHXB202108017","chicago":"Chang, Cheng, Wei Chen, Ye Chen, Yonghua Chen, Yu Chen, Feng Ding, Chunhai Fan, et al. “Recent Progress on Two-Dimensional Materials.” Acta Physico-Chimica Sinica. Peking University, 2021. https://doi.org/10.3866/PKU.WHXB202108017.","ista":"Chang C, Chen W, Chen Y, Chen Y, Chen Y, Ding F, Fan C, Fan HJ, Fan Z, Gong C, Gong Y, He Q, Hong X, Hu S, Hu W, Huang W, Huang Y, Ji W, Li D, Li LJ, Li Q, Lin L, Ling C, Liu M, Liu N, Liu Z, Loh KP, Ma J, Miao F, Peng H, Shao M, Song L, Su S, Sun S, Tan C, Tang Z, Wang D, Wang H, Wang J, Wang X, Wang X, Wee ATS, Wei Z, Wu Y, Wu ZS, Xiong J, Xiong Q, Xu W, Yin P, Zeng H, Zeng Z, Zhai T, Zhang H, Zhang H, Zhang Q, Zhang T, Zhang X, Zhao LD, Zhao M, Zhao W, Zhao Y, Zhou KG, Zhou X, Zhou Y, Zhu H, Zhang H, Liu Z. 2021. Recent progress on two-dimensional materials. Acta Physico-Chimica Sinica. 37(12), 2108017."},"title":"Recent progress on two-dimensional materials","author":[{"first_name":"Cheng","id":"9E331C2E-9F27-11E9-AE48-5033E6697425","last_name":"Chang","full_name":"Chang, Cheng","orcid":"0000-0002-9515-4277"},{"first_name":"Wei","last_name":"Chen","full_name":"Chen, Wei"},{"last_name":"Chen","full_name":"Chen, Ye","first_name":"Ye"},{"first_name":"Yonghua","last_name":"Chen","full_name":"Chen, Yonghua"},{"first_name":"Yu","last_name":"Chen","full_name":"Chen, Yu"},{"full_name":"Ding, Feng","last_name":"Ding","first_name":"Feng"},{"first_name":"Chunhai","full_name":"Fan, Chunhai","last_name":"Fan"},{"last_name":"Fan","full_name":"Fan, Hong Jin","first_name":"Hong Jin"},{"first_name":"Zhanxi","full_name":"Fan, Zhanxi","last_name":"Fan"},{"first_name":"Cheng","full_name":"Gong, Cheng","last_name":"Gong"},{"last_name":"Gong","full_name":"Gong, Yongji","first_name":"Yongji"},{"first_name":"Qiyuan","full_name":"He, Qiyuan","last_name":"He"},{"first_name":"Xun","last_name":"Hong","full_name":"Hong, Xun"},{"last_name":"Hu","full_name":"Hu, Sheng","first_name":"Sheng"},{"first_name":"Weida","last_name":"Hu","full_name":"Hu, Weida"},{"last_name":"Huang","full_name":"Huang, Wei","first_name":"Wei"},{"first_name":"Yuan","last_name":"Huang","full_name":"Huang, Yuan"},{"first_name":"Wei","last_name":"Ji","full_name":"Ji, Wei"},{"last_name":"Li","full_name":"Li, Dehui","first_name":"Dehui"},{"last_name":"Li","full_name":"Li, Lain Jong","first_name":"Lain Jong"},{"first_name":"Qiang","last_name":"Li","full_name":"Li, Qiang"},{"first_name":"Li","last_name":"Lin","full_name":"Lin, Li"},{"full_name":"Ling, Chongyi","last_name":"Ling","first_name":"Chongyi"},{"full_name":"Liu, Minghua","last_name":"Liu","first_name":"Minghua"},{"last_name":"Liu","full_name":"Liu, Nan","first_name":"Nan"},{"first_name":"Zhuang","full_name":"Liu, Zhuang","last_name":"Liu"},{"first_name":"Kian Ping","last_name":"Loh","full_name":"Loh, Kian Ping"},{"first_name":"Jianmin","full_name":"Ma, Jianmin","last_name":"Ma"},{"last_name":"Miao","full_name":"Miao, Feng","first_name":"Feng"},{"first_name":"Hailin","last_name":"Peng","full_name":"Peng, Hailin"},{"first_name":"Mingfei","full_name":"Shao, Mingfei","last_name":"Shao"},{"full_name":"Song, Li","last_name":"Song","first_name":"Li"},{"full_name":"Su, Shao","last_name":"Su","first_name":"Shao"},{"full_name":"Sun, Shuo","last_name":"Sun","first_name":"Shuo"},{"first_name":"Chaoliang","last_name":"Tan","full_name":"Tan, Chaoliang"},{"full_name":"Tang, Zhiyong","last_name":"Tang","first_name":"Zhiyong"},{"full_name":"Wang, Dingsheng","last_name":"Wang","first_name":"Dingsheng"},{"first_name":"Huan","last_name":"Wang","full_name":"Wang, Huan"},{"full_name":"Wang, Jinlan","last_name":"Wang","first_name":"Jinlan"},{"first_name":"Xin","full_name":"Wang, Xin","last_name":"Wang"},{"first_name":"Xinran","last_name":"Wang","full_name":"Wang, Xinran"},{"full_name":"Wee, Andrew T.S.","last_name":"Wee","first_name":"Andrew T.S."},{"last_name":"Wei","full_name":"Wei, Zhongming","first_name":"Zhongming"},{"last_name":"Wu","full_name":"Wu, Yuen","first_name":"Yuen"},{"last_name":"Wu","full_name":"Wu, Zhong Shuai","first_name":"Zhong Shuai"},{"first_name":"Jie","last_name":"Xiong","full_name":"Xiong, Jie"},{"last_name":"Xiong","full_name":"Xiong, Qihua","first_name":"Qihua"},{"last_name":"Xu","full_name":"Xu, Weigao","first_name":"Weigao"},{"first_name":"Peng","last_name":"Yin","full_name":"Yin, Peng"},{"last_name":"Zeng","full_name":"Zeng, Haibo","first_name":"Haibo"},{"first_name":"Zhiyuan","last_name":"Zeng","full_name":"Zeng, Zhiyuan"},{"first_name":"Tianyou","full_name":"Zhai, Tianyou","last_name":"Zhai"},{"first_name":"Han","last_name":"Zhang","full_name":"Zhang, Han"},{"last_name":"Zhang","full_name":"Zhang, Hui","first_name":"Hui"},{"full_name":"Zhang, Qichun","last_name":"Zhang","first_name":"Qichun"},{"last_name":"Zhang","full_name":"Zhang, Tierui","first_name":"Tierui"},{"last_name":"Zhang","full_name":"Zhang, Xiang","first_name":"Xiang"},{"full_name":"Zhao, Li Dong","last_name":"Zhao","first_name":"Li Dong"},{"first_name":"Meiting","full_name":"Zhao, Meiting","last_name":"Zhao"},{"full_name":"Zhao, Weijie","last_name":"Zhao","first_name":"Weijie"},{"full_name":"Zhao, Yunxuan","last_name":"Zhao","first_name":"Yunxuan"},{"last_name":"Zhou","full_name":"Zhou, Kai Ge","first_name":"Kai Ge"},{"full_name":"Zhou, Xing","last_name":"Zhou","first_name":"Xing"},{"first_name":"Yu","full_name":"Zhou, Yu","last_name":"Zhou"},{"first_name":"Hongwei","last_name":"Zhu","full_name":"Zhu, Hongwei"},{"first_name":"Hua","last_name":"Zhang","full_name":"Zhang, Hua"},{"first_name":"Zhongfan","full_name":"Liu, Zhongfan","last_name":"Liu"}],"article_processing_charge":"No","quality_controlled":"1","publisher":"Peking University","oa":1,"day":"13","publication":"Acta Physico-Chimica Sinica","year":"2021","doi":"10.3866/PKU.WHXB202108017","date_published":"2021-10-13T00:00:00Z","date_created":"2024-01-14T23:00:58Z","_id":"14800","status":"public","article_type":"review","type":"journal_article","date_updated":"2024-01-17T11:29:33Z","department":[{"_id":"MaIb"}],"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Research on two-dimensional (2D) materials has been explosively increasing in last seventeen years in varying subjects including condensed matter physics, electronic engineering, materials science, and chemistry since the mechanical exfoliation of graphene in 2004. Starting from graphene, 2D materials now have become a big family with numerous members and diverse categories. The unique structural features and physicochemical properties of 2D materials make them one class of the most appealing candidates for a wide range of potential applications. In particular, we have seen some major breakthroughs made in the field of 2D materials in last five years not only in developing novel synthetic methods and exploring new structures/properties but also in identifying innovative applications and pushing forward commercialisation. In this review, we provide a critical summary on the recent progress made in the field of 2D materials with a particular focus on last five years. After a brief background introduction, we first discuss the major synthetic methods for 2D materials, including the mechanical exfoliation, liquid exfoliation, vapor phase deposition, and wet-chemical synthesis as well as phase engineering of 2D materials belonging to the field of phase engineering of nanomaterials (PEN). We then introduce the superconducting/optical/magnetic properties and chirality of 2D materials along with newly emerging magic angle 2D superlattices. Following that, the promising applications of 2D materials in electronics, optoelectronics, catalysis, energy storage, solar cells, biomedicine, sensors, environments, etc. are described sequentially. Thereafter, we present the theoretic calculations and simulations of 2D materials. Finally, after concluding the current progress, we provide some personal discussions on the existing challenges and future outlooks in this rapidly developing field. "}],"month":"10","intvolume":" 37","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.3866/PKU.WHXB202108017"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1001-4861"]},"publication_status":"published","issue":"12","volume":37},{"date_published":"2021-10-06T00:00:00Z","doi":"10.1007/978-3-030-88494-9_3","date_created":"2021-10-31T23:01:31Z","page":"42-61","day":"06","publication":"21st International Conference on Runtime Verification","isi":1,"year":"2021","publisher":"Springer Nature","quality_controlled":"1","oa":1,"acknowledgement":"We thank Christoph Lampert and Alex Greengold for fruitful discussions. This research was supported in part by the Simons Institute for the Theory of Computing, the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award), and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411.","title":"Into the unknown: active monitoring of neural networks","author":[{"first_name":"Anna","id":"CBA4D1A8-0FE8-11E9-BDE6-07BFE5697425","full_name":"Lukina, Anna","last_name":"Lukina"},{"last_name":"Schilling","orcid":"0000-0003-3658-1065","full_name":"Schilling, Christian","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","first_name":"Christian"},{"full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"}],"article_processing_charge":"No","external_id":{"isi":["000719383800003"],"arxiv":["2009.06429"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Lukina A, Schilling C, Henzinger TA. 2021. Into the unknown: active monitoring of neural networks. 21st International Conference on Runtime Verification. RV: Runtime Verification, LNCS, vol. 12974, 42–61.","chicago":"Lukina, Anna, Christian Schilling, and Thomas A Henzinger. “Into the Unknown: Active Monitoring of Neural Networks.” In 21st International Conference on Runtime Verification, 12974:42–61. Cham: Springer Nature, 2021. https://doi.org/10.1007/978-3-030-88494-9_3.","apa":"Lukina, A., Schilling, C., & Henzinger, T. A. (2021). Into the unknown: active monitoring of neural networks. In 21st International Conference on Runtime Verification (Vol. 12974, pp. 42–61). Cham: Springer Nature. https://doi.org/10.1007/978-3-030-88494-9_3","ama":"Lukina A, Schilling C, Henzinger TA. Into the unknown: active monitoring of neural networks. In: 21st International Conference on Runtime Verification. Vol 12974. Cham: Springer Nature; 2021:42-61. doi:10.1007/978-3-030-88494-9_3","short":"A. Lukina, C. Schilling, T.A. Henzinger, in:, 21st International Conference on Runtime Verification, Springer Nature, Cham, 2021, pp. 42–61.","ieee":"A. Lukina, C. Schilling, and T. A. Henzinger, “Into the unknown: active monitoring of neural networks,” in 21st International Conference on Runtime Verification, Virtual, 2021, vol. 12974, pp. 42–61.","mla":"Lukina, Anna, et al. “Into the Unknown: Active Monitoring of Neural Networks.” 21st International Conference on Runtime Verification, vol. 12974, Springer Nature, 2021, pp. 42–61, doi:10.1007/978-3-030-88494-9_3."},"project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"name":"The Wittgenstein Prize","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"related_material":{"record":[{"id":"13234","status":"public","relation":"extended_version"}]},"volume":"12974 ","ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0302-9743"],"isbn":["9-783-0308-8493-2"],"eissn":["1611-3349"],"eisbn":["978-3-030-88494-9"]},"publication_status":"published","month":"10","place":"Cham","alternative_title":["LNCS"],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2009.06429"}],"oa_version":"Preprint","abstract":[{"text":"Neural-network classifiers achieve high accuracy when predicting the class of an input that they were trained to identify. Maintaining this accuracy in dynamic environments, where inputs frequently fall outside the fixed set of initially known classes, remains a challenge. The typical approach is to detect inputs from novel classes and retrain the classifier on an augmented dataset. However, not only the classifier but also the detection mechanism needs to adapt in order to distinguish between newly learned and yet unknown input classes. To address this challenge, we introduce an algorithmic framework for active monitoring of a neural network. A monitor wrapped in our framework operates in parallel with the neural network and interacts with a human user via a series of interpretable labeling queries for incremental adaptation. In addition, we propose an adaptive quantitative monitor to improve precision. An experimental evaluation on a diverse set of benchmarks with varying numbers of classes confirms the benefits of our active monitoring framework in dynamic scenarios.","lang":"eng"}],"department":[{"_id":"ToHe"}],"date_updated":"2024-01-30T12:06:56Z","status":"public","keyword":["monitoring","neural networks","novelty detection"],"type":"conference","conference":{"name":"RV: Runtime Verification","location":"Virtual","end_date":"2021-10-14","start_date":"2021-10-11"},"_id":"10206"},{"type":"journal_article","article_type":"original","status":"public","_id":"14889","department":[{"_id":"RoSe"}],"date_updated":"2024-02-05T10:02:45Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2005.02098"}],"scopus_import":"1","intvolume":" 3","month":"10","abstract":[{"text":"We consider the Fröhlich Hamiltonian with large coupling constant α. For initial data of Pekar product form with coherent phonon field and with the electron minimizing the corresponding energy, we provide a norm approximation of the evolution, valid up to times of order α2. The approximation is given in terms of a Pekar product state, evolved through the Landau-Pekar equations, corrected by a Bogoliubov dynamics taking quantum fluctuations into account. This allows us to show that the Landau-Pekar equations approximately describe the evolution of the electron- and one-phonon reduced density matrices under the Fröhlich dynamics up to times of order α2.","lang":"eng"}],"oa_version":"Preprint","ec_funded":1,"volume":3,"issue":"4","publication_status":"published","publication_identifier":{"issn":["2578-5893"],"eissn":["2578-5885"]},"language":[{"iso":"eng"}],"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"},{"grant_number":"694227","name":"Analysis of quantum many-body systems","call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"external_id":{"arxiv":["2005.02098"]},"article_processing_charge":"No","author":[{"last_name":"Leopold","orcid":"0000-0002-0495-6822","full_name":"Leopold, Nikolai K","first_name":"Nikolai K","id":"4BC40BEC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Mitrouskas, David Johannes","last_name":"Mitrouskas","first_name":"David Johannes","id":"cbddacee-2b11-11eb-a02e-a2e14d04e52d"},{"full_name":"Rademacher, Simone Anna Elvira","orcid":"0000-0001-5059-4466","last_name":"Rademacher","first_name":"Simone Anna Elvira","id":"856966FE-A408-11E9-977E-802DE6697425"},{"last_name":"Schlein","full_name":"Schlein, Benjamin","first_name":"Benjamin"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","last_name":"Seiringer"}],"title":"Landau–Pekar equations and quantum fluctuations for the dynamics of a strongly coupled polaron","citation":{"ista":"Leopold NK, Mitrouskas DJ, Rademacher SAE, Schlein B, Seiringer R. 2021. Landau–Pekar equations and quantum fluctuations for the dynamics of a strongly coupled polaron. Pure and Applied Analysis. 3(4), 653–676.","chicago":"Leopold, Nikolai K, David Johannes Mitrouskas, Simone Anna Elvira Rademacher, Benjamin Schlein, and Robert Seiringer. “Landau–Pekar Equations and Quantum Fluctuations for the Dynamics of a Strongly Coupled Polaron.” Pure and Applied Analysis. Mathematical Sciences Publishers, 2021. https://doi.org/10.2140/paa.2021.3.653.","ieee":"N. K. Leopold, D. J. Mitrouskas, S. A. E. Rademacher, B. Schlein, and R. Seiringer, “Landau–Pekar equations and quantum fluctuations for the dynamics of a strongly coupled polaron,” Pure and Applied Analysis, vol. 3, no. 4. Mathematical Sciences Publishers, pp. 653–676, 2021.","short":"N.K. Leopold, D.J. Mitrouskas, S.A.E. Rademacher, B. Schlein, R. Seiringer, Pure and Applied Analysis 3 (2021) 653–676.","apa":"Leopold, N. K., Mitrouskas, D. J., Rademacher, S. A. E., Schlein, B., & Seiringer, R. (2021). Landau–Pekar equations and quantum fluctuations for the dynamics of a strongly coupled polaron. Pure and Applied Analysis. Mathematical Sciences Publishers. https://doi.org/10.2140/paa.2021.3.653","ama":"Leopold NK, Mitrouskas DJ, Rademacher SAE, Schlein B, Seiringer R. Landau–Pekar equations and quantum fluctuations for the dynamics of a strongly coupled polaron. Pure and Applied Analysis. 2021;3(4):653-676. doi:10.2140/paa.2021.3.653","mla":"Leopold, Nikolai K., et al. “Landau–Pekar Equations and Quantum Fluctuations for the Dynamics of a Strongly Coupled Polaron.” Pure and Applied Analysis, vol. 3, no. 4, Mathematical Sciences Publishers, 2021, pp. 653–76, doi:10.2140/paa.2021.3.653."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"publisher":"Mathematical Sciences Publishers","quality_controlled":"1","acknowledgement":"Financial support by the European Union’s Horizon 2020 research and innovation programme\r\nunder the Marie Skłodowska-Curie grant agreement No. 754411 (S.R.) and the European\r\nResearch Council under grant agreement No. 694227 (N.L. and R.S.), as well as by the SNSF\r\nEccellenza project PCEFP2 181153 (N.L.), the NCCR SwissMAP (N.L. and B.S.) and by the\r\nDeutsche Forschungsgemeinschaft (DFG) through the Research Training Group 1838: Spectral\r\nTheory and Dynamics of Quantum Systems (D.M.) is gratefully acknowledged. B.S. gratefully\r\nacknowledges financial support from the Swiss National Science Foundation through the Grant\r\n“Dynamical and energetic properties of Bose-Einstein condensates” and from the European\r\nResearch Council through the ERC-AdG CLaQS (grant agreement No 834782). D.M. thanks\r\nMarcel Griesemer for helpful discussions.","page":"653-676","date_created":"2024-01-28T23:01:43Z","date_published":"2021-10-01T00:00:00Z","doi":"10.2140/paa.2021.3.653","year":"2021","publication":"Pure and Applied Analysis","day":"01"},{"intvolume":" 3","month":"10","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1912.11004"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"lang":"eng","text":"We consider a system of N interacting bosons in the mean-field scaling regime and construct corrections to the Bogoliubov dynamics that approximate the true N-body dynamics in norm to arbitrary precision. The N-independent corrections are given in terms of the solutions of the Bogoliubov and Hartree equations and satisfy a generalized form of Wick's theorem. We determine the n-point correlation functions of the excitations around the condensate, as well as the reduced densities of the N-body system, to arbitrary accuracy, given only the knowledge of the two-point functions of a quasi-free state and the solution of the Hartree equation. In this way, the complex problem of computing all n-point correlation functions for an interacting N-body system is essentially reduced to the problem of solving the Hartree equation and the PDEs for the Bogoliubov two-point functions."}],"ec_funded":1,"issue":"4","volume":3,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["2578-5893"],"eissn":["2578-5885"]},"status":"public","type":"journal_article","article_type":"original","_id":"14890","department":[{"_id":"RoSe"}],"date_updated":"2024-02-05T09:26:31Z","oa":1,"quality_controlled":"1","publisher":"Mathematical Sciences Publishers","acknowledgement":"We are grateful for the hospitality of Central China Normal University (CCNU),\r\nwhere parts of this work were done, and thank Phan Th`anh Nam, Simone\r\nRademacher, Robert Seiringer and Stefan Teufel for helpful discussions. L.B. gratefully acknowledges the support by the German Research Foundation (DFG) within the Research\r\nTraining Group 1838 “Spectral Theory and Dynamics of Quantum Systems”, and the funding\r\nfrom the European Union’s Horizon 2020 research and innovation programme under the Marie\r\nSk lodowska-Curie Grant Agreement No. 754411.","date_created":"2024-01-28T23:01:43Z","date_published":"2021-10-01T00:00:00Z","doi":"10.2140/paa.2021.3.677","page":"677-726","publication":"Pure and Applied Analysis","day":"01","year":"2021","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"title":"Beyond Bogoliubov dynamics","external_id":{"arxiv":["1912.11004"]},"article_processing_charge":"No","author":[{"id":"A2E3BCBE-5FCC-11E9-AA4B-76F3E5697425","first_name":"Lea","last_name":"Bossmann","full_name":"Bossmann, Lea","orcid":"0000-0002-6854-1343"},{"id":"40AC02DC-F248-11E8-B48F-1D18A9856A87","first_name":"Sören P","last_name":"Petrat","orcid":"0000-0002-9166-5889","full_name":"Petrat, Sören P"},{"first_name":"Peter","last_name":"Pickl","full_name":"Pickl, Peter"},{"first_name":"Avy","last_name":"Soffer","full_name":"Soffer, Avy"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Bossmann L, Petrat SP, Pickl P, Soffer A. 2021. Beyond Bogoliubov dynamics. Pure and Applied Analysis. 3(4), 677–726.","chicago":"Bossmann, Lea, Sören P Petrat, Peter Pickl, and Avy Soffer. “Beyond Bogoliubov Dynamics.” Pure and Applied Analysis. Mathematical Sciences Publishers, 2021. https://doi.org/10.2140/paa.2021.3.677.","short":"L. Bossmann, S.P. Petrat, P. Pickl, A. Soffer, Pure and Applied Analysis 3 (2021) 677–726.","ieee":"L. Bossmann, S. P. Petrat, P. Pickl, and A. Soffer, “Beyond Bogoliubov dynamics,” Pure and Applied Analysis, vol. 3, no. 4. Mathematical Sciences Publishers, pp. 677–726, 2021.","ama":"Bossmann L, Petrat SP, Pickl P, Soffer A. Beyond Bogoliubov dynamics. Pure and Applied Analysis. 2021;3(4):677-726. doi:10.2140/paa.2021.3.677","apa":"Bossmann, L., Petrat, S. P., Pickl, P., & Soffer, A. (2021). Beyond Bogoliubov dynamics. Pure and Applied Analysis. Mathematical Sciences Publishers. https://doi.org/10.2140/paa.2021.3.677","mla":"Bossmann, Lea, et al. “Beyond Bogoliubov Dynamics.” Pure and Applied Analysis, vol. 3, no. 4, Mathematical Sciences Publishers, 2021, pp. 677–726, doi:10.2140/paa.2021.3.677."}},{"_id":"15013","type":"journal_article","article_type":"original","status":"public","date_updated":"2024-02-19T08:30:00Z","department":[{"_id":"LaEr"}],"abstract":[{"lang":"eng","text":"We consider random n×n matrices X with independent and centered entries and a general variance profile. We show that the spectral radius of X converges with very high probability to the square root of the spectral radius of the variance matrix of X when n tends to infinity. We also establish the optimal rate of convergence, that is a new result even for general i.i.d. matrices beyond the explicitly solvable Gaussian cases. The main ingredient is the proof of the local inhomogeneous circular law [arXiv:1612.07776] at the spectral edge."}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1907.13631","open_access":"1"}],"month":"05","intvolume":" 2","publication_identifier":{"issn":["2690-0998"],"eissn":["2690-1005"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":2,"issue":"2","ec_funded":1,"project":[{"name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"}],"citation":{"mla":"Alt, Johannes, et al. “Spectral Radius of Random Matrices with Independent Entries.” Probability and Mathematical Physics, vol. 2, no. 2, Mathematical Sciences Publishers, 2021, pp. 221–80, doi:10.2140/pmp.2021.2.221.","short":"J. Alt, L. Erdös, T.H. Krüger, Probability and Mathematical Physics 2 (2021) 221–280.","ieee":"J. Alt, L. Erdös, and T. H. Krüger, “Spectral radius of random matrices with independent entries,” Probability and Mathematical Physics, vol. 2, no. 2. Mathematical Sciences Publishers, pp. 221–280, 2021.","ama":"Alt J, Erdös L, Krüger TH. Spectral radius of random matrices with independent entries. Probability and Mathematical Physics. 2021;2(2):221-280. doi:10.2140/pmp.2021.2.221","apa":"Alt, J., Erdös, L., & Krüger, T. H. (2021). Spectral radius of random matrices with independent entries. Probability and Mathematical Physics. Mathematical Sciences Publishers. https://doi.org/10.2140/pmp.2021.2.221","chicago":"Alt, Johannes, László Erdös, and Torben H Krüger. “Spectral Radius of Random Matrices with Independent Entries.” Probability and Mathematical Physics. Mathematical Sciences Publishers, 2021. https://doi.org/10.2140/pmp.2021.2.221.","ista":"Alt J, Erdös L, Krüger TH. 2021. Spectral radius of random matrices with independent entries. Probability and Mathematical Physics. 2(2), 221–280."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Alt","full_name":"Alt, Johannes","first_name":"Johannes","id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Erdös, László","orcid":"0000-0001-5366-9603","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László"},{"first_name":"Torben H","id":"3020C786-F248-11E8-B48F-1D18A9856A87","last_name":"Krüger","orcid":"0000-0002-4821-3297","full_name":"Krüger, Torben H"}],"article_processing_charge":"No","external_id":{"arxiv":["1907.13631"]},"title":"Spectral radius of random matrices with independent entries","acknowledgement":"Partially supported by ERC Starting Grant RandMat No. 715539 and the SwissMap grant of Swiss National Science Foundation. Partially supported by ERC Advanced Grant RanMat No. 338804. Partially supported by the Hausdorff Center for Mathematics in Bonn.","publisher":"Mathematical Sciences Publishers","quality_controlled":"1","oa":1,"year":"2021","day":"21","publication":"Probability and Mathematical Physics","page":"221-280","doi":"10.2140/pmp.2021.2.221","date_published":"2021-05-21T00:00:00Z","date_created":"2024-02-18T23:01:03Z"},{"year":"2021","has_accepted_license":"1","isi":1,"publication":"Proceedings of the National Academy of Sciences","day":"14","date_created":"2021-08-11T14:11:43Z","doi":"10.1073/pnas.2113046118","date_published":"2021-12-14T00:00:00Z","acknowledgement":"We gratefully thank Julie Neveu and Dr. Amanda Barranco of the Grégory Vert laboratory for help preparing plants in France, Dr. Zuzana Gelova for help and advice with protoplast generation, Dr. Stéphane Vassilopoulos and Dr. Florian Schur for advice regarding EM tomography, Alejandro Marquiegui Alvaro for help with material generation, and Dr. Lukasz Kowalski for generously gifting us the mWasabi protein. This research was supported by the Scientific Service Units of Institute of Science and Technology Austria (IST Austria) through resources provided by the Electron Microscopy Facility, Lab Support Facility (particularly Dorota Jaworska), and the Bioimaging Facility. We acknowledge the Advanced Microscopy Facility of the Vienna BioCenter Core Facilities for use of the 3D SIM. For the mass spectrometry analysis of proteins, we acknowledge the University of Natural Resources and Life Sciences (BOKU) Core Facility Mass Spectrometry. This work was supported by the following funds: A.J. is supported by funding from the Austrian Science Fund I3630B25 to J.F. P.M. and E.B. are supported by Agence Nationale de la Recherche ANR-11-EQPX-0029 Morphoscope2 and ANR-10-INBS-04 France BioImaging. S.Y.B. is supported by the NSF No. 1121998 and 1614915. J.W. and D.V.D. are supported by the European Research Council Grant 682436 (to D.V.D.), a China Scholarship Council Grant 201508440249 (to J.W.), and by a Ghent University Special Research Co-funding Grant ST01511051 (to J.W.).","oa":1,"publisher":"National Academy of Sciences","quality_controlled":"1","citation":{"ista":"Johnson AJ, Dahhan DA, Gnyliukh N, Kaufmann W, Zheden V, Costanzo T, Mahou P, Hrtyan M, Wang J, Aguilera Servin JL, van Damme D, Beaurepaire E, Loose M, Bednarek SY, Friml J. 2021. The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis. Proceedings of the National Academy of Sciences. 118(51), e2113046118.","chicago":"Johnson, Alexander J, Dana A Dahhan, Nataliia Gnyliukh, Walter Kaufmann, Vanessa Zheden, Tommaso Costanzo, Pierre Mahou, et al. “The TPLATE Complex Mediates Membrane Bending during Plant Clathrin-Mediated Endocytosis.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2113046118.","apa":"Johnson, A. J., Dahhan, D. A., Gnyliukh, N., Kaufmann, W., Zheden, V., Costanzo, T., … Friml, J. (2021). The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2113046118","ama":"Johnson AJ, Dahhan DA, Gnyliukh N, et al. The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis. Proceedings of the National Academy of Sciences. 2021;118(51). doi:10.1073/pnas.2113046118","ieee":"A. J. Johnson et al., “The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis,” Proceedings of the National Academy of Sciences, vol. 118, no. 51. National Academy of Sciences, 2021.","short":"A.J. Johnson, D.A. Dahhan, N. Gnyliukh, W. Kaufmann, V. Zheden, T. Costanzo, P. Mahou, M. Hrtyan, J. Wang, J.L. Aguilera Servin, D. van Damme, E. Beaurepaire, M. Loose, S.Y. Bednarek, J. Friml, Proceedings of the National Academy of Sciences 118 (2021).","mla":"Johnson, Alexander J., et al. “The TPLATE Complex Mediates Membrane Bending during Plant Clathrin-Mediated Endocytosis.” Proceedings of the National Academy of Sciences, vol. 118, no. 51, e2113046118, National Academy of Sciences, 2021, doi:10.1073/pnas.2113046118."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000736417600043"],"pmid":["34907016"]},"article_processing_charge":"No","author":[{"full_name":"Johnson, Alexander J","orcid":"0000-0002-2739-8843","last_name":"Johnson","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander J"},{"full_name":"Dahhan, Dana A","last_name":"Dahhan","first_name":"Dana A"},{"id":"390C1120-F248-11E8-B48F-1D18A9856A87","first_name":"Nataliia","full_name":"Gnyliukh, Nataliia","orcid":"0000-0002-2198-0509","last_name":"Gnyliukh"},{"full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315","last_name":"Kaufmann","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","first_name":"Walter"},{"last_name":"Zheden","full_name":"Zheden, Vanessa","orcid":"0000-0002-9438-4783","first_name":"Vanessa","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87"},{"id":"D93824F4-D9BA-11E9-BB12-F207E6697425","first_name":"Tommaso","last_name":"Costanzo","full_name":"Costanzo, Tommaso","orcid":"0000-0001-9732-3815"},{"first_name":"Pierre","full_name":"Mahou, Pierre","last_name":"Mahou"},{"first_name":"Mónika","id":"45A71A74-F248-11E8-B48F-1D18A9856A87","last_name":"Hrtyan","full_name":"Hrtyan, Mónika"},{"first_name":"Jie","full_name":"Wang, Jie","last_name":"Wang"},{"first_name":"Juan L","id":"2A67C376-F248-11E8-B48F-1D18A9856A87","full_name":"Aguilera Servin, Juan L","orcid":"0000-0002-2862-8372","last_name":"Aguilera Servin"},{"full_name":"van Damme, Daniël","last_name":"van Damme","first_name":"Daniël"},{"last_name":"Beaurepaire","full_name":"Beaurepaire, Emmanuel","first_name":"Emmanuel"},{"last_name":"Loose","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"},{"first_name":"Sebastian Y","last_name":"Bednarek","full_name":"Bednarek, Sebastian Y"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"title":"The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis","article_number":"e2113046118","project":[{"call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants"}],"publication_status":"published","publication_identifier":{"eissn":["1091-6490"]},"language":[{"iso":"eng"}],"file":[{"file_name":"2021_PNAS_Johnson.pdf","date_created":"2021-12-15T08:59:40Z","file_size":2757340,"date_updated":"2021-12-15T08:59:40Z","creator":"cchlebak","success":1,"checksum":"8d01e72e22c4fb1584e72d8601947069","file_id":"10546","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"volume":118,"issue":"51","related_material":{"link":[{"url":"https://doi.org/10.1101/2021.04.26.441441","relation":"earlier_version"}],"record":[{"relation":"dissertation_contains","status":"public","id":"14510"},{"status":"public","id":"14988","relation":"research_data"}]},"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"abstract":[{"lang":"eng","text":"Clathrin-mediated endocytosis is the major route of entry of cargos into cells and thus underpins many physiological processes. During endocytosis, an area of flat membrane is remodeled by proteins to create a spherical vesicle against intracellular forces. The protein machinery which mediates this membrane bending in plants is unknown. However, it is known that plant endocytosis is actin independent, thus indicating that plants utilize a unique mechanism to mediate membrane bending against high-turgor pressure compared to other model systems. Here, we investigate the TPLATE complex, a plant-specific endocytosis protein complex. It has been thought to function as a classical adaptor functioning underneath the clathrin coat. However, by using biochemical and advanced live microscopy approaches, we found that TPLATE is peripherally associated with clathrin-coated vesicles and localizes at the rim of endocytosis events. As this localization is more fitting to the protein machinery involved in membrane bending during endocytosis, we examined cells in which the TPLATE complex was disrupted and found that the clathrin structures present as flat patches. This suggests a requirement of the TPLATE complex for membrane bending during plant clathrin–mediated endocytosis. Next, we used in vitro biophysical assays to confirm that the TPLATE complex possesses protein domains with intrinsic membrane remodeling activity. These results redefine the role of the TPLATE complex and implicate it as a key component of the evolutionarily distinct plant endocytosis mechanism, which mediates endocytic membrane bending against the high-turgor pressure in plant cells."}],"pmid":1,"oa_version":"Published Version","intvolume":" 118","month":"12","date_updated":"2024-02-19T11:06:09Z","ddc":["580"],"file_date_updated":"2021-12-15T08:59:40Z","department":[{"_id":"JiFr"},{"_id":"MaLo"},{"_id":"EvBe"},{"_id":"EM-Fac"},{"_id":"NanoFab"}],"_id":"9887","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public"},{"year":"2021","publication_status":"published","publication_identifier":{"isbn":["9780470016176"],"eisbn":["9780470015902"]},"publication":"Encyclopedia of Life Sciences","language":[{"iso":"eng"}],"day":"28","date_created":"2024-02-14T12:05:50Z","doi":"10.1002/9780470015902.a0029355","volume":2,"date_published":"2021-05-28T00:00:00Z","abstract":[{"text":"Hybrid zones are narrow geographic regions where different populations, races or interbreeding species meet and mate, producing mixed ‘hybrid’ offspring. They are relatively common and can be found in a diverse range of organisms and environments. The study of hybrid zones has played an important role in our understanding of the origin of species, with hybrid zones having been described as ‘natural laboratories’. This is because they allow us to study,in situ, the conditions and evolutionary forces that enable divergent taxa to remain distinct despite some ongoing gene exchange between them.","lang":"eng"}],"oa_version":"None","quality_controlled":"1","publisher":"Wiley","intvolume":" 2","month":"05","citation":{"ista":"Stankowski S, Shipilina D, Westram AM. 2021.Hybrid Zones. In: Encyclopedia of Life Sciences. vol. 2.","chicago":"Stankowski, Sean, Daria Shipilina, and Anja M Westram. “Hybrid Zones.” In Encyclopedia of Life Sciences, Vol. 2. ELS. Wiley, 2021. https://doi.org/10.1002/9780470015902.a0029355.","apa":"Stankowski, S., Shipilina, D., & Westram, A. M. (2021). Hybrid Zones. In Encyclopedia of Life Sciences (Vol. 2). Wiley. https://doi.org/10.1002/9780470015902.a0029355","ama":"Stankowski S, Shipilina D, Westram AM. Hybrid Zones. In: Encyclopedia of Life Sciences. Vol 2. eLS. Wiley; 2021. doi:10.1002/9780470015902.a0029355","short":"S. Stankowski, D. Shipilina, A.M. Westram, in:, Encyclopedia of Life Sciences, Wiley, 2021.","ieee":"S. Stankowski, D. Shipilina, and A. M. Westram, “Hybrid Zones,” in Encyclopedia of Life Sciences, vol. 2, Wiley, 2021.","mla":"Stankowski, Sean, et al. “Hybrid Zones.” Encyclopedia of Life Sciences, vol. 2, Wiley, 2021, doi:10.1002/9780470015902.a0029355."},"date_updated":"2024-02-19T09:54:18Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski","full_name":"Stankowski, Sean"},{"orcid":"0000-0002-1145-9226","full_name":"Shipilina, Daria","last_name":"Shipilina","first_name":"Daria","id":"428A94B0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M"}],"department":[{"_id":"NiBa"}],"title":"Hybrid Zones","_id":"14984","series_title":"eLS","type":"book_chapter","status":"public"},{"abstract":[{"text":"The goal of zero-shot learning is to construct a classifier that can identify object classes for which no training examples are available. When training data for some of the object classes is available but not for others, the name generalized zero-shot learning is commonly used.\r\nIn a wider sense, the phrase zero-shot is also used to describe other machine learning-based approaches that require no training data from the problem of interest, such as zero-shot action recognition or zero-shot machine translation.","lang":"eng"}],"oa_version":"None","edition":"2","quality_controlled":"1","publisher":"Springer","place":"Cham","month":"10","year":"2021","publication_status":"published","publication_identifier":{"isbn":["9783030634155"],"eisbn":["9783030634162"]},"publication":"Computer Vision","language":[{"iso":"eng"}],"day":"13","page":"1395-1397","date_created":"2024-02-14T14:05:32Z","date_published":"2021-10-13T00:00:00Z","doi":"10.1007/978-3-030-63416-2_874","_id":"14987","type":"book_chapter","status":"public","citation":{"ista":"Lampert C. 2021.Zero-Shot Learning. In: Computer Vision. , 1395–1397.","chicago":"Lampert, Christoph. “Zero-Shot Learning.” In Computer Vision, edited by Katsushi Ikeuchi, 2nd ed., 1395–97. Cham: Springer, 2021. https://doi.org/10.1007/978-3-030-63416-2_874.","ieee":"C. Lampert, “Zero-Shot Learning,” in Computer Vision, 2nd ed., K. Ikeuchi, Ed. Cham: Springer, 2021, pp. 1395–1397.","short":"C. Lampert, in:, K. Ikeuchi (Ed.), Computer Vision, 2nd ed., Springer, Cham, 2021, pp. 1395–1397.","ama":"Lampert C. Zero-Shot Learning. In: Ikeuchi K, ed. Computer Vision. 2nd ed. Cham: Springer; 2021:1395-1397. doi:10.1007/978-3-030-63416-2_874","apa":"Lampert, C. (2021). Zero-Shot Learning. In K. Ikeuchi (Ed.), Computer Vision (2nd ed., pp. 1395–1397). Cham: Springer. https://doi.org/10.1007/978-3-030-63416-2_874","mla":"Lampert, Christoph. “Zero-Shot Learning.” Computer Vision, edited by Katsushi Ikeuchi, 2nd ed., Springer, 2021, pp. 1395–97, doi:10.1007/978-3-030-63416-2_874."},"date_updated":"2024-02-19T10:59:04Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","last_name":"Lampert"}],"editor":[{"last_name":"Ikeuchi","full_name":"Ikeuchi, Katsushi","first_name":"Katsushi"}],"department":[{"_id":"ChLa"}],"title":"Zero-Shot Learning"},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"research_data_reference","status":"public","_id":"14988","article_processing_charge":"No","author":[{"first_name":"Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","last_name":"Johnson","full_name":"Johnson, Alexander J","orcid":"0000-0002-2739-8843"}],"department":[{"_id":"JiFr"}],"title":"Raw data from Johnson et al, PNAS, 2021","citation":{"ieee":"A. J. Johnson, “Raw data from Johnson et al, PNAS, 2021.” Zenodo, 2021.","short":"A.J. Johnson, (2021).","apa":"Johnson, A. J. (2021). Raw data from Johnson et al, PNAS, 2021. Zenodo. https://doi.org/10.5281/ZENODO.5747100","ama":"Johnson AJ. Raw data from Johnson et al, PNAS, 2021. 2021. doi:10.5281/ZENODO.5747100","mla":"Johnson, Alexander J. Raw Data from Johnson et Al, PNAS, 2021. Zenodo, 2021, doi:10.5281/ZENODO.5747100.","ista":"Johnson AJ. 2021. Raw data from Johnson et al, PNAS, 2021, Zenodo, 10.5281/ZENODO.5747100.","chicago":"Johnson, Alexander J. “Raw Data from Johnson et Al, PNAS, 2021.” Zenodo, 2021. https://doi.org/10.5281/ZENODO.5747100."},"date_updated":"2024-02-19T11:06:09Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["580"],"oa":1,"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.5747100","open_access":"1"}],"publisher":"Zenodo","month":"12","abstract":[{"lang":"eng","text":"Raw data generated from the publication - The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis by Johnson et al., 2021 In PNAS"}],"oa_version":"Published Version","date_created":"2024-02-14T14:13:48Z","date_published":"2021-12-01T00:00:00Z","doi":"10.5281/ZENODO.5747100","related_material":{"record":[{"status":"public","id":"9887","relation":"used_in_publication"}]},"year":"2021","has_accepted_license":"1","day":"01"},{"month":"07","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2107.03695"}],"oa_version":"Preprint","acknowledgement":"This research was supported by the Scientific Service Units of IST Austria through resources provided by the MIBA Machine Shop and the nanofabrication facility. JS and AG were supported by funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement No.754411.","abstract":[{"lang":"eng","text":"Superconductor-semiconductor hybrids are platforms for realizing effective p-wave superconductivity. Spin-orbit coupling, combined with the proximity effect, causes the two-dimensional semiconductor to inherit p±ip intraband pairing, and application of magnetic field can then result in transitions to the normal state, partial Bogoliubov Fermi surfaces, or topological phases with Majorana modes. Experimentally probing the hybrid superconductor-semiconductor interface is challenging due to the shunting effect of the conventional superconductor. Consequently, the nature of induced pairing remains an open question. Here, we use the circuit quantum electrodynamics architecture to probe induced superconductivity in a two dimensional Al-InAs hybrid system. We observe a strong suppression of superfluid density and enhanced dissipation driven by magnetic field, which cannot be accounted for by the depairing theory of an s-wave superconductor. These observations are explained by a picture of independent intraband p±ip superconductors giving way to partial Bogoliubov Fermi surfaces, and allow for the first characterization of key properties of the hybrid superconducting system."}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"related_material":{"record":[{"id":"10851","status":"public","relation":"later_version"},{"id":"9636","status":"public","relation":"research_data"}]},"date_published":"2021-07-08T00:00:00Z","ec_funded":1,"date_created":"2021-09-21T08:41:02Z","day":"08","language":[{"iso":"eng"}],"publication":"arXiv","year":"2021","publication_status":"submitted","status":"public","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"type":"preprint","article_number":"2107.03695","_id":"10029","title":"Breakdown of induced p±ip pairing in a superconductor-semiconductor hybrid","department":[{"_id":"MaSe"},{"_id":"AnHi"},{"_id":"MiLe"}],"author":[{"id":"29C8C0B4-F248-11E8-B48F-1D18A9856A87","first_name":"Duc T","full_name":"Phan, Duc T","last_name":"Phan"},{"first_name":"Jorden L","id":"5479D234-2D30-11EA-89CC-40953DDC885E","last_name":"Senior","full_name":"Senior, Jorden L","orcid":"0000-0002-0672-9295"},{"id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","first_name":"Areg","full_name":"Ghazaryan, Areg","orcid":"0000-0001-9666-3543","last_name":"Ghazaryan"},{"first_name":"M.","full_name":"Hatefipour, M.","last_name":"Hatefipour"},{"first_name":"W. M.","last_name":"Strickland","full_name":"Strickland, W. M."},{"first_name":"J.","full_name":"Shabani, J.","last_name":"Shabani"},{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym","last_name":"Serbyn","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym"},{"full_name":"Higginbotham, Andrew P","orcid":"0000-0003-2607-2363","last_name":"Higginbotham","first_name":"Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"arxiv":["2107.03695"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-02-21T12:36:52Z","citation":{"chicago":"Phan, Duc T, Jorden L Senior, Areg Ghazaryan, M. Hatefipour, W. M. Strickland, J. Shabani, Maksym Serbyn, and Andrew P Higginbotham. “Breakdown of Induced P±ip Pairing in a Superconductor-Semiconductor Hybrid.” ArXiv, n.d.","ista":"Phan DT, Senior JL, Ghazaryan A, Hatefipour M, Strickland WM, Shabani J, Serbyn M, Higginbotham AP. Breakdown of induced p±ip pairing in a superconductor-semiconductor hybrid. arXiv, 2107.03695.","mla":"Phan, Duc T., et al. “Breakdown of Induced P±ip Pairing in a Superconductor-Semiconductor Hybrid.” ArXiv, 2107.03695.","apa":"Phan, D. T., Senior, J. L., Ghazaryan, A., Hatefipour, M., Strickland, W. M., Shabani, J., … Higginbotham, A. P. (n.d.). Breakdown of induced p±ip pairing in a superconductor-semiconductor hybrid. arXiv.","ama":"Phan DT, Senior JL, Ghazaryan A, et al. Breakdown of induced p±ip pairing in a superconductor-semiconductor hybrid. arXiv.","short":"D.T. Phan, J.L. Senior, A. Ghazaryan, M. Hatefipour, W.M. Strickland, J. Shabani, M. Serbyn, A.P. Higginbotham, ArXiv (n.d.).","ieee":"D. T. 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Data for ‘Breakdown of induced p ± ip pairing in a superconductor-semiconductor hybrid’, Institute of Science and Technology Austria.","chicago":"Higginbotham, Andrew P. “Data for ‘Breakdown of Induced p ± Ip Pairing in a Superconductor-Semiconductor Hybrid.’” Institute of Science and Technology Austria, 2021."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"publisher":"Institute of Science and Technology Austria","oa_version":"Submitted Version","date_created":"2021-07-07T20:43:10Z","related_material":{"record":[{"id":"10029","status":"public","relation":"used_in_publication"}]},"date_published":"2021-01-01T00:00:00Z","year":"2021","has_accepted_license":"1","file":[{"checksum":"18e90687ec7bbd75f8bfea4d8293fb30","file_id":"9637","success":1,"content_type":"application/zip","access_level":"open_access","relation":"main_file","date_created":"2021-07-07T20:37:28Z","file_name":"figures_data.zip","date_updated":"2021-07-07T20:37:28Z","file_size":3345244,"creator":"ahigginb"}]},{"day":"02","publication":"Science","isi":1,"year":"2021","doi":"10.1126/science.abf1513","date_published":"2021-07-02T00:00:00Z","date_created":"2020-12-02T10:51:52Z","acknowledgement":"The authors thank A. Higginbotham, E. J. H. Lee and F. R. Martins for helpful discussions. This research was supported by the Scientific Service Units of IST Austria through resources provided by the MIBA Machine Shop and the nanofabrication facility; the NOMIS Foundation and Microsoft; the European Union’s Horizon 2020 research and innovation program under the Marie SklodowskaCurie grant agreement No 844511; the FETOPEN Grant Agreement No. 828948; the European Research Commission through the grant agreement HEMs-DAM No 716655; the Spanish Ministry of Science and Innovation through Grants PGC2018-097018-B-I00, PCI2018-093026, FIS2016-80434-P (AEI/FEDER, EU), RYC2011-09345 (Ram´on y Cajal Programme), and the Mar´ıa de Maeztu Programme for Units of Excellence in R&D (CEX2018-000805-M); the CSIC Research Platform on Quantum Technologies PTI-001.","quality_controlled":"1","publisher":"American Association for the Advancement of Science","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Valentini, Marco, Fernando Peñaranda, Andrea C Hofmann, Matthias Brauns, Robert Hauschild, Peter Krogstrup, Pablo San-Jose, Elsa Prada, Ramón Aguado, and Georgios Katsaros. “Nontopological Zero-Bias Peaks in Full-Shell Nanowires Induced by Flux-Tunable Andreev States.” Science. American Association for the Advancement of Science, 2021. https://doi.org/10.1126/science.abf1513.","ista":"Valentini M, Peñaranda F, Hofmann AC, Brauns M, Hauschild R, Krogstrup P, San-Jose P, Prada E, Aguado R, Katsaros G. 2021. Nontopological zero-bias peaks in full-shell nanowires induced by flux-tunable Andreev states. Science. 373(6550), 82–88.","mla":"Valentini, Marco, et al. “Nontopological Zero-Bias Peaks in Full-Shell Nanowires Induced by Flux-Tunable Andreev States.” Science, vol. 373, no. 6550, 82–88, American Association for the Advancement of Science, 2021, doi:10.1126/science.abf1513.","apa":"Valentini, M., Peñaranda, F., Hofmann, A. C., Brauns, M., Hauschild, R., Krogstrup, P., … Katsaros, G. (2021). Nontopological zero-bias peaks in full-shell nanowires induced by flux-tunable Andreev states. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.abf1513","ama":"Valentini M, Peñaranda F, Hofmann AC, et al. Nontopological zero-bias peaks in full-shell nanowires induced by flux-tunable Andreev states. Science. 2021;373(6550). doi:10.1126/science.abf1513","short":"M. Valentini, F. Peñaranda, A.C. Hofmann, M. Brauns, R. Hauschild, P. Krogstrup, P. San-Jose, E. Prada, R. Aguado, G. Katsaros, Science 373 (2021).","ieee":"M. Valentini et al., “Nontopological zero-bias peaks in full-shell nanowires induced by flux-tunable Andreev states,” Science, vol. 373, no. 6550. 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In this study, we demonstrate that the appearance of subgap states in such structures is actually governed by the junction region in tunneling spectroscopy measurements and not the full-shell nanowire itself. Short tunneling regions never show subgap states, whereas longer junctions always do. This can be understood in terms of quantum dots forming in the junction and hosting Andreev levels in the Yu-Shiba-Rusinov regime. The intricate magnetic field dependence of the Andreev levels, through both the Zeeman and Little-Parks effects, may result in robust zero-bias peaks—features that could be easily misinterpreted as originating from Majorana zero modes but are unrelated to topological superconductivity."}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"month":"07","intvolume":" 373","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2008.02348"}],"date_updated":"2024-02-21T12:40:09Z","department":[{"_id":"GeKa"},{"_id":"Bio"}],"_id":"8910","status":"public","type":"journal_article","article_type":"original"},{"doi":"10.15479/AT:ISTA:9323","date_published":"2021-04-14T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","id":"8909","status":"public"}]},"contributor":[{"id":"4C473F58-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel","contributor_type":"project_member","last_name":"Jirovec"}],"date_created":"2021-04-14T09:50:22Z","day":"14","file":[{"content_type":"application/x-zip-compressed","relation":"main_file","access_level":"open_access","success":1,"checksum":"c569d2a2ce1694445cdbca19cf8ae023","file_id":"9324","file_size":221832287,"date_updated":"2021-04-14T09:48:47Z","creator":"djirovec","file_name":"DataRepositorySTqubit.zip","date_created":"2021-04-14T09:48:47Z"},{"checksum":"845bdf87430718ad6aff47eda7b5fc92","file_id":"9325","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/octet-stream","date_created":"2021-04-14T09:49:30Z","file_name":"ReadMe","creator":"djirovec","date_updated":"2021-04-14T09:49:30Z","file_size":4323}],"has_accepted_license":"1","year":"2021","month":"04","publisher":"Institute of Science and Technology Austria","oa":1,"oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"file_date_updated":"2021-04-14T09:49:30Z","title":"Research data for \"A singlet-triplet hole spin qubit planar Ge\"","department":[{"_id":"GradSch"},{"_id":"GeKa"}],"author":[{"full_name":"Jirovec, Daniel","orcid":"0000-0002-7197-4801","last_name":"Jirovec","first_name":"Daniel","id":"4C473F58-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","ddc":["530"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Jirovec D. 2021. Research data for ‘A singlet-triplet hole spin qubit planar Ge’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:9323.","chicago":"Jirovec, Daniel. “Research Data for ‘A Singlet-Triplet Hole Spin Qubit Planar Ge.’” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9323.","short":"D. Jirovec, (2021).","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. https://doi.org/10.15479/AT:ISTA:9323","ama":"Jirovec D. Research data for “A singlet-triplet hole spin qubit planar Ge.” 2021. doi:10.15479/AT:ISTA:9323","mla":"Jirovec, Daniel. Research Data for “A Singlet-Triplet Hole Spin Qubit Planar Ge.” Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9323."},"date_updated":"2024-02-21T12:39:15Z","status":"public","type":"research_data","tmp":{"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)","short":"CC0 (1.0)"},"_id":"9323"},{"oa":1,"publisher":"Institute of Science and Technology Austria","abstract":[{"lang":"eng","text":"This .zip File contains the transport data for \"Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states\" by M. Valentini, et. al. \r\nThe measurements were done using Labber Software and the data is stored in the hdf5 file format.\r\nInstructions of how to read the data are in \"Notebook_Valentini.pdf\"."}],"acknowledged_ssus":[{"_id":"NanoFab"}],"oa_version":"Published Version","date_created":"2021-05-14T12:07:53Z","contributor":[{"id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","contributor_type":"contact_person","first_name":"Marco","last_name":"Valentini"}],"doi":"10.15479/AT:ISTA:9389","related_material":{"record":[{"status":"public","id":"8910","relation":"used_in_publication"}]},"date_published":"2021-01-01T00:00:00Z","year":"2021","has_accepted_license":"1","file":[{"creator":"mvalenti","file_size":10572981,"date_updated":"2021-05-14T11:42:23Z","file_name":"Notebook_Valentini.pdf","date_created":"2021-05-14T11:42:23Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"9390","checksum":"80a905c4eef24dab6fb247e81a3d67f5"},{"creator":"mvalenti","date_updated":"2021-05-14T11:56:48Z","file_size":99076111,"date_created":"2021-05-14T11:56:48Z","file_name":"Experimental_data.zip","access_level":"open_access","relation":"main_file","content_type":"application/x-zip-compressed","checksum":"1e61a7e63949448a8db0091cdac23570","file_id":"9391"}],"tmp":{"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)","short":"CC0 (1.0)"},"type":"research_data","status":"public","_id":"9389","article_processing_charge":"No","author":[{"id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","first_name":"Marco","full_name":"Valentini, Marco","last_name":"Valentini"}],"file_date_updated":"2021-05-14T11:56:48Z","title":"Research data for \"Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states\"","department":[{"_id":"GradSch"},{"_id":"GeKa"}],"citation":{"chicago":"Valentini, Marco. “Research Data for ‘Non-Topological Zero Bias Peaks in Full-Shell Nanowires Induced by Flux Tunable Andreev States.’” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9389.","ista":"Valentini M. 2021. 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Valentini, “Research data for ‘Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states.’” Institute of Science and Technology Austria, 2021."},"date_updated":"2024-02-21T12:40:09Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["530"]},{"project":[{"grant_number":"844511","name":"Majorana bound states in Ge/SiGe heterostructures","call_identifier":"H2020","_id":"26A151DA-B435-11E9-9278-68D0E5697425"},{"name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS","grant_number":"862046","call_identifier":"H2020","_id":"237E5020-32DE-11EA-91FC-C7463DDC885E"}],"article_number":"L022005","article_processing_charge":"No","external_id":{"arxiv":["2012.00322"]},"author":[{"full_name":"Aggarwal, Kushagra","orcid":"0000-0001-9985-9293","last_name":"Aggarwal","id":"b22ab905-3539-11eb-84c3-fc159dcd79cb","first_name":"Kushagra"},{"last_name":"Hofmann","full_name":"Hofmann, Andrea C","id":"340F461A-F248-11E8-B48F-1D18A9856A87","first_name":"Andrea C"},{"first_name":"Daniel","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7197-4801","full_name":"Jirovec, Daniel","last_name":"Jirovec"},{"first_name":"Ivan","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","last_name":"Prieto Gonzalez","full_name":"Prieto Gonzalez, Ivan","orcid":"0000-0002-7370-5357"},{"first_name":"Amir","last_name":"Sammak","full_name":"Sammak, Amir"},{"first_name":"Marc","full_name":"Botifoll, Marc","last_name":"Botifoll"},{"first_name":"Sara","full_name":"Martí-Sánchez, Sara","last_name":"Martí-Sánchez"},{"full_name":"Veldhorst, Menno","last_name":"Veldhorst","first_name":"Menno"},{"full_name":"Arbiol, Jordi","last_name":"Arbiol","first_name":"Jordi"},{"last_name":"Scappucci","full_name":"Scappucci, Giordano","first_name":"Giordano"},{"first_name":"Jeroen","full_name":"Danon, Jeroen","last_name":"Danon"},{"full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X","last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios"}],"title":"Enhancement of proximity-induced superconductivity in a planar Ge hole gas","citation":{"ista":"Aggarwal K, Hofmann AC, Jirovec D, Prieto Gonzalez I, Sammak A, Botifoll M, Martí-Sánchez S, Veldhorst M, Arbiol J, Scappucci G, Danon J, Katsaros G. 2021. Enhancement of proximity-induced superconductivity in a planar Ge hole gas. Physical Review Research. 3(2), L022005.","chicago":"Aggarwal, Kushagra, Andrea C Hofmann, Daniel Jirovec, Ivan Prieto Gonzalez, Amir Sammak, Marc Botifoll, Sara Martí-Sánchez, et al. “Enhancement of Proximity-Induced Superconductivity in a Planar Ge Hole Gas.” Physical Review Research. American Physical Society, 2021. https://doi.org/10.1103/physrevresearch.3.l022005.","apa":"Aggarwal, K., Hofmann, A. C., Jirovec, D., Prieto Gonzalez, I., Sammak, A., Botifoll, M., … Katsaros, G. (2021). Enhancement of proximity-induced superconductivity in a planar Ge hole gas. Physical Review Research. American Physical Society. https://doi.org/10.1103/physrevresearch.3.l022005","ama":"Aggarwal K, Hofmann AC, Jirovec D, et al. Enhancement of proximity-induced superconductivity in a planar Ge hole gas. Physical Review Research. 2021;3(2). doi:10.1103/physrevresearch.3.l022005","short":"K. Aggarwal, A.C. Hofmann, D. Jirovec, I. Prieto Gonzalez, A. Sammak, M. Botifoll, S. Martí-Sánchez, M. Veldhorst, J. Arbiol, G. Scappucci, J. Danon, G. Katsaros, Physical Review Research 3 (2021).","ieee":"K. Aggarwal et al., “Enhancement of proximity-induced superconductivity in a planar Ge hole gas,” Physical Review Research, vol. 3, no. 2. American Physical Society, 2021.","mla":"Aggarwal, Kushagra, et al. “Enhancement of Proximity-Induced Superconductivity in a Planar Ge Hole Gas.” Physical Review Research, vol. 3, no. 2, L022005, American Physical Society, 2021, doi:10.1103/physrevresearch.3.l022005."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa":1,"publisher":"American Physical Society","quality_controlled":"1","acknowledgement":"This research and related results were made possible with the support of the NOMIS Foundation. This research was supported by the Scientific Service Units of IST Austria through resources provided by the MIBA Machine Shop and the nanofabrication facility, the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant agreement No. 844511 Grant Agreement No. 862046. ICN2 acknowledge funding from Generalitat de Catalunya 2017 SGR 327. ICN2 is supported by the Severo Ochoa program from Spanish MINECO (Grant No. SEV-2017-0706) and is funded by the CERCA Programme/Generalitat de Catalunya. Part of the present work has been performed in the framework of Universitat Autnoma de Barcelona Materials Science PhD program. The HAADF-STEM microscopy was conducted in the Laboratorio de Microscopias Avanzadas at Instituto de Nanociencia de Aragon-Universidad de Zaragoza. Authors acknowledge the LMA-INA for offering access to their instruments and expertise. We acknowledge support from CSIC Research Platform on Quantum Technologies PTI-001. This project has received funding from the European Union's Horizon 2020 research and innovation programme under Grant Agreement No. 823717 ESTEEM3. M.B. acknowledges support from SUR Generalitat de Catalunya and the EU Social Fund; project ref. 2020 FI 00103. G.S. and M.V. acknowledge support through a projectruimte grant associated with the Netherlands Organization of Scientific Research (NWO). J.D. acknowledges support through FRIPRO-project 274853, which is funded by the Research Council of Norway.","date_created":"2021-12-16T18:50:57Z","doi":"10.1103/physrevresearch.3.l022005","date_published":"2021-04-15T00:00:00Z","year":"2021","has_accepted_license":"1","publication":"Physical Review Research","day":"15","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","keyword":["general engineering"],"status":"public","_id":"10559","file_date_updated":"2021-12-17T08:12:37Z","department":[{"_id":"GeKa"}],"date_updated":"2024-02-21T12:41:26Z","ddc":["620"],"scopus_import":"1","intvolume":" 3","month":"04","abstract":[{"text":"Hole gases in planar germanium can have high mobilities in combination with strong spin-orbit interaction and electrically tunable g factors, and are therefore emerging as a promising platform for creating hybrid superconductor-semiconductor devices. A key challenge towards hybrid Ge-based quantum technologies is the design of high-quality interfaces and superconducting contacts that are robust against magnetic fields. In this work, by combining the assets of aluminum, which provides good contact to the Ge, and niobium, which has a significant superconducting gap, we demonstrate highly transparent low-disordered JoFETs with relatively large ICRN products that are capable of withstanding high magnetic fields. We furthermore demonstrate the ability of phase-biasing individual JoFETs, opening up an avenue to explore topological superconductivity in planar Ge. The persistence of superconductivity in the reported hybrid devices beyond 1.8 T paves the way towards integrating spin qubits and proximity-induced superconductivity on the same chip.","lang":"eng"}],"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"oa_version":"Published Version","ec_funded":1,"issue":"2","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"8831"},{"relation":"research_data","id":"8834","status":"public"}]},"volume":3,"publication_status":"published","publication_identifier":{"issn":["2643-1564"]},"language":[{"iso":"eng"}],"file":[{"success":1,"checksum":"60a1bc9c9b616b1b155044bb8cfc6484","file_id":"10561","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2021_PhysRevResearch_Aggarwal.pdf","date_created":"2021-12-17T08:12:37Z","file_size":1917512,"date_updated":"2021-12-17T08:12:37Z","creator":"cchlebak"}]},{"oa_version":"Published Version","pmid":1,"acknowledged_ssus":[{"_id":"ScienComp"}],"abstract":[{"text":"While sexual reproduction is widespread among many taxa, asexual lineages have repeatedly evolved from sexual ancestors. Despite extensive research on the evolution of sex, it is still unclear whether this switch represents a major transition requiring major molecular reorganization, and how convergent the changes involved are. In this study, we investigated the phylogenetic relationship and patterns of gene expression of sexual and asexual lineages of Eurasian Artemia brine shrimp, to assess how gene expression patterns are affected by the transition to asexuality. We find only a few genes that are consistently associated with the evolution of asexuality, suggesting that this shift may not require an extensive overhauling of the meiotic machinery. While genes with sex-biased expression have high rates of expression divergence within Eurasian Artemia, neither female- nor male-biased genes appear to show unusual evolutionary patterns after sexuality is lost, contrary to theoretical expectations.","lang":"eng"}],"month":"09","intvolume":" 288","scopus_import":"1","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"76e7f253b7040bca2ad76f82bd7c45c0","file_id":"10172","success":1,"date_updated":"2021-10-22T11:48:02Z","file_size":995806,"creator":"cchlebak","date_created":"2021-10-22T11:48:02Z","file_name":"2021_ProRoSocBBioSci_Huylmans.pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0962-8452"],"eissn":["1471-2954"]},"publication_status":"published","related_material":{"link":[{"relation":"supplementary_material","url":"https://doi.org/10.6084/m9.figshare.c.5615488.v1"}],"record":[{"id":"9949","status":"public","relation":"research_data"}]},"volume":288,"issue":"1959","ec_funded":1,"_id":"10166","status":"public","keyword":["asexual reproduction","parthenogenesis","sex-biased genes","sexual conflict","automixis","crustaceans"],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["595"],"date_updated":"2024-02-21T12:40:29Z","department":[{"_id":"BeVi"}],"file_date_updated":"2021-10-22T11:48:02Z","acknowledgement":"We thank the Vicoso laboratory, Thomas Lenormand and Tanja Schwander for helpful discussions, the group of Gonzalo Gajardo, especially Cristian Gallardo-Escárate and Margarita Parraguez Donoso, for sequencing data and advice, and the IST Scientific Computing Group for their support. This work was supported by the European Research Council under the European Union's Horizon 2020 research and innovation program (grant agreement no. 715257).","publisher":"The Royal Society","quality_controlled":"1","oa":1,"day":"22","publication":"Proceedings of the Royal Society B: Biological Sciences","isi":1,"has_accepted_license":"1","year":"2021","doi":"10.1098/rspb.2021.1720","date_published":"2021-09-22T00:00:00Z","date_created":"2021-10-21T07:46:06Z","article_number":"20211720","project":[{"name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","grant_number":"715257","call_identifier":"H2020","_id":"250BDE62-B435-11E9-9278-68D0E5697425"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Huylmans AK, Macon A, Hontoria F, Vicoso B. 2021. Transitions to asexuality and evolution of gene expression in Artemia brine shrimp. Proceedings of the Royal Society B: Biological Sciences. 288(1959), 20211720.","chicago":"Huylmans, Ann K, Ariana Macon, Francisco Hontoria, and Beatriz Vicoso. “Transitions to Asexuality and Evolution of Gene Expression in Artemia Brine Shrimp.” Proceedings of the Royal Society B: Biological Sciences. The Royal Society, 2021. https://doi.org/10.1098/rspb.2021.1720.","apa":"Huylmans, A. K., Macon, A., Hontoria, F., & Vicoso, B. (2021). Transitions to asexuality and evolution of gene expression in Artemia brine shrimp. Proceedings of the Royal Society B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rspb.2021.1720","ama":"Huylmans AK, Macon A, Hontoria F, Vicoso B. Transitions to asexuality and evolution of gene expression in Artemia brine shrimp. Proceedings of the Royal Society B: Biological Sciences. 2021;288(1959). doi:10.1098/rspb.2021.1720","ieee":"A. K. Huylmans, A. Macon, F. Hontoria, and B. Vicoso, “Transitions to asexuality and evolution of gene expression in Artemia brine shrimp,” Proceedings of the Royal Society B: Biological Sciences, vol. 288, no. 1959. The Royal Society, 2021.","short":"A.K. Huylmans, A. Macon, F. Hontoria, B. Vicoso, Proceedings of the Royal Society B: Biological Sciences 288 (2021).","mla":"Huylmans, Ann K., et al. “Transitions to Asexuality and Evolution of Gene Expression in Artemia Brine Shrimp.” Proceedings of the Royal Society B: Biological Sciences, vol. 288, no. 1959, 20211720, The Royal Society, 2021, doi:10.1098/rspb.2021.1720."},"title":"Transitions to asexuality and evolution of gene expression in Artemia brine shrimp","author":[{"last_name":"Huylmans","full_name":"Huylmans, Ann K","orcid":"0000-0001-8871-4961","first_name":"Ann K","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Macon","full_name":"Macon, Ariana","first_name":"Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hontoria, Francisco","last_name":"Hontoria","first_name":"Francisco"},{"full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz"}],"external_id":{"isi":["000697643700001"],"pmid":["34547909"]},"article_processing_charge":"Yes (via OA deal)"}]