[{"language":[{"iso":"eng"}],"conference":{"name":"CALDAM: Conference on Algorithms and Discrete Applied Mathematics","end_date":"2021-02-13","start_date":"2021-02-11","location":"Rupnagar, India"},"date_published":"2021-01-28T00:00:00Z","doi":"10.1007/978-3-030-67899-9_28","quality_controlled":"1","page":"346-358","publication":"Conference on Algorithms and Discrete Applied Mathematics","citation":{"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.","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","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.","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.","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.","short":"A. Bloch-Hansen, N. Samei, R. Solis-Oba, in:, Conference on Algorithms and Discrete Applied Mathematics, Springer Nature, 2021, pp. 346–358."},"month":"01","day":"28","article_processing_charge":"No","publication_identifier":{"issn":["0302-9743"],"isbn":["9783030678982"],"eissn":["1611-3349"]},"scopus_import":"1","date_created":"2021-03-07T23:01:25Z","date_updated":"2023-10-10T09:29:08Z","volume":12601,"oa_version":"None","author":[{"full_name":"Bloch-Hansen, Andrew","last_name":"Bloch-Hansen","first_name":"Andrew"},{"full_name":"Samei, Nasim","id":"C1531CAE-36E9-11EA-845F-33AA3DDC885E","first_name":"Nasim","last_name":"Samei"},{"first_name":"Roberto","last_name":"Solis-Oba","full_name":"Solis-Oba, Roberto"}],"status":"public","title":"Experimental evaluation of a local search approximation algorithm for the multiway cut problem","publication_status":"published","publisher":"Springer Nature","intvolume":" 12601","department":[{"_id":"VlKo"}],"year":"2021","_id":"9227","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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"}],"alternative_title":["LNCS"],"type":"conference"},{"type":"journal_article","issue":"2","abstract":[{"lang":"eng","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."}],"intvolume":" 93","title":"An inertial subgradient extragradient algorithm extended to pseudomonotone equilibrium problems","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8817","oa_version":"None","scopus_import":"1","article_processing_charge":"No","day":"01","page":"213-242","article_type":"original","citation":{"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","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.","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.","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","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.","short":"Y. Shehu, O.S. Iyiola, D.V. Thong, N.T.C. Van, Mathematical Methods of Operations Research 93 (2021) 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."},"publication":"Mathematical Methods of Operations Research","date_published":"2021-04-01T00:00:00Z","ec_funded":1,"department":[{"_id":"VlKo"}],"publisher":"Springer Nature","publication_status":"published","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).","year":"2021","volume":93,"date_updated":"2023-10-10T09:30:23Z","date_created":"2020-11-29T23:01:18Z","author":[{"full_name":"Shehu, Yekini","id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9224-7139","first_name":"Yekini","last_name":"Shehu"},{"full_name":"Iyiola, Olaniyi S.","first_name":"Olaniyi S.","last_name":"Iyiola"},{"full_name":"Thong, Duong Viet","first_name":"Duong Viet","last_name":"Thong"},{"full_name":"Van, Nguyen Thi Cam","first_name":"Nguyen Thi Cam","last_name":"Van"}],"publication_identifier":{"eissn":["1432-5217"],"issn":["1432-2994"]},"month":"04","project":[{"call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice","_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000590497300001"]},"language":[{"iso":"eng"}],"doi":"10.1007/s00186-020-00730-w"},{"issue":"2","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."}],"type":"journal_article","oa_version":"None","intvolume":" 76","status":"public","title":"New convergence results for inertial Krasnoselskii–Mann iterations in Hilbert spaces with applications","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9315","article_processing_charge":"No","day":"25","scopus_import":"1","date_published":"2021-03-25T00:00:00Z","article_type":"original","citation":{"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.","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.","short":"O.S. Iyiola, Y. Shehu, Results in Mathematics 76 (2021).","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.","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.","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"},"publication":"Results in Mathematics","article_number":"75","volume":76,"date_created":"2021-04-11T22:01:14Z","date_updated":"2023-10-10T09:47:33Z","author":[{"full_name":"Iyiola, Olaniyi S.","last_name":"Iyiola","first_name":"Olaniyi S."},{"id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9224-7139","first_name":"Yekini","last_name":"Shehu","full_name":"Shehu, Yekini"}],"department":[{"_id":"VlKo"}],"publisher":"Springer Nature","publication_status":"published","year":"2021","acknowledgement":"The research of this author is supported by the Postdoctoral Fellowship from Institute of Science and Technology (IST), Austria.","publication_identifier":{"eissn":["1420-9012"],"issn":["1422-6383"]},"month":"03","language":[{"iso":"eng"}],"doi":"10.1007/s00025-021-01381-x","isi":1,"quality_controlled":"1","external_id":{"isi":["000632917700001"]}},{"day":"14","article_processing_charge":"No","scopus_import":"1","date_published":"2021-04-14T00:00:00Z","article_type":"original","publication":"Optimization","citation":{"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","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","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.","ista":"Ogbuisi FU, Shehu Y, Yao JC. 2021. Convergence analysis of new inertial method for the split common null point problem. Optimization.","short":"F.U. Ogbuisi, Y. Shehu, J.C. Yao, Optimization (2021).","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.","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."},"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."}],"type":"journal_article","oa_version":"None","title":"Convergence analysis of new inertial method for the split common null point problem","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9365","month":"04","publication_identifier":{"eissn":["1029-4945"],"issn":["0233-1934"]},"language":[{"iso":"eng"}],"doi":"10.1080/02331934.2021.1914035","quality_controlled":"1","isi":1,"project":[{"_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160","name":"Discrete Optimization in Computer Vision: Theory and Practice","call_identifier":"FP7"}],"external_id":{"isi":["000640109300001"]},"ec_funded":1,"date_created":"2021-05-02T22:01:29Z","date_updated":"2023-10-10T09:48:41Z","author":[{"last_name":"Ogbuisi","first_name":"Ferdinard U.","full_name":"Ogbuisi, Ferdinard U."},{"orcid":"0000-0001-9224-7139","id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87","last_name":"Shehu","first_name":"Yekini","full_name":"Shehu, Yekini"},{"last_name":"Yao","first_name":"Jen Chih","full_name":"Yao, Jen Chih"}],"publication_status":"published","department":[{"_id":"VlKo"}],"publisher":"Taylor and Francis","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).","year":"2021"},{"date_published":"2021-11-18T00:00:00Z","page":"1382–1390","article_type":"original","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.","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.","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","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.","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.","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."},"publication":"Nature Physics","has_accepted_license":"1","article_processing_charge":"No","day":"18","scopus_import":"1","file":[{"content_type":"application/pdf","file_size":40285498,"creator":"channezo","access_level":"open_access","file_name":"50145_4_merged_1630498627.pdf","checksum":"5d6d76750a71d7cb632bb15417c38ef7","success":1,"date_updated":"2023-10-11T09:31:43Z","date_created":"2023-10-11T09:31:43Z","relation":"main_file","file_id":"14420"}],"oa_version":"Submitted Version","intvolume":" 17","ddc":["530"],"status":"public","title":"Cell monolayers sense curvature by exploiting active mechanics and nuclear mechanoadaptation","_id":"10365","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"12","abstract":[{"lang":"eng","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."}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1038/s41567-021-01374-1","project":[{"name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020","grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E"},{"call_identifier":"FWF","name":"Active mechano-chemical description of the cell cytoskeleton","_id":"268294B6-B435-11E9-9278-68D0E5697425","grant_number":"P31639"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000720204300004"]},"oa":1,"publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"month":"11","volume":17,"date_created":"2021-11-28T23:01:29Z","date_updated":"2023-10-16T06:31:54Z","related_material":{"link":[{"relation":"press_release","description":"News on IST Webpage","url":"https://ist.ac.at/en/news/how-cells-feel-curvature/"}]},"author":[{"full_name":"Luciano, Marine","last_name":"Luciano","first_name":"Marine"},{"id":"31D2C804-F248-11E8-B48F-1D18A9856A87","first_name":"Shi-lei","last_name":"Xue","full_name":"Xue, Shi-lei"},{"full_name":"De Vos, Winnok H.","first_name":"Winnok H.","last_name":"De Vos"},{"full_name":"Redondo-Morata, Lorena","last_name":"Redondo-Morata","first_name":"Lorena"},{"full_name":"Surin, Mathieu","last_name":"Surin","first_name":"Mathieu"},{"full_name":"Lafont, Frank","first_name":"Frank","last_name":"Lafont"},{"full_name":"Hannezo, Edouard B","first_name":"Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561"},{"full_name":"Gabriele, Sylvain","last_name":"Gabriele","first_name":"Sylvain"}],"department":[{"_id":"EdHa"}],"publisher":"Springer Nature","publication_status":"published","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.","year":"2021","ec_funded":1,"file_date_updated":"2023-10-11T09:31:43Z"},{"date_published":"2021-02-08T00:00:00Z","publication":"Autophagy","citation":{"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.","short":"D.J. Klionsky, A.K. Abdel-Aziz, S. Abdelfatah, M. Abdellatif, A. Abdoli, S. Abel, H. Abeliovich, M.H. Abildgaard, Y.P. Abudu, A. Acevedo-Arozena, I.E. Adamopoulos, K. Adeli, T.E. Adolph, A. Adornetto, E. Aflaki, G. Agam, A. Agarwal, B.B. Aggarwal, M. Agnello, P. Agostinis, J.N. Agrewala, A. Agrotis, P.V. Aguilar, S.T. Ahmad, Z.M. Ahmed, U. Ahumada-Castro, S. Aits, S. Aizawa, Y. Akkoc, T. Akoumianaki, H.A. Akpinar, A.M. Al-Abd, L. Al-Akra, A. Al-Gharaibeh, M.A. Alaoui-Jamali, S. Alberti, E. Alcocer-Gómez, C. Alessandri, M. Ali, M.A. Alim Al-Bari, S. Aliwaini, J. Alizadeh, E. Almacellas, A. Almasan, A. Alonso, G.D. Alonso, N. Altan-Bonnet, D.C. Altieri, É.M.C. Álvarez, S. Alves, C. Alves Da Costa, M.M. Alzaharna, M. Amadio, C. Amantini, C. Amaral, S. Ambrosio, A.O. Amer, V. Ammanathan, Z. An, S.U. Andersen, S.A. Andrabi, M. Andrade-Silva, A.M. Andres, S. Angelini, D. Ann, U.C. Anozie, M.Y. Ansari, P. Antas, A. Antebi, Z. Antón, T. Anwar, L. Apetoh, N. Apostolova, T. Araki, Y. Araki, K. Arasaki, W.L. Araújo, J. Araya, C. Arden, M.A. Arévalo, S. Arguelles, E. Arias, J. Arikkath, H. Arimoto, A.R. Ariosa, D. Armstrong-James, L. Arnauné-Pelloquin, A. Aroca, D.S. Arroyo, I. Arsov, R. Artero, D.M.L. Asaro, M. Aschner, M. Ashrafizadeh, O. Ashur-Fabian, A.G. Atanasov, A.K. Au, P. Auberger, H.W. Auner, L. Aurelian, R. Autelli, L. Avagliano, Y. Ávalos, S. Aveic, C.A. Aveleira, T. Avin-Wittenberg, Y. Aydin, S. Ayton, S. Ayyadevara, M. Azzopardi, M. Baba, J.M. Backer, S.K. Backues, D.H. Bae, O.N. Bae, S.H. Bae, E.H. Baehrecke, A. Baek, S.H. Baek, S.H. Baek, G. Bagetta, A. Bagniewska-Zadworna, H. Bai, J. Bai, X. Bai, Y. Bai, N. Bairagi, S. Baksi, T. Balbi, C.T. Baldari, W. Balduini, A. Ballabio, M. Ballester, S. Balazadeh, R. Balzan, R. Bandopadhyay, S. Banerjee, S. Banerjee, Á. Bánréti, Y. Bao, M.S. Baptista, A. Baracca, C. Barbati, A. Bargiela, D. Barilà, P.G. Barlow, S.J. Barmada, E. Barreiro, G.E. Barreto, J. Bartek, B. Bartel, A. Bartolome, G.R. Barve, S.H. Basagoudanavar, D.C. Bassham, R.C. Bast, A. Basu, H. Batoko, I. Batten, E.E. Baulieu, B.L. Baumgarner, J. Bayry, R. Beale, I. Beau, F. Beaumatin, L.R.G. Bechara, G.R. Beck, M.F. Beers, J. Begun, C. Behrends, G.M.N. Behrens, R. Bei, E. Bejarano, S. Bel, C. Behl, A. Belaid, N. Belgareh-Touzé, C. Bellarosa, F. 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Tumtas, M.J. Tuñón, S. Turcotte, B. Turk, V. Turk, B.J. Turner, R.I. Tuxworth, J.K. Tyler, E.V. Tyutereva, Y. Uchiyama, A. Ugun-Klusek, H.H. Uhlig, M. Ułamek-Kozioł, I.V. Ulasov, M. Umekawa, C. Ungermann, R. Unno, S. Urbe, E. Uribe-Carretero, S. Üstün, V.N. Uversky, T. Vaccari, M.I. Vaccaro, B.F. Vahsen, H. Vakifahmetoglu-Norberg, R. Valdor, M.J. Valente, A. Valko, R.B. Vallee, A.M. Valverde, G. Van Den Berghe, S. Van Der Veen, L. Van Kaer, J. Van Loosdregt, S.J.L. Van Wijk, W. Vandenberghe, I. Vanhorebeek, M.A. Vannier-Santos, N. Vannini, M.C. Vanrell, C. Vantaggiato, G. Varano, I. Varela-Nieto, M. Varga, M.H. Vasconcelos, S. Vats, D.G. Vavvas, I. Vega-Naredo, S. Vega-Rubin-De-Celis, G. Velasco, A.P. Velázquez, T. Vellai, E. Vellenga, F. Velotti, M. Verdier, P. Verginis, I. Vergne, P. Verkade, M. Verma, P. Verstreken, T. Vervliet, J. Vervoorts, A.T. Vessoni, V.M. Victor, M. Vidal, C. Vidoni, O.V. Vieira, R.D. Vierstra, S. Viganó, H. Vihinen, V. Vijayan, M. Vila, M. Vilar, J.M. 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Tong, Autophagy 17 (2021) 1–382.","mla":"Klionsky, Daniel J., et al. “Guidelines for the Use and Interpretation of Assays for Monitoring Autophagy (4th Edition).” Autophagy, vol. 17, no. 1, Taylor & Francis, 2021, pp. 1–382, doi:10.1080/15548627.2020.1797280.","ieee":"D. J. Klionsky et al., “Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition),” Autophagy, vol. 17, no. 1. Taylor & Francis, pp. 1–382, 2021.","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","ista":"Klionsky DJ et al. 2021. Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition). Autophagy. 17(1), 1–382.","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"},"article_type":"review","page":"1-382","day":"08","article_processing_charge":"No","scopus_import":"1","oa_version":"Published Version","_id":"9298","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)","status":"public","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"}],"issue":"1","type":"journal_article","doi":"10.1080/15548627.2020.1797280","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1080/15548627.2020.1797280","open_access":"1"}],"external_id":{"pmid":["33634751"],"isi":["000636121800001"]},"oa":1,"quality_controlled":"1","isi":1,"month":"02","publication_identifier":{"issn":["1554-8627"],"eissn":["1554-8635"]},"author":[{"last_name":"Klionsky","first_name":"Daniel J.","full_name":"Klionsky, Daniel J."},{"full_name":"Abdel-Aziz, Amal Kamal","first_name":"Amal Kamal","last_name":"Abdel-Aziz"},{"last_name":"Abdelfatah","first_name":"Sara","full_name":"Abdelfatah, Sara"},{"last_name":"Abdellatif","first_name":"Mahmoud","full_name":"Abdellatif, Mahmoud"},{"last_name":"Abdoli","first_name":"Asghar","full_name":"Abdoli, Asghar"},{"last_name":"Abel","first_name":"Steffen","full_name":"Abel, Steffen"},{"full_name":"Abeliovich, Hagai","last_name":"Abeliovich","first_name":"Hagai"},{"last_name":"Abildgaard","first_name":"Marie H.","full_name":"Abildgaard, Marie H."},{"full_name":"Abudu, Yakubu Princely","first_name":"Yakubu Princely","last_name":"Abudu"},{"first_name":"Abraham","last_name":"Acevedo-Arozena","full_name":"Acevedo-Arozena, Abraham"},{"first_name":"Iannis E.","last_name":"Adamopoulos","full_name":"Adamopoulos, Iannis E."},{"full_name":"Adeli, Khosrow","first_name":"Khosrow","last_name":"Adeli"},{"full_name":"Adolph, Timon E.","first_name":"Timon E.","last_name":"Adolph"},{"full_name":"Adornetto, Annagrazia","first_name":"Annagrazia","last_name":"Adornetto"},{"full_name":"Aflaki, Elma","last_name":"Aflaki","first_name":"Elma"},{"full_name":"Agam, Galila","last_name":"Agam","first_name":"Galila"},{"full_name":"Agarwal, Anupam","last_name":"Agarwal","first_name":"Anupam"},{"full_name":"Aggarwal, Bharat B.","last_name":"Aggarwal","first_name":"Bharat B."},{"last_name":"Agnello","first_name":"Maria","full_name":"Agnello, Maria"},{"full_name":"Agostinis, Patrizia","first_name":"Patrizia","last_name":"Agostinis"},{"full_name":"Agrewala, Javed N.","last_name":"Agrewala","first_name":"Javed N."},{"first_name":"Alexander","last_name":"Agrotis","full_name":"Agrotis, Alexander"},{"full_name":"Aguilar, Patricia V.","first_name":"Patricia V.","last_name":"Aguilar"},{"last_name":"Ahmad","first_name":"S. 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Due to space and other limitations, it is not possible to include all other sources of financial support.","pmid":1,"publication_status":"published","publisher":"Taylor & Francis","department":[{"_id":"JiFr"},{"_id":"CaHe"}]},{"date_updated":"2023-10-17T07:39:01Z","date_created":"2020-11-08T23:01:25Z","volume":33,"author":[{"id":"35827D50-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8314-0177","first_name":"Timothy D","last_name":"Browning","full_name":"Browning, Timothy D"},{"full_name":"Heath-Brown, Roger","first_name":"Roger","last_name":"Heath-Brown"}],"publication_status":"published","department":[{"_id":"TiBr"}],"publisher":"De Gruyter","year":"2021","month":"01","publication_identifier":{"issn":["0933-7741"],"eissn":["1435-5337"]},"language":[{"iso":"eng"}],"doi":"10.1515/forum-2020-0074","isi":1,"quality_controlled":"1","project":[{"name":"New frontiers of the Manin conjecture","call_identifier":"FWF","_id":"26AEDAB2-B435-11E9-9278-68D0E5697425","grant_number":"P32428"}],"external_id":{"arxiv":["2003.09593"],"isi":["000604750900008"]},"main_file_link":[{"url":"https://arxiv.org/abs/2003.09593","open_access":"1"}],"oa":1,"abstract":[{"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.","lang":"eng"}],"issue":"1","type":"journal_article","oa_version":"Preprint","title":"The geometric sieve for quadrics","status":"public","intvolume":" 33","_id":"8742","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2021-01-01T00:00:00Z","article_type":"original","page":"147-165","publication":"Forum Mathematicum","citation":{"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","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.","ista":"Browning TD, Heath-Brown R. 2021. The geometric sieve for quadrics. Forum Mathematicum. 33(1), 147–165.","ama":"Browning TD, Heath-Brown R. The geometric sieve for quadrics. Forum Mathematicum. 2021;33(1):147-165. doi:10.1515/forum-2020-0074","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.","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."}},{"publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"KrPi"}],"publication_status":"published","year":"2021","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","date_updated":"2023-10-17T09:24:07Z","date_created":"2021-09-23T07:31:44Z","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"10044"},{"id":"10049","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"637"},{"status":"public","relation":"part_of_dissertation","id":"10041"},{"relation":"part_of_dissertation","status":"public","id":"6430"},{"id":"10048","relation":"part_of_dissertation","status":"public"}]},"author":[{"full_name":"Klein, Karen","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87","last_name":"Klein","first_name":"Karen"}],"license":"https://creativecommons.org/licenses/by/4.0/","ec_funded":1,"file_date_updated":"2022-03-10T12:15:18Z","project":[{"name":"Teaching Old Crypto New Tricks","call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"supervisor":[{"orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak","first_name":"Krzysztof Z","full_name":"Pietrzak, Krzysztof Z"}],"degree_awarded":"PhD","doi":"10.15479/at:ista:10035","publication_identifier":{"issn":["2663-337X"]},"month":"09","title":"On the adaptive security of graph-based games","ddc":["519"],"status":"public","_id":"10035","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"date_created":"2021-10-04T12:22:33Z","date_updated":"2021-10-04T12:22:33Z","success":1,"checksum":"73a44345c683e81f3e765efbf86fdcc5","file_id":"10082","relation":"main_file","creator":"cchlebak","file_size":2104726,"content_type":"application/pdf","file_name":"thesis_pdfa.pdf","access_level":"open_access"},{"access_level":"closed","file_name":"thesis_final (1).zip","file_size":9538359,"content_type":"application/x-zip-compressed","creator":"cchlebak","relation":"source_file","file_id":"10085","checksum":"7b80df30a0e686c3ef6a56d4e1c59e29","date_updated":"2022-03-10T12:15:18Z","date_created":"2021-10-05T07:04:37Z"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"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]).","lang":"eng"}],"page":"276","citation":{"mla":"Klein, Karen. On the Adaptive Security of Graph-Based Games. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10035.","short":"K. Klein, On the Adaptive Security of Graph-Based Games, Institute of Science and Technology Austria, 2021.","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.","ama":"Klein K. On the adaptive security of graph-based games. 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.","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","ieee":"K. Klein, “On the adaptive security of graph-based games,” Institute of Science and Technology Austria, 2021."},"date_published":"2021-09-23T00:00:00Z","has_accepted_license":"1","article_processing_charge":"No","day":"23"},{"year":"2021","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).","publisher":"Springer Nature","department":[{"_id":"KrPi"}],"publication_status":"published","related_material":{"record":[{"id":"10048","relation":"earlier_version","status":"public"}]},"author":[{"id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","first_name":"Chethan","last_name":"Kamath Hosdurg","full_name":"Kamath Hosdurg, Chethan"},{"full_name":"Klein, Karen","first_name":"Karen","last_name":"Klein","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pietrzak","first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Pietrzak, Krzysztof Z"},{"full_name":"Walter, Michael","id":"488F98B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3186-2482","first_name":"Michael","last_name":"Walter"}],"volume":13043,"date_created":"2021-12-05T23:01:43Z","date_updated":"2023-10-17T09:24:07Z","ec_funded":1,"external_id":{"isi":["000728364000019"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://ia.cr/2021/059"}],"project":[{"grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Teaching Old Crypto New Tricks"}],"isi":1,"quality_controlled":"1","doi":"10.1007/978-3-030-90453-1_19","conference":{"name":"TCC: Theory of Cryptography","start_date":"2021-11-08","location":"Raleigh, NC, United States","end_date":"2021-11-11"},"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0302-9743"],"isbn":["9-783-0309-0452-4"],"eissn":["1611-3349"]},"month":"11","_id":"10410","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 13043","status":"public","title":"The cost of adaptivity in security games on graphs","oa_version":"Preprint","type":"conference","alternative_title":["LNCS"],"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 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.","lang":"eng"}],"citation":{"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.","short":"C. Kamath Hosdurg, K. Klein, K.Z. Pietrzak, M. Walter, in:, 19th International Conference, Springer Nature, 2021, pp. 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.","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","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.","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.","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"},"publication":"19th International Conference","page":"550-581","date_published":"2021-11-04T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"04"},{"oa_version":"Preprint","date_updated":"2023-10-17T09:24:08Z","date_created":"2021-09-27T12:52:05Z","related_material":{"record":[{"relation":"later_version","status":"public","id":"10410"},{"id":"10035","status":"public","relation":"dissertation_contains"}]},"author":[{"last_name":"Kamath Hosdurg","first_name":"Chethan","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","full_name":"Kamath Hosdurg, Chethan"},{"first_name":"Karen","last_name":"Klein","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87","full_name":"Klein, Karen"},{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z"},{"full_name":"Walter, Michael","id":"488F98B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3186-2482","first_name":"Michael","last_name":"Walter"}],"publisher":"International Association for Cryptologic Research","department":[{"_id":"KrPi"}],"status":"public","title":"The cost of adaptivity in security games on graphs","publication_status":"published","_id":"10048","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2021","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"}],"type":"conference","language":[{"iso":"eng"}],"date_published":"2021-07-08T00:00:00Z","conference":{"end_date":"2021-11-11","location":"Raleigh, NC, United States","start_date":"2021-11-08","name":"TCC: Theory of Cryptography Conference"},"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://ia.cr/2021/059"}],"citation":{"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.","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.","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.","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.","short":"C. Kamath Hosdurg, K. Klein, K.Z. Pietrzak, M. Walter, in:, 19th Theory of Cryptography Conference 2021, International Association for Cryptologic Research, 2021.","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."},"publication":"19th Theory of Cryptography Conference 2021","article_processing_charge":"No","day":"08","month":"07"},{"date_updated":"2023-10-17T11:26:45Z","date_created":"2022-02-06T23:01:33Z","volume":14,"author":[{"full_name":"Leopold, Nikolai K","first_name":"Nikolai K","last_name":"Leopold","id":"4BC40BEC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0495-6822"},{"full_name":"Rademacher, Simone Anna Elvira","orcid":"0000-0001-5059-4466","id":"856966FE-A408-11E9-977E-802DE6697425","last_name":"Rademacher","first_name":"Simone Anna Elvira"},{"full_name":"Schlein, Benjamin","last_name":"Schlein","first_name":"Benjamin"},{"full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","first_name":"Robert"}],"publication_status":"published","publisher":"Mathematical Sciences Publishers","department":[{"_id":"RoSe"}],"year":"2021","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","ec_funded":1,"language":[{"iso":"eng"}],"doi":"10.2140/APDE.2021.14.2079","quality_controlled":"1","isi":1,"project":[{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227","call_identifier":"H2020","name":"Analysis of quantum many-body systems"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1904.12532"}],"external_id":{"isi":["000733976600004"],"arxiv":["1904.12532"]},"month":"11","publication_identifier":{"issn":["2157-5045"],"eissn":["1948-206X"]},"oa_version":"Preprint","title":" The Landau–Pekar equations: Adiabatic theorem and accuracy","status":"public","intvolume":" 14","_id":"10738","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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"}],"issue":"7","type":"journal_article","date_published":"2021-11-10T00:00:00Z","article_type":"original","page":"2079-2100","publication":"Analysis and PDE","citation":{"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","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.","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.","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","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.","short":"N.K. Leopold, S.A.E. Rademacher, B. Schlein, R. Seiringer, Analysis and PDE 14 (2021) 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."},"day":"10","article_processing_charge":"No","scopus_import":"1"},{"oa":1,"project":[{"_id":"268A44D6-B435-11E9-9278-68D0E5697425","grant_number":"805223","call_identifier":"H2020","name":"Elastic Coordination for Scalable Machine Learning"}],"doi":"10.15479/at:ista:10429","language":[{"iso":"eng"}],"supervisor":[{"first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian"}],"degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"month":"12","year":"2021","department":[{"_id":"GradSch"},{"_id":"DaAl"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","related_material":{"record":[{"id":"10432","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"6673"},{"relation":"part_of_dissertation","status":"public","id":"5965"},{"status":"public","relation":"part_of_dissertation","id":"10435"}]},"author":[{"full_name":"Nadiradze, Giorgi","id":"3279A00C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5634-0731","first_name":"Giorgi","last_name":"Nadiradze"}],"date_created":"2021-12-08T21:52:28Z","date_updated":"2023-10-17T11:48:55Z","ec_funded":1,"file_date_updated":"2022-03-28T12:55:12Z","citation":{"ista":"Nadiradze G. 2021. On achieving scalability through relaxation. Institute of Science and Technology Austria.","ieee":"G. Nadiradze, “On achieving scalability through relaxation,” Institute of Science and Technology Austria, 2021.","apa":"Nadiradze, G. (2021). On achieving scalability through relaxation. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10429","ama":"Nadiradze G. On achieving scalability through relaxation. 2021. doi:10.15479/at:ista:10429","chicago":"Nadiradze, Giorgi. “On Achieving Scalability through Relaxation.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10429.","mla":"Nadiradze, Giorgi. On Achieving Scalability through Relaxation. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10429.","short":"G. Nadiradze, On Achieving Scalability through Relaxation, Institute of Science and Technology Austria, 2021."},"page":"132","date_published":"2021-12-09T00:00:00Z","has_accepted_license":"1","article_processing_charge":"No","day":"09","_id":"10429","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","ddc":["000"],"title":"On achieving scalability through relaxation","file":[{"file_name":"Thesis_Final_09_12_2021.pdf","access_level":"open_access","creator":"gnadirad","file_size":2370859,"content_type":"application/pdf","file_id":"10436","relation":"main_file","date_created":"2021-12-09T17:47:49Z","date_updated":"2021-12-09T17:47:49Z","success":1,"checksum":"6bf14e9a523387328f016c0689f5e10e"},{"creator":"gnadirad","file_size":2596924,"content_type":"application/zip","access_level":"closed","file_name":"Thesis_Final_09_12_2021.zip","checksum":"914d6c5ca86bd0add471971a8f4c4341","date_created":"2021-12-09T17:47:49Z","date_updated":"2022-03-28T12:55:12Z","file_id":"10437","relation":"source_file"}],"oa_version":"Published Version","type":"dissertation","alternative_title":["ISTA Thesis"],"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"}]},{"day":"01","month":"12","article_processing_charge":"No","conference":{"start_date":"2021-12-06","location":"Sydney, Australia","end_date":"2021-12-14","name":"NeurIPS: Neural Information Processing Systems"},"date_published":"2021-12-01T00:00:00Z","language":[{"iso":"eng"}],"publication":"35th Conference on Neural Information Processing Systems","citation":{"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.","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.","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.","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.","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.","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."},"external_id":{"arxiv":["1910.12308"]},"oa":1,"main_file_link":[{"url":"https://papers.nips.cc/paper/2021/hash/362c99307cdc3f2d8b410652386a9dd1-Abstract.html","open_access":"1"}],"quality_controlled":"1","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"},{"_id":"268A44D6-B435-11E9-9278-68D0E5697425","grant_number":"805223","name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020"}],"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"}],"ec_funded":1,"type":"conference","author":[{"id":"3279A00C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5634-0731","first_name":"Giorgi","last_name":"Nadiradze","full_name":"Nadiradze, Giorgi"},{"full_name":"Sabour, Amirmojtaba","id":"bcc145fd-e77f-11ea-ae8b-80d661dbff67","first_name":"Amirmojtaba","last_name":"Sabour"},{"full_name":"Davies, Peter","orcid":"0000-0002-5646-9524","id":"11396234-BB50-11E9-B24C-90FCE5697425","last_name":"Davies","first_name":"Peter"},{"first_name":"Shigang","last_name":"Li","full_name":"Li, Shigang"},{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10429"}]},"date_created":"2021-12-09T10:59:12Z","date_updated":"2023-10-17T11:48:56Z","oa_version":"Published Version","year":"2021","_id":"10435","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","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Asynchronous decentralized SGD with quantized and local updates","publication_status":"published","publisher":"Neural Information Processing Systems Foundation","department":[{"_id":"DaAl"}]},{"oa_version":"Preprint","intvolume":" 35","status":"public","title":"PCA initialization for approximate message passing in rotationally invariant models","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"10593","abstract":[{"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.","lang":"eng"}],"type":"conference","date_published":"2021-12-01T00:00:00Z","page":"29616-29629","citation":{"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.","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.","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.","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.","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.","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.","short":"M. Mondelli, R. Venkataramanan, in:, 35th Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2021, pp. 29616–29629."},"publication":"35th Conference on Neural Information Processing Systems","article_processing_charge":"No","day":"01","scopus_import":"1","volume":35,"date_updated":"2023-10-17T11:48:23Z","date_created":"2022-01-03T10:50:02Z","author":[{"full_name":"Mondelli, Marco","id":"27EB676C-8706-11E9-9510-7717E6697425","orcid":"0000-0002-3242-7020","first_name":"Marco","last_name":"Mondelli"},{"last_name":"Venkataramanan","first_name":"Ramji","full_name":"Venkataramanan, Ramji"}],"publisher":"Neural Information Processing Systems Foundation","department":[{"_id":"MaMo"}],"publication_status":"published","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","year":"2021","language":[{"iso":"eng"}],"conference":{"end_date":"2021-12-14","location":"Virtual","start_date":"2021-12-06","name":"NeurIPS: Neural Information Processing Systems"},"project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"}],"quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/2106.02356","open_access":"1"}],"external_id":{"arxiv":["2106.02356"]},"publication_identifier":{"isbn":["9781713845393"],"issn":["1049-5258"]},"month":"12"},{"publication_identifier":{"isbn":["9781713845393"],"issn":["1049-5258"]},"month":"12","conference":{"name":"35th Conference on Neural Information Processing Systems","start_date":"2021-12-06","location":"Virtual","end_date":"2021-12-14"},"language":[{"iso":"eng"}],"oa":1,"external_id":{"arxiv":["2102.09671"]},"main_file_link":[{"url":"https://arxiv.org/abs/2102.09671","open_access":"1"}],"project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"quality_controlled":"1","author":[{"first_name":"Quynh","last_name":"Nguyen","full_name":"Nguyen, Quynh"},{"full_name":"Bréchet, Pierre","first_name":"Pierre","last_name":"Bréchet"},{"full_name":"Mondelli, Marco","last_name":"Mondelli","first_name":"Marco","orcid":"0000-0002-3242-7020","id":"27EB676C-8706-11E9-9510-7717E6697425"}],"volume":35,"date_created":"2022-01-03T10:56:20Z","date_updated":"2023-10-17T11:48:40Z","year":"2021","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).","department":[{"_id":"MaMo"}],"publisher":"Neural Information Processing Systems Foundation","publication_status":"published","article_processing_charge":"No","day":"01","date_published":"2021-12-01T00:00:00Z","citation":{"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.","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.","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.","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.","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.","short":"Q. Nguyen, P. Bréchet, M. Mondelli, in:, 35th Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2021.","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."},"publication":"35th Conference on Neural Information Processing Systems","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"}],"type":"conference","oa_version":"Preprint","_id":"10594","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 35","title":"When are solutions connected in deep networks?","status":"public"},{"file_date_updated":"2021-08-09T12:23:13Z","article_number":"045005","volume":6,"date_updated":"2023-10-17T12:54:54Z","date_created":"2021-08-08T22:01:25Z","author":[{"first_name":"Sonia","last_name":"Mobassem","full_name":"Mobassem, Sonia"},{"last_name":"Lambert","first_name":"Nicholas J.","full_name":"Lambert, Nicholas J."},{"orcid":"0000-0001-6249-5860","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","last_name":"Rueda Sanchez","first_name":"Alfredo R","full_name":"Rueda Sanchez, Alfredo R"},{"first_name":"Johannes M","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M"},{"first_name":"Gerd","last_name":"Leuchs","full_name":"Leuchs, Gerd"},{"first_name":"Harald G.L.","last_name":"Schwefel","full_name":"Schwefel, Harald G.L."}],"department":[{"_id":"JoFi"}],"publisher":"IOP Publishing","publication_status":"published","year":"2021","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.","publication_identifier":{"eissn":["2058-9565"]},"month":"07","language":[{"iso":"eng"}],"doi":"10.1088/2058-9565/ac0f36","isi":1,"quality_controlled":"1","external_id":{"isi":["000673081500001"],"arxiv":["2008.08764"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"issue":"4","abstract":[{"lang":"eng","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."}],"type":"journal_article","oa_version":"Published Version","file":[{"file_name":"2021_QuantumScienceTechnology_Mobassem.pdf","access_level":"open_access","creator":"cchlebak","file_size":2366118,"content_type":"application/pdf","file_id":"9836","relation":"main_file","date_created":"2021-08-09T12:23:13Z","date_updated":"2021-08-09T12:23:13Z","checksum":"b15c2c228487a75002c3b52d56f23d5c"}],"intvolume":" 6","status":"public","ddc":["530"],"title":"Thermal noise in electro-optic devices at cryogenic temperatures","_id":"9815","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes","has_accepted_license":"1","day":"15","scopus_import":"1","date_published":"2021-07-15T00:00:00Z","article_type":"original","citation":{"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.","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).","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.","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","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.","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.","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"},"publication":"Quantum Science and Technology"},{"month":"08","publication_identifier":{"eissn":["2693-5015"]},"language":[{"iso":"eng"}],"doi":"10.21203/rs.3.rs-750965/v1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"file_date_updated":"2021-08-31T14:02:19Z","date_created":"2021-08-31T12:54:16Z","date_updated":"2023-10-17T13:06:29Z","author":[{"first_name":"Deqing","last_name":"Cao","full_name":"Cao, Deqing"},{"full_name":"Shen, Xiaoxiao","last_name":"Shen","first_name":"Xiaoxiao"},{"last_name":"Wang","first_name":"Aiping","full_name":"Wang, Aiping"},{"full_name":"Yu, Fengjiao","first_name":"Fengjiao","last_name":"Yu"},{"first_name":"Yuping","last_name":"Wu","full_name":"Wu, Yuping"},{"first_name":"Siqi","last_name":"Shi","full_name":"Shi, Siqi"},{"orcid":"0000-0003-2902-5319","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","last_name":"Freunberger","first_name":"Stefan Alexander","full_name":"Freunberger, Stefan Alexander"},{"full_name":"Chen, Yuhui","first_name":"Yuhui","last_name":"Chen"}],"related_material":{"record":[{"relation":"later_version","status":"public","id":"10813"}]},"publication_status":"submitted","publisher":"Research Square","department":[{"_id":"StFr"}],"year":"2021","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. ","day":"18","article_processing_charge":"No","has_accepted_license":"1","keyword":["Catalysis","Energy engineering","Materials theory and modeling"],"date_published":"2021-08-18T00:00:00Z","page":"21","publication":"Research Square","citation":{"short":"D. Cao, X. Shen, A. Wang, F. Yu, Y. Wu, S. Shi, S.A. Freunberger, Y. Chen, Research Square (n.d.).","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.","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.","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","ieee":"D. Cao et al., “Sharp kinetic acceleration potentials during mediated redox catalysis of insulators,” Research Square. Research Square.","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","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."},"abstract":[{"lang":"eng","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."}],"type":"preprint","file":[{"creator":"cchlebak","file_size":1019662,"content_type":"application/pdf","access_level":"open_access","file_name":"2021_ResearchSquare_Cao.pdf","success":1,"checksum":"1878e91c29d5769ed5a827b0b7addf00","date_created":"2021-08-31T14:02:19Z","date_updated":"2021-08-31T14:02:19Z","file_id":"9979","relation":"main_file"}],"oa_version":"Preprint","ddc":["541"],"title":"Sharp kinetic acceleration potentials during mediated redox catalysis of insulators","status":"public","_id":"9978","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"pmid":1,"year":"2021","publisher":"SAGE Publications","department":[{"_id":"GaNo"}],"publication_status":"published","author":[{"first_name":"N","last_name":"Tournier","full_name":"Tournier, N"},{"first_name":"S","last_name":"Goutal","full_name":"Goutal, S"},{"first_name":"S","last_name":"Mairinger","full_name":"Mairinger, S"},{"full_name":"Lozano, IH","last_name":"Lozano","first_name":"IH"},{"full_name":"Filip, T","first_name":"T","last_name":"Filip"},{"full_name":"Sauberer, M","last_name":"Sauberer","first_name":"M"},{"first_name":"F","last_name":"Caillé","full_name":"Caillé, F"},{"first_name":"L","last_name":"Breuil","full_name":"Breuil, L"},{"full_name":"Stanek, J","last_name":"Stanek","first_name":"J"},{"last_name":"Freeman","first_name":"AF","full_name":"Freeman, AF"},{"full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","first_name":"Gaia"},{"full_name":"Truillet, C","first_name":"C","last_name":"Truillet"},{"full_name":"Wanek, T","first_name":"T","last_name":"Wanek"},{"last_name":"Langer","first_name":"O","full_name":"Langer, O"}],"volume":41,"date_updated":"2023-10-18T06:45:30Z","date_created":"2020-11-06T08:39:01Z","publication_identifier":{"eissn":["1559-7016"],"issn":["0271-678x"]},"month":"07","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8221757/"}],"external_id":{"isi":["000664214100012"],"pmid":["33081568"]},"oa":1,"quality_controlled":"1","isi":1,"doi":"10.1177/0271678X20965500","language":[{"iso":"eng"}],"type":"journal_article","issue":"7","abstract":[{"lang":"eng","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."}],"_id":"8730","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 41","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","status":"public","oa_version":"Published Version","scopus_import":"1","article_processing_charge":"No","day":"01","citation":{"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.","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","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.","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","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.","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.","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."},"publication":"Journal of Cerebral Blood Flow and Metabolism","page":"1634-1646","article_type":"original","date_published":"2021-07-01T00:00:00Z"},{"scopus_import":"1","day":"22","article_processing_charge":"No","has_accepted_license":"1","article_type":"original","page":"1256-1273","publication":"Evolution","citation":{"ieee":"S. Stankowski and M. Ravinet, “Defining the speciation continuum,” Evolution, vol. 75, no. 6. Oxford University Press, pp. 1256–1273, 2021.","apa":"Stankowski, S., & Ravinet, M. (2021). Defining the speciation continuum. Evolution. Oxford University Press. https://doi.org/10.1111/evo.14215","ista":"Stankowski S, Ravinet M. 2021. Defining the speciation continuum. Evolution. 75(6), 1256–1273.","ama":"Stankowski S, Ravinet M. Defining the speciation continuum. Evolution. 2021;75(6):1256-1273. doi:10.1111/evo.14215","chicago":"Stankowski, Sean, and Mark Ravinet. “Defining the Speciation Continuum.” Evolution. Oxford University Press, 2021. https://doi.org/10.1111/evo.14215.","short":"S. Stankowski, M. Ravinet, Evolution 75 (2021) 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."},"date_published":"2021-03-22T00:00:00Z","type":"journal_article","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"}],"issue":"6","status":"public","title":"Defining the speciation continuum","ddc":["570"],"intvolume":" 75","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9383","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"10921","date_created":"2022-03-25T12:02:04Z","date_updated":"2022-03-25T12:02:04Z","checksum":"96f6ccf15d95a4e9f7c0b27eee570fa6","success":1,"file_name":"2021_Evolution_Stankowski.pdf","access_level":"open_access","file_size":719991,"content_type":"application/pdf","creator":"kschuh"}],"month":"03","publication_identifier":{"issn":["0014-3820"],"eissn":["1558-5646"]},"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"external_id":{"isi":["000647226400001"]},"language":[{"iso":"eng"}],"doi":"10.1111/evo.14215","license":"https://creativecommons.org/licenses/by-nc/4.0/","file_date_updated":"2022-03-25T12:02:04Z","publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Oxford University Press","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.","year":"2021","date_updated":"2023-10-18T08:16:01Z","date_created":"2021-05-09T22:01:39Z","volume":75,"author":[{"full_name":"Stankowski, Sean","last_name":"Stankowski","first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E"},{"full_name":"Ravinet, Mark","last_name":"Ravinet","first_name":"Mark"}]},{"author":[{"full_name":"Li, Lanxin","first_name":"Lanxin","last_name":"Li","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5607-272X"},{"orcid":"0000-0001-7241-2328","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","last_name":"Verstraeten","first_name":"Inge","full_name":"Verstraeten, Inge"},{"full_name":"Roosjen, Mark","last_name":"Roosjen","first_name":"Mark"},{"full_name":"Takahashi, Koji","last_name":"Takahashi","first_name":"Koji"},{"orcid":"0000-0002-7244-7237","id":"3922B506-F248-11E8-B48F-1D18A9856A87","last_name":"Rodriguez Solovey","first_name":"Lesia","full_name":"Rodriguez Solovey, Lesia"},{"last_name":"Merrin","first_name":"Jack","orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87","full_name":"Merrin, Jack"},{"full_name":"Chen, Jian","last_name":"Chen","first_name":"Jian"},{"full_name":"Shabala, Lana","first_name":"Lana","last_name":"Shabala"},{"full_name":"Smet, Wouter","last_name":"Smet","first_name":"Wouter"},{"full_name":"Ren, Hong","first_name":"Hong","last_name":"Ren"},{"full_name":"Vanneste, Steffen","last_name":"Vanneste","first_name":"Steffen"},{"full_name":"Shabala, Sergey","first_name":"Sergey","last_name":"Shabala"},{"full_name":"De Rybel, Bert","last_name":"De Rybel","first_name":"Bert"},{"full_name":"Weijers, Dolf","last_name":"Weijers","first_name":"Dolf"},{"first_name":"Toshinori","last_name":"Kinoshita","full_name":"Kinoshita, Toshinori"},{"first_name":"William M.","last_name":"Gray","full_name":"Gray, William M."},{"full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}],"related_material":{"record":[{"id":"10095","relation":"earlier_version","status":"public"}],"link":[{"url":"https://ist.ac.at/en/news/stop-and-grow/","description":"News on IST Webpage","relation":"press_release"}]},"date_created":"2021-11-07T23:01:25Z","date_updated":"2023-10-18T08:30:53Z","volume":599,"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.","year":"2021","pmid":1,"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"JiFr"},{"_id":"NanoFab"}],"ec_funded":1,"doi":"10.1038/s41586-021-04037-6","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"Bio"}],"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://www.doi.org/10.21203/rs.3.rs-266395/v3","open_access":"1"}],"external_id":{"pmid":["34707283"],"isi":["000713338100006"]},"oa":1,"quality_controlled":"1","isi":1,"project":[{"grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020"},{"grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF"},{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"},{"name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root","grant_number":"25351","_id":"26B4D67E-B435-11E9-9278-68D0E5697425"}],"month":"11","publication_identifier":{"eissn":["14764687"],"issn":["00280836"]},"oa_version":"Preprint","_id":"10223","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"Cell surface and intracellular auxin signalling for H+ fluxes in root growth","intvolume":" 599","abstract":[{"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.","lang":"eng"}],"issue":"7884","type":"journal_article","date_published":"2021-11-11T00:00:00Z","publication":"Nature","citation":{"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.","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.","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.","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","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.","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","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."},"article_type":"original","page":"273-277","day":"11","article_processing_charge":"No","scopus_import":"1","keyword":["Multidisciplinary"]},{"month":"04","publication_identifier":{"eissn":["2296-634X"]},"language":[{"iso":"eng"}],"doi":"10.3389/fcell.2021.649433","quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000644419500001"],"pmid":["33928084"]},"file_date_updated":"2021-05-11T15:09:23Z","article_number":"649433","date_created":"2021-05-09T22:01:37Z","date_updated":"2023-10-18T08:19:49Z","volume":9,"author":[{"orcid":"0000-0002-8176-4824","id":"516F03FA-93A3-11EA-A7C5-D6BE3DDC885E","last_name":"Bolger-Munro","first_name":"Madison","full_name":"Bolger-Munro, Madison"},{"last_name":"Choi","first_name":"Kate","full_name":"Choi, Kate"},{"full_name":"Cheung, Faith","last_name":"Cheung","first_name":"Faith"},{"first_name":"Yi Tian","last_name":"Liu","full_name":"Liu, Yi Tian"},{"first_name":"May","last_name":"Dang-Lawson","full_name":"Dang-Lawson, May"},{"full_name":"Deretic, Nikola","last_name":"Deretic","first_name":"Nikola"},{"full_name":"Keane, Connor","first_name":"Connor","last_name":"Keane"},{"full_name":"Gold, Michael R.","first_name":"Michael R.","last_name":"Gold"}],"publication_status":"published","publisher":"Frontiers Media","department":[{"_id":"CaHe"}],"acknowledgement":"We thank the UBC Life Sciences Institute Imaging Facility andthe UBC Flow Cytometry Facility.","year":"2021","pmid":1,"day":"13","article_processing_charge":"No","has_accepted_license":"1","keyword":["B cell","actin","immune synapse","cell spreading","cofilin","WDR1 (AIP1)","LIM domain kinase","B cell receptor (BCR)"],"scopus_import":"1","date_published":"2021-04-13T00:00:00Z","article_type":"original","publication":"Frontiers in Cell and Developmental Biology","citation":{"ama":"Bolger-Munro M, Choi K, Cheung F, et al. The Wdr1-LIMK-Cofilin axis controls B cell antigen receptor-induced actin remodeling and signaling at the immune synapse. Frontiers in Cell and Developmental Biology. 2021;9. doi: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.","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.","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","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).","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."},"abstract":[{"lang":"eng","text":"When B cells encounter membrane-bound antigens, the formation and coalescence of B cell antigen receptor (BCR) microclusters amplifies BCR signaling. The ability of B cells to probe the surface of antigen-presenting cells (APCs) and respond to APC-bound antigens requires remodeling of the actin cytoskeleton. Initial BCR signaling stimulates actin-related protein (Arp) 2/3 complex-dependent actin polymerization, which drives B cell spreading as well as the centripetal movement and coalescence of BCR microclusters at the B cell-APC synapse. Sustained actin polymerization depends on concomitant actin filament depolymerization, which enables the recycling of actin monomers and Arp2/3 complexes. Cofilin-mediated severing of actin filaments is a rate-limiting step in the morphological changes that occur during immune synapse formation. Hence, regulators of cofilin activity such as WD repeat-containing protein 1 (Wdr1), LIM domain kinase (LIMK), and coactosin-like 1 (Cotl1) may also be essential for actin-dependent processes in B cells. Wdr1 enhances cofilin-mediated actin disassembly. Conversely, Cotl1 competes with cofilin for binding to actin and LIMK phosphorylates cofilin and prevents it from binding to actin filaments. We now show that Wdr1 and LIMK have distinct roles in BCR-induced assembly of the peripheral actin structures that drive B cell spreading, and that cofilin, Wdr1, and LIMK all contribute to the actin-dependent amplification of BCR signaling at the immune synapse. Depleting Cotl1 had no effect on these processes. Thus, the Wdr1-LIMK-cofilin axis is critical for BCR-induced actin remodeling and for B cell responses to APC-bound antigens."}],"type":"journal_article","oa_version":"Published Version","file":[{"date_updated":"2021-05-11T15:09:23Z","date_created":"2021-05-11T15:09:23Z","success":1,"checksum":"8c8a03575d2f7583f88dc3b658b0976b","file_id":"9386","relation":"main_file","creator":"kschuh","file_size":4076024,"content_type":"application/pdf","file_name":"2021_Frontiers_Cell_Bolger-Munro.pdf","access_level":"open_access"}],"title":"The Wdr1-LIMK-Cofilin axis controls B cell antigen receptor-induced actin remodeling and signaling at the immune synapse","ddc":["570"],"status":"public","intvolume":" 9","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9379"},{"pmid":1,"acknowledgement":"The authors would like to thank Ulisse Ferrari for useful discussions and feedback.","year":"2021","department":[{"_id":"GaTk"}],"publisher":"Public Library of Science","publication_status":"published","author":[{"full_name":"Chalk, Matthew J","id":"2BAAC544-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7782-4436","first_name":"Matthew J","last_name":"Chalk"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","first_name":"Gašper","last_name":"Tkačik","full_name":"Tkačik, Gašper"},{"full_name":"Marre, Olivier","first_name":"Olivier","last_name":"Marre"}],"volume":16,"date_updated":"2023-10-18T08:17:42Z","date_created":"2021-05-02T22:01:28Z","article_number":"e0248940","file_date_updated":"2021-05-04T13:22:19Z","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000641474900072"],"pmid":["33857170"]},"isi":1,"quality_controlled":"1","doi":"10.1371/journal.pone.0248940","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["19326203"]},"month":"04","_id":"9362","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 16","ddc":["570"],"title":"Inferring the function performed by a recurrent neural network","status":"public","file":[{"success":1,"checksum":"c52da133850307d2031f552d998f00e8","date_updated":"2021-05-04T13:22:19Z","date_created":"2021-05-04T13:22:19Z","file_id":"9371","relation":"main_file","creator":"kschuh","file_size":2768282,"content_type":"application/pdf","access_level":"open_access","file_name":"2021_pone_Chalk.pdf"}],"oa_version":"Published Version","type":"journal_article","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"}],"citation":{"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.","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.","short":"M.J. Chalk, G. Tkačik, O. Marre, PLoS ONE 16 (2021).","ista":"Chalk MJ, Tkačik G, Marre O. 2021. Inferring the function performed by a recurrent neural network. PLoS ONE. 16(4), e0248940.","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.","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"},"publication":"PLoS ONE","article_type":"original","date_published":"2021-04-15T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"15"},{"scopus_import":"1","keyword":["auxin","growth","cell wall","xyloglucans","hypocotyls","gravitropism"],"has_accepted_license":"1","article_processing_charge":"Yes","day":"26","citation":{"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","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.","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.","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","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.","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).","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."},"publication":"International Journal of Molecular Sciences","article_type":"original","date_published":"2021-08-26T00:00:00Z","type":"journal_article","issue":"17","abstract":[{"lang":"eng","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."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9986","intvolume":" 22","status":"public","title":"Xyloglucan remodeling defines auxin-dependent differential tissue expansion in plants","ddc":["575"],"file":[{"creator":"cchlebak","file_size":2162247,"content_type":"application/pdf","file_name":"2021_IntJMolecularSciences_Velasquez.pdf","access_level":"open_access","date_created":"2021-09-06T12:50:19Z","date_updated":"2021-09-07T09:04:53Z","checksum":"6b7055cf89f1b7ed8594c3fdf56f000b","file_id":"9988","relation":"main_file"}],"oa_version":"Published Version","publication_identifier":{"issn":["1661-6596"],"eissn":["1422-0067"]},"month":"08","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["34502129"],"isi":["000694347100001"]},"isi":1,"quality_controlled":"1","doi":"10.3390/ijms22179222","language":[{"iso":"eng"}],"article_number":"9222","file_date_updated":"2021-09-07T09:04:53Z","pmid":1,"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","year":"2021","department":[{"_id":"EvBe"}],"publisher":"MDPI","publication_status":"published","author":[{"last_name":"Velasquez","first_name":"Silvia Melina","full_name":"Velasquez, Silvia Melina"},{"last_name":"Guo","first_name":"Xiaoyuan","full_name":"Guo, Xiaoyuan"},{"last_name":"Gallemi","first_name":"Marçal","orcid":"0000-0003-4675-6893","id":"460C6802-F248-11E8-B48F-1D18A9856A87","full_name":"Gallemi, Marçal"},{"first_name":"Bibek","last_name":"Aryal","full_name":"Aryal, Bibek"},{"full_name":"Venhuizen, Peter","first_name":"Peter","last_name":"Venhuizen"},{"full_name":"Barbez, Elke","first_name":"Elke","last_name":"Barbez"},{"full_name":"Dünser, Kai Alexander","first_name":"Kai Alexander","last_name":"Dünser"},{"full_name":"Darino, Martin","last_name":"Darino","first_name":"Martin"},{"full_name":"Pӗnčík, Aleš","last_name":"Pӗnčík","first_name":"Aleš"},{"first_name":"Ondřej","last_name":"Novák","full_name":"Novák, Ondřej"},{"full_name":"Kalyna, Maria","last_name":"Kalyna","first_name":"Maria"},{"first_name":"Gregory","last_name":"Mouille","full_name":"Mouille, Gregory"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","first_name":"Eva","last_name":"Benková","full_name":"Benková, Eva"},{"full_name":"Bhalerao, Rishikesh P.","first_name":"Rishikesh P.","last_name":"Bhalerao"},{"full_name":"Mravec, Jozef","last_name":"Mravec","first_name":"Jozef"},{"first_name":"Jürgen","last_name":"Kleine-Vehn","full_name":"Kleine-Vehn, Jürgen"}],"volume":22,"date_updated":"2023-10-31T19:29:38Z","date_created":"2021-09-05T22:01:24Z"},{"page":"1846-1857","article_type":"original","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.","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","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.","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","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.","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.","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."},"publication":"Plant, Cell & Environment","date_published":"2021-06-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"01","intvolume":" 44","title":"INDITTO2 transposon conveys auxin-mediated DRO1 transcription for rice drought avoidance","status":"public","ddc":["580"],"_id":"9189","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","file":[{"access_level":"open_access","file_name":"Zhao PlantCellEnv 2021_accepted.pdf","content_type":"application/pdf","file_size":8437528,"creator":"amally","relation":"main_file","file_id":"14481","checksum":"a812418fede076741c9c4dc07f317068","success":1,"date_updated":"2023-11-02T17:02:11Z","date_created":"2023-11-02T17:02:11Z"}],"type":"journal_article","issue":"6","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."}],"isi":1,"quality_controlled":"1","oa":1,"external_id":{"isi":["000625398600001"],"pmid":["33576018"]},"language":[{"iso":"eng"}],"doi":"10.1111/pce.14029","publication_identifier":{"issn":["0140-7791"],"eissn":["1365-3040"]},"month":"06","department":[{"_id":"JiFr"}],"publisher":"Wiley","publication_status":"published","pmid":1,"year":"2021","volume":44,"date_updated":"2023-11-07T08:18:36Z","date_created":"2021-02-24T10:07:21Z","author":[{"first_name":"Y","last_name":"Zhao","full_name":"Zhao, Y"},{"full_name":"Wu, L","first_name":"L","last_name":"Wu"},{"full_name":"Fu, Q","last_name":"Fu","first_name":"Q"},{"last_name":"Wang","first_name":"D","full_name":"Wang, D"},{"first_name":"J","last_name":"Li","full_name":"Li, J"},{"full_name":"Yao, B","last_name":"Yao","first_name":"B"},{"full_name":"Yu, S","last_name":"Yu","first_name":"S"},{"first_name":"L","last_name":"Jiang","full_name":"Jiang, L"},{"first_name":"J","last_name":"Qian","full_name":"Qian, J"},{"full_name":"Zhou, X","first_name":"X","last_name":"Zhou"},{"full_name":"Han, L","last_name":"Han","first_name":"L"},{"last_name":"Zhao","first_name":"S","full_name":"Zhao, S"},{"full_name":"Ma, C","first_name":"C","last_name":"Ma"},{"first_name":"Y","last_name":"Zhang","full_name":"Zhang, Y"},{"first_name":"C","last_name":"Luo","full_name":"Luo, C"},{"last_name":"Dong","first_name":"Q","full_name":"Dong, Q"},{"full_name":"Li, S","first_name":"S","last_name":"Li"},{"first_name":"L","last_name":"Zhang","full_name":"Zhang, L"},{"full_name":"Jiang, X","first_name":"X","last_name":"Jiang"},{"last_name":"Li","first_name":"Y","full_name":"Li, Y"},{"last_name":"Luo","first_name":"H","full_name":"Luo, H"},{"last_name":"Li","first_name":"K","full_name":"Li, K"},{"full_name":"Yang, J","first_name":"J","last_name":"Yang"},{"full_name":"Luo, Q","last_name":"Luo","first_name":"Q"},{"full_name":"Li, L","last_name":"Li","first_name":"L"},{"last_name":"Peng","first_name":"S","full_name":"Peng, S"},{"full_name":"Huang, H","first_name":"H","last_name":"Huang"},{"full_name":"Zuo, Z","last_name":"Zuo","first_name":"Z"},{"full_name":"Liu, C","last_name":"Liu","first_name":"C"},{"first_name":"L","last_name":"Wang","full_name":"Wang, L"},{"first_name":"C","last_name":"Li","full_name":"Li, C"},{"full_name":"He, X","last_name":"He","first_name":"X"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří"},{"full_name":"Du, Y","first_name":"Y","last_name":"Du"}],"file_date_updated":"2023-11-02T17:02:11Z"},{"doi":"10.48550/arXiv.2106.11217","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2106.11217"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2106.11217","open_access":"1"}],"project":[{"grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems","call_identifier":"H2020"},{"call_identifier":"H2020","name":"Optimal Transport and Stochastic Dynamics","_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117"},{"name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","grant_number":"F6504"}],"month":"07","author":[{"full_name":"Feliciangeli, Dario","orcid":"0000-0003-0754-8530","id":"41A639AA-F248-11E8-B48F-1D18A9856A87","last_name":"Feliciangeli","first_name":"Dario"},{"first_name":"Augusto","last_name":"Gerolin","full_name":"Gerolin, Augusto"},{"id":"30AD2CBC-F248-11E8-B48F-1D18A9856A87","last_name":"Portinale","first_name":"Lorenzo","full_name":"Portinale, Lorenzo"}],"related_material":{"record":[{"id":"9733","status":"public","relation":"dissertation_contains"},{"id":"10030","relation":"dissertation_contains","status":"public"},{"id":"12911","relation":"later_version","status":"public"}]},"date_updated":"2023-11-14T13:21:01Z","date_created":"2021-08-06T09:07:12Z","year":"2021","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].","publication_status":"submitted","department":[{"_id":"RoSe"},{"_id":"JaMa"}],"ec_funded":1,"article_number":"2106.11217","date_published":"2021-07-21T00:00:00Z","publication":"arXiv","citation":{"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.","short":"D. Feliciangeli, A. Gerolin, L. Portinale, ArXiv (n.d.).","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.","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","ista":"Feliciangeli D, Gerolin A, Portinale L. A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature. arXiv, 2106.11217.","ieee":"D. Feliciangeli, A. Gerolin, and L. Portinale, “A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature,” arXiv. .","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"},"day":"21","article_processing_charge":"No","has_accepted_license":"1","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9792","title":"A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature","status":"public","ddc":["510"],"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"}],"type":"preprint"},{"day":"10","has_accepted_license":"1","article_processing_charge":"Yes","scopus_import":"1","date_published":"2021-12-10T00:00:00Z","publication":"Molecular Therapy - Methods and Clinical Development","citation":{"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.","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","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.","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","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.","short":"M.E. Maes, G.M. Wögenstein, G. Colombo, R. Casado Polanco, S. Siegert, Molecular Therapy - Methods and Clinical Development 23 (2021) 210–224.","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."},"article_type":"original","page":"210-224","abstract":[{"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","lang":"eng"}],"type":"journal_article","file":[{"file_name":"2021_MolTherMethodsClinDev_Maes.pdf","access_level":"open_access","creator":"cchlebak","content_type":"application/pdf","file_size":4794147,"file_id":"10657","relation":"main_file","date_created":"2022-01-24T07:43:09Z","date_updated":"2022-01-24T07:43:09Z","success":1,"checksum":"77dc540e8011c5475031bdf6ccef20a6"}],"oa_version":"Published Version","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"10655","title":"Optimizing AAV2/6 microglial targeting identified enhanced efficiency in the photoreceptor degenerative environment","status":"public","ddc":["570"],"intvolume":" 23","month":"12","publication_identifier":{"eissn":["2329-0501"]},"doi":"10.1016/j.omtm.2021.09.006","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000748748500019"]},"quality_controlled":"1","isi":1,"project":[{"grant_number":"715571","_id":"25D4A630-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Microglia action towards neuronal circuit formation and function in health and disease"}],"file_date_updated":"2022-01-24T07:43:09Z","ec_funded":1,"author":[{"id":"3838F452-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9642-1085","first_name":"Margaret E","last_name":"Maes","full_name":"Maes, Margaret E"},{"last_name":"Wögenstein","first_name":"Gabriele M.","full_name":"Wögenstein, Gabriele M."},{"full_name":"Colombo, Gloria","first_name":"Gloria","last_name":"Colombo","id":"3483CF6C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9434-8902"},{"full_name":"Casado Polanco, Raquel","orcid":"0000-0001-8293-4568","id":"15240fc1-dbcd-11ea-9d1d-ac5a786425fd","last_name":"Casado Polanco","first_name":"Raquel"},{"full_name":"Siegert, Sandra","first_name":"Sandra","last_name":"Siegert","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8635-0877"}],"date_created":"2022-01-23T23:01:28Z","date_updated":"2023-11-16T13:12:03Z","volume":23,"year":"2021","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 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.","publication_status":"published","department":[{"_id":"SaSi"},{"_id":"SiHi"}],"publisher":"Elsevier"},{"month":"12","publication_identifier":{"eissn":["2666-1667"]},"doi":"10.1016/j.xpro.2021.101012","acknowledged_ssus":[{"_id":"Bio"}],"language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","project":[{"grant_number":"715571","_id":"25D4A630-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Microglia action towards neuronal circuit formation and function in health and disease"}],"file_date_updated":"2021-12-20T08:58:40Z","ec_funded":1,"article_number":"101012","author":[{"last_name":"Venturino","first_name":"Alessandro","orcid":"0000-0003-2356-9403","id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","full_name":"Venturino, Alessandro"},{"first_name":"Sandra","last_name":"Siegert","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8635-0877","full_name":"Siegert, Sandra"}],"date_updated":"2023-11-16T13:11:04Z","date_created":"2021-12-19T23:01:32Z","volume":2,"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.","year":"2021","publication_status":"published","publisher":"Elsevier ; Cell Press","department":[{"_id":"SaSi"}],"day":"17","has_accepted_license":"1","article_processing_charge":"Yes","scopus_import":"1","date_published":"2021-12-17T00:00:00Z","publication":"STAR Protocols","citation":{"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.","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.","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","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","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.","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."},"article_type":"original","abstract":[{"lang":"eng","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)."}],"issue":"4","type":"journal_article","file":[{"access_level":"open_access","file_name":"2021_STARProt_Venturino.pdf","content_type":"application/pdf","file_size":6207060,"creator":"cchlebak","relation":"main_file","file_id":"10570","checksum":"9ea2501056c5df99e84726b845e9b976","success":1,"date_created":"2021-12-20T08:58:40Z","date_updated":"2021-12-20T08:58:40Z"}],"oa_version":"Published Version","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"10565","status":"public","title":"Minimally invasive protocols and quantification for microglia-mediated perineuronal net disassembly in mouse brain","ddc":["573"],"intvolume":" 2"},{"article_number":"100939","file_date_updated":"2021-11-22T08:23:58Z","ec_funded":1,"year":"2021","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.","publication_status":"published","department":[{"_id":"SiHi"}],"publisher":"Cell Press","author":[{"orcid":"0000-0002-3183-8207","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","last_name":"Amberg","first_name":"Nicole","full_name":"Amberg, Nicole"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","first_name":"Simon","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon"}],"date_created":"2021-11-21T23:01:28Z","date_updated":"2023-11-16T13:08:03Z","volume":2,"month":"11","publication_identifier":{"eissn":["2666-1667"]},"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","project":[{"name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020","grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425"},{"_id":"268F8446-B435-11E9-9278-68D0E5697425","grant_number":"T0101031","name":"Role of Eed in neural stem cell lineage progression","call_identifier":"FWF"},{"name":"Molecular Mechanisms of Neural Stem Cell Lineage Progression","grant_number":"F07805","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E"}],"doi":"10.1016/j.xpro.2021.100939","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"language":[{"iso":"eng"}],"type":"journal_article","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"}],"issue":"4","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"10321","ddc":["573"],"title":"Genetic mosaic dissection of candidate genes in mice using mosaic analysis with double markers","status":"public","intvolume":" 2","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"10329","date_created":"2021-11-22T08:23:58Z","date_updated":"2021-11-22T08:23:58Z","checksum":"9e3f6d06bf583e7a8b6a9e9a60500a28","success":1,"file_name":"2021_STARProtocols_Amberg.pdf","access_level":"open_access","content_type":"application/pdf","file_size":7309464,"creator":"cchlebak"}],"scopus_import":"1","day":"10","article_processing_charge":"Yes","has_accepted_license":"1","publication":"STAR Protocols","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.","short":"N. Amberg, S. Hippenmeyer, STAR Protocols 2 (2021).","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.","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","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.","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","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."},"article_type":"original","date_published":"2021-11-10T00:00:00Z"},{"isi":1,"quality_controlled":"1","project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A"},{"_id":"2674F658-B435-11E9-9278-68D0E5697425","grant_number":"M02495","name":"Protein structure and function in filopodia across scales","call_identifier":"FWF"}],"external_id":{"isi":["000720259500002"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"language":[{"iso":"eng"}],"doi":"10.1016/j.jsb.2021.107808","month":"11","publication_identifier":{"issn":["1047-8477"]},"publication_status":"published","department":[{"_id":"FlSc"}],"publisher":"Elsevier ","year":"2021","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_updated":"2023-11-21T08:36:02Z","date_created":"2021-11-15T12:21:42Z","volume":213,"author":[{"full_name":"Dimchev, Georgi A","orcid":"0000-0001-8370-6161","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","last_name":"Dimchev","first_name":"Georgi A"},{"last_name":"Amiri","first_name":"Behnam","full_name":"Amiri, Behnam"},{"full_name":"Fäßler, Florian","first_name":"Florian","last_name":"Fäßler","id":"404F5528-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7149-769X"},{"full_name":"Falcke, Martin","first_name":"Martin","last_name":"Falcke"},{"first_name":"Florian KM","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM"}],"related_material":{"record":[{"id":"14502","relation":"software","status":"public"}]},"article_number":"107808","file_date_updated":"2021-11-15T13:11:27Z","article_type":"original","publication":"Journal of Structural Biology","citation":{"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.","short":"G.A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, F.K. Schur, Journal of Structural Biology 213 (2021).","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.","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","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.","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.","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"},"date_published":"2021-11-03T00:00:00Z","keyword":["Structural Biology"],"scopus_import":"1","day":"03","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","title":"Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data","ddc":["572"],"status":"public","intvolume":" 213","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"10290","oa_version":"Published Version","file":[{"creator":"cchlebak","file_size":16818304,"content_type":"application/pdf","file_name":"2021_JournalStructBiol_Dimchev.pdf","access_level":"open_access","date_updated":"2021-11-15T13:11:27Z","date_created":"2021-11-15T13:11:27Z","success":1,"checksum":"6b209e4d44775d4e02b50f78982c15fa","file_id":"10291","relation":"main_file"}],"type":"journal_article","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."}],"issue":"4"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9969","status":"public","title":"LightPIR: Privacy-preserving route discovery for payment channel networks","oa_version":"Submitted Version","type":"conference","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."}],"citation":{"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).","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.","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","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","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.","mla":"Pietrzak, Krzysztof Z., et al. LightPIR: Privacy-Preserving Route Discovery for Payment Channel Networks. IEEE, 2021, doi:10.23919/IFIPNetworking52078.2021.9472205.","short":"K.Z. Pietrzak, I. Salem, S. Schmid, M.X. Yeo, in:, IEEE, 2021."},"date_published":"2021-06-21T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"21","year":"2021","publisher":"IEEE","department":[{"_id":"KrPi"}],"publication_status":"published","related_material":{"record":[{"id":"14506","status":"public","relation":"dissertation_contains"}]},"author":[{"full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak","first_name":"Krzysztof Z"},{"last_name":"Salem","first_name":"Iosif","full_name":"Salem, Iosif"},{"full_name":"Schmid, Stefan","first_name":"Stefan","last_name":"Schmid"},{"first_name":"Michelle X","last_name":"Yeo","id":"2D82B818-F248-11E8-B48F-1D18A9856A87","full_name":"Yeo, Michelle X"}],"date_created":"2021-08-29T22:01:16Z","date_updated":"2023-11-30T10:54:50Z","ec_funded":1,"oa":1,"external_id":{"arxiv":["2104.04293"],"isi":["000853016800008"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2104.04293"}],"project":[{"grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","name":"Teaching Old Crypto New Tricks","call_identifier":"H2020"}],"quality_controlled":"1","isi":1,"doi":"10.23919/IFIPNetworking52078.2021.9472205","conference":{"location":"Espoo and Helsinki, Finland","start_date":"2021-06-21","end_date":"2021-06-24","name":"2021 IFIP Networking Conference (IFIP Networking)"},"language":[{"iso":"eng"}],"publication_identifier":{"eisbn":["978-3-9031-7639-3"],"eissn":["1861-2288"],"isbn":["978-1-6654-4501-6"]},"month":"06"},{"type":"conference","abstract":[{"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.","lang":"eng"}],"title":"Proving non-termination by program reversal","status":"public","_id":"9644","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","scopus_import":"1","article_processing_charge":"No","day":"01","page":"1033-1048","citation":{"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.","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.","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.","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.","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."},"publication":"Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation","date_published":"2021-06-01T00:00:00Z","ec_funded":1,"publisher":"Association for Computing Machinery","department":[{"_id":"KrCh"}],"publication_status":"published","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.","year":"2021","date_created":"2021-07-11T22:01:17Z","date_updated":"2023-11-30T10:55:37Z","related_material":{"record":[{"id":"14539","status":"public","relation":"dissertation_contains"}]},"author":[{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"first_name":"Ehsan Kafshdar","last_name":"Goharshady","full_name":"Goharshady, Ehsan Kafshdar"},{"full_name":"Novotný, Petr","last_name":"Novotný","first_name":"Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87"},{"id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4681-1699","first_name":"Dorde","last_name":"Zikelic","full_name":"Zikelic, Dorde"}],"publication_identifier":{"isbn":["9781450383912"]},"month":"06","project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020"}],"quality_controlled":"1","isi":1,"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/2104.01189","open_access":"1"}],"external_id":{"arxiv":["2104.01189"],"isi":["000723661700067"]},"language":[{"iso":"eng"}],"doi":"10.1145/3453483.3454093","conference":{"name":"PLDI: Programming Language Design and Implementation","start_date":"2021-06-20","location":"Online","end_date":"2021-06-26"}},{"date_published":"2021-07-01T00:00:00Z","publication":"Quantum","citation":{"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","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.","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","ista":"Sack S, Serbyn M. 2021. Quantum annealing initialization of the quantum approximate optimization algorithm. Quantum. 5, 491.","short":"S. Sack, M. Serbyn, Quantum 5 (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.","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."},"article_type":"original","day":"01","has_accepted_license":"1","article_processing_charge":"Yes","scopus_import":"1","file":[{"date_updated":"2021-08-06T06:44:31Z","date_created":"2021-08-06T06:44:31Z","checksum":"9706c2bb8e748e9b5b138381995a7f6f","relation":"main_file","file_id":"9774","content_type":"application/pdf","file_size":2312482,"creator":"cchlebak","file_name":"2021_Quantum_Sack.pdf","access_level":"open_access"}],"oa_version":"Published Version","_id":"9760","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Quantum annealing initialization of the quantum approximate optimization algorithm","ddc":["530"],"status":"public","intvolume":" 5","abstract":[{"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.","lang":"eng"}],"type":"journal_article","doi":"10.22331/Q-2021-07-01-491","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000669830600001"],"arxiv":["2101.05742"]},"isi":1,"quality_controlled":"1","project":[{"name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020","grant_number":"850899","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E"}],"month":"07","publication_identifier":{"eissn":["2521-327X"]},"author":[{"full_name":"Sack, Stefan","id":"dd622248-f6e0-11ea-865d-ce382a1c81a5","orcid":"0000-0001-5400-8508","first_name":"Stefan","last_name":"Sack"},{"full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","first_name":"Maksym"}],"related_material":{"record":[{"id":"14622","relation":"dissertation_contains","status":"public"}]},"date_created":"2021-08-01T22:01:21Z","date_updated":"2023-12-13T14:47:25Z","volume":5,"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).","year":"2021","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"MaSe"}],"publisher":"Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften","file_date_updated":"2021-08-06T06:44:31Z","ec_funded":1,"article_number":"491"},{"abstract":[{"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.","lang":"eng"}],"alternative_title":["LNCS"],"type":"conference","oa_version":"Preprint","status":"public","title":"On lexicographic proof rules for probabilistic termination","intvolume":" 13047","_id":"10414","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"10","article_processing_charge":"No","scopus_import":"1","date_published":"2021-11-10T00:00:00Z","page":"619-639","publication":"24th International Symposium on Formal Methods","citation":{"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","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.","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","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.","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.","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.","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."},"ec_funded":1,"date_updated":"2024-01-17T08:19:41Z","date_created":"2021-12-05T23:01:45Z","volume":13047,"author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"last_name":"Goharshady","first_name":"Ehsan Kafshdar","full_name":"Goharshady, Ehsan Kafshdar"},{"full_name":"Novotný, Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","first_name":"Petr","last_name":"Novotný"},{"full_name":"Zárevúcky, Jiří","first_name":"Jiří","last_name":"Zárevúcky"},{"full_name":"Zikelic, Dorde","last_name":"Zikelic","first_name":"Dorde","orcid":"0000-0002-4681-1699","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"14539","status":"public","relation":"dissertation_contains"},{"id":"14778","status":"public","relation":"later_version"}]},"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"KrCh"}],"year":"2021","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.","month":"11","publication_identifier":{"isbn":["9-783-0309-0869-0"],"eissn":["1611-3349"],"eisbn":["978-3-030-90870-6"],"issn":["0302-9743"]},"language":[{"iso":"eng"}],"conference":{"name":"FM: Formal Methods","end_date":"2021-11-26","start_date":"2021-11-20","location":"Virtual"},"doi":"10.1007/978-3-030-90870-6_33","isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818"},{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"}],"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/2108.02188","open_access":"1"}],"external_id":{"isi":["000758218600033"],"arxiv":["2108.02188"]}},{"department":[{"_id":"MaIb"}],"publisher":"Peking University","publication_status":"published","year":"2021","volume":37,"date_updated":"2024-01-17T11:29:33Z","date_created":"2024-01-14T23:00:58Z","author":[{"id":"9E331C2E-9F27-11E9-AE48-5033E6697425","orcid":"0000-0002-9515-4277","first_name":"Cheng","last_name":"Chang","full_name":"Chang, Cheng"},{"full_name":"Chen, Wei","last_name":"Chen","first_name":"Wei"},{"last_name":"Chen","first_name":"Ye","full_name":"Chen, 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"},{"full_name":"Fan, Chunhai","last_name":"Fan","first_name":"Chunhai"},{"last_name":"Fan","first_name":"Hong Jin","full_name":"Fan, Hong Jin"},{"full_name":"Fan, Zhanxi","first_name":"Zhanxi","last_name":"Fan"},{"full_name":"Gong, Cheng","first_name":"Cheng","last_name":"Gong"},{"first_name":"Yongji","last_name":"Gong","full_name":"Gong, Yongji"},{"full_name":"He, Qiyuan","last_name":"He","first_name":"Qiyuan"},{"first_name":"Xun","last_name":"Hong","full_name":"Hong, Xun"},{"full_name":"Hu, Sheng","last_name":"Hu","first_name":"Sheng"},{"full_name":"Hu, Weida","first_name":"Weida","last_name":"Hu"},{"full_name":"Huang, Wei","first_name":"Wei","last_name":"Huang"},{"last_name":"Huang","first_name":"Yuan","full_name":"Huang, Yuan"},{"first_name":"Wei","last_name":"Ji","full_name":"Ji, Wei"},{"full_name":"Li, Dehui","first_name":"Dehui","last_name":"Li"},{"first_name":"Lain Jong","last_name":"Li","full_name":"Li, Lain Jong"},{"full_name":"Li, Qiang","last_name":"Li","first_name":"Qiang"},{"full_name":"Lin, Li","last_name":"Lin","first_name":"Li"},{"full_name":"Ling, Chongyi","last_name":"Ling","first_name":"Chongyi"},{"first_name":"Minghua","last_name":"Liu","full_name":"Liu, Minghua"},{"first_name":"Nan","last_name":"Liu","full_name":"Liu, Nan"},{"full_name":"Liu, Zhuang","first_name":"Zhuang","last_name":"Liu"},{"last_name":"Loh","first_name":"Kian Ping","full_name":"Loh, Kian Ping"},{"full_name":"Ma, Jianmin","first_name":"Jianmin","last_name":"Ma"},{"full_name":"Miao, Feng","last_name":"Miao","first_name":"Feng"},{"full_name":"Peng, Hailin","last_name":"Peng","first_name":"Hailin"},{"full_name":"Shao, Mingfei","last_name":"Shao","first_name":"Mingfei"},{"first_name":"Li","last_name":"Song","full_name":"Song, Li"},{"full_name":"Su, Shao","first_name":"Shao","last_name":"Su"},{"full_name":"Sun, Shuo","last_name":"Sun","first_name":"Shuo"},{"first_name":"Chaoliang","last_name":"Tan","full_name":"Tan, Chaoliang"},{"last_name":"Tang","first_name":"Zhiyong","full_name":"Tang, Zhiyong"},{"first_name":"Dingsheng","last_name":"Wang","full_name":"Wang, Dingsheng"},{"last_name":"Wang","first_name":"Huan","full_name":"Wang, Huan"},{"last_name":"Wang","first_name":"Jinlan","full_name":"Wang, Jinlan"},{"first_name":"Xin","last_name":"Wang","full_name":"Wang, Xin"},{"full_name":"Wang, Xinran","first_name":"Xinran","last_name":"Wang"},{"last_name":"Wee","first_name":"Andrew T.S.","full_name":"Wee, Andrew T.S."},{"first_name":"Zhongming","last_name":"Wei","full_name":"Wei, Zhongming"},{"last_name":"Wu","first_name":"Yuen","full_name":"Wu, Yuen"},{"full_name":"Wu, Zhong Shuai","first_name":"Zhong Shuai","last_name":"Wu"},{"full_name":"Xiong, Jie","first_name":"Jie","last_name":"Xiong"},{"full_name":"Xiong, Qihua","first_name":"Qihua","last_name":"Xiong"},{"last_name":"Xu","first_name":"Weigao","full_name":"Xu, Weigao"},{"last_name":"Yin","first_name":"Peng","full_name":"Yin, Peng"},{"last_name":"Zeng","first_name":"Haibo","full_name":"Zeng, Haibo"},{"first_name":"Zhiyuan","last_name":"Zeng","full_name":"Zeng, Zhiyuan"},{"last_name":"Zhai","first_name":"Tianyou","full_name":"Zhai, Tianyou"},{"full_name":"Zhang, Han","first_name":"Han","last_name":"Zhang"},{"full_name":"Zhang, Hui","last_name":"Zhang","first_name":"Hui"},{"full_name":"Zhang, Qichun","last_name":"Zhang","first_name":"Qichun"},{"full_name":"Zhang, Tierui","first_name":"Tierui","last_name":"Zhang"},{"first_name":"Xiang","last_name":"Zhang","full_name":"Zhang, Xiang"},{"full_name":"Zhao, Li Dong","last_name":"Zhao","first_name":"Li Dong"},{"full_name":"Zhao, Meiting","last_name":"Zhao","first_name":"Meiting"},{"full_name":"Zhao, Weijie","last_name":"Zhao","first_name":"Weijie"},{"full_name":"Zhao, Yunxuan","first_name":"Yunxuan","last_name":"Zhao"},{"full_name":"Zhou, Kai Ge","first_name":"Kai Ge","last_name":"Zhou"},{"full_name":"Zhou, Xing","last_name":"Zhou","first_name":"Xing"},{"full_name":"Zhou, Yu","last_name":"Zhou","first_name":"Yu"},{"full_name":"Zhu, Hongwei","last_name":"Zhu","first_name":"Hongwei"},{"full_name":"Zhang, Hua","first_name":"Hua","last_name":"Zhang"},{"full_name":"Liu, Zhongfan","last_name":"Liu","first_name":"Zhongfan"}],"article_number":"2108017","quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://doi.org/10.3866/PKU.WHXB202108017","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.3866/PKU.WHXB202108017","publication_identifier":{"issn":["1001-4861"]},"month":"10","intvolume":" 37","status":"public","title":"Recent progress on two-dimensional materials","_id":"14800","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","type":"journal_article","issue":"12","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. "}],"article_type":"review","citation":{"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.","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.","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).","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.","ieee":"C. Chang et al., “Recent progress on two-dimensional materials,” Acta Physico-Chimica Sinica, vol. 37, no. 12. Peking University, 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"},"publication":"Acta Physico-Chimica Sinica","date_published":"2021-10-13T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"13"},{"related_material":{"record":[{"status":"public","relation":"extended_version","id":"13234"}]},"author":[{"full_name":"Lukina, Anna","first_name":"Anna","last_name":"Lukina","id":"CBA4D1A8-0FE8-11E9-BDE6-07BFE5697425"},{"full_name":"Schilling, Christian","last_name":"Schilling","first_name":"Christian","orcid":"0000-0003-3658-1065","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A"}],"volume":"12974 ","date_updated":"2024-01-30T12:06:56Z","date_created":"2021-10-31T23:01:31Z","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.","year":"2021","publisher":"Springer Nature","department":[{"_id":"ToHe"}],"publication_status":"published","ec_funded":1,"place":"Cham","doi":"10.1007/978-3-030-88494-9_3","conference":{"end_date":"2021-10-14","location":"Virtual","start_date":"2021-10-11","name":"RV: Runtime Verification"},"language":[{"iso":"eng"}],"external_id":{"arxiv":["2009.06429"],"isi":["000719383800003"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2009.06429"}],"oa":1,"project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"},{"call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","publication_identifier":{"eissn":["1611-3349"],"isbn":["9-783-0308-8493-2"],"eisbn":["978-3-030-88494-9"],"issn":["0302-9743"]},"month":"10","oa_version":"Preprint","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10206","title":"Into the unknown: active monitoring of neural networks","status":"public","abstract":[{"lang":"eng","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."}],"type":"conference","alternative_title":["LNCS"],"date_published":"2021-10-06T00:00:00Z","citation":{"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","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.","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.","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","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.","short":"A. Lukina, C. Schilling, T.A. Henzinger, in:, 21st International Conference on Runtime Verification, Springer Nature, Cham, 2021, pp. 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."},"publication":"21st International Conference on Runtime Verification","page":"42-61","article_processing_charge":"No","day":"06","scopus_import":"1","keyword":["monitoring","neural networks","novelty detection"]},{"date_created":"2024-01-28T23:01:43Z","date_updated":"2024-02-05T10:02:45Z","volume":3,"author":[{"full_name":"Leopold, Nikolai K","id":"4BC40BEC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0495-6822","first_name":"Nikolai K","last_name":"Leopold"},{"full_name":"Mitrouskas, David Johannes","id":"cbddacee-2b11-11eb-a02e-a2e14d04e52d","last_name":"Mitrouskas","first_name":"David Johannes"},{"first_name":"Simone Anna Elvira","last_name":"Rademacher","id":"856966FE-A408-11E9-977E-802DE6697425","orcid":"0000-0001-5059-4466","full_name":"Rademacher, Simone Anna Elvira"},{"full_name":"Schlein, Benjamin","first_name":"Benjamin","last_name":"Schlein"},{"orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","first_name":"Robert","full_name":"Seiringer, Robert"}],"publication_status":"published","department":[{"_id":"RoSe"}],"publisher":"Mathematical Sciences Publishers","year":"2021","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.","ec_funded":1,"language":[{"iso":"eng"}],"doi":"10.2140/paa.2021.3.653","quality_controlled":"1","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"},{"name":"Analysis of quantum many-body systems","call_identifier":"H2020","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"oa":1,"external_id":{"arxiv":["2005.02098"]},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2005.02098","open_access":"1"}],"month":"10","publication_identifier":{"issn":["2578-5893"],"eissn":["2578-5885"]},"oa_version":"Preprint","status":"public","title":"Landau–Pekar equations and quantum fluctuations for the dynamics of a strongly coupled polaron","intvolume":" 3","_id":"14889","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","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."}],"issue":"4","type":"journal_article","date_published":"2021-10-01T00:00:00Z","article_type":"original","page":"653-676","publication":"Pure and Applied Analysis","citation":{"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","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.","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.","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","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.","short":"N.K. Leopold, D.J. Mitrouskas, S.A.E. Rademacher, B. Schlein, R. Seiringer, Pure and Applied Analysis 3 (2021) 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."},"day":"01","article_processing_charge":"No","scopus_import":"1"},{"quality_controlled":"1","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"external_id":{"arxiv":["1912.11004"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1912.11004"}],"language":[{"iso":"eng"}],"doi":"10.2140/paa.2021.3.677","month":"10","publication_identifier":{"issn":["2578-5893"],"eissn":["2578-5885"]},"publication_status":"published","department":[{"_id":"RoSe"}],"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.","year":"2021","date_created":"2024-01-28T23:01:43Z","date_updated":"2024-02-05T09:26:31Z","volume":3,"author":[{"full_name":"Bossmann, Lea","orcid":"0000-0002-6854-1343","id":"A2E3BCBE-5FCC-11E9-AA4B-76F3E5697425","last_name":"Bossmann","first_name":"Lea"},{"orcid":"0000-0002-9166-5889","id":"40AC02DC-F248-11E8-B48F-1D18A9856A87","last_name":"Petrat","first_name":"Sören P","full_name":"Petrat, Sören P"},{"full_name":"Pickl, Peter","first_name":"Peter","last_name":"Pickl"},{"last_name":"Soffer","first_name":"Avy","full_name":"Soffer, Avy"}],"ec_funded":1,"article_type":"original","page":"677-726","publication":"Pure and Applied Analysis","citation":{"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.","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.","short":"L. Bossmann, S.P. Petrat, P. Pickl, A. Soffer, Pure and Applied Analysis 3 (2021) 677–726.","ista":"Bossmann L, Petrat SP, Pickl P, Soffer A. 2021. Beyond Bogoliubov dynamics. Pure and Applied Analysis. 3(4), 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.","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","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"},"date_published":"2021-10-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","status":"public","title":"Beyond Bogoliubov dynamics","intvolume":" 3","_id":"14890","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","type":"journal_article","abstract":[{"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.","lang":"eng"}],"issue":"4"},{"scopus_import":"1","day":"21","article_processing_charge":"No","article_type":"original","page":"221-280","publication":"Probability and Mathematical Physics","citation":{"short":"J. Alt, L. Erdös, T.H. Krüger, Probability and Mathematical Physics 2 (2021) 221–280.","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.","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.","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","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.","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","ista":"Alt J, Erdös L, Krüger TH. 2021. Spectral radius of random matrices with independent entries. Probability and Mathematical Physics. 2(2), 221–280."},"date_published":"2021-05-21T00:00:00Z","type":"journal_article","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."}],"issue":"2","title":"Spectral radius of random matrices with independent entries","status":"public","intvolume":" 2","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15013","oa_version":"Preprint","month":"05","publication_identifier":{"issn":["2690-0998"],"eissn":["2690-1005"]},"quality_controlled":"1","project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804","name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7"}],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1907.13631","open_access":"1"}],"external_id":{"arxiv":["1907.13631"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.2140/pmp.2021.2.221","ec_funded":1,"publication_status":"published","publisher":"Mathematical Sciences Publishers","department":[{"_id":"LaEr"}],"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.","year":"2021","date_updated":"2024-02-19T08:30:00Z","date_created":"2024-02-18T23:01:03Z","volume":2,"author":[{"id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes","last_name":"Alt","full_name":"Alt, Johannes"},{"last_name":"Erdös","first_name":"László","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","full_name":"Erdös, László"},{"orcid":"0000-0002-4821-3297","id":"3020C786-F248-11E8-B48F-1D18A9856A87","last_name":"Krüger","first_name":"Torben H","full_name":"Krüger, Torben H"}]},{"pmid":1,"year":"2021","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.).","publisher":"National Academy of Sciences","department":[{"_id":"JiFr"},{"_id":"MaLo"},{"_id":"EvBe"},{"_id":"EM-Fac"},{"_id":"NanoFab"}],"publication_status":"published","related_material":{"record":[{"id":"14510","status":"public","relation":"dissertation_contains"},{"id":"14988","relation":"research_data","status":"public"}],"link":[{"relation":"earlier_version","url":"https://doi.org/10.1101/2021.04.26.441441"}]},"author":[{"orcid":"0000-0002-2739-8843","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","last_name":"Johnson","first_name":"Alexander J","full_name":"Johnson, Alexander J"},{"last_name":"Dahhan","first_name":"Dana A","full_name":"Dahhan, Dana A"},{"full_name":"Gnyliukh, Nataliia","orcid":"0000-0002-2198-0509","id":"390C1120-F248-11E8-B48F-1D18A9856A87","last_name":"Gnyliukh","first_name":"Nataliia"},{"full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","last_name":"Kaufmann","first_name":"Walter"},{"id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9438-4783","first_name":"Vanessa","last_name":"Zheden","full_name":"Zheden, Vanessa"},{"first_name":"Tommaso","last_name":"Costanzo","id":"D93824F4-D9BA-11E9-BB12-F207E6697425","orcid":"0000-0001-9732-3815","full_name":"Costanzo, Tommaso"},{"full_name":"Mahou, Pierre","first_name":"Pierre","last_name":"Mahou"},{"id":"45A71A74-F248-11E8-B48F-1D18A9856A87","last_name":"Hrtyan","first_name":"Mónika","full_name":"Hrtyan, Mónika"},{"full_name":"Wang, Jie","last_name":"Wang","first_name":"Jie"},{"full_name":"Aguilera Servin, Juan L","orcid":"0000-0002-2862-8372","id":"2A67C376-F248-11E8-B48F-1D18A9856A87","last_name":"Aguilera Servin","first_name":"Juan L"},{"full_name":"van Damme, Daniël","last_name":"van Damme","first_name":"Daniël"},{"full_name":"Beaurepaire, Emmanuel","first_name":"Emmanuel","last_name":"Beaurepaire"},{"full_name":"Loose, Martin","last_name":"Loose","first_name":"Martin","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sebastian Y","last_name":"Bednarek","full_name":"Bednarek, Sebastian Y"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří"}],"volume":118,"date_updated":"2024-02-19T11:06:09Z","date_created":"2021-08-11T14:11:43Z","article_number":"e2113046118","file_date_updated":"2021-12-15T08:59:40Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["34907016"],"isi":["000736417600043"]},"oa":1,"project":[{"_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630","call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants"}],"isi":1,"quality_controlled":"1","doi":"10.1073/pnas.2113046118","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"publication_identifier":{"eissn":["1091-6490"]},"month":"12","_id":"9887","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 118","ddc":["580"],"title":"The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis","status":"public","oa_version":"Published Version","file":[{"success":1,"checksum":"8d01e72e22c4fb1584e72d8601947069","date_created":"2021-12-15T08:59:40Z","date_updated":"2021-12-15T08:59:40Z","file_id":"10546","relation":"main_file","creator":"cchlebak","file_size":2757340,"content_type":"application/pdf","access_level":"open_access","file_name":"2021_PNAS_Johnson.pdf"}],"type":"journal_article","issue":"51","abstract":[{"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.","lang":"eng"}],"citation":{"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","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.","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.","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","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.","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."},"publication":"Proceedings of the National Academy of Sciences","article_type":"original","date_published":"2021-12-14T00:00:00Z","article_processing_charge":"No","has_accepted_license":"1","day":"14"},{"language":[{"iso":"eng"}],"doi":"10.1002/9780470015902.a0029355","date_published":"2021-05-28T00:00:00Z","quality_controlled":"1","publication":"Encyclopedia of Life Sciences","citation":{"ama":"Stankowski S, Shipilina D, Westram AM. Hybrid Zones. In: Encyclopedia of Life Sciences. Vol 2. eLS. Wiley; 2021. doi:10.1002/9780470015902.a0029355","ista":"Stankowski S, Shipilina D, Westram AM. 2021.Hybrid Zones. In: Encyclopedia of Life Sciences. vol. 2.","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","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.","short":"S. Stankowski, D. Shipilina, A.M. Westram, in:, Encyclopedia of Life Sciences, Wiley, 2021.","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."},"month":"05","day":"28","publication_identifier":{"isbn":["9780470016176"],"eisbn":["9780470015902"]},"article_processing_charge":"No","series_title":"eLS","date_created":"2024-02-14T12:05:50Z","date_updated":"2024-02-19T09:54:18Z","oa_version":"None","volume":2,"author":[{"full_name":"Stankowski, Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski","first_name":"Sean"},{"full_name":"Shipilina, Daria","last_name":"Shipilina","first_name":"Daria","orcid":"0000-0002-1145-9226","id":"428A94B0-F248-11E8-B48F-1D18A9856A87"},{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","first_name":"Anja M","last_name":"Westram","full_name":"Westram, Anja M"}],"status":"public","publication_status":"published","title":"Hybrid Zones","intvolume":" 2","publisher":"Wiley","department":[{"_id":"NiBa"}],"year":"2021","_id":"14984","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","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."}],"type":"book_chapter"},{"page":"1395-1397","quality_controlled":"1","citation":{"short":"C. Lampert, in:, K. Ikeuchi (Ed.), Computer Vision, 2nd ed., Springer, Cham, 2021, pp. 1395–1397.","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.","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.","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","ieee":"C. Lampert, “Zero-Shot Learning,” in Computer Vision, 2nd ed., K. Ikeuchi, Ed. Cham: Springer, 2021, pp. 1395–1397.","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","ista":"Lampert C. 2021.Zero-Shot Learning. In: Computer Vision. , 1395–1397."},"publication":"Computer Vision","language":[{"iso":"eng"}],"date_published":"2021-10-13T00:00:00Z","doi":"10.1007/978-3-030-63416-2_874","publication_identifier":{"isbn":["9783030634155"],"eisbn":["9783030634162"]},"article_processing_charge":"No","month":"10","day":"13","publisher":"Springer","department":[{"_id":"ChLa"}],"editor":[{"first_name":"Katsushi","last_name":"Ikeuchi","full_name":"Ikeuchi, Katsushi"}],"title":"Zero-Shot Learning","publication_status":"published","status":"public","year":"2021","_id":"14987","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","date_updated":"2024-02-19T10:59:04Z","date_created":"2024-02-14T14:05:32Z","edition":"2","author":[{"full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","first_name":"Christoph"}],"place":"Cham","type":"book_chapter","abstract":[{"lang":"eng","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."}]},{"abstract":[{"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","lang":"eng"}],"type":"research_data_reference","author":[{"id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2739-8843","first_name":"Alexander J","last_name":"Johnson","full_name":"Johnson, Alexander J"}],"related_material":{"record":[{"id":"9887","status":"public","relation":"used_in_publication"}]},"date_updated":"2024-02-19T11:06:09Z","date_created":"2024-02-14T14:13:48Z","oa_version":"Published Version","_id":"14988","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2021","status":"public","ddc":["580"],"title":"Raw data from Johnson et al, PNAS, 2021","department":[{"_id":"JiFr"}],"publisher":"Zenodo","month":"12","day":"01","has_accepted_license":"1","article_processing_charge":"No","doi":"10.5281/ZENODO.5747100","date_published":"2021-12-01T00:00:00Z","citation":{"mla":"Johnson, Alexander J. Raw Data from Johnson et Al, PNAS, 2021. Zenodo, 2021, doi:10.5281/ZENODO.5747100.","short":"A.J. Johnson, (2021).","chicago":"Johnson, Alexander J. “Raw Data from Johnson et Al, PNAS, 2021.” Zenodo, 2021. https://doi.org/10.5281/ZENODO.5747100.","ama":"Johnson AJ. Raw data from Johnson et al, PNAS, 2021. 2021. doi:10.5281/ZENODO.5747100","ista":"Johnson AJ. 2021. Raw data from Johnson et al, PNAS, 2021, Zenodo, 10.5281/ZENODO.5747100.","ieee":"A. J. Johnson, “Raw data from Johnson et al, PNAS, 2021.” Zenodo, 2021.","apa":"Johnson, A. J. (2021). Raw data from Johnson et al, PNAS, 2021. Zenodo. https://doi.org/10.5281/ZENODO.5747100"},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.5747100"}]},{"abstract":[{"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.","lang":"eng"}],"ec_funded":1,"article_number":"2107.03695","type":"preprint","author":[{"full_name":"Phan, Duc T","id":"29C8C0B4-F248-11E8-B48F-1D18A9856A87","first_name":"Duc T","last_name":"Phan"},{"full_name":"Senior, Jorden L","first_name":"Jorden L","last_name":"Senior","id":"5479D234-2D30-11EA-89CC-40953DDC885E","orcid":"0000-0002-0672-9295"},{"first_name":"Areg","last_name":"Ghazaryan","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9666-3543","full_name":"Ghazaryan, Areg"},{"first_name":"M.","last_name":"Hatefipour","full_name":"Hatefipour, M."},{"full_name":"Strickland, W. M.","first_name":"W. M.","last_name":"Strickland"},{"full_name":"Shabani, J.","last_name":"Shabani","first_name":"J."},{"orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","first_name":"Maksym","full_name":"Serbyn, Maksym"},{"full_name":"Higginbotham, Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2607-2363","first_name":"Andrew P","last_name":"Higginbotham"}],"related_material":{"record":[{"relation":"later_version","status":"public","id":"10851"},{"id":"9636","relation":"research_data","status":"public"}]},"date_created":"2021-09-21T08:41:02Z","date_updated":"2024-02-21T12:36:52Z","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"10029","year":"2021","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.","status":"public","title":"Breakdown of induced p±ip pairing in a superconductor-semiconductor hybrid","publication_status":"submitted","department":[{"_id":"MaSe"},{"_id":"AnHi"},{"_id":"MiLe"}],"month":"07","day":"08","article_processing_charge":"No","date_published":"2021-07-08T00:00:00Z","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"language":[{"iso":"eng"}],"publication":"arXiv","oa":1,"external_id":{"arxiv":["2107.03695"]},"citation":{"ama":"Phan DT, Senior JL, Ghazaryan A, et al. Breakdown of induced p±ip pairing in a superconductor-semiconductor hybrid. arXiv.","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.","ieee":"D. T. Phan et al., “Breakdown of induced p±ip pairing in a superconductor-semiconductor hybrid,” arXiv. .","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.","mla":"Phan, Duc T., et al. “Breakdown of Induced P±ip Pairing in a Superconductor-Semiconductor Hybrid.” ArXiv, 2107.03695.","short":"D.T. Phan, J.L. Senior, A. Ghazaryan, M. Hatefipour, W.M. Strickland, J. Shabani, M. Serbyn, A.P. Higginbotham, ArXiv (n.d.).","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."},"main_file_link":[{"url":"https://arxiv.org/abs/2107.03695","open_access":"1"}],"project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}]},{"article_processing_charge":"No","has_accepted_license":"1","month":"03","day":"29","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"citation":{"ista":"Katsaros G. 2021. Raw transport data for: Enhancement of proximity induced superconductivity in planar germanium, Institute of Science and Technology Austria, 10.15479/AT:ISTA:9291.","apa":"Katsaros, G. (2021). Raw transport data for: Enhancement of proximity induced superconductivity in planar germanium. 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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).","lang":"eng"}],"file_date_updated":"2021-04-01T07:52:56Z","department":[{"_id":"GeKa"}],"publisher":"Institute of Science and Technology Austria","status":"public","ddc":["530"],"title":"Raw transport data for: Enhancement of proximity induced superconductivity in planar germanium","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9291","year":"2021","oa_version":"Published Version","file":[{"checksum":"635df3c08fc13c3dac008cd421aefbe4","success":1,"date_updated":"2021-03-27T13:46:17Z","date_created":"2021-03-27T13:46:17Z","relation":"main_file","file_id":"9292","content_type":"application/x-zip-compressed","file_size":10616071,"creator":"gkatsaro","access_level":"open_access","file_name":"Raw Data- Enhancement of Superconductivity in a Planar Ge hole gas.zip"},{"access_level":"open_access","file_name":"README.txt","file_size":470,"content_type":"text/plain","creator":"dernst","relation":"main_file","file_id":"9302","checksum":"12b3ca69ae7509a346711baae0b02a75","success":1,"date_created":"2021-04-01T07:52:56Z","date_updated":"2021-04-01T07:52:56Z"}],"date_created":"2021-03-27T13:47:49Z","date_updated":"2024-02-21T12:37:14Z","author":[{"orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","last_name":"Katsaros","first_name":"Georgios","full_name":"Katsaros, Georgios"}]},{"related_material":{"record":[{"id":"10029","status":"public","relation":"used_in_publication"}]},"author":[{"orcid":"0000-0003-2607-2363","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","last_name":"Higginbotham","first_name":"Andrew P","full_name":"Higginbotham, Andrew P"}],"file":[{"success":1,"checksum":"18e90687ec7bbd75f8bfea4d8293fb30","date_updated":"2021-07-07T20:37:28Z","date_created":"2021-07-07T20:37:28Z","file_id":"9637","relation":"main_file","creator":"ahigginb","content_type":"application/zip","file_size":3345244,"access_level":"open_access","file_name":"figures_data.zip"}],"oa_version":"Submitted Version","date_updated":"2024-02-21T12:36:52Z","date_created":"2021-07-07T20:43:10Z","year":"2021","_id":"9636","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Institute of Science and Technology Austria","department":[{"_id":"AnHi"}],"status":"public","title":"Data for \"Breakdown of induced p ± ip pairing in a superconductor-semiconductor hybrid\"","file_date_updated":"2021-07-07T20:37:28Z","type":"research_data","date_published":"2021-01-01T00:00:00Z","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"citation":{"short":"A.P. Higginbotham, (2021).","mla":"Higginbotham, Andrew P. Data for “Breakdown of Induced p ± Ip Pairing in a Superconductor-Semiconductor Hybrid.” Institute of Science and Technology Austria, 2021.","chicago":"Higginbotham, Andrew P. “Data for ‘Breakdown of Induced p ± Ip Pairing in a Superconductor-Semiconductor Hybrid.’” Institute of Science and Technology Austria, 2021.","ama":"Higginbotham AP. Data for “Breakdown of induced p ± ip pairing in a superconductor-semiconductor hybrid.” 2021.","ieee":"A. P. Higginbotham, “Data for ‘Breakdown of induced p ± ip pairing in a superconductor-semiconductor hybrid.’” Institute of Science and Technology Austria, 2021.","apa":"Higginbotham, A. P. (2021). Data for “Breakdown of induced p ± ip pairing in a superconductor-semiconductor hybrid.” Institute of Science and Technology Austria.","ista":"Higginbotham AP. 2021. Data for ‘Breakdown of induced p ± ip pairing in a superconductor-semiconductor hybrid’, Institute of Science and Technology Austria."},"oa":1,"article_processing_charge":"No","has_accepted_license":"1"},{"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"language":[{"iso":"eng"}],"doi":"10.1126/science.abf1513","isi":1,"quality_controlled":"1","project":[{"name":"Hybrid Semiconductor - Superconductor Quantum Devices","_id":"262116AA-B435-11E9-9278-68D0E5697425"},{"grant_number":"844511","_id":"26A151DA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Majorana bound states in Ge/SiGe heterostructures"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2008.02348"}],"external_id":{"arxiv":["2008.02348"],"isi":["000677843100034"]},"oa":1,"month":"07","publication_identifier":{"issn":["00368075"],"eissn":["10959203"]},"date_updated":"2024-02-21T12:40:09Z","date_created":"2020-12-02T10:51:52Z","volume":373,"author":[{"id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","last_name":"Valentini","first_name":"Marco","full_name":"Valentini, Marco"},{"full_name":"Peñaranda, Fernando","first_name":"Fernando","last_name":"Peñaranda"},{"id":"340F461A-F248-11E8-B48F-1D18A9856A87","first_name":"Andrea C","last_name":"Hofmann","full_name":"Hofmann, Andrea C"},{"last_name":"Brauns","first_name":"Matthias","id":"33F94E3C-F248-11E8-B48F-1D18A9856A87","full_name":"Brauns, Matthias"},{"full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","first_name":"Robert"},{"full_name":"Krogstrup, Peter","first_name":"Peter","last_name":"Krogstrup"},{"full_name":"San-Jose, Pablo","first_name":"Pablo","last_name":"San-Jose"},{"full_name":"Prada, Elsa","last_name":"Prada","first_name":"Elsa"},{"full_name":"Aguado, Ramón","first_name":"Ramón","last_name":"Aguado"},{"full_name":"Katsaros, Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8342-202X","first_name":"Georgios","last_name":"Katsaros"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/unfinding-a-split-electron/","description":"News on IST Homepage","relation":"press_release"}],"record":[{"id":"13286","status":"public","relation":"dissertation_contains"},{"status":"public","relation":"research_data","id":"9389"}]},"publication_status":"published","publisher":"American Association for the Advancement of Science","department":[{"_id":"GeKa"},{"_id":"Bio"}],"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.","year":"2021","ec_funded":1,"article_number":"82-88","date_published":"2021-07-02T00:00:00Z","article_type":"original","publication":"Science","citation":{"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.","ieee":"M. Valentini et al., “Nontopological zero-bias peaks in full-shell nanowires induced by flux-tunable Andreev states,” Science, vol. 373, no. 6550. American Association for the Advancement of Science, 2021.","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","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.","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.","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)."},"day":"02","article_processing_charge":"No","scopus_import":"1","oa_version":"Submitted Version","title":"Nontopological zero-bias peaks in full-shell nanowires induced by flux-tunable Andreev states","status":"public","intvolume":" 373","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8910","abstract":[{"lang":"eng","text":"A semiconducting nanowire fully wrapped by a superconducting shell has been proposed as a platform for obtaining Majorana modes at small magnetic fields. 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."}],"issue":"6550","type":"journal_article"},{"article_processing_charge":"No","has_accepted_license":"1","month":"04","day":"14","date_published":"2021-04-14T00:00:00Z","doi":"10.15479/AT:ISTA:9323","citation":{"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.","short":"D. Jirovec, (2021).","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.","ama":"Jirovec D. Research data for “A singlet-triplet hole spin qubit planar Ge.” 2021. doi:10.15479/AT:ISTA:9323","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.","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"},"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa":1,"file_date_updated":"2021-04-14T09:49:30Z","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"}],"type":"research_data","contributor":[{"id":"4C473F58-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel","contributor_type":"project_member","last_name":"Jirovec"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"8909"}]},"author":[{"last_name":"Jirovec","first_name":"Daniel","orcid":"0000-0002-7197-4801","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","full_name":"Jirovec, Daniel"}],"oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"DataRepositorySTqubit.zip","creator":"djirovec","content_type":"application/x-zip-compressed","file_size":221832287,"file_id":"9324","relation":"main_file","success":1,"checksum":"c569d2a2ce1694445cdbca19cf8ae023","date_updated":"2021-04-14T09:48:47Z","date_created":"2021-04-14T09:48:47Z"},{"date_updated":"2021-04-14T09:49:30Z","date_created":"2021-04-14T09:49:30Z","checksum":"845bdf87430718ad6aff47eda7b5fc92","success":1,"relation":"main_file","file_id":"9325","file_size":4323,"content_type":"application/octet-stream","creator":"djirovec","file_name":"ReadMe","access_level":"open_access"}],"date_updated":"2024-02-21T12:39:15Z","date_created":"2021-04-14T09:50:22Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9323","year":"2021","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"GeKa"}],"status":"public","ddc":["530"],"title":"Research data for \"A singlet-triplet hole spin qubit planar Ge\""},{"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"8910"}]},"contributor":[{"id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","first_name":"Marco","contributor_type":"contact_person","last_name":"Valentini"}],"author":[{"first_name":"Marco","last_name":"Valentini","id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","full_name":"Valentini, Marco"}],"file":[{"file_name":"Notebook_Valentini.pdf","access_level":"open_access","content_type":"application/pdf","file_size":10572981,"creator":"mvalenti","relation":"main_file","file_id":"9390","date_created":"2021-05-14T11:42:23Z","date_updated":"2021-05-14T11:42:23Z","checksum":"80a905c4eef24dab6fb247e81a3d67f5"},{"file_size":99076111,"content_type":"application/x-zip-compressed","creator":"mvalenti","access_level":"open_access","file_name":"Experimental_data.zip","checksum":"1e61a7e63949448a8db0091cdac23570","date_updated":"2021-05-14T11:56:48Z","date_created":"2021-05-14T11:56:48Z","relation":"main_file","file_id":"9391"}],"oa_version":"Published Version","date_updated":"2024-02-21T12:40:09Z","date_created":"2021-05-14T12:07:53Z","_id":"9389","year":"2021","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"GradSch"},{"_id":"GeKa"}],"publisher":"Institute of Science and Technology Austria","ddc":["530"],"status":"public","title":"Research data for \"Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states\"","file_date_updated":"2021-05-14T11:56:48Z","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\"."}],"type":"research_data","doi":"10.15479/AT:ISTA:9389","date_published":"2021-01-01T00:00:00Z","acknowledged_ssus":[{"_id":"NanoFab"}],"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa":1,"citation":{"apa":"Valentini, M. (2021). Research data for “Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:9389","ieee":"M. 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.","ista":"Valentini M. 2021. Research data for ‘Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:9389.","ama":"Valentini M. Research data for “Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states.” 2021. doi:10.15479/AT:ISTA:9389","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.","short":"M. Valentini, (2021).","mla":"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, doi:10.15479/AT:ISTA:9389."},"has_accepted_license":"1","article_processing_charge":"No"},{"day":"15","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","keyword":["general engineering"],"date_published":"2021-04-15T00:00:00Z","publication":"Physical Review Research","citation":{"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","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.","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.","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","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.","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).","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."},"article_type":"original","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"}],"issue":"2","type":"journal_article","oa_version":"Published Version","file":[{"creator":"cchlebak","content_type":"application/pdf","file_size":1917512,"file_name":"2021_PhysRevResearch_Aggarwal.pdf","access_level":"open_access","date_updated":"2021-12-17T08:12:37Z","date_created":"2021-12-17T08:12:37Z","success":1,"checksum":"60a1bc9c9b616b1b155044bb8cfc6484","file_id":"10561","relation":"main_file"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"10559","status":"public","ddc":["620"],"title":"Enhancement of proximity-induced superconductivity in a planar Ge hole gas","intvolume":" 3","month":"04","publication_identifier":{"issn":["2643-1564"]},"doi":"10.1103/physrevresearch.3.l022005","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"language":[{"iso":"eng"}],"external_id":{"arxiv":["2012.00322"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","project":[{"name":"Majorana bound states in Ge/SiGe heterostructures","call_identifier":"H2020","_id":"26A151DA-B435-11E9-9278-68D0E5697425","grant_number":"844511"},{"call_identifier":"H2020","name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS","grant_number":"862046","_id":"237E5020-32DE-11EA-91FC-C7463DDC885E"}],"file_date_updated":"2021-12-17T08:12:37Z","ec_funded":1,"article_number":"L022005","author":[{"first_name":"Kushagra","last_name":"Aggarwal","id":"b22ab905-3539-11eb-84c3-fc159dcd79cb","orcid":"0000-0001-9985-9293","full_name":"Aggarwal, Kushagra"},{"full_name":"Hofmann, Andrea C","last_name":"Hofmann","first_name":"Andrea C","id":"340F461A-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-7197-4801","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","last_name":"Jirovec","first_name":"Daniel","full_name":"Jirovec, Daniel"},{"full_name":"Prieto Gonzalez, Ivan","first_name":"Ivan","last_name":"Prieto Gonzalez","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7370-5357"},{"full_name":"Sammak, Amir","first_name":"Amir","last_name":"Sammak"},{"last_name":"Botifoll","first_name":"Marc","full_name":"Botifoll, Marc"},{"last_name":"Martí-Sánchez","first_name":"Sara","full_name":"Martí-Sánchez, Sara"},{"first_name":"Menno","last_name":"Veldhorst","full_name":"Veldhorst, Menno"},{"last_name":"Arbiol","first_name":"Jordi","full_name":"Arbiol, Jordi"},{"first_name":"Giordano","last_name":"Scappucci","full_name":"Scappucci, Giordano"},{"first_name":"Jeroen","last_name":"Danon","full_name":"Danon, Jeroen"},{"full_name":"Katsaros, Georgios","first_name":"Georgios","last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8342-202X"}],"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"8831"},{"status":"public","relation":"research_data","id":"8834"}]},"date_created":"2021-12-16T18:50:57Z","date_updated":"2024-02-21T12:41:26Z","volume":3,"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.","year":"2021","publication_status":"published","department":[{"_id":"GeKa"}],"publisher":"American Physical Society"},{"pmid":1,"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).","year":"2021","publisher":"The Royal Society","department":[{"_id":"BeVi"}],"publication_status":"published","related_material":{"link":[{"relation":"supplementary_material","url":"https://doi.org/10.6084/m9.figshare.c.5615488.v1"}],"record":[{"relation":"research_data","status":"public","id":"9949"}]},"author":[{"full_name":"Huylmans, Ann K","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8871-4961","first_name":"Ann K","last_name":"Huylmans"},{"id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","last_name":"Macon","first_name":"Ariana","full_name":"Macon, Ariana"},{"last_name":"Hontoria","first_name":"Francisco","full_name":"Hontoria, Francisco"},{"full_name":"Vicoso, Beatriz","first_name":"Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306"}],"volume":288,"date_created":"2021-10-21T07:46:06Z","date_updated":"2024-02-21T12:40:29Z","article_number":"20211720","ec_funded":1,"file_date_updated":"2021-10-22T11:48:02Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["34547909"],"isi":["000697643700001"]},"project":[{"_id":"250BDE62-B435-11E9-9278-68D0E5697425","grant_number":"715257","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","call_identifier":"H2020"}],"isi":1,"quality_controlled":"1","doi":"10.1098/rspb.2021.1720","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"publication_identifier":{"eissn":["1471-2954"],"issn":["0962-8452"]},"month":"09","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10166","intvolume":" 288","title":"Transitions to asexuality and evolution of gene expression in Artemia brine shrimp","ddc":["595"],"status":"public","file":[{"creator":"cchlebak","file_size":995806,"content_type":"application/pdf","access_level":"open_access","file_name":"2021_ProRoSocBBioSci_Huylmans.pdf","success":1,"checksum":"76e7f253b7040bca2ad76f82bd7c45c0","date_updated":"2021-10-22T11:48:02Z","date_created":"2021-10-22T11:48:02Z","file_id":"10172","relation":"main_file"}],"oa_version":"Published Version","type":"journal_article","issue":"1959","abstract":[{"lang":"eng","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."}],"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.","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.","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","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.","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.","short":"A.K. Huylmans, A. Macon, F. Hontoria, B. Vicoso, Proceedings of the Royal Society B: Biological Sciences 288 (2021)."},"publication":"Proceedings of the Royal Society B: Biological Sciences","article_type":"original","date_published":"2021-09-22T00:00:00Z","scopus_import":"1","keyword":["asexual reproduction","parthenogenesis","sex-biased genes","sexual conflict","automixis","crustaceans"],"article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"22"},{"doi":"10.15479/AT:ISTA:9192","date_published":"2021-02-26T00:00:00Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"citation":{"chicago":"Surendranadh, Parvathy, Louise S Arathoon, Carina Baskett, David Field, Melinda Pickup, and Nicholas H Barton. “Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9192.","mla":"Surendranadh, Parvathy, et al. Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus. Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9192.","short":"P. Surendranadh, L.S. Arathoon, C. Baskett, D. Field, M. Pickup, N.H. Barton, (2021).","ista":"Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. 2021. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus, Institute of Science and Technology Austria, 10.15479/AT:ISTA:9192.","apa":"Surendranadh, P., Arathoon, L. S., Baskett, C., Field, D., Pickup, M., & Barton, N. H. (2021). Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:9192","ieee":"P. Surendranadh, L. S. Arathoon, C. Baskett, D. Field, M. Pickup, and N. H. Barton, “Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus.” Institute of Science and Technology Austria, 2021.","ama":"Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. 2021. doi:10.15479/AT:ISTA:9192"},"oa":1,"month":"02","day":"26","article_processing_charge":"No","has_accepted_license":"1","author":[{"first_name":"Parvathy","last_name":"Surendranadh","id":"455235B8-F248-11E8-B48F-1D18A9856A87","full_name":"Surendranadh, Parvathy"},{"first_name":"Louise S","last_name":"Arathoon","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1771-714X","full_name":"Arathoon, Louise S"},{"full_name":"Baskett, Carina","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7354-8574","first_name":"Carina","last_name":"Baskett"},{"full_name":"Field, David","first_name":"David","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478"},{"orcid":"0000-0001-6118-0541","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","last_name":"Pickup","first_name":"Melinda","full_name":"Pickup, Melinda"},{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"11411"},{"relation":"later_version","status":"public","id":"11321"},{"id":"8254","status":"public","relation":"earlier_version"}]},"contributor":[{"id":"455235B8-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member","last_name":"Surendranadh","first_name":"Parvathy"},{"id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","first_name":"Louise S","contributor_type":"project_member","last_name":"Arathoon"},{"id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member","last_name":"Baskett","first_name":"Carina"},{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478","first_name":"David","contributor_type":"project_member","last_name":"Field"},{"contributor_type":"project_member","last_name":"Pickup","first_name":"Melinda","orcid":"0000-0001-6118-0541","id":"2C78037E-F248-11E8-B48F-1D18A9856A87"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","contributor_type":"project_leader","last_name":"Barton"}],"date_updated":"2024-02-21T12:41:09Z","date_created":"2021-02-24T17:49:21Z","file":[{"access_level":"open_access","file_name":"Data_Code.zip","creator":"larathoo","file_size":5934452,"content_type":"application/x-zip-compressed","file_id":"9193","relation":"main_file","success":1,"checksum":"f85537815809a8a4b7da9d01163f88c0","date_updated":"2021-02-24T17:45:13Z","date_created":"2021-02-24T17:45:13Z"}],"oa_version":"Published Version","_id":"9192","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2021","status":"public","ddc":["576"],"title":"Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"abstract":[{"text":"Here are the research data underlying the publication \" Effects of fine-scale population structure on inbreeding in a long-term study of snapdragons (Antirrhinum majus).\" Further information are summed up in the README document.","lang":"eng"}],"file_date_updated":"2021-02-24T17:45:13Z","type":"research_data"},{"publisher":"Institute of Science and Technology Austria","department":[{"_id":"BeVi"}],"status":"public","title":"Data from Hyulmans et al 2021, \"Transitions to asexuality and evolution of gene expression in Artemia brine shrimp\"","_id":"9949","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2021","file":[{"relation":"main_file","file_id":"9950","checksum":"90461837eed66beac6fa302993cf0ca9","success":1,"date_created":"2021-08-21T13:43:59Z","date_updated":"2021-08-21T13:43:59Z","access_level":"open_access","file_name":"Data.zip","file_size":139188306,"content_type":"application/zip","creator":"bvicoso"}],"oa_version":"None","date_updated":"2024-02-21T12:40:30Z","date_created":"2021-08-21T13:44:22Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"10166"}]},"author":[{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","first_name":"Beatriz","last_name":"Vicoso","full_name":"Vicoso, Beatriz"}],"type":"research_data","file_date_updated":"2021-08-21T13:43:59Z","citation":{"ama":"Vicoso B. Data from Hyulmans et al 2021, “Transitions to asexuality and evolution of gene expression in Artemia brine shrimp.” 2021. doi:10.15479/AT:ISTA:9949","apa":"Vicoso, B. (2021). Data from Hyulmans et al 2021, “Transitions to asexuality and evolution of gene expression in Artemia brine shrimp.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:9949","ieee":"B. Vicoso, “Data from Hyulmans et al 2021, ‘Transitions to asexuality and evolution of gene expression in Artemia brine shrimp.’” Institute of Science and Technology Austria, 2021.","ista":"Vicoso B. 2021. Data from Hyulmans et al 2021, ‘Transitions to asexuality and evolution of gene expression in Artemia brine shrimp’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:9949.","short":"B. Vicoso, (2021).","mla":"Vicoso, Beatriz. Data from Hyulmans et Al 2021, “Transitions to Asexuality and Evolution of Gene Expression in Artemia Brine Shrimp.” Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9949.","chicago":"Vicoso, Beatriz. “Data from Hyulmans et Al 2021, ‘Transitions to Asexuality and Evolution of Gene Expression in Artemia Brine Shrimp.’” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9949."},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"doi":"10.15479/AT:ISTA:9949","date_published":"2021-08-24T00:00:00Z","article_processing_charge":"No","has_accepted_license":"1","day":"24","month":"08"},{"article_processing_charge":"Yes","has_accepted_license":"1","day":"07","keyword":["Modelling and Simulation","Genetics","Molecular Biology","Antibiotics","Drug interactions"],"date_published":"2021-01-07T00:00:00Z","citation":{"chicago":"Kavcic, Bor, Gašper Tkačik, and Mark Tobias Bollenbach. “Minimal Biophysical Model of Combined Antibiotic Action.” PLOS Computational Biology. Public Library of Science, 2021. https://doi.org/10.1371/journal.pcbi.1008529.","mla":"Kavcic, Bor, et al. “Minimal Biophysical Model of Combined Antibiotic Action.” PLOS Computational Biology, vol. 17, e1008529, Public Library of Science, 2021, doi:10.1371/journal.pcbi.1008529.","short":"B. Kavcic, G. Tkačik, M.T. Bollenbach, PLOS Computational Biology 17 (2021).","ista":"Kavcic B, Tkačik G, Bollenbach MT. 2021. Minimal biophysical model of combined antibiotic action. PLOS Computational Biology. 17, e1008529.","ieee":"B. Kavcic, G. Tkačik, and M. T. Bollenbach, “Minimal biophysical model of combined antibiotic action,” PLOS Computational Biology, vol. 17. Public Library of Science, 2021.","apa":"Kavcic, B., Tkačik, G., & Bollenbach, M. T. (2021). Minimal biophysical model of combined antibiotic action. PLOS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1008529","ama":"Kavcic B, Tkačik G, Bollenbach MT. Minimal biophysical model of combined antibiotic action. PLOS Computational Biology. 2021;17. doi:10.1371/journal.pcbi.1008529"},"publication":"PLOS Computational Biology","article_type":"original","abstract":[{"lang":"eng","text":"Phenomenological relations such as Ohm’s or Fourier’s law have a venerable history in physics but are still scarce in biology. This situation restrains predictive theory. Here, we build on bacterial “growth laws,” which capture physiological feedback between translation and cell growth, to construct a minimal biophysical model for the combined action of ribosome-targeting antibiotics. Our model predicts drug interactions like antagonism or synergy solely from responses to individual drugs. We provide analytical results for limiting cases, which agree well with numerical results. We systematically refine the model by including direct physical interactions of different antibiotics on the ribosome. In a limiting case, our model provides a mechanistic underpinning for recent predictions of higher-order interactions that were derived using entropy maximization. We further refine the model to include the effects of antibiotics that mimic starvation and the presence of resistance genes. We describe the impact of a starvation-mimicking antibiotic on drug interactions analytically and verify it experimentally. Our extended model suggests a change in the type of drug interaction that depends on the strength of resistance, which challenges established rescaling paradigms. We experimentally show that the presence of unregulated resistance genes can lead to altered drug interaction, which agrees with the prediction of the model. While minimal, the model is readily adaptable and opens the door to predicting interactions of second and higher-order in a broad range of biological systems."}],"type":"journal_article","oa_version":"Published Version","file":[{"file_size":3690053,"content_type":"application/pdf","creator":"dernst","file_name":"2021_PlosComBio_Kavcic.pdf","access_level":"open_access","date_updated":"2021-02-04T12:30:48Z","date_created":"2021-02-04T12:30:48Z","checksum":"e29f2b42651bef8e034781de8781ffac","success":1,"relation":"main_file","file_id":"9092"}],"_id":"8997","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 17","title":"Minimal biophysical model of combined antibiotic action","ddc":["570"],"status":"public","publication_identifier":{"issn":["1553-7358"]},"month":"01","doi":"10.1371/journal.pcbi.1008529","language":[{"iso":"eng"}],"external_id":{"isi":["000608045000010"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"name":"Revealing the mechanisms underlying drug interactions","call_identifier":"FWF","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","grant_number":"P27201-B22"},{"call_identifier":"FWF","name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","file_date_updated":"2021-02-04T12:30:48Z","article_number":"e1008529","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"7673"},{"id":"8930","status":"public","relation":"research_data"}]},"author":[{"full_name":"Kavcic, Bor","first_name":"Bor","last_name":"Kavcic","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6041-254X"},{"full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","first_name":"Gašper"},{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X","first_name":"Tobias","last_name":"Bollenbach","full_name":"Bollenbach, Tobias"}],"volume":17,"date_created":"2021-01-08T07:16:18Z","date_updated":"2024-02-21T12:41:41Z","acknowledgement":"This work was supported in part by Tum stipend of Knafelj foundation (to B.K.), Austrian Science Fund (FWF) standalone grants P 27201-B22 (to T.B.) and P 28844(to G.T.), HFSP program Grant RGP0042/2013 (to T.B.), German Research Foundation (DFG) individual grant BO 3502/2-1 (to T.B.), and German Research Foundation (DFG) Collaborative Research Centre (SFB) 1310 (to T.B.). ","year":"2021","publisher":"Public Library of Science","department":[{"_id":"GaTk"}],"publication_status":"published"},{"file_date_updated":"2021-03-23T10:12:58Z","ec_funded":1,"article_number":"e65993","date_created":"2021-03-23T10:11:46Z","date_updated":"2024-02-21T12:41:57Z","volume":10,"author":[{"id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1391-8377","first_name":"Anna A","last_name":"Nagy-Staron","full_name":"Nagy-Staron, Anna A"},{"id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3768-877X","first_name":"Kathrin","last_name":"Tomasek","full_name":"Tomasek, Kathrin"},{"full_name":"Caruso Carter, Caroline","last_name":"Caruso Carter","first_name":"Caroline"},{"full_name":"Sonnleitner, Elisabeth","last_name":"Sonnleitner","first_name":"Elisabeth"},{"first_name":"Bor","last_name":"Kavcic","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6041-254X","full_name":"Kavcic, Bor"},{"first_name":"Tiago","last_name":"Paixão","full_name":"Paixão, Tiago"},{"orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","first_name":"Calin C","full_name":"Guet, Calin C"}],"related_material":{"record":[{"id":"8951","relation":"research_data","status":"public"}]},"publication_status":"published","publisher":"eLife Sciences Publications","department":[{"_id":"GaTk"},{"_id":"CaGu"}],"year":"2021","acknowledgement":"We thank J Bollback, L Hurst, M Lagator, C Nizak, O Rivoire, M Savageau, G Tkacik, and B Vicozo\r\nfor helpful discussions; A Dolinar and A Greshnova for technical assistance; T Bollenbach for supplying the strain JW0336; C Rusnac, and members of the Guet lab for comments. The research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement n˚\r\n628377 (ANS) and an Austrian Science Fund (FWF) grant n˚ I 3901-B32 (CCG).","month":"03","publication_identifier":{"issn":["2050-084X"]},"language":[{"iso":"eng"}],"doi":"10.7554/elife.65993","isi":1,"quality_controlled":"1","project":[{"grant_number":"628377","_id":"2517526A-B435-11E9-9278-68D0E5697425","name":"The Systems Biology of Transcriptional Read-Through in Bacteria: from Synthetic Networks to Genomic Studies","call_identifier":"FP7"},{"_id":"268BFA92-B435-11E9-9278-68D0E5697425","grant_number":"I03901","name":"CyberCircuits: Cybergenetic circuits to test composability of gene networks","call_identifier":"FWF"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000631050900001"]},"abstract":[{"text":"Gene expression levels are influenced by multiple coexisting molecular mechanisms. Some of these interactions such as those of transcription factors and promoters have been studied extensively. However, predicting phenotypes of gene regulatory networks (GRNs) remains a major challenge. Here, we use a well-defined synthetic GRN to study in Escherichia coli how network phenotypes depend on local genetic context, i.e. the genetic neighborhood of a transcription factor and its relative position. We show that one GRN with fixed topology can display not only quantitatively but also qualitatively different phenotypes, depending solely on the local genetic context of its components. Transcriptional read-through is the main molecular mechanism that places one transcriptional unit (TU) within two separate regulons without the need for complex regulatory sequences. We propose that relative order of individual TUs, with its potential for combinatorial complexity, plays an important role in shaping phenotypes of GRNs.","lang":"eng"}],"type":"journal_article","file":[{"checksum":"3c2f44058c2dd45a5a1027f09d263f8e","success":1,"date_updated":"2021-03-23T10:12:58Z","date_created":"2021-03-23T10:12:58Z","relation":"main_file","file_id":"9284","file_size":1390469,"content_type":"application/pdf","creator":"bkavcic","access_level":"open_access","file_name":"elife-65993-v2.pdf"}],"oa_version":"Published Version","ddc":["570"],"status":"public","title":"Local genetic context shapes the function of a gene regulatory network","intvolume":" 10","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9283","day":"08","article_processing_charge":"Yes","has_accepted_license":"1","keyword":["Genetics and Molecular Biology"],"date_published":"2021-03-08T00:00:00Z","article_type":"original","publication":"eLife","citation":{"short":"A.A. Nagy-Staron, K. Tomasek, C. Caruso Carter, E. Sonnleitner, B. Kavcic, T. Paixão, C.C. Guet, ELife 10 (2021).","mla":"Nagy-Staron, Anna A., et al. “Local Genetic Context Shapes the Function of a Gene Regulatory Network.” ELife, vol. 10, e65993, eLife Sciences Publications, 2021, doi:10.7554/elife.65993.","chicago":"Nagy-Staron, Anna A, Kathrin Tomasek, Caroline Caruso Carter, Elisabeth Sonnleitner, Bor Kavcic, Tiago Paixão, and Calin C Guet. “Local Genetic Context Shapes the Function of a Gene Regulatory Network.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/elife.65993.","ama":"Nagy-Staron AA, Tomasek K, Caruso Carter C, et al. Local genetic context shapes the function of a gene regulatory network. eLife. 2021;10. doi:10.7554/elife.65993","ieee":"A. A. Nagy-Staron et al., “Local genetic context shapes the function of a gene regulatory network,” eLife, vol. 10. eLife Sciences Publications, 2021.","apa":"Nagy-Staron, A. A., Tomasek, K., Caruso Carter, C., Sonnleitner, E., Kavcic, B., Paixão, T., & Guet, C. C. (2021). Local genetic context shapes the function of a gene regulatory network. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.65993","ista":"Nagy-Staron AA, Tomasek K, Caruso Carter C, Sonnleitner E, Kavcic B, Paixão T, Guet CC. 2021. Local genetic context shapes the function of a gene regulatory network. eLife. 10, e65993."}},{"volume":40,"date_created":"2021-10-27T07:08:19Z","date_updated":"2024-02-28T12:52:48Z","author":[{"full_name":"Alderighi, Thomas","last_name":"Alderighi","first_name":"Thomas"},{"full_name":"Malomo, Luigi","first_name":"Luigi","last_name":"Malomo"},{"full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","first_name":"Bernd"},{"first_name":"Paolo","last_name":"Cignoni","full_name":"Cignoni, Paolo"},{"full_name":"Pietroni, Nico","first_name":"Nico","last_name":"Pietroni"}],"publisher":"Association for Computing Machinery","department":[{"_id":"BeBi"}],"publication_status":"published","acknowledgement":"The authors thank Marco Callieri for all his precious help with the resin casts. The models used in the paper are courtesy of the Stanford 3D Scanning Repository, the AIM@SHAPE Shape Repository, and Thingi10K Repository. The research was partially funded by the European Research Council (ERC) MATERIALIZABLE: Intelligent fabrication-oriented computational design and modeling (grant no. 715767).","year":"2021","ec_funded":1,"file_date_updated":"2021-10-27T07:08:07Z","article_number":"272","language":[{"iso":"eng"}],"doi":"10.1145/3478513.3480555","project":[{"_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000729846700077"]},"oa":1,"main_file_link":[{"url":"http://vcg.isti.cnr.it/Publications/2021/AMBCP21","open_access":"1"}],"publication_identifier":{"eissn":["1557-7368 "],"issn":["0730-0301"]},"month":"12","oa_version":"Submitted Version","file":[{"file_id":"10185","relation":"main_file","date_created":"2021-10-27T07:08:07Z","date_updated":"2021-10-27T07:08:07Z","checksum":"384ece7a9ad1026787ba9560b04336d5","file_name":"rigidmolds-authorversion.pdf","access_level":"open_access","creator":"bbickel","content_type":"application/pdf","file_size":107708317}],"intvolume":" 40","title":"Volume decomposition for two-piece rigid casting","status":"public","ddc":["000"],"_id":"10184","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"6","abstract":[{"text":"We introduce a novel technique to automatically decompose an input object’s volume into a set of parts that can be represented by two opposite height fields. Such decomposition enables the manufacturing of individual parts using two-piece reusable rigid molds. Our decomposition strategy relies on a new energy formulation that utilizes a pre-computed signal on the mesh volume representing the accessibility for a predefined set of extraction directions. Thanks to this novel formulation, our method allows for efficient optimization of a fabrication-aware partitioning of volumes in a completely\r\nautomatic way. We demonstrate the efficacy of our approach by generating valid volume partitionings for a wide range of complex objects and physically reproducing several of them.","lang":"eng"}],"type":"journal_article","date_published":"2021-12-01T00:00:00Z","article_type":"original","citation":{"ama":"Alderighi T, Malomo L, Bickel B, Cignoni P, Pietroni N. Volume decomposition for two-piece rigid casting. ACM Transactions on Graphics. 2021;40(6). doi:10.1145/3478513.3480555","ieee":"T. Alderighi, L. Malomo, B. Bickel, P. Cignoni, and N. Pietroni, “Volume decomposition for two-piece rigid casting,” ACM Transactions on Graphics, vol. 40, no. 6. Association for Computing Machinery, 2021.","apa":"Alderighi, T., Malomo, L., Bickel, B., Cignoni, P., & Pietroni, N. (2021). Volume decomposition for two-piece rigid casting. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3478513.3480555","ista":"Alderighi T, Malomo L, Bickel B, Cignoni P, Pietroni N. 2021. Volume decomposition for two-piece rigid casting. ACM Transactions on Graphics. 40(6), 272.","short":"T. Alderighi, L. Malomo, B. Bickel, P. Cignoni, N. Pietroni, ACM Transactions on Graphics 40 (2021).","mla":"Alderighi, Thomas, et al. “Volume Decomposition for Two-Piece Rigid Casting.” ACM Transactions on Graphics, vol. 40, no. 6, 272, Association for Computing Machinery, 2021, doi:10.1145/3478513.3480555.","chicago":"Alderighi, Thomas, Luigi Malomo, Bernd Bickel, Paolo Cignoni, and Nico Pietroni. “Volume Decomposition for Two-Piece Rigid Casting.” ACM Transactions on Graphics. Association for Computing Machinery, 2021. https://doi.org/10.1145/3478513.3480555."},"publication":"ACM Transactions on Graphics","has_accepted_license":"1","article_processing_charge":"No","day":"01"},{"date_published":"2021-06-01T00:00:00Z","article_type":"original","citation":{"chicago":"Czumaj, Artur, Peter Davies, and Merav Parter. “Graph Sparsification for Derandomizing Massively Parallel Computation with Low Space.” ACM Transactions on Algorithms. Association for Computing Machinery, 2021. https://doi.org/10.1145/3451992.","short":"A. Czumaj, P. Davies, M. Parter, ACM Transactions on Algorithms 17 (2021).","mla":"Czumaj, Artur, et al. “Graph Sparsification for Derandomizing Massively Parallel Computation with Low Space.” ACM Transactions on Algorithms, vol. 17, no. 2, 16, Association for Computing Machinery, 2021, doi:10.1145/3451992.","ieee":"A. Czumaj, P. Davies, and M. Parter, “Graph sparsification for derandomizing massively parallel computation with low space,” ACM Transactions on Algorithms, vol. 17, no. 2. Association for Computing Machinery, 2021.","apa":"Czumaj, A., Davies, P., & Parter, M. (2021). Graph sparsification for derandomizing massively parallel computation with low space. ACM Transactions on Algorithms. Association for Computing Machinery. https://doi.org/10.1145/3451992","ista":"Czumaj A, Davies P, Parter M. 2021. Graph sparsification for derandomizing massively parallel computation with low space. ACM Transactions on Algorithms. 17(2), 16.","ama":"Czumaj A, Davies P, Parter M. Graph sparsification for derandomizing massively parallel computation with low space. ACM Transactions on Algorithms. 2021;17(2). doi:10.1145/3451992"},"publication":"ACM Transactions on Algorithms","article_processing_charge":"No","has_accepted_license":"1","day":"01","oa_version":"Submitted Version","file":[{"success":1,"checksum":"a21c627683890c309a68f6389302c408","date_updated":"2021-06-10T19:33:56Z","date_created":"2021-06-10T19:33:56Z","file_id":"9542","relation":"main_file","creator":"pdavies","content_type":"application/pdf","file_size":587404,"access_level":"open_access","file_name":"MISMM-arxiv.pdf"}],"intvolume":" 17","status":"public","title":"Graph sparsification for derandomizing massively parallel computation with low space","ddc":["000"],"_id":"9541","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"2","abstract":[{"text":"The Massively Parallel Computation (MPC) model is an emerging model that distills core aspects of distributed and parallel computation, developed as a tool to solve combinatorial (typically graph) problems in systems of many machines with limited space. Recent work has focused on the regime in which machines have sublinear (in n, the number of nodes in the input graph) space, with randomized algorithms presented for the fundamental problems of Maximal Matching and Maximal Independent Set. However, there have been no prior corresponding deterministic algorithms. A major challenge underlying the sublinear space setting is that the local space of each machine might be too small to store all edges incident to a single node. This poses a considerable obstacle compared to classical models in which each node is assumed to know and have easy access to its incident edges. To overcome this barrier, we introduce a new graph sparsification technique that deterministically computes a low-degree subgraph, with the additional property that solving the problem on this subgraph provides significant progress towards solving the problem for the original input graph. Using this framework to derandomize the well-known algorithm of Luby [SICOMP’86], we obtain O(log Δ + log log n)-round deterministic MPC algorithms for solving the problems of Maximal Matching and Maximal Independent Set with O(nɛ) space on each machine for any constant ɛ > 0. These algorithms also run in O(log Δ) rounds in the closely related model of CONGESTED CLIQUE, improving upon the state-of-the-art bound of O(log 2Δ) rounds by Censor-Hillel et al. [DISC’17].","lang":"eng"}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1145/3451992","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"isi":1,"quality_controlled":"1","external_id":{"arxiv":["1912.05390"],"isi":["000661311300006"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1912.05390"}],"oa":1,"publication_identifier":{"eissn":["1549-6333"],"issn":["1549-6325"]},"month":"06","volume":17,"date_updated":"2024-02-28T12:53:09Z","date_created":"2021-06-10T19:31:05Z","related_material":{"record":[{"id":"7802","status":"public","relation":"earlier_version"}]},"author":[{"first_name":"Artur","last_name":"Czumaj","full_name":"Czumaj, Artur"},{"full_name":"Davies, Peter","orcid":"0000-0002-5646-9524","id":"11396234-BB50-11E9-B24C-90FCE5697425","last_name":"Davies","first_name":"Peter"},{"last_name":"Parter","first_name":"Merav","full_name":"Parter, Merav"}],"publisher":"Association for Computing Machinery","department":[{"_id":"DaAl"}],"publication_status":"published","acknowledgement":"Institute of Science and Technology Austria (IST Austria). Email: peter.davies@ist.ac.at. Work partially\r\ndone at the Department of Computer Science and Centre for Discrete Mathematics and its Applications (DIMAP),University of Warwick. Research partially supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 754411, the Centre for Discrete Mathematics and its Applications, a Weizmann-UK Making Connections Grant, and EPSRC award EP/N011163/1.","year":"2021","ec_funded":1,"file_date_updated":"2021-06-10T19:33:56Z","article_number":"16"},{"publication_status":"published","publisher":"American Physical Society ","department":[{"_id":"MiLe"}],"year":"2021","acknowledgement":"We acknowledge helpful discussions with W. G. Unruh and A. Rodriguez. F. S. is supported by European Union’s\r\nHorizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant No. 754411. M. L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). W. H. Z. is\r\nsupported by Department of Energy under the Los\r\nAlamos National Laboratory LDRD Program as well as by the U.S. Department of Energy, Office of Science, Basic\r\nEnergy Sciences, Materials Sciences and Engineering Division, Condensed Matter Theory Program. R. V. K. is supported by NSERC of Canada.\r\n","date_updated":"2024-02-29T12:34:10Z","date_created":"2021-10-13T09:21:33Z","volume":127,"author":[{"full_name":"Suzuki, Fumika","id":"650C99FC-1079-11EA-A3C0-73AE3DDC885E","orcid":"0000-0003-4982-5970","first_name":"Fumika","last_name":"Suzuki"},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","first_name":"Mikhail","last_name":"Lemeshko","full_name":"Lemeshko, Mikhail"},{"full_name":"Zurek, Wojciech H.","last_name":"Zurek","first_name":"Wojciech H."},{"first_name":"Roman V.","last_name":"Krems","full_name":"Krems, Roman V."}],"article_number":"160602","ec_funded":1,"quality_controlled":"1","isi":1,"project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"},{"call_identifier":"H2020","name":"Angulon: physics and applications of a new quasiparticle","grant_number":"801770","_id":"2688CF98-B435-11E9-9278-68D0E5697425"}],"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/2011.06279","open_access":"1"}],"external_id":{"arxiv":["2011.06279"],"isi":["000707495700001"]},"language":[{"iso":"eng"}],"doi":"10.1103/physrevlett.127.160602","month":"10","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"title":"Anderson localization of composite particles","status":"public","intvolume":" 127","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"10134","oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"We investigate the effect of coupling between translational and internal degrees of freedom of composite quantum particles on their localization in a random potential. We show that entanglement between the two degrees of freedom weakens localization due to the upper bound imposed on the inverse participation ratio by purity of a quantum state. We perform numerical calculations for a two-particle system bound by a harmonic force in a 1D disordered lattice and a rigid rotor in a 2D disordered lattice. We illustrate that the coupling has a dramatic effect on localization properties, even with a small number of internal states participating in quantum dynamics."}],"issue":"16","article_type":"original","publication":"Physical Review Letters","citation":{"ista":"Suzuki F, Lemeshko M, Zurek WH, Krems RV. 2021. Anderson localization of composite particles. Physical Review Letters. 127(16), 160602.","ieee":"F. Suzuki, M. Lemeshko, W. H. Zurek, and R. V. Krems, “Anderson localization of composite particles,” Physical Review Letters, vol. 127, no. 16. American Physical Society , 2021.","apa":"Suzuki, F., Lemeshko, M., Zurek, W. H., & Krems, R. V. (2021). Anderson localization of composite particles. Physical Review Letters. American Physical Society . https://doi.org/10.1103/physrevlett.127.160602","ama":"Suzuki F, Lemeshko M, Zurek WH, Krems RV. Anderson localization of composite particles. Physical Review Letters. 2021;127(16). doi:10.1103/physrevlett.127.160602","chicago":"Suzuki, Fumika, Mikhail Lemeshko, Wojciech H. Zurek, and Roman V. Krems. “Anderson Localization of Composite Particles.” Physical Review Letters. American Physical Society , 2021. https://doi.org/10.1103/physrevlett.127.160602.","mla":"Suzuki, Fumika, et al. “Anderson Localization of Composite Particles.” Physical Review Letters, vol. 127, no. 16, 160602, American Physical Society , 2021, doi:10.1103/physrevlett.127.160602.","short":"F. Suzuki, M. Lemeshko, W.H. Zurek, R.V. Krems, Physical Review Letters 127 (2021)."},"date_published":"2021-10-12T00:00:00Z","keyword":["General Physics and Astronomy"],"scopus_import":"1","day":"12","article_processing_charge":"No"},{"language":[{"iso":"eng"}],"conference":{"name":"SPAA: Symposium on Parallelism in Algorithms and Architectures ","end_date":"2021-07-08","location":" Virtual Event, United States","start_date":"2021-07-06"},"doi":"10.1145/3409964.3461785","quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Coordination in constrained and natural distributed systems","grant_number":"840605","_id":"26A5D39A-B435-11E9-9278-68D0E5697425"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2005.07761"}],"oa":1,"external_id":{"arxiv":["2005.07761"]},"month":"07","publication_identifier":{"isbn":["9781450380706"]},"date_updated":"2024-03-05T07:13:12Z","date_created":"2021-07-18T22:01:22Z","author":[{"full_name":"Brandt, Sebastian","last_name":"Brandt","first_name":"Sebastian"},{"full_name":"Keller, Barbara","last_name":"Keller","first_name":"Barbara"},{"full_name":"Rybicki, Joel","first_name":"Joel","last_name":"Rybicki","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6432-6646"},{"last_name":"Suomela","first_name":"Jukka","full_name":"Suomela, Jukka"},{"first_name":"Jara","last_name":"Uitto","full_name":"Uitto, Jara"}],"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"15074"}]},"publication_status":"published","department":[{"_id":"DaAl"}],"acknowledgement":"We thank Orr Fischer, Juho Hirvonen, and Tuomo Lempiäinen for valuable discussions. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 840605.","year":"2021","ec_funded":1,"date_published":"2021-07-06T00:00:00Z","page":"129-139","publication":"Annual ACM Symposium on Parallelism in Algorithms and Architectures","citation":{"ama":"Brandt S, Keller B, Rybicki J, Suomela J, Uitto J. Efficient load-balancing through distributed token dropping. In: Annual ACM Symposium on Parallelism in Algorithms and Architectures. ; 2021:129-139. doi:10.1145/3409964.3461785","apa":"Brandt, S., Keller, B., Rybicki, J., Suomela, J., & Uitto, J. (2021). Efficient load-balancing through distributed token dropping. In Annual ACM Symposium on Parallelism in Algorithms and Architectures (pp. 129–139). Virtual Event, United States. https://doi.org/10.1145/3409964.3461785","ieee":"S. Brandt, B. Keller, J. Rybicki, J. Suomela, and J. Uitto, “Efficient load-balancing through distributed token dropping,” in Annual ACM Symposium on Parallelism in Algorithms and Architectures, Virtual Event, United States, 2021, pp. 129–139.","ista":"Brandt S, Keller B, Rybicki J, Suomela J, Uitto J. 2021. Efficient load-balancing through distributed token dropping. Annual ACM Symposium on Parallelism in Algorithms and Architectures. SPAA: Symposium on Parallelism in Algorithms and Architectures , 129–139.","short":"S. Brandt, B. Keller, J. Rybicki, J. Suomela, J. Uitto, in:, Annual ACM Symposium on Parallelism in Algorithms and Architectures, 2021, pp. 129–139.","mla":"Brandt, Sebastian, et al. “Efficient Load-Balancing through Distributed Token Dropping.” Annual ACM Symposium on Parallelism in Algorithms and Architectures, 2021, pp. 129–39, doi:10.1145/3409964.3461785.","chicago":"Brandt, Sebastian, Barbara Keller, Joel Rybicki, Jukka Suomela, and Jara Uitto. “Efficient Load-Balancing through Distributed Token Dropping.” In Annual ACM Symposium on Parallelism in Algorithms and Architectures, 129–39, 2021. https://doi.org/10.1145/3409964.3461785."},"day":"06","article_processing_charge":"No","scopus_import":"1","oa_version":"Preprint","title":"Efficient load-balancing through distributed token dropping","status":"public","_id":"9678","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","abstract":[{"lang":"eng","text":"We introduce a new graph problem, the token dropping game, and we show how to solve it efficiently in a distributed setting. We use the token dropping game as a tool to design an efficient distributed algorithm for stable orientations and more generally for locally optimal semi-matchings. The prior work by Czygrinow et al. (DISC 2012) finds a stable orientation in O(Δ^5) rounds in graphs of maximum degree Δ, while we improve it to O(Δ^4) and also prove a lower bound of Ω(Δ). For the more general problem of locally optimal semi-matchings, the prior upper bound is O(S^5) and our new algorithm runs in O(C · S^4) rounds, which is an improvement for C = o(S); here C and S are the maximum degrees of customers and servers, respectively."}],"type":"conference"},{"file_date_updated":"2021-12-27T10:36:40Z","ec_funded":1,"date_updated":"2024-03-05T07:35:53Z","date_created":"2020-08-24T06:24:04Z","author":[{"full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"id":"3279A00C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5634-0731","first_name":"Giorgi","last_name":"Nadiradze","full_name":"Nadiradze, Giorgi"},{"full_name":"Sabour, Amirmojtaba","first_name":"Amirmojtaba","last_name":"Sabour","id":"bcc145fd-e77f-11ea-ae8b-80d661dbff67"}],"related_material":{"record":[{"id":"15077","relation":"earlier_version","status":"public"}],"link":[{"relation":"earlier_version","url":"https://doi.org/10.4230/LIPIcs.ICALP.2020.7"}]},"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"DaAl"}],"year":"2021","acknowledgement":"The authors sincerely thank Thomas Sauerwald and George Giakkoupis for insightful discussions, and Mohsen Ghaffari, Yuval Peres, and Udi Wieder for feedback on earlier versions of this draft. We also thank the ICALP anonymous reviewers for their very useful comments. Open access funding provided by Institute of Science and Technology (IST Austria). Funding was provided by European Research Council (Grant No. PR1042ERC01).","month":"12","publication_identifier":{"issn":["0178-4617"],"eissn":["1432-0541"]},"language":[{"iso":"eng"}],"conference":{"end_date":"2020-07-11","start_date":"2020-07-08","location":"Virtual, Online; Germany","name":"ICALP: International Colloquium on Automata, Languages, and Programming "},"doi":"10.1007/s00453-021-00905-9","quality_controlled":"1","isi":1,"project":[{"grant_number":"805223","_id":"268A44D6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Elastic Coordination for Scalable Machine Learning"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2003.09297"],"isi":["000734004600001"]},"abstract":[{"lang":"eng","text":"We consider the following dynamic load-balancing process: given an underlying graph G with n nodes, in each step t≥ 0, one unit of load is created, and placed at a randomly chosen graph node. In the same step, the chosen node picks a random neighbor, and the two nodes balance their loads by averaging them. We are interested in the expected gap between the minimum and maximum loads at nodes as the process progresses, and its dependence on n and on the graph structure. Variants of the above graphical balanced allocation process have been studied previously by Peres, Talwar, and Wieder [Peres et al., 2015], and by Sauerwald and Sun [Sauerwald and Sun, 2015]. These authors left as open the question of characterizing the gap in the case of cycle graphs in the dynamic case, where weights are created during the algorithm’s execution. For this case, the only known upper bound is of 𝒪(n log n), following from a majorization argument due to [Peres et al., 2015], which analyzes a related graphical allocation process. In this paper, we provide an upper bound of 𝒪 (√n log n) on the expected gap of the above process for cycles of length n. We introduce a new potential analysis technique, which enables us to bound the difference in load between k-hop neighbors on the cycle, for any k ≤ n/2. We complement this with a \"gap covering\" argument, which bounds the maximum value of the gap by bounding its value across all possible subsets of a certain structure, and recursively bounding the gaps within each subset. We provide analytical and experimental evidence that our upper bound on the gap is tight up to a logarithmic factor. "}],"type":"journal_article","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2021_Algorithmica_Alistarh.pdf","creator":"cchlebak","file_size":525950,"content_type":"application/pdf","file_id":"10577","relation":"main_file","success":1,"checksum":"21169b25b0c8e17b21e12af22bff9870","date_created":"2021-12-27T10:36:40Z","date_updated":"2021-12-27T10:36:40Z"}],"status":"public","title":"Dynamic averaging load balancing on cycles","ddc":["000"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8286","day":"24","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","scopus_import":"1","date_published":"2021-12-24T00:00:00Z","article_type":"original","publication":"Algorithmica","citation":{"ama":"Alistarh D-A, Nadiradze G, Sabour A. Dynamic averaging load balancing on cycles. Algorithmica. 2021. doi:10.1007/s00453-021-00905-9","ista":"Alistarh D-A, Nadiradze G, Sabour A. 2021. Dynamic averaging load balancing on cycles. Algorithmica.","ieee":"D.-A. Alistarh, G. Nadiradze, and A. Sabour, “Dynamic averaging load balancing on cycles,” Algorithmica. Springer Nature, 2021.","apa":"Alistarh, D.-A., Nadiradze, G., & Sabour, A. (2021). Dynamic averaging load balancing on cycles. Algorithmica. Virtual, Online; Germany: Springer Nature. https://doi.org/10.1007/s00453-021-00905-9","mla":"Alistarh, Dan-Adrian, et al. “Dynamic Averaging Load Balancing on Cycles.” Algorithmica, Springer Nature, 2021, doi:10.1007/s00453-021-00905-9.","short":"D.-A. Alistarh, G. Nadiradze, A. Sabour, Algorithmica (2021).","chicago":"Alistarh, Dan-Adrian, Giorgi Nadiradze, and Amirmojtaba Sabour. “Dynamic Averaging Load Balancing on Cycles.” Algorithmica. Springer Nature, 2021. https://doi.org/10.1007/s00453-021-00905-9."}},{"alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"This thesis is the result of the research carried out by the author during his PhD at IST Austria between 2017 and 2021. It mainly focuses on the Fröhlich polaron model, specifically to its regime of strong coupling. This model, which is rigorously introduced and discussed in the introduction, has been of great interest in condensed matter physics and field theory for more than eighty years. It is used to describe an electron interacting with the atoms of a solid material (the strength of this interaction is modeled by the presence of a coupling constant α in the Hamiltonian of the system). The particular regime examined here, which is mathematically described by considering the limit α →∞, displays many interesting features related to the emergence of classical behavior, which allows for a simplified effective description of the system under analysis. The properties, the range of validity and a quantitative analysis of the precision of such classical approximations are the main object of the present work. We specify our investigation to the study of the ground state energy of the system, its dynamics and its effective mass. For each of these problems, we provide in the introduction an overview of the previously known results and a detailed account of the original contributions by the author.","lang":"eng"}],"status":"public","ddc":["515","519","539"],"title":"The polaron at strong coupling","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"9733","oa_version":"Published Version","file":[{"file_size":1958710,"content_type":"application/pdf","creator":"dfelicia","file_name":"Thesis_FeliciangeliA.pdf","access_level":"open_access","date_updated":"2021-09-06T09:28:56Z","date_created":"2021-08-19T14:03:48Z","checksum":"e88bb8ca43948abe060eb2d2fa719881","relation":"main_file","file_id":"9944"},{"relation":"source_file","file_id":"9945","checksum":"72810843abee83705853505b3f8348aa","date_created":"2021-08-19T14:06:35Z","date_updated":"2022-03-10T12:13:57Z","access_level":"closed","file_name":"thesis.7z","file_size":3771669,"content_type":"application/octet-stream","creator":"dfelicia"}],"day":"20","has_accepted_license":"1","article_processing_charge":"No","page":"180","citation":{"chicago":"Feliciangeli, Dario. “The Polaron at Strong Coupling.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9733.","short":"D. Feliciangeli, The Polaron at Strong Coupling, Institute of Science and Technology Austria, 2021.","mla":"Feliciangeli, Dario. The Polaron at Strong Coupling. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9733.","apa":"Feliciangeli, D. (2021). The polaron at strong coupling. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9733","ieee":"D. Feliciangeli, “The polaron at strong coupling,” Institute of Science and Technology Austria, 2021.","ista":"Feliciangeli D. 2021. The polaron at strong coupling. Institute of Science and Technology Austria.","ama":"Feliciangeli D. The polaron at strong coupling. 2021. doi:10.15479/at:ista:9733"},"date_published":"2021-08-20T00:00:00Z","license":"https://creativecommons.org/licenses/by-nd/4.0/","file_date_updated":"2022-03-10T12:13:57Z","ec_funded":1,"publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"RoSe"},{"_id":"JaMa"}],"year":"2021","date_created":"2021-07-27T15:48:30Z","date_updated":"2024-03-06T12:30:44Z","author":[{"full_name":"Feliciangeli, Dario","last_name":"Feliciangeli","first_name":"Dario","orcid":"0000-0003-0754-8530","id":"41A639AA-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"9787","relation":"part_of_dissertation","status":"public"},{"id":"9792","status":"public","relation":"part_of_dissertation"},{"id":"9225","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"9781"},{"relation":"part_of_dissertation","status":"public","id":"9791"}]},"month":"08","publication_identifier":{"issn":["2663-337X"]},"project":[{"grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425","name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020"},{"name":"Analysis of quantum many-body systems","call_identifier":"H2020","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"},{"name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","grant_number":"F6504"}],"tmp":{"short":"CC BY-ND (4.0)","image":"/image/cc_by_nd.png","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode"},"oa":1,"degree_awarded":"PhD","supervisor":[{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","first_name":"Robert","last_name":"Seiringer","full_name":"Seiringer, Robert"},{"full_name":"Maas, Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0845-1338","first_name":"Jan","last_name":"Maas"}],"language":[{"iso":"eng"}],"doi":"10.15479/at:ista:9733"},{"abstract":[{"lang":"eng","text":"As the size and complexity of models and datasets grow, so does the need for communication-efficient variants of stochastic gradient descent that can be deployed to perform parallel model training. One popular communication-compression method for data-parallel SGD is QSGD (Alistarh et al., 2017), which quantizes and encodes gradients to reduce communication costs. The baseline variant of QSGD provides strong theoretical guarantees, however, for practical purposes, the authors proposed a heuristic variant which we call QSGDinf, which demonstrated impressive empirical gains for distributed training of large neural networks. In this paper, we build on this work to propose a new gradient quantization scheme, and show that it has both stronger theoretical guarantees than QSGD, and matches and exceeds the empirical performance of the QSGDinf heuristic and of other compression methods."}],"issue":"114","type":"journal_article","oa_version":"Published Version","file":[{"file_id":"9595","relation":"main_file","success":1,"checksum":"6428aa8bcb67768b6949c99b55d5281d","date_updated":"2021-06-23T07:09:41Z","date_created":"2021-06-23T07:09:41Z","access_level":"open_access","file_name":"2021_JournalOfMachineLearningResearch_Ramezani-Kebrya.pdf","creator":"asandaue","content_type":"application/pdf","file_size":11237154}],"title":"NUQSGD: Provably communication-efficient data-parallel SGD via nonuniform quantization","status":"public","ddc":["000"],"intvolume":" 22","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9571","day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2021-04-01T00:00:00Z","article_type":"original","page":"1−43","publication":"Journal of Machine Learning Research","citation":{"ieee":"A. Ramezani-Kebrya, F. Faghri, I. Markov, V. Aksenov, D.-A. Alistarh, and D. M. Roy, “NUQSGD: Provably communication-efficient data-parallel SGD via nonuniform quantization,” Journal of Machine Learning Research, vol. 22, no. 114. Journal of Machine Learning Research, p. 1−43, 2021.","apa":"Ramezani-Kebrya, A., Faghri, F., Markov, I., Aksenov, V., Alistarh, D.-A., & Roy, D. M. (2021). NUQSGD: Provably communication-efficient data-parallel SGD via nonuniform quantization. Journal of Machine Learning Research. Journal of Machine Learning Research.","ista":"Ramezani-Kebrya A, Faghri F, Markov I, Aksenov V, Alistarh D-A, Roy DM. 2021. NUQSGD: Provably communication-efficient data-parallel SGD via nonuniform quantization. Journal of Machine Learning Research. 22(114), 1−43.","ama":"Ramezani-Kebrya A, Faghri F, Markov I, Aksenov V, Alistarh D-A, Roy DM. NUQSGD: Provably communication-efficient data-parallel SGD via nonuniform quantization. Journal of Machine Learning Research. 2021;22(114):1−43.","chicago":"Ramezani-Kebrya, Ali, Fartash Faghri, Ilya Markov, Vitalii Aksenov, Dan-Adrian Alistarh, and Daniel M. Roy. “NUQSGD: Provably Communication-Efficient Data-Parallel SGD via Nonuniform Quantization.” Journal of Machine Learning Research. Journal of Machine Learning Research, 2021.","short":"A. Ramezani-Kebrya, F. Faghri, I. Markov, V. Aksenov, D.-A. Alistarh, D.M. Roy, Journal of Machine Learning Research 22 (2021) 1−43.","mla":"Ramezani-Kebrya, Ali, et al. “NUQSGD: Provably Communication-Efficient Data-Parallel SGD via Nonuniform Quantization.” Journal of Machine Learning Research, vol. 22, no. 114, Journal of Machine Learning Research, 2021, p. 1−43."},"file_date_updated":"2021-06-23T07:09:41Z","date_updated":"2024-03-06T12:22:07Z","date_created":"2021-06-20T22:01:33Z","volume":22,"author":[{"last_name":"Ramezani-Kebrya","first_name":"Ali","full_name":"Ramezani-Kebrya, Ali"},{"last_name":"Faghri","first_name":"Fartash","full_name":"Faghri, Fartash"},{"last_name":"Markov","first_name":"Ilya","full_name":"Markov, Ilya"},{"id":"2980135A-F248-11E8-B48F-1D18A9856A87","first_name":"Vitalii","last_name":"Aksenov","full_name":"Aksenov, Vitalii"},{"full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Daniel M.","last_name":"Roy","full_name":"Roy, Daniel M."}],"publication_status":"published","department":[{"_id":"DaAl"}],"publisher":"Journal of Machine Learning Research","year":"2021","month":"04","publication_identifier":{"eissn":["15337928"],"issn":["15324435"]},"language":[{"iso":"eng"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["1908.06077"]},"oa":1,"main_file_link":[{"url":"https://www.jmlr.org/papers/v22/20-255.html","open_access":"1"}]},{"month":"02","publication_identifier":{"eissn":["1097-4199"]},"quality_controlled":"1","project":[{"_id":"260018B0-B435-11E9-9278-68D0E5697425","grant_number":"725780","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020"}],"oa":1,"main_file_link":[{"url":"https://doi.org/10.1101/2020.06.14.151258","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1016/j.neuron.2020.11.028","ec_funded":1,"publication_status":"published","department":[{"_id":"SiHi"}],"publisher":"Elsevier","year":"2021","acknowledgement":"We thank M. Mishina for GluD2fl frozen embryos, T.C. Südhof and J.I. Morgan for Cbln1fl mice, L. Anderson for help in generating the MADM alleles, W. Joo for a previously unpublished construct, M. Yuzaki, K. Shen, J. Ding, and members of the Luo lab, including J.M. Kebschull, H. Li, J. Li, T. Li, C.M. McLaughlin, D. Pederick, J. Ren, D.C. Wang and C. Xu for discussions and critiques of the manuscript, and M. Yuzaki for supporting Y.H.T. during the final phase of this project. Y.H.T. was supported by a JSPS fellowship; S.A.S. was supported by a Stanford Graduate Fellowship and an NSF Predoctoral Fellowship; L.J. is supported by a Stanford Graduate Fellowship and an NSF Predoctoral Fellowship; M.J.W. is supported by a Burroughs Wellcome Fund CASI Award. This work was supported by an NIH grant (R01-NS050538) to L.L.; the European Research Council (ERC) under the European Union's Horizon 2020 research and innovations programme (No. 725780 LinPro) to S.H.; and Simons and James S. McDonnell Foundations and an NSF CAREER award to S.G.; L.L. is an HHMI investigator.","date_updated":"2024-03-06T12:12:48Z","date_created":"2020-09-21T11:59:47Z","volume":109,"author":[{"first_name":"Yukari H.","last_name":"Takeo","full_name":"Takeo, Yukari H."},{"full_name":"Shuster, S. Andrew","last_name":"Shuster","first_name":"S. Andrew"},{"full_name":"Jiang, Linnie","first_name":"Linnie","last_name":"Jiang"},{"full_name":"Hu, Miley","first_name":"Miley","last_name":"Hu"},{"first_name":"David J.","last_name":"Luginbuhl","full_name":"Luginbuhl, David J."},{"first_name":"Thomas","last_name":"Rülicke","full_name":"Rülicke, Thomas"},{"last_name":"Contreras","first_name":"Ximena","id":"475990FE-F248-11E8-B48F-1D18A9856A87","full_name":"Contreras, Ximena"},{"orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","first_name":"Simon","full_name":"Hippenmeyer, Simon"},{"full_name":"Wagner, Mark J.","last_name":"Wagner","first_name":"Mark J."},{"full_name":"Ganguli, Surya","first_name":"Surya","last_name":"Ganguli"},{"last_name":"Luo","first_name":"Liqun","full_name":"Luo, Liqun"}],"scopus_import":"1","day":"17","article_processing_charge":"No","article_type":"original","page":"P629-644.E8","publication":"Neuron","citation":{"ista":"Takeo YH, Shuster SA, Jiang L, Hu M, Luginbuhl DJ, Rülicke T, Contreras X, Hippenmeyer S, Wagner MJ, Ganguli S, Luo L. 2021. GluD2- and Cbln1-mediated competitive synaptogenesis shapes the dendritic arbors of cerebellar Purkinje cells. Neuron. 109(4), P629–644.E8.","ieee":"Y. H. Takeo et al., “GluD2- and Cbln1-mediated competitive synaptogenesis shapes the dendritic arbors of cerebellar Purkinje cells,” Neuron, vol. 109, no. 4. Elsevier, p. P629–644.E8, 2021.","apa":"Takeo, Y. H., Shuster, S. A., Jiang, L., Hu, M., Luginbuhl, D. J., Rülicke, T., … Luo, L. (2021). GluD2- and Cbln1-mediated competitive synaptogenesis shapes the dendritic arbors of cerebellar Purkinje cells. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2020.11.028","ama":"Takeo YH, Shuster SA, Jiang L, et al. GluD2- and Cbln1-mediated competitive synaptogenesis shapes the dendritic arbors of cerebellar Purkinje cells. Neuron. 2021;109(4):P629-644.E8. doi:10.1016/j.neuron.2020.11.028","chicago":"Takeo, Yukari H., S. Andrew Shuster, Linnie Jiang, Miley Hu, David J. Luginbuhl, Thomas Rülicke, Ximena Contreras, et al. “GluD2- and Cbln1-Mediated Competitive Synaptogenesis Shapes the Dendritic Arbors of Cerebellar Purkinje Cells.” Neuron. Elsevier, 2021. https://doi.org/10.1016/j.neuron.2020.11.028.","mla":"Takeo, Yukari H., et al. “GluD2- and Cbln1-Mediated Competitive Synaptogenesis Shapes the Dendritic Arbors of Cerebellar Purkinje Cells.” Neuron, vol. 109, no. 4, Elsevier, 2021, p. P629–644.E8, doi:10.1016/j.neuron.2020.11.028.","short":"Y.H. Takeo, S.A. Shuster, L. Jiang, M. Hu, D.J. Luginbuhl, T. Rülicke, X. Contreras, S. Hippenmeyer, M.J. Wagner, S. Ganguli, L. Luo, Neuron 109 (2021) P629–644.E8."},"date_published":"2021-02-17T00:00:00Z","type":"journal_article","abstract":[{"text":"The synaptotrophic hypothesis posits that synapse formation stabilizes dendritic branches, yet this hypothesis has not been causally tested in vivo in the mammalian brain. Presynaptic ligand cerebellin-1 (Cbln1) and postsynaptic receptor GluD2 mediate synaptogenesis between granule cells and Purkinje cells in the molecular layer of the cerebellar cortex. Here we show that sparse but not global knockout of GluD2 causes under-elaboration of Purkinje cell dendrites in the deep molecular layer and overelaboration in the superficial molecular layer. Developmental, overexpression, structure-function, and genetic epistasis analyses indicate that dendrite morphogenesis defects result from competitive synaptogenesis in a Cbln1/GluD2-dependent manner. A generative model of dendritic growth based on competitive synaptogenesis largely recapitulates GluD2 sparse and global knockout phenotypes. Our results support the synaptotrophic hypothesis at initial stages of dendrite development, suggest a second mode in which cumulative synapse formation inhibits further dendrite growth, and highlight the importance of competition in dendrite morphogenesis.","lang":"eng"}],"issue":"4","title":"GluD2- and Cbln1-mediated competitive synaptogenesis shapes the dendritic arbors of cerebellar Purkinje cells","status":"public","intvolume":" 109","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8544","oa_version":"Preprint"},{"day":"08","month":"07","article_processing_charge":"No","publication":"arXiv","main_file_link":[{"url":"https://arxiv.org/abs/2107.03720","open_access":"1"}],"external_id":{"arxiv":["2107.03720"]},"citation":{"ieee":"D. Feliciangeli, S. A. E. Rademacher, and R. Seiringer, “The effective mass problem for the Landau-Pekar equations,” arXiv. .","apa":"Feliciangeli, D., Rademacher, S. A. E., & Seiringer, R. (n.d.). The effective mass problem for the Landau-Pekar equations. arXiv.","ista":"Feliciangeli D, Rademacher SAE, Seiringer R. The effective mass problem for the Landau-Pekar equations. arXiv, 2107.03720.","ama":"Feliciangeli D, Rademacher SAE, Seiringer R. The effective mass problem for the Landau-Pekar equations. arXiv.","chicago":"Feliciangeli, Dario, Simone Anna Elvira Rademacher, and Robert Seiringer. “The Effective Mass Problem for the Landau-Pekar Equations.” ArXiv, n.d.","short":"D. Feliciangeli, S.A.E. Rademacher, R. Seiringer, ArXiv (n.d.).","mla":"Feliciangeli, Dario, et al. “The Effective Mass Problem for the Landau-Pekar Equations.” ArXiv, 2107.03720."},"oa":1,"project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"},{"name":"Analysis of quantum many-body systems","call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227"}],"date_published":"2021-07-08T00:00:00Z","language":[{"iso":"eng"}],"article_number":"2107.03720 ","type":"preprint","abstract":[{"lang":"eng","text":"We provide a definition of the effective mass for the classical polaron described by the Landau-Pekar equations. It is based on a novel variational principle, minimizing the energy functional over states with given (initial) velocity. The resulting formula for the polaron's effective mass agrees with the prediction by Landau and Pekar."}],"ec_funded":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9791","acknowledgement":"We thank Herbert Spohn for helpful comments. Funding from the European Union’s Horizon 2020 research and innovation programme under the ERC grant agreement No. 694227 (D.F. and R.S.) and under the Marie Skłodowska-Curie Grant Agreement No. 754411 (S.R.) is gratefully acknowledged..","year":"2021","status":"public","ddc":["510"],"publication_status":"submitted","title":"The effective mass problem for the Landau-Pekar equations","department":[{"_id":"RoSe"}],"author":[{"first_name":"Dario","last_name":"Feliciangeli","id":"41A639AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0754-8530","full_name":"Feliciangeli, Dario"},{"full_name":"Rademacher, Simone Anna Elvira","first_name":"Simone Anna Elvira","last_name":"Rademacher","id":"856966FE-A408-11E9-977E-802DE6697425","orcid":"0000-0001-5059-4466"},{"full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","first_name":"Robert"}],"related_material":{"record":[{"status":"public","relation":"later_version","id":"10755"},{"relation":"dissertation_contains","status":"public","id":"9733"}]},"date_created":"2021-08-06T08:49:45Z","date_updated":"2024-03-06T12:30:45Z","oa_version":"Preprint"},{"scopus_import":"1","day":"07","article_processing_charge":"No","publication":"Neuron","citation":{"chicago":"Mlynarski, Wiktor F, Michal Hledik, Thomas R Sokolowski, and Gašper Tkačik. “Statistical Analysis and Optimality of Neural Systems.” Neuron. Cell Press, 2021. https://doi.org/10.1016/j.neuron.2021.01.020.","mla":"Mlynarski, Wiktor F., et al. “Statistical Analysis and Optimality of Neural Systems.” Neuron, vol. 109, no. 7, Cell Press, 2021, p. 1227–1241.e5, doi:10.1016/j.neuron.2021.01.020.","short":"W.F. Mlynarski, M. Hledik, T.R. Sokolowski, G. Tkačik, Neuron 109 (2021) 1227–1241.e5.","ista":"Mlynarski WF, Hledik M, Sokolowski TR, Tkačik G. 2021. Statistical analysis and optimality of neural systems. Neuron. 109(7), 1227–1241.e5.","ieee":"W. F. Mlynarski, M. Hledik, T. R. Sokolowski, and G. Tkačik, “Statistical analysis and optimality of neural systems,” Neuron, vol. 109, no. 7. Cell Press, p. 1227–1241.e5, 2021.","apa":"Mlynarski, W. F., Hledik, M., Sokolowski, T. R., & Tkačik, G. (2021). Statistical analysis and optimality of neural systems. Neuron. Cell Press. https://doi.org/10.1016/j.neuron.2021.01.020","ama":"Mlynarski WF, Hledik M, Sokolowski TR, Tkačik G. Statistical analysis and optimality of neural systems. Neuron. 2021;109(7):1227-1241.e5. doi:10.1016/j.neuron.2021.01.020"},"page":"1227-1241.e5","date_published":"2021-04-07T00:00:00Z","type":"journal_article","abstract":[{"text":"Normative theories and statistical inference provide complementary approaches for the study of biological systems. A normative theory postulates that organisms have adapted to efficiently solve essential tasks, and proceeds to mathematically work out testable consequences of such optimality; parameters that maximize the hypothesized organismal function can be derived ab initio, without reference to experimental data. In contrast, statistical inference focuses on efficient utilization of data to learn model parameters, without reference to any a priori notion of biological function, utility, or fitness. Traditionally, these two approaches were developed independently and applied separately. Here we unify them in a coherent Bayesian framework that embeds a normative theory into a family of maximum-entropy “optimization priors.” This family defines a smooth interpolation between a data-rich inference regime (characteristic of “bottom-up” statistical models), and a data-limited ab inito prediction regime (characteristic of “top-down” normative theory). We demonstrate the applicability of our framework using data from the visual cortex, and argue that the flexibility it affords is essential to address a number of fundamental challenges relating to inference and prediction in complex, high-dimensional biological problems.","lang":"eng"}],"issue":"7","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7553","status":"public","title":"Statistical analysis and optimality of neural systems","intvolume":" 109","oa_version":"Preprint","month":"04","oa":1,"external_id":{"isi":["000637809600006"]},"main_file_link":[{"url":"https://doi.org/10.1101/848374","open_access":"1"}],"quality_controlled":"1","isi":1,"project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"doi":"10.1016/j.neuron.2021.01.020","language":[{"iso":"eng"}],"ec_funded":1,"year":"2021","acknowledgement":"The authors thank Dario Ringach for providing the V1 receptive fields and Olivier Marre for providing the retinal receptive fields. W.M. was funded by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 754411. M.H. was funded in part by Human Frontiers Science grant no. HFSP RGP0032/2018.","publication_status":"published","publisher":"Cell Press","department":[{"_id":"GaTk"}],"author":[{"last_name":"Mlynarski","first_name":"Wiktor F","id":"358A453A-F248-11E8-B48F-1D18A9856A87","full_name":"Mlynarski, Wiktor F"},{"id":"4171253A-F248-11E8-B48F-1D18A9856A87","last_name":"Hledik","first_name":"Michal","full_name":"Hledik, Michal"},{"first_name":"Thomas R","last_name":"Sokolowski","id":"3E999752-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1287-3779","full_name":"Sokolowski, Thomas R"},{"orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","first_name":"Gašper","full_name":"Tkačik, Gašper"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/can-evolution-be-predicted/","description":"News on IST Homepage","relation":"press_release"}],"record":[{"relation":"dissertation_contains","status":"public","id":"15020"}]},"date_updated":"2024-03-06T14:22:51Z","date_created":"2020-02-28T11:00:12Z","volume":109},{"related_material":{"record":[{"id":"12480","relation":"later_version","status":"public"}]},"author":[{"full_name":"Mondelli, Marco","first_name":"Marco","last_name":"Mondelli","id":"27EB676C-8706-11E9-9510-7717E6697425","orcid":"0000-0002-3242-7020"},{"last_name":"Venkataramanan","first_name":"Ramji","full_name":"Venkataramanan, Ramji"}],"volume":130,"date_updated":"2024-03-07T10:36:53Z","date_created":"2022-01-03T11:34:22Z","acknowledgement":"The authors would like to thank Andrea Montanari 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.","year":"2021","editor":[{"last_name":"Banerjee","first_name":"Arindam","full_name":"Banerjee, Arindam"},{"full_name":"Fukumizu, Kenji","last_name":"Fukumizu","first_name":"Kenji"}],"publisher":"ML Research Press","department":[{"_id":"MaMo"}],"publication_status":"published","publication_identifier":{"issn":["2640-3498"]},"month":"04","conference":{"location":"Virtual, San Diego, CA, United States","start_date":"2021-04-13","end_date":"2021-04-15","name":"AISTATS: Artificial Intelligence and Statistics"},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://proceedings.mlr.press/v130/mondelli21a.html"}],"external_id":{"arxiv":["2010.03460"]},"oa":1,"project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"}],"quality_controlled":"1","abstract":[{"lang":"eng","text":" We consider the problem of estimating a signal from measurements obtained via a generalized linear model. We focus on estimators based on approximate message passing (AMP), a family of iterative algorithms with many appealing features: the performance of AMP in the high-dimensional limit can be succinctly characterized under suitable model assumptions; AMP can also be tailored to the empirical distribution of the signal entries, and for a wide class of estimation problems, AMP is conjectured to be optimal among all polynomial-time algorithms. However, a major issue of AMP is that in many models (such as phase retrieval), it requires an initialization correlated with the ground-truth signal and independent from the measurement matrix. Assuming that such an initialization is available is typically not realistic. In this paper, we solve this problem by proposing an AMP algorithm initialized with a spectral estimator. With such an initialization, the standard AMP analysis fails since the spectral estimator depends in a complicated way on the design matrix. Our main contribution is a rigorous characterization of the performance of AMP with spectral initialization in the high-dimensional limit. The key technical idea is to define and analyze a two-phase artificial AMP algorithm that first produces the spectral estimator, and then closely approximates the iterates of the true AMP. We also provide numerical results that demonstrate the validity of the proposed approach. "}],"type":"conference","alternative_title":["Proceedings of Machine Learning Research"],"oa_version":"Preprint","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"10598","intvolume":" 130","title":"Approximate message passing with spectral initialization for generalized linear models","status":"public","article_processing_charge":"Yes (via OA deal)","day":"01","scopus_import":"1","date_published":"2021-04-01T00:00:00Z","citation":{"ista":"Mondelli M, Venkataramanan R. 2021. Approximate message passing with spectral initialization for generalized linear models. Proceedings of The 24th International Conference on Artificial Intelligence and Statistics. AISTATS: Artificial Intelligence and Statistics, Proceedings of Machine Learning Research, vol. 130, 397–405.","ieee":"M. Mondelli and R. Venkataramanan, “Approximate message passing with spectral initialization for generalized linear models,” in Proceedings of The 24th International Conference on Artificial Intelligence and Statistics, Virtual, San Diego, CA, United States, 2021, vol. 130, pp. 397–405.","apa":"Mondelli, M., & Venkataramanan, R. (2021). Approximate message passing with spectral initialization for generalized linear models. In A. Banerjee & K. Fukumizu (Eds.), Proceedings of The 24th International Conference on Artificial Intelligence and Statistics (Vol. 130, pp. 397–405). Virtual, San Diego, CA, United States: ML Research Press.","ama":"Mondelli M, Venkataramanan R. Approximate message passing with spectral initialization for generalized linear models. In: Banerjee A, Fukumizu K, eds. Proceedings of The 24th International Conference on Artificial Intelligence and Statistics. Vol 130. ML Research Press; 2021:397-405.","chicago":"Mondelli, Marco, and Ramji Venkataramanan. “Approximate Message Passing with Spectral Initialization for Generalized Linear Models.” In Proceedings of The 24th International Conference on Artificial Intelligence and Statistics, edited by Arindam Banerjee and Kenji Fukumizu, 130:397–405. ML Research Press, 2021.","mla":"Mondelli, Marco, and Ramji Venkataramanan. “Approximate Message Passing with Spectral Initialization for Generalized Linear Models.” Proceedings of The 24th International Conference on Artificial Intelligence and Statistics, edited by Arindam Banerjee and Kenji Fukumizu, vol. 130, ML Research Press, 2021, pp. 397–405.","short":"M. Mondelli, R. Venkataramanan, in:, A. Banerjee, K. Fukumizu (Eds.), Proceedings of The 24th International Conference on Artificial Intelligence and Statistics, ML Research Press, 2021, pp. 397–405."},"publication":"Proceedings of The 24th International Conference on Artificial Intelligence and Statistics","page":"397-405"},{"date_published":"2021-02-25T00:00:00Z","citation":{"chicago":"Shehu, Yekini, Qiao-Li Dong, Lu-Lu Liu, and Jen-Chih Yao. “New Strong Convergence Method for the Sum of Two Maximal Monotone Operators.” Optimization and Engineering. Springer Nature, 2021. https://doi.org/10.1007/s11081-020-09544-5.","mla":"Shehu, Yekini, et al. “New Strong Convergence Method for the Sum of Two Maximal Monotone Operators.” Optimization and Engineering, vol. 22, Springer Nature, 2021, pp. 2627–53, doi:10.1007/s11081-020-09544-5.","short":"Y. Shehu, Q.-L. Dong, L.-L. Liu, J.-C. Yao, Optimization and Engineering 22 (2021) 2627–2653.","ista":"Shehu Y, Dong Q-L, Liu L-L, Yao J-C. 2021. New strong convergence method for the sum of two maximal monotone operators. Optimization and Engineering. 22, 2627–2653.","ieee":"Y. Shehu, Q.-L. Dong, L.-L. Liu, and J.-C. Yao, “New strong convergence method for the sum of two maximal monotone operators,” Optimization and Engineering, vol. 22. Springer Nature, pp. 2627–2653, 2021.","apa":"Shehu, Y., Dong, Q.-L., Liu, L.-L., & Yao, J.-C. (2021). New strong convergence method for the sum of two maximal monotone operators. Optimization and Engineering. Springer Nature. https://doi.org/10.1007/s11081-020-09544-5","ama":"Shehu Y, Dong Q-L, Liu L-L, Yao J-C. New strong convergence method for the sum of two maximal monotone operators. Optimization and Engineering. 2021;22:2627-2653. doi:10.1007/s11081-020-09544-5"},"publication":"Optimization and Engineering","page":"2627-2653","article_type":"original","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"25","scopus_import":"1","oa_version":"Published Version","file":[{"file_id":"8197","relation":"main_file","success":1,"date_updated":"2020-08-03T15:24:39Z","date_created":"2020-08-03T15:24:39Z","access_level":"open_access","file_name":"2020_OptimizationEngineering_Shehu.pdf","creator":"dernst","content_type":"application/pdf","file_size":2137860}],"_id":"8196","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 22","title":"New strong convergence method for the sum of two maximal monotone operators","ddc":["510"],"status":"public","abstract":[{"text":"This paper aims to obtain a strong convergence result for a Douglas–Rachford splitting method with inertial extrapolation step for finding a zero of the sum of two set-valued maximal monotone operators without any further assumption of uniform monotonicity on any of the involved maximal monotone operators. Furthermore, our proposed method is easy to implement and the inertial factor in our proposed method is a natural choice. Our method of proof is of independent interest. Finally, some numerical implementations are given to confirm the theoretical analysis.","lang":"eng"}],"type":"journal_article","doi":"10.1007/s11081-020-09544-5","language":[{"iso":"eng"}],"external_id":{"isi":["000559345400001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"},{"grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425","name":"Discrete Optimization in Computer Vision: Theory and Practice","call_identifier":"FP7"}],"isi":1,"quality_controlled":"1","publication_identifier":{"issn":["1389-4420"],"eissn":["1573-2924"]},"month":"02","author":[{"full_name":"Shehu, Yekini","first_name":"Yekini","last_name":"Shehu","id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9224-7139"},{"last_name":"Dong","first_name":"Qiao-Li","full_name":"Dong, Qiao-Li"},{"last_name":"Liu","first_name":"Lu-Lu","full_name":"Liu, Lu-Lu"},{"full_name":"Yao, Jen-Chih","last_name":"Yao","first_name":"Jen-Chih"}],"volume":22,"date_updated":"2024-03-07T14:39:29Z","date_created":"2020-08-03T14:29:57Z","year":"2021","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). 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). The authors are grateful to the anonymous referees and the handling Editor for their comments and suggestions which have improved the earlier version of the manuscript greatly.","department":[{"_id":"VlKo"}],"publisher":"Springer Nature","publication_status":"published","ec_funded":1,"file_date_updated":"2020-08-03T15:24:39Z"},{"type":"journal_article","abstract":[{"text":"In the worldwide endeavor for disruptive quantum technologies, germanium is emerging as a versatile material to realize devices capable of encoding, processing, or transmitting quantum information. These devices leverage special properties of the germanium valence-band states, commonly known as holes, such as their inherently strong spin-orbit coupling and the ability to host superconducting pairing correlations. In this Review, we initially introduce the physics of holes in low-dimensional germanium structures with key insights from a theoretical perspective. We then examine the material science progress underpinning germanium-based planar heterostructures and nanowires. We review the most significant experimental results demonstrating key building blocks for quantum technology, such as an electrically driven universal quantum gate set with spin qubits in quantum dots and superconductor-semiconductor devices for hybrid quantum systems. We conclude by identifying the most promising prospects\r\ntoward scalable quantum information processing. ","lang":"eng"}],"title":"The germanium quantum information route","status":"public","intvolume":" 6","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"8911","oa_version":"Preprint","scopus_import":"1","day":"01","article_processing_charge":"No","article_type":"original","page":"926–943 ","publication":"Nature Reviews Materials","citation":{"short":"G. Scappucci, C. Kloeffel, F.A. Zwanenburg, D. Loss, M. Myronov, J.-J. Zhang, S.D. Franceschi, G. Katsaros, M. Veldhorst, Nature Reviews Materials 6 (2021) 926–943.","mla":"Scappucci, Giordano, et al. “The Germanium Quantum Information Route.” Nature Reviews Materials, vol. 6, Springer Nature, 2021, pp. 926–943, doi:10.1038/s41578-020-00262-z.","chicago":"Scappucci, Giordano, Christoph Kloeffel, Floris A. Zwanenburg, Daniel Loss, Maksym Myronov, Jian-Jun Zhang, Silvano De Franceschi, Georgios Katsaros, and Menno Veldhorst. “The Germanium Quantum Information Route.” Nature Reviews Materials. Springer Nature, 2021. https://doi.org/10.1038/s41578-020-00262-z.","ama":"Scappucci G, Kloeffel C, Zwanenburg FA, et al. The germanium quantum information route. Nature Reviews Materials. 2021;6:926–943. doi:10.1038/s41578-020-00262-z","apa":"Scappucci, G., Kloeffel, C., Zwanenburg, F. A., Loss, D., Myronov, M., Zhang, J.-J., … Veldhorst, M. (2021). The germanium quantum information route. Nature Reviews Materials. Springer Nature. https://doi.org/10.1038/s41578-020-00262-z","ieee":"G. Scappucci et al., “The germanium quantum information route,” Nature Reviews Materials, vol. 6. Springer Nature, pp. 926–943, 2021.","ista":"Scappucci G, Kloeffel C, Zwanenburg FA, Loss D, Myronov M, Zhang J-J, Franceschi SD, Katsaros G, Veldhorst M. 2021. The germanium quantum information route. Nature Reviews Materials. 6, 926–943."},"date_published":"2021-10-01T00:00:00Z","ec_funded":1,"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"GeKa"}],"year":"2021","acknowledgement":"G.S., M.W.,F.A.Z acknowledge financial support from The Netherlands Organization for Scientific Research (NWO). F.Z., D.L., G.K. acknowledge funding from the European Union’s Horizon 2020 research and innovation programme under Grand Agreement Nr. 862046. G.K. acknowledges funding from FP7 ERC Starting Grant 335497, FWF Y 715-N30, FWF P-30207. S.D. acknowledges support from the European Union’s Horizon 2020 program under Grant\r\nAgreement No. 81050 and from the Agence Nationale de la Recherche through the TOPONANO and CMOSQSPIN projects. J.Z. acknowledges support from the National Key R&D Program of China (Grant No. 2016YFA0301701) and Strategic Priority Research Program of CAS (Grant No. XDB30000000). D.L. and C.K. acknowledge the Swiss National Science Foundation and NCCR QSIT.","date_updated":"2024-03-07T14:48:57Z","date_created":"2020-12-02T10:52:51Z","volume":6,"author":[{"full_name":"Scappucci, Giordano","last_name":"Scappucci","first_name":"Giordano"},{"first_name":"Christoph","last_name":"Kloeffel","full_name":"Kloeffel, Christoph"},{"last_name":"Zwanenburg","first_name":"Floris A.","full_name":"Zwanenburg, Floris A."},{"first_name":"Daniel","last_name":"Loss","full_name":"Loss, Daniel"},{"last_name":"Myronov","first_name":"Maksym","full_name":"Myronov, Maksym"},{"full_name":"Zhang, Jian-Jun","last_name":"Zhang","first_name":"Jian-Jun"},{"first_name":"Silvano De","last_name":"Franceschi","full_name":"Franceschi, Silvano De"},{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8342-202X","first_name":"Georgios","last_name":"Katsaros","full_name":"Katsaros, Georgios"},{"full_name":"Veldhorst, Menno","last_name":"Veldhorst","first_name":"Menno"}],"month":"10","publication_identifier":{"eissn":["2058-8437"]},"isi":1,"quality_controlled":"1","project":[{"_id":"25517E86-B435-11E9-9278-68D0E5697425","grant_number":"335497","name":"Towards Spin qubits and Majorana fermions in Germanium selfassembled hut-wires","call_identifier":"FP7"},{"grant_number":"Y00715","_id":"2552F888-B435-11E9-9278-68D0E5697425","name":"Loch Spin-Qubits und Majorana-Fermionen in Germanium","call_identifier":"FWF"},{"name":"Hole spin orbit qubits in Ge quantum wells","call_identifier":"FWF","grant_number":"P30207","_id":"2641CE5E-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000600826100003"],"arxiv":["2004.08133"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2004.08133"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1038/s41578-020-00262-z"},{"_id":"8338","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"On mutually diagonal nets on (confocal) quadrics and 3-dimensional webs","status":"public","intvolume":" 66","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"Canonical parametrisations of classical confocal coordinate systems are introduced and exploited to construct non-planar analogues of incircular (IC) nets on individual quadrics and systems of confocal quadrics. Intimate connections with classical deformations of quadrics that are isometric along asymptotic lines and circular cross-sections of quadrics are revealed. The existence of octahedral webs of surfaces of Blaschke type generated by asymptotic and characteristic lines that are diagonally related to lines of curvature is proved theoretically and established constructively. Appropriate samplings (grids) of these webs lead to three-dimensional extensions of non-planar IC nets. Three-dimensional octahedral grids composed of planes and spatially extending (checkerboard) IC-nets are shown to arise in connection with systems of confocal quadrics in Minkowski space. In this context, the Laguerre geometric notion of conical octahedral grids of planes is introduced. The latter generalise the octahedral grids derived from systems of confocal quadrics in Minkowski space. An explicit construction of conical octahedral grids is presented. The results are accompanied by various illustrations which are based on the explicit formulae provided by the theory.","lang":"eng"}],"publication":"Discrete and Computational Geometry","citation":{"short":"A. Akopyan, A.I. Bobenko, W.K. Schief, J. Techter, Discrete and Computational Geometry 66 (2021) 938–976.","mla":"Akopyan, Arseniy, et al. “On Mutually Diagonal Nets on (Confocal) Quadrics and 3-Dimensional Webs.” Discrete and Computational Geometry, vol. 66, Springer Nature, 2021, pp. 938–76, doi:10.1007/s00454-020-00240-w.","chicago":"Akopyan, Arseniy, Alexander I. Bobenko, Wolfgang K. Schief, and Jan Techter. “On Mutually Diagonal Nets on (Confocal) Quadrics and 3-Dimensional Webs.” Discrete and Computational Geometry. Springer Nature, 2021. https://doi.org/10.1007/s00454-020-00240-w.","ama":"Akopyan A, Bobenko AI, Schief WK, Techter J. On mutually diagonal nets on (confocal) quadrics and 3-dimensional webs. Discrete and Computational Geometry. 2021;66:938-976. doi:10.1007/s00454-020-00240-w","ieee":"A. Akopyan, A. I. Bobenko, W. K. Schief, and J. Techter, “On mutually diagonal nets on (confocal) quadrics and 3-dimensional webs,” Discrete and Computational Geometry, vol. 66. Springer Nature, pp. 938–976, 2021.","apa":"Akopyan, A., Bobenko, A. I., Schief, W. K., & Techter, J. (2021). On mutually diagonal nets on (confocal) quadrics and 3-dimensional webs. Discrete and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-020-00240-w","ista":"Akopyan A, Bobenko AI, Schief WK, Techter J. 2021. On mutually diagonal nets on (confocal) quadrics and 3-dimensional webs. Discrete and Computational Geometry. 66, 938–976."},"article_type":"original","page":"938-976","date_published":"2021-10-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","acknowledgement":"This research was supported by the DFG Collaborative Research Center TRR 109 “Discretization in Geometry and Dynamics”. W.K.S. was also supported by the Australian Research Council (DP1401000851). A.V.A. was also supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 78818 Alpha).","year":"2021","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"HeEd"}],"author":[{"full_name":"Akopyan, Arseniy","orcid":"0000-0002-2548-617X","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","last_name":"Akopyan","first_name":"Arseniy"},{"full_name":"Bobenko, Alexander I.","last_name":"Bobenko","first_name":"Alexander I."},{"last_name":"Schief","first_name":"Wolfgang K.","full_name":"Schief, Wolfgang K."},{"full_name":"Techter, Jan","last_name":"Techter","first_name":"Jan"}],"date_updated":"2024-03-07T14:51:11Z","date_created":"2020-09-06T22:01:13Z","volume":66,"ec_funded":1,"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1908.00856"}],"external_id":{"isi":["000564488500002"],"arxiv":["1908.00856"]},"isi":1,"quality_controlled":"1","project":[{"name":"Alpha Shape Theory Extended","call_identifier":"H2020","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","grant_number":"788183"}],"doi":"10.1007/s00454-020-00240-w","language":[{"iso":"eng"}],"month":"10","publication_identifier":{"issn":["0179-5376"],"eissn":["1432-0444"]}},{"date_published":"2021-12-01T00:00:00Z","publication":"Distributed Computing","citation":{"ama":"Censor-Hillel K, Dory M, Korhonen J, Leitersdorf D. Fast approximate shortest paths in the congested clique. Distributed Computing. 2021;34:463-487. doi:10.1007/s00446-020-00380-5","apa":"Censor-Hillel, K., Dory, M., Korhonen, J., & Leitersdorf, D. (2021). Fast approximate shortest paths in the congested clique. Distributed Computing. Springer Nature. https://doi.org/10.1007/s00446-020-00380-5","ieee":"K. Censor-Hillel, M. Dory, J. Korhonen, and D. Leitersdorf, “Fast approximate shortest paths in the congested clique,” Distributed Computing, vol. 34. Springer Nature, pp. 463–487, 2021.","ista":"Censor-Hillel K, Dory M, Korhonen J, Leitersdorf D. 2021. Fast approximate shortest paths in the congested clique. Distributed Computing. 34, 463–487.","short":"K. Censor-Hillel, M. Dory, J. Korhonen, D. Leitersdorf, Distributed Computing 34 (2021) 463–487.","mla":"Censor-Hillel, Keren, et al. “Fast Approximate Shortest Paths in the Congested Clique.” Distributed Computing, vol. 34, Springer Nature, 2021, pp. 463–87, doi:10.1007/s00446-020-00380-5.","chicago":"Censor-Hillel, Keren, Michal Dory, Janne Korhonen, and Dean Leitersdorf. “Fast Approximate Shortest Paths in the Congested Clique.” Distributed Computing. Springer Nature, 2021. https://doi.org/10.1007/s00446-020-00380-5."},"article_type":"original","page":"463-487","day":"01","article_processing_charge":"Yes (via OA deal)","scopus_import":"1","oa_version":"Published Version","_id":"7939","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Fast approximate shortest paths in the congested clique","status":"public","intvolume":" 34","abstract":[{"text":"We design fast deterministic algorithms for distance computation in the Congested Clique model. Our key contributions include:\r\n A (2+ϵ)-approximation for all-pairs shortest paths in O(log2n/ϵ) rounds on unweighted undirected graphs. With a small additional additive factor, this also applies for weighted graphs. This is the first sub-polynomial constant-factor approximation for APSP in this model.\r\n A (1+ϵ)-approximation for multi-source shortest paths from O(n−−√) sources in O(log2n/ϵ) rounds on weighted undirected graphs. This is the first sub-polynomial algorithm obtaining this approximation for a set of sources of polynomial size.\r\n\r\nOur main techniques are new distance tools that are obtained via improved algorithms for sparse matrix multiplication, which we leverage to construct efficient hopsets and shortest paths. Furthermore, our techniques extend to additional distance problems for which we improve upon the state-of-the-art, including diameter approximation, and an exact single-source shortest paths algorithm for weighted undirected graphs in O~(n1/6) rounds. ","lang":"eng"}],"type":"journal_article","doi":"10.1007/s00446-020-00380-5","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/s00446-020-00380-5"}],"external_id":{"arxiv":["1903.05956"],"isi":["000556444600001"]},"oa":1,"quality_controlled":"1","isi":1,"project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"month":"12","publication_identifier":{"issn":["0178-2770"],"eissn":["1432-0452"]},"author":[{"full_name":"Censor-Hillel, Keren","first_name":"Keren","last_name":"Censor-Hillel"},{"last_name":"Dory","first_name":"Michal","full_name":"Dory, Michal"},{"full_name":"Korhonen, Janne","id":"C5402D42-15BC-11E9-A202-CA2BE6697425","first_name":"Janne","last_name":"Korhonen"},{"first_name":"Dean","last_name":"Leitersdorf","full_name":"Leitersdorf, Dean"}],"related_material":{"record":[{"id":"6933","relation":"earlier_version","status":"public"}]},"date_created":"2020-06-07T22:00:54Z","date_updated":"2024-03-07T14:43:39Z","volume":34,"acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). We thank Mohsen Ghaffari, Michael Elkin and Merav Parter for fruitful discussions. This project has received funding from the European Union’s Horizon 2020 Research And Innovation Program under Grant Agreement No. 755839.","year":"2021","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"DaAl"}]},{"date_published":"2021-09-01T00:00:00Z","citation":{"short":"J.-D. Boissonnat, R. Dyer, A. Ghosh, A. Lieutier, M. Wintraecken, Discrete and Computational Geometry 66 (2021) 666–686.","mla":"Boissonnat, Jean-Daniel, et al. “Local Conditions for Triangulating Submanifolds of Euclidean Space.” Discrete and Computational Geometry, vol. 66, Springer Nature, 2021, pp. 666–86, doi:10.1007/s00454-020-00233-9.","chicago":"Boissonnat, Jean-Daniel, Ramsay Dyer, Arijit Ghosh, Andre Lieutier, and Mathijs Wintraecken. “Local Conditions for Triangulating Submanifolds of Euclidean Space.” Discrete and Computational Geometry. Springer Nature, 2021. https://doi.org/10.1007/s00454-020-00233-9.","ama":"Boissonnat J-D, Dyer R, Ghosh A, Lieutier A, Wintraecken M. Local conditions for triangulating submanifolds of Euclidean space. Discrete and Computational Geometry. 2021;66:666-686. doi:10.1007/s00454-020-00233-9","apa":"Boissonnat, J.-D., Dyer, R., Ghosh, A., Lieutier, A., & Wintraecken, M. (2021). Local conditions for triangulating submanifolds of Euclidean space. Discrete and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-020-00233-9","ieee":"J.-D. Boissonnat, R. Dyer, A. Ghosh, A. Lieutier, and M. Wintraecken, “Local conditions for triangulating submanifolds of Euclidean space,” Discrete and Computational Geometry, vol. 66. Springer Nature, pp. 666–686, 2021.","ista":"Boissonnat J-D, Dyer R, Ghosh A, Lieutier A, Wintraecken M. 2021. Local conditions for triangulating submanifolds of Euclidean space. Discrete and Computational Geometry. 66, 666–686."},"publication":"Discrete and Computational Geometry","page":"666-686","article_type":"original","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"01","scopus_import":"1","oa_version":"Published Version","_id":"8248","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 66","ddc":["510"],"status":"public","title":"Local conditions for triangulating submanifolds of Euclidean space","abstract":[{"lang":"eng","text":"We consider the following setting: suppose that we are given a manifold M in Rd with positive reach. Moreover assume that we have an embedded simplical complex A without boundary, whose vertex set lies on the manifold, is sufficiently dense and such that all simplices in A have sufficient quality. We prove that if, locally, interiors of the projection of the simplices onto the tangent space do not intersect, then A is a triangulation of the manifold, that is, they are homeomorphic."}],"type":"journal_article","doi":"10.1007/s00454-020-00233-9","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"main_file_link":[{"url":"https://doi.org/10.1007/s00454-020-00233-9","open_access":"1"}],"external_id":{"isi":["000558119300001"]},"project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","publication_identifier":{"issn":["0179-5376"],"eissn":["1432-0444"]},"month":"09","author":[{"last_name":"Boissonnat","first_name":"Jean-Daniel","full_name":"Boissonnat, Jean-Daniel"},{"full_name":"Dyer, Ramsay","last_name":"Dyer","first_name":"Ramsay"},{"first_name":"Arijit","last_name":"Ghosh","full_name":"Ghosh, Arijit"},{"full_name":"Lieutier, Andre","last_name":"Lieutier","first_name":"Andre"},{"first_name":"Mathijs","last_name":"Wintraecken","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7472-2220","full_name":"Wintraecken, Mathijs"}],"volume":66,"date_updated":"2024-03-07T14:54:59Z","date_created":"2020-08-11T07:11:51Z","acknowledgement":"Open access funding provided by the Institute of Science and Technology (IST Austria). Arijit Ghosh is supported by the Ramanujan Fellowship (No. SB/S2/RJN-064/2015), India.\r\nThis work has been funded by the European Research Council under the European Union’s ERC Grant Agreement number 339025 GUDHI (Algorithmic Foundations of Geometric Understanding in Higher Dimensions). The third author is supported by Ramanujan Fellowship (No. SB/S2/RJN-064/2015), India. The fifth author also received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411.","year":"2021","publisher":"Springer Nature","department":[{"_id":"HeEd"}],"publication_status":"published","ec_funded":1},{"doi":"10.1109/TIT.2020.3038806","language":[{"iso":"eng"}],"external_id":{"arxiv":["1711.01339"]},"quality_controlled":"1","month":"09","publication_identifier":{"issn":["0018-9448"],"eissn":["1557-9654"]},"author":[{"full_name":"Fazeli, Arman","first_name":"Arman","last_name":"Fazeli"},{"first_name":"Hamed","last_name":"Hassani","full_name":"Hassani, Hamed"},{"full_name":"Mondelli, Marco","first_name":"Marco","last_name":"Mondelli","id":"27EB676C-8706-11E9-9510-7717E6697425","orcid":"0000-0002-3242-7020"},{"full_name":"Vardy, Alexander","first_name":"Alexander","last_name":"Vardy"}],"related_material":{"record":[{"id":"6665","status":"public","relation":"earlier_version"}]},"date_updated":"2024-03-07T12:18:50Z","date_created":"2021-01-10T23:01:18Z","volume":67,"year":"2021","publication_status":"published","department":[{"_id":"MaMo"}],"publisher":"IEEE","date_published":"2021-09-01T00:00:00Z","publication":"IEEE Transactions on Information Theory","citation":{"mla":"Fazeli, Arman, et al. “Binary Linear Codes with Optimal Scaling: Polar Codes with Large Kernels.” IEEE Transactions on Information Theory, vol. 67, no. 9, IEEE, 2021, pp. 5693–710, doi:10.1109/TIT.2020.3038806.","short":"A. Fazeli, H. Hassani, M. Mondelli, A. Vardy, IEEE Transactions on Information Theory 67 (2021) 5693–5710.","chicago":"Fazeli, Arman, Hamed Hassani, Marco Mondelli, and Alexander Vardy. “Binary Linear Codes with Optimal Scaling: Polar Codes with Large Kernels.” IEEE Transactions on Information Theory. IEEE, 2021. https://doi.org/10.1109/TIT.2020.3038806.","ama":"Fazeli A, Hassani H, Mondelli M, Vardy A. Binary linear codes with optimal scaling: Polar codes with large kernels. IEEE Transactions on Information Theory. 2021;67(9):5693-5710. doi:10.1109/TIT.2020.3038806","ista":"Fazeli A, Hassani H, Mondelli M, Vardy A. 2021. Binary linear codes with optimal scaling: Polar codes with large kernels. IEEE Transactions on Information Theory. 67(9), 5693–5710.","ieee":"A. Fazeli, H. Hassani, M. Mondelli, and A. Vardy, “Binary linear codes with optimal scaling: Polar codes with large kernels,” IEEE Transactions on Information Theory, vol. 67, no. 9. IEEE, pp. 5693–5710, 2021.","apa":"Fazeli, A., Hassani, H., Mondelli, M., & Vardy, A. (2021). Binary linear codes with optimal scaling: Polar codes with large kernels. IEEE Transactions on Information Theory. IEEE. https://doi.org/10.1109/TIT.2020.3038806"},"article_type":"original","page":"5693-5710","day":"01","article_processing_charge":"No","scopus_import":"1","oa_version":"Preprint","_id":"9002","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Binary linear codes with optimal scaling: Polar codes with large kernels","intvolume":" 67","abstract":[{"lang":"eng","text":" We prove that, for the binary erasure channel (BEC), the polar-coding paradigm gives rise to codes that not only approach the Shannon limit but do so under the best possible scaling of their block length as a function of the gap to capacity. This result exhibits the first known family of binary codes that attain both optimal scaling and quasi-linear complexity of encoding and decoding. Our proof is based on the construction and analysis of binary polar codes with large kernels. When communicating reliably at rates within ε>0 of capacity, the code length n often scales as O(1/εμ), where the constant μ is called the scaling exponent. It is known that the optimal scaling exponent is μ=2, and it is achieved by random linear codes. The scaling exponent of conventional polar codes (based on the 2×2 kernel) on the BEC is μ=3.63. This falls far short of the optimal scaling guaranteed by random codes. Our main contribution is a rigorous proof of the following result: for the BEC, there exist ℓ×ℓ binary kernels, such that polar codes constructed from these kernels achieve scaling exponent μ(ℓ) that tends to the optimal value of 2 as ℓ grows. We furthermore characterize precisely how large ℓ needs to be as a function of the gap between μ(ℓ) and 2. The resulting binary codes maintain the recursive structure of conventional polar codes, and thereby achieve construction complexity O(n) and encoding/decoding complexity O(nlogn)."}],"issue":"9","type":"journal_article"},{"oa_version":"Published Version","file":[{"checksum":"f0a7745d48afa09ea7025e876a0145a8","success":1,"date_updated":"2020-11-24T13:11:39Z","date_created":"2020-11-24T13:11:39Z","relation":"main_file","file_id":"8800","content_type":"application/pdf","file_size":2527276,"creator":"dernst","access_level":"open_access","file_name":"2020_WIREs_DevBio_KuzmiczKowalska.pdf"}],"status":"public","ddc":["570"],"title":"Regulation of size and scale in vertebrate spinal cord development","_id":"7883","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"All vertebrates have a spinal cord with dimensions and shape specific to their species. Yet how species‐specific organ size and shape are achieved is a fundamental unresolved question in biology. The formation and sculpting of organs begins during embryonic development. As it develops, the spinal cord extends in anterior–posterior direction in synchrony with the overall growth of the body. The dorsoventral (DV) and apicobasal lengths of the spinal cord neuroepithelium also change, while at the same time a characteristic pattern of neural progenitor subtypes along the DV axis is established and elaborated. At the basis of these changes in tissue size and shape are biophysical determinants, such as the change in cell number, cell size and shape, and anisotropic tissue growth. These processes are controlled by global tissue‐scale regulators, such as morphogen signaling gradients as well as mechanical forces. Current challenges in the field are to uncover how these tissue‐scale regulatory mechanisms are translated to the cellular and molecular level, and how regulation of distinct cellular processes gives rise to an overall defined size. Addressing these questions will help not only to achieve a better understanding of how size is controlled, but also of how tissue size is coordinated with the specification of pattern."}],"type":"journal_article","date_published":"2021-04-15T00:00:00Z","article_type":"original","citation":{"ama":"Kuzmicz-Kowalska K, Kicheva A. Regulation of size and scale in vertebrate spinal cord development. Wiley Interdisciplinary Reviews: Developmental Biology. 2021. doi:10.1002/wdev.383","ista":"Kuzmicz-Kowalska K, Kicheva A. 2021. Regulation of size and scale in vertebrate spinal cord development. Wiley Interdisciplinary Reviews: Developmental Biology., e383.","ieee":"K. Kuzmicz-Kowalska and A. Kicheva, “Regulation of size and scale in vertebrate spinal cord development,” Wiley Interdisciplinary Reviews: Developmental Biology. Wiley, 2021.","apa":"Kuzmicz-Kowalska, K., & Kicheva, A. (2021). Regulation of size and scale in vertebrate spinal cord development. Wiley Interdisciplinary Reviews: Developmental Biology. Wiley. https://doi.org/10.1002/wdev.383","mla":"Kuzmicz-Kowalska, Katarzyna, and Anna Kicheva. “Regulation of Size and Scale in Vertebrate Spinal Cord Development.” Wiley Interdisciplinary Reviews: Developmental Biology, e383, Wiley, 2021, doi:10.1002/wdev.383.","short":"K. Kuzmicz-Kowalska, A. Kicheva, Wiley Interdisciplinary Reviews: Developmental Biology (2021).","chicago":"Kuzmicz-Kowalska, Katarzyna, and Anna Kicheva. “Regulation of Size and Scale in Vertebrate Spinal Cord Development.” Wiley Interdisciplinary Reviews: Developmental Biology. Wiley, 2021. https://doi.org/10.1002/wdev.383."},"publication":"Wiley Interdisciplinary Reviews: Developmental Biology","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"15","scopus_import":"1","date_updated":"2024-03-07T15:03:00Z","date_created":"2020-05-24T22:01:00Z","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"14323"}]},"author":[{"last_name":"Kuzmicz-Kowalska","first_name":"Katarzyna","id":"4CED352A-F248-11E8-B48F-1D18A9856A87","full_name":"Kuzmicz-Kowalska, Katarzyna"},{"first_name":"Anna","last_name":"Kicheva","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4509-4998","full_name":"Kicheva, Anna"}],"department":[{"_id":"AnKi"}],"publisher":"Wiley","publication_status":"published","pmid":1,"acknowledgement":"Austrian Academy of Sciences, Grant/Award Number: DOC fellowship for Katarzyna Kuzmicz-Kowalska; Austrian Science Fund, Grant/Award Number: F78 (Stem Cell Modulation); H2020 European Research Council, Grant/Award Number: 680037","year":"2021","ec_funded":1,"file_date_updated":"2020-11-24T13:11:39Z","article_number":"e383","language":[{"iso":"eng"}],"doi":"10.1002/wdev.383","project":[{"name":"Coordination of Patterning And Growth In the Spinal Cord","call_identifier":"H2020","_id":"B6FC0238-B512-11E9-945C-1524E6697425","grant_number":"680037"},{"_id":"267AF0E4-B435-11E9-9278-68D0E5697425","name":"The role of morphogens in the regulation of neural tube growth"},{"_id":"059DF620-7A3F-11EA-A408-12923DDC885E","grant_number":"F07802","name":"Morphogen control of growth and pattern in the spinal cord"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000531419400001"],"pmid":["32391980"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"publication_identifier":{"issn":["17597684"],"eissn":["17597692"]},"month":"04"},{"page":"1166-1198","article_type":"original","citation":{"chicago":"Brown, Adam, and Bei Wang. “Sheaf-Theoretic Stratification Learning from Geometric and Topological Perspectives.” Discrete and Computational Geometry. Springer Nature, 2021. https://doi.org/10.1007/s00454-020-00206-y.","mla":"Brown, Adam, and Bei Wang. “Sheaf-Theoretic Stratification Learning from Geometric and Topological Perspectives.” Discrete and Computational Geometry, vol. 65, Springer Nature, 2021, pp. 1166–98, doi:10.1007/s00454-020-00206-y.","short":"A. Brown, B. Wang, Discrete and Computational Geometry 65 (2021) 1166–1198.","ista":"Brown A, Wang B. 2021. Sheaf-theoretic stratification learning from geometric and topological perspectives. Discrete and Computational Geometry. 65, 1166–1198.","ieee":"A. Brown and B. Wang, “Sheaf-theoretic stratification learning from geometric and topological perspectives,” Discrete and Computational Geometry, vol. 65. Springer Nature, pp. 1166–1198, 2021.","apa":"Brown, A., & Wang, B. (2021). Sheaf-theoretic stratification learning from geometric and topological perspectives. Discrete and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-020-00206-y","ama":"Brown A, Wang B. Sheaf-theoretic stratification learning from geometric and topological perspectives. Discrete and Computational Geometry. 2021;65:1166-1198. doi:10.1007/s00454-020-00206-y"},"publication":"Discrete and Computational Geometry","date_published":"2021-06-01T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"01","intvolume":" 65","status":"public","title":"Sheaf-theoretic stratification learning from geometric and topological perspectives","ddc":["510"],"_id":"7905","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","file":[{"date_updated":"2020-11-25T09:06:41Z","date_created":"2020-11-25T09:06:41Z","checksum":"487a84ea5841b75f04f66d7ebd71b67e","success":1,"relation":"main_file","file_id":"8803","content_type":"application/pdf","file_size":1013730,"creator":"dernst","file_name":"2020_DiscreteCompGeometry_Brown.pdf","access_level":"open_access"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"We investigate a sheaf-theoretic interpretation of stratification learning from geometric and topological perspectives. Our main result is the construction of stratification learning algorithms framed in terms of a sheaf on a partially ordered set with the Alexandroff topology. We prove that the resulting decomposition is the unique minimal stratification for which the strata are homogeneous and the given sheaf is constructible. In particular, when we choose to work with the local homology sheaf, our algorithm gives an alternative to the local homology transfer algorithm given in Bendich et al. (Proceedings of the 23rd Annual ACM-SIAM Symposium on Discrete Algorithms, pp. 1355–1370, ACM, New York, 2012), and the cohomology stratification algorithm given in Nanda (Found. Comput. Math. 20(2), 195–222, 2020). Additionally, we give examples of stratifications based on the geometric techniques of Breiding et al. (Rev. Mat. Complut. 31(3), 545–593, 2018), illustrating how the sheaf-theoretic approach can be used to study stratifications from both topological and geometric perspectives. This approach also points toward future applications of sheaf theory in the study of topological data analysis by illustrating the utility of the language of sheaf theory in generalizing existing algorithms."}],"project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000536324700001"],"arxiv":["1712.07734"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/s00454-020-00206-y","publication_identifier":{"eissn":["1432-0444"],"issn":["0179-5376"]},"month":"06","publisher":"Springer Nature","department":[{"_id":"HeEd"}],"publication_status":"published","year":"2021","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). This work was partially supported by NSF IIS-1513616 and NSF ABI-1661375. The authors would like to thank the anonymous referees for their insightful comments.","volume":65,"date_created":"2020-05-30T10:26:04Z","date_updated":"2024-03-07T15:01:58Z","author":[{"last_name":"Brown","first_name":"Adam","id":"70B7FDF6-608D-11E9-9333-8535E6697425","full_name":"Brown, Adam"},{"first_name":"Bei","last_name":"Wang","full_name":"Wang, Bei"}],"file_date_updated":"2020-11-25T09:06:41Z"},{"month":"02","publication_identifier":{"eissn":["14322064"],"issn":["01788051"]},"language":[{"iso":"eng"}],"doi":"10.1007/s00440-020-01003-7","quality_controlled":"1","isi":1,"project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"},{"grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"arxiv":["1908.00969"],"isi":["000572724600002"]},"file_date_updated":"2020-10-05T14:53:40Z","ec_funded":1,"date_updated":"2024-03-07T15:07:53Z","date_created":"2020-10-04T22:01:37Z","author":[{"orcid":"0000-0002-4901-7992","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","last_name":"Cipolloni","first_name":"Giorgio","full_name":"Cipolloni, Giorgio"},{"full_name":"Erdös, László","first_name":"László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603"},{"first_name":"Dominik J","last_name":"Schröder","id":"408ED176-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2904-1856","full_name":"Schröder, Dominik J"}],"publication_status":"published","department":[{"_id":"LaEr"}],"publisher":"Springer Nature","year":"2021","day":"01","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","scopus_import":"1","date_published":"2021-02-01T00:00:00Z","article_type":"original","publication":"Probability Theory and Related Fields","citation":{"ista":"Cipolloni G, Erdös L, Schröder DJ. 2021. Edge universality for non-Hermitian random matrices. Probability Theory and Related Fields.","apa":"Cipolloni, G., Erdös, L., & Schröder, D. J. (2021). Edge universality for non-Hermitian random matrices. Probability Theory and Related Fields. Springer Nature. https://doi.org/10.1007/s00440-020-01003-7","ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “Edge universality for non-Hermitian random matrices,” Probability Theory and Related Fields. Springer Nature, 2021.","ama":"Cipolloni G, Erdös L, Schröder DJ. Edge universality for non-Hermitian random matrices. Probability Theory and Related Fields. 2021. doi:10.1007/s00440-020-01003-7","chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Edge Universality for Non-Hermitian Random Matrices.” Probability Theory and Related Fields. Springer Nature, 2021. https://doi.org/10.1007/s00440-020-01003-7.","mla":"Cipolloni, Giorgio, et al. “Edge Universality for Non-Hermitian Random Matrices.” Probability Theory and Related Fields, Springer Nature, 2021, doi:10.1007/s00440-020-01003-7.","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Probability Theory and Related Fields (2021)."},"abstract":[{"lang":"eng","text":"We consider large non-Hermitian real or complex random matrices X with independent, identically distributed centred entries. We prove that their local eigenvalue statistics near the spectral edge, the unit circle, coincide with those of the Ginibre ensemble, i.e. when the matrix elements of X are Gaussian. This result is the non-Hermitian counterpart of the universality of the Tracy–Widom distribution at the spectral edges of the Wigner ensemble."}],"type":"journal_article","oa_version":"Published Version","file":[{"creator":"dernst","file_size":497032,"content_type":"application/pdf","access_level":"open_access","file_name":"2020_ProbTheory_Cipolloni.pdf","success":1,"checksum":"611ae28d6055e1e298d53a57beb05ef4","date_updated":"2020-10-05T14:53:40Z","date_created":"2020-10-05T14:53:40Z","file_id":"8612","relation":"main_file"}],"ddc":["510"],"status":"public","title":"Edge universality for non-Hermitian random matrices","_id":"8601","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"date_published":"2021-09-01T00:00:00Z","page":"2109-2126","article_type":"original","citation":{"ista":"Shehu Y, Gibali A. 2021. New inertial relaxed method for solving split feasibilities. Optimization Letters. 15, 2109–2126.","apa":"Shehu, Y., & Gibali, A. (2021). New inertial relaxed method for solving split feasibilities. Optimization Letters. Springer Nature. https://doi.org/10.1007/s11590-020-01603-1","ieee":"Y. Shehu and A. Gibali, “New inertial relaxed method for solving split feasibilities,” Optimization Letters, vol. 15. Springer Nature, pp. 2109–2126, 2021.","ama":"Shehu Y, Gibali A. New inertial relaxed method for solving split feasibilities. Optimization Letters. 2021;15:2109-2126. doi:10.1007/s11590-020-01603-1","chicago":"Shehu, Yekini, and Aviv Gibali. “New Inertial Relaxed Method for Solving Split Feasibilities.” Optimization Letters. Springer Nature, 2021. https://doi.org/10.1007/s11590-020-01603-1.","mla":"Shehu, Yekini, and Aviv Gibali. “New Inertial Relaxed Method for Solving Split Feasibilities.” Optimization Letters, vol. 15, Springer Nature, 2021, pp. 2109–26, doi:10.1007/s11590-020-01603-1.","short":"Y. Shehu, A. Gibali, Optimization Letters 15 (2021) 2109–2126."},"publication":"Optimization Letters","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"01","scopus_import":"1","oa_version":"Published Version","file":[{"checksum":"63c5f31cd04626152a19f97a2476281b","success":1,"date_created":"2024-03-07T14:58:51Z","date_updated":"2024-03-07T14:58:51Z","relation":"main_file","file_id":"15089","file_size":2148882,"content_type":"application/pdf","creator":"kschuh","access_level":"open_access","file_name":"2021_OptimizationLetters_Shehu.pdf"}],"intvolume":" 15","status":"public","title":"New inertial relaxed method for solving split feasibilities","ddc":["510"],"_id":"7925","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"In this paper, we introduce a relaxed CQ method with alternated inertial step for solving split feasibility problems. We give convergence of the sequence generated by our method under some suitable assumptions. Some numerical implementations from sparse signal and image deblurring are reported to show the efficiency of our method."}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1007/s11590-020-01603-1","project":[{"call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice","_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000537342300001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"publication_identifier":{"eissn":["1862-4480"],"issn":["1862-4472"]},"month":"09","volume":15,"date_created":"2020-06-04T11:28:33Z","date_updated":"2024-03-07T15:00:43Z","author":[{"full_name":"Shehu, Yekini","orcid":"0000-0001-9224-7139","id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87","last_name":"Shehu","first_name":"Yekini"},{"first_name":"Aviv","last_name":"Gibali","full_name":"Gibali, Aviv"}],"department":[{"_id":"VlKo"}],"publisher":"Springer Nature","publication_status":"published","year":"2021","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). The authors are grateful to the referees for their insightful comments which have improved the earlier version of the manuscript greatly. The first 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).","ec_funded":1,"file_date_updated":"2024-03-07T14:58:51Z"},{"oa_version":"Submitted Version","file":[{"content_type":"application/pdf","file_size":38574802,"creator":"cziletti","file_name":"VandaeletalAuthorVersion2021.pdf","access_level":"open_access","date_created":"2021-07-08T12:27:55Z","date_updated":"2021-12-02T23:30:05Z","checksum":"7eb580abd8893cdb0b410cf41bc8c263","relation":"main_file","file_id":"9639","embargo":"2021-12-01"}],"ddc":["570"],"status":"public","title":"Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses","intvolume":" 16","_id":"9438","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"Rigorous investigation of synaptic transmission requires analysis of unitary synaptic events by simultaneous recording from presynaptic terminals and postsynaptic target neurons. However, this has been achieved at only a limited number of model synapses, including the squid giant synapse and the mammalian calyx of Held. Cortical presynaptic terminals have been largely inaccessible to direct presynaptic recording, due to their small size. Here, we describe a protocol for improved subcellular patch-clamp recording in rat and mouse brain slices, with the synapse in a largely intact environment. Slice preparation takes ~2 h, recording ~3 h and post hoc morphological analysis 2 d. Single presynaptic hippocampal mossy fiber terminals are stimulated minimally invasively in the bouton-attached configuration, in which the cytoplasmic content remains unperturbed, or in the whole-bouton configuration, in which the cytoplasmic composition can be precisely controlled. Paired pre–postsynaptic recordings can be integrated with biocytin labeling and morphological analysis, allowing correlative investigation of synapse structure and function. Paired recordings can be obtained from mossy fiber terminals in slices from both rats and mice, implying applicability to genetically modified synapses. Paired recordings can also be performed together with axon tract stimulation or optogenetic activation, allowing comparison of unitary and compound synaptic events in the same target cell. Finally, paired recordings can be combined with spontaneous event analysis, permitting collection of miniature events generated at a single identified synapse. In conclusion, the subcellular patch-clamp techniques detailed here should facilitate analysis of biophysics, plasticity and circuit function of cortical synapses in the mammalian central nervous system."}],"issue":"6","type":"journal_article","date_published":"2021-06-01T00:00:00Z","article_type":"original","page":"2947–2967","publication":"Nature Protocols","citation":{"ista":"Vandael DH, Okamoto Y, Borges Merjane C, Vargas Barroso VM, Suter B, Jonas PM. 2021. Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses. Nature Protocols. 16(6), 2947–2967.","ieee":"D. H. Vandael, Y. Okamoto, C. Borges Merjane, V. M. Vargas Barroso, B. Suter, and P. M. Jonas, “Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses,” Nature Protocols, vol. 16, no. 6. Springer Nature, pp. 2947–2967, 2021.","apa":"Vandael, D. H., Okamoto, Y., Borges Merjane, C., Vargas Barroso, V. M., Suter, B., & Jonas, P. M. (2021). Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses. Nature Protocols. Springer Nature. https://doi.org/10.1038/s41596-021-00526-0","ama":"Vandael DH, Okamoto Y, Borges Merjane C, Vargas Barroso VM, Suter B, Jonas PM. Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses. Nature Protocols. 2021;16(6):2947–2967. doi:10.1038/s41596-021-00526-0","chicago":"Vandael, David H, Yuji Okamoto, Carolina Borges Merjane, Victor M Vargas Barroso, Benjamin Suter, and Peter M Jonas. “Subcellular Patch-Clamp Techniques for Single-Bouton Stimulation and Simultaneous Pre- and Postsynaptic Recording at Cortical Synapses.” Nature Protocols. Springer Nature, 2021. https://doi.org/10.1038/s41596-021-00526-0.","mla":"Vandael, David H., et al. “Subcellular Patch-Clamp Techniques for Single-Bouton Stimulation and Simultaneous Pre- and Postsynaptic Recording at Cortical Synapses.” Nature Protocols, vol. 16, no. 6, Springer Nature, 2021, pp. 2947–2967, doi:10.1038/s41596-021-00526-0.","short":"D.H. Vandael, Y. Okamoto, C. Borges Merjane, V.M. Vargas Barroso, B. Suter, P.M. Jonas, Nature Protocols 16 (2021) 2947–2967."},"day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_created":"2021-05-30T22:01:24Z","date_updated":"2023-08-10T22:30:51Z","volume":16,"author":[{"full_name":"Vandael, David H","first_name":"David H","last_name":"Vandael","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7577-1676"},{"full_name":"Okamoto, Yuji","first_name":"Yuji","last_name":"Okamoto","id":"3337E116-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0408-6094"},{"full_name":"Borges Merjane, Carolina","orcid":"0000-0003-0005-401X","id":"4305C450-F248-11E8-B48F-1D18A9856A87","last_name":"Borges Merjane","first_name":"Carolina"},{"full_name":"Vargas Barroso, Victor M","id":"2F55A9DE-F248-11E8-B48F-1D18A9856A87","last_name":"Vargas Barroso","first_name":"Victor M"},{"last_name":"Suter","first_name":"Benjamin","orcid":"0000-0002-9885-6936","id":"4952F31E-F248-11E8-B48F-1D18A9856A87","full_name":"Suter, Benjamin"},{"full_name":"Jonas, Peter M","last_name":"Jonas","first_name":"Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","department":[{"_id":"PeJo"}],"publisher":"Springer Nature","year":"2021","acknowledgement":"This project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 692692 to P.J.) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award to P.J., V 739-B27 to C.B.M.). We are grateful to F. Marr and C. Altmutter for excellent technical assistance and cell reconstruction, E. Kralli-Beller for manuscript editing, and the Scientific Service Units of IST Austria, especially T. Asenov and Miba machine shop, for maximally efficient support.","pmid":1,"file_date_updated":"2021-12-02T23:30:05Z","ec_funded":1,"acknowledged_ssus":[{"_id":"M-Shop"}],"language":[{"iso":"eng"}],"doi":"10.1038/s41596-021-00526-0","quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","grant_number":"692692","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"_id":"25C5A090-B435-11E9-9278-68D0E5697425","grant_number":"Z00312","call_identifier":"FWF","name":"The Wittgenstein Prize"},{"name":"Structural plasticity at mossy fiber-CA3 synapses","call_identifier":"FWF","grant_number":"V00739","_id":"2696E7FE-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000650528700003"],"pmid":["33990799"]},"oa":1,"month":"06","publication_identifier":{"issn":["17542189"],"eissn":["17502799"]}},{"status":"public","ddc":["575"],"title":"Wound healing in the Arabidopsis root meristem","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"9992","file":[{"relation":"source_file","file_id":"9993","checksum":"c763064adaa720e16066c1a4f9682bbb","date_created":"2021-09-09T07:29:48Z","date_updated":"2021-09-15T22:30:26Z","access_level":"closed","embargo_to":"open_access","file_name":"Thesis_vupload.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":25179004,"creator":"lhoermaye"},{"relation":"main_file","file_id":"9996","embargo":"2021-09-09","date_updated":"2021-09-15T22:30:26Z","date_created":"2021-09-09T14:25:08Z","checksum":"53911b06e93d7cdbbf4c7f4c162fa70f","file_name":"Thesis_vfinal_pdfa.pdf","access_level":"open_access","content_type":"application/pdf","file_size":6246900,"creator":"lhoermaye"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"lang":"eng","text":"Blood – this is what animals use to heal wounds fast and efficient. Plants do not have blood circulation and their cells cannot move. However, plants have evolved remarkable capacities to regenerate tissues and organs preventing further damage. In my PhD research, I studied the wound healing in the Arabidopsis root. I used a UV laser to ablate single cells in the root tip and observed the consequent wound healing. Interestingly, the inner adjacent cells induced a\r\ndivision plane switch and subsequently adopted the cell type of the killed cell to replace it. We termed this form of wound healing “restorative divisions”. This initial observation triggered the questions of my PhD studies: How and why do cells orient their division planes, how do they feel the wound and why does this happen only in inner adjacent cells.\r\nFor answering these questions, I used a quite simple experimental setup: 5 day - old seedlings were stained with propidium iodide to visualize cell walls and dead cells; ablation was carried out using a special laser cutter and a confocal microscope. Adaptation of the novel vertical microscope system made it possible to observe wounds in real time. This revealed that restorative divisions occur at increased frequency compared to normal divisions. Additionally,\r\nthe major plant hormone auxin accumulates in wound adjacent cells and drives the expression of the wound-stress responsive transcription factor ERF115. Using this as a marker gene for wound responses, we found that an important part of wound signalling is the sensing of the collapse of the ablated cell. The collapse causes a radical pressure drop, which results in strong tissue deformations. These deformations manifest in an invasion of the now free spot specifically by the inner adjacent cells within seconds, probably because of higher pressure of the inner tissues. Long-term imaging revealed that those deformed cells continuously expand towards the wound hole and that this is crucial for the restorative division. These wound-expanding cells exhibit an abnormal, biphasic polarity of microtubule arrays\r\nbefore the division. Experiments inhibiting cell expansion suggest that it is the biphasic stretching that induces those MT arrays. Adapting the micromanipulator aspiration system from animal scientists at our institute confirmed the hypothesis that stretching influences microtubule stability. In conclusion, this shows that microtubules react to tissue deformation\r\nand this facilitates the observed division plane switch. This puts mechanical cues and tensions at the most prominent position for explaining the growth and wound healing properties of plants. Hence, it shines light onto the importance of understanding mechanical signal transduction. "}],"page":"168","citation":{"ama":"Hörmayer L. Wound healing in the Arabidopsis root meristem. 2021. doi:10.15479/at:ista:9992","ista":"Hörmayer L. 2021. Wound healing in the Arabidopsis root meristem. Institute of Science and Technology Austria.","apa":"Hörmayer, L. (2021). Wound healing in the Arabidopsis root meristem. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9992","ieee":"L. Hörmayer, “Wound healing in the Arabidopsis root meristem,” Institute of Science and Technology Austria, 2021.","mla":"Hörmayer, Lukas. Wound Healing in the Arabidopsis Root Meristem. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9992.","short":"L. Hörmayer, Wound Healing in the Arabidopsis Root Meristem, Institute of Science and Technology Austria, 2021.","chicago":"Hörmayer, Lukas. “Wound Healing in the Arabidopsis Root Meristem.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9992."},"date_published":"2021-09-13T00:00:00Z","article_processing_charge":"No","has_accepted_license":"1","day":"13","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"publication_status":"published","year":"2021","date_created":"2021-09-09T07:37:20Z","date_updated":"2023-09-07T13:38:33Z","related_material":{"record":[{"id":"6351","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"6943"},{"id":"8002","status":"public","relation":"part_of_dissertation"}]},"author":[{"last_name":"Hörmayer","first_name":"Lukas","orcid":"0000-0001-8295-2926","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","full_name":"Hörmayer, Lukas"}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","ec_funded":1,"file_date_updated":"2021-09-15T22:30:26Z","project":[{"call_identifier":"FWF","name":"RNA-directed DNA methylation in plant development","grant_number":"P29988","_id":"262EF96E-B435-11E9-9278-68D0E5697425"},{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"language":[{"iso":"eng"}],"supervisor":[{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"degree_awarded":"PhD","doi":"10.15479/at:ista:9992","publication_identifier":{"issn":["2663-337X"]},"month":"09"},{"publication_status":"published","department":[{"_id":"PeJo"}],"publisher":"Springer Nature","year":"2021","acknowledgement":"We thank A. Aertsen, N. Kopell, W. Maass, A. Roth, F. Stella and T. Vogels for critically reading earlier versions of the manuscript. We are grateful to F. Marr and C. Altmutter for excellent technical assistance, E. Kralli-Beller for manuscript editing, and the Scientific Service Units of IST Austria for efficient support. Finally, we thank T. Carnevale, L. Erdös, M. Hines, D. Nykamp and D. Schröder for useful discussions, and R. Friedrich and S. Wiechert for sharing unpublished data. This project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 692692, P.J.) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award to P.J. and P 31815 to S.J.G.).","date_updated":"2023-08-10T22:30:10Z","date_created":"2022-03-04T08:32:36Z","volume":1,"author":[{"full_name":"Guzmán, José","orcid":"0000-0003-2209-5242","id":"30CC5506-F248-11E8-B48F-1D18A9856A87","last_name":"Guzmán","first_name":"José"},{"last_name":"Schlögl","first_name":"Alois","orcid":"0000-0002-5621-8100","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","full_name":"Schlögl, Alois"},{"full_name":"Espinoza Martinez, Claudia ","last_name":"Espinoza Martinez","first_name":"Claudia ","orcid":"0000-0003-4710-2082","id":"31FFEE2E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zhang, Xiaomin","first_name":"Xiaomin","last_name":"Zhang","id":"423EC9C2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Suter","first_name":"Benjamin","orcid":"0000-0002-9885-6936","id":"4952F31E-F248-11E8-B48F-1D18A9856A87","full_name":"Suter, Benjamin"},{"orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","first_name":"Peter M","full_name":"Jonas, Peter M"}],"related_material":{"record":[{"relation":"software","status":"public","id":"10110"}],"link":[{"relation":"press_release","url":"https://ista.ac.at/en/news/spot-the-difference/"}]},"file_date_updated":"2022-06-18T22:30:03Z","ec_funded":1,"quality_controlled":"1","project":[{"name":"Biophysics and circuit function of a giant cortical glumatergic synapse","call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","grant_number":"692692"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425"}],"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/647800","open_access":"1"}],"oa":1,"acknowledged_ssus":[{"_id":"SSU"}],"language":[{"iso":"eng"}],"doi":"10.1038/s43588-021-00157-1","month":"12","publication_identifier":{"issn":["2662-8457"]},"title":"How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network","ddc":["610"],"status":"public","intvolume":" 1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"10816","oa_version":"Submitted Version","file":[{"creator":"patrickd","file_size":1699466,"content_type":"application/pdf","file_name":"Guzmanetal2021.pdf","access_level":"open_access","date_created":"2022-06-02T12:51:07Z","date_updated":"2022-06-18T22:30:03Z","checksum":"9fec5b667909ef52be96d502e4f8c2ae","embargo":"2022-06-17","file_id":"11430","relation":"main_file"},{"relation":"supplementary_material","title":"Supplementary Material","file_id":"11431","embargo":"2022-06-17","date_updated":"2022-06-18T22:30:03Z","date_created":"2022-06-02T12:53:47Z","checksum":"52a005b13a114e3c3a28fa6bbe8b1a8d","file_name":"Guzmanetal2021Suppl.pdf","access_level":"open_access","file_size":3005651,"content_type":"application/pdf","creator":"patrickd"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Pattern separation is a fundamental brain computation that converts small differences in input patterns into large differences in output patterns. Several synaptic mechanisms of pattern separation have been proposed, including code expansion, inhibition and plasticity; however, which of these mechanisms play a role in the entorhinal cortex (EC)–dentate gyrus (DG)–CA3 circuit, a classical pattern separation circuit, remains unclear. Here we show that a biologically realistic, full-scale EC–DG–CA3 circuit model, including granule cells (GCs) and parvalbumin-positive inhibitory interneurons (PV+-INs) in the DG, is an efficient pattern separator. Both external gamma-modulated inhibition and internal lateral inhibition mediated by PV+-INs substantially contributed to pattern separation. Both local connectivity and fast signaling at GC–PV+-IN synapses were important for maximum effectiveness. Similarly, mossy fiber synapses with conditional detonator properties contributed to pattern separation. By contrast, perforant path synapses with Hebbian synaptic plasticity and direct EC–CA3 connection shifted the network towards pattern completion. Our results demonstrate that the specific properties of cells and synapses optimize higher-order computations in biological networks and might be useful to improve the deep learning capabilities of technical networks."}],"issue":"12","article_type":"original","page":"830-842","publication":"Nature Computational Science","citation":{"ama":"Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network. Nature Computational Science. 2021;1(12):830-842. doi:10.1038/s43588-021-00157-1","ista":"Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. 2021. 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Springer Nature. https://doi.org/10.1038/s43588-021-00157-1","mla":"Guzmán, José, et al. “How Connectivity Rules and Synaptic Properties Shape the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3 Network.” Nature Computational Science, vol. 1, no. 12, Springer Nature, 2021, pp. 830–42, doi:10.1038/s43588-021-00157-1.","short":"J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, P.M. Jonas, Nature Computational Science 1 (2021) 830–842.","chicago":"Guzmán, José, Alois Schlögl, Claudia Espinoza Martinez, Xiaomin Zhang, Benjamin Suter, and Peter M Jonas. “How Connectivity Rules and Synaptic Properties Shape the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3 Network.” Nature Computational Science. 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Several synaptic mechanisms of pattern separation have been proposed, including code expansion, inhibition and plasticity; however, which of these mechanisms play a role in the entorhinal cortex (EC)–dentate gyrus (DG)–CA3 circuit, a classical pattern separation circuit, remains unclear. Here we show that a biologically realistic, full-scale EC–DG–CA3 circuit model, including granule cells (GCs) and parvalbumin-positive inhibitory interneurons (PV+-INs) in the DG, is an efficient pattern separator. Both external gamma-modulated inhibition and internal lateral inhibition mediated by PV+-INs substantially contributed to pattern separation. Both local connectivity and fast signaling at GC–PV+-IN synapses were important for maximum effectiveness. Similarly, mossy fiber synapses with conditional detonator properties contributed to pattern separation. By contrast, perforant path synapses with Hebbian synaptic plasticity and direct EC–CA3 connection shifted the network towards pattern completion. Our results demonstrate that the specific properties of cells and synapses optimize higher-order computations in biological networks and might be useful to improve the deep learning capabilities of technical networks."}],"file_date_updated":"2021-10-08T08:46:04Z","license":"https://opensource.org/licenses/GPL-3.0"},{"publication_status":"submitted","title":"The structure of hippocampal CA1 interactions optimizes spatial coding across experience","status":"public","publisher":"Cold Spring Harbor Laboratory","department":[{"_id":"GradSch"},{"_id":"JoCs"},{"_id":"GaTk"}],"_id":"10077","acknowledgement":"We thank Peter Baracskay, Karola Kaefer and Hugo Malagon-Vina for the acquisition of the data. We thank Federico Stella for comments on an earlier version of the manuscript. MN was supported by European Union Horizon 2020 grant 665385, JC was supported by European Research Council consolidator grant 281511, GT was supported by the Austrian Science Fund (FWF) grant P34015, CS was supported by an IST fellow grant, National Institute of Mental Health Award 1R01MH125571-01, by the National Science Foundation under NSF Award No. 1922658 and a Google faculty award.","year":"2021","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2024-03-28T23:30:16Z","date_created":"2021-10-04T06:23:34Z","oa_version":"Preprint","author":[{"last_name":"Nardin","first_name":"Michele","orcid":"0000-0001-8849-6570","id":"30BD0376-F248-11E8-B48F-1D18A9856A87","full_name":"Nardin, Michele"},{"orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari","first_name":"Jozsef L","full_name":"Csicsvari, Jozsef L"},{"full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","first_name":"Gašper"},{"id":"3933349E-F248-11E8-B48F-1D18A9856A87","last_name":"Savin","first_name":"Cristina","full_name":"Savin, Cristina"}],"related_material":{"record":[{"id":"11932","status":"public","relation":"dissertation_contains"}]},"type":"preprint","abstract":[{"text":"Although much is known about how single neurons in the hippocampus represent an animal’s position, how cell-cell interactions contribute to spatial coding remains poorly understood. Using a novel statistical estimator and theoretical modeling, both developed in the framework of maximum entropy models, we reveal highly structured cell-to-cell interactions whose statistics depend on familiar vs. novel environment. In both conditions the circuit interactions optimize the encoding of spatial information, but for regimes that differ in the signal-to-noise ratio of their spatial inputs. Moreover, the topology of the interactions facilitates linear decodability, making the information easy to read out by downstream circuits. These findings suggest that the efficient coding hypothesis is not applicable only to individual neuron properties in the sensory periphery, but also to neural interactions in the central brain.","lang":"eng"}],"ec_funded":1,"project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program"},{"grant_number":"281511","_id":"257A4776-B435-11E9-9278-68D0E5697425","name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex","call_identifier":"FP7"},{"name":"Efficient coding with biophysical realism","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6","grant_number":"P34015"}],"publication":"bioRxiv","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2021.09.28.460602","open_access":"1"}],"citation":{"short":"M. Nardin, J.L. Csicsvari, G. Tkačik, C. Savin, BioRxiv (n.d.).","mla":"Nardin, Michele, et al. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” BioRxiv, Cold Spring Harbor Laboratory, doi:10.1101/2021.09.28.460602.","chicago":"Nardin, Michele, Jozsef L Csicsvari, Gašper Tkačik, and Cristina Savin. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” BioRxiv. Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/2021.09.28.460602.","ama":"Nardin M, Csicsvari JL, Tkačik G, Savin C. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. bioRxiv. doi:10.1101/2021.09.28.460602","ieee":"M. Nardin, J. L. Csicsvari, G. Tkačik, and C. Savin, “The structure of hippocampal CA1 interactions optimizes spatial coding across experience,” bioRxiv. Cold Spring Harbor Laboratory.","apa":"Nardin, M., Csicsvari, J. L., Tkačik, G., & Savin, C. (n.d.). The structure of hippocampal CA1 interactions optimizes spatial coding across experience. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2021.09.28.460602","ista":"Nardin M, Csicsvari JL, Tkačik G, Savin C. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. bioRxiv, 10.1101/2021.09.28.460602."},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1101/2021.09.28.460602","date_published":"2021-09-29T00:00:00Z","day":"29","month":"09","article_processing_charge":"No"},{"type":"journal_article","abstract":[{"lang":"eng","text":"Aprotic alkali metal–O2 batteries face two major obstacles to their chemistry occurring efficiently, the insulating nature of the formed alkali superoxides/peroxides and parasitic reactions that are caused by the highly reactive singlet oxygen (1O2). Redox mediators are recognized to be key for improving rechargeability. However, it is unclear how they affect 1O2 formation, which hinders strategies for their improvement. Here we clarify the mechanism of mediated peroxide and superoxide oxidation and thus explain how redox mediators either enhance or suppress 1O2 formation. We show that charging commences with peroxide oxidation to a superoxide intermediate and that redox potentials above ~3.5 V versus Li/Li+ drive 1O2 evolution from superoxide oxidation, while disproportionation always generates some 1O2. We find that 1O2 suppression requires oxidation to be faster than the generation of 1O2 from disproportionation. Oxidation rates decrease with growing driving force following Marcus inverted-region behaviour, establishing a region of maximum rate."}],"issue":"5","_id":"9250","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation","status":"public","ddc":["540"],"intvolume":" 13","oa_version":"Submitted Version","file":[{"file_name":"2021_NatureChem_Petit_acceptedVersion.pdf","access_level":"open_access","creator":"dernst","file_size":1811448,"content_type":"application/pdf","file_id":"9276","embargo":"2021-09-15","relation":"main_file","date_updated":"2021-09-16T22:30:03Z","date_created":"2021-03-22T11:46:00Z","checksum":"3ee3f8dd79ed1b7bb0929fce184c8012"}],"scopus_import":"1","keyword":["General Chemistry","General Chemical Engineering"],"day":"15","has_accepted_license":"1","article_processing_charge":"No","publication":"Nature Chemistry","citation":{"apa":"Petit, Y. K., Mourad, E., Prehal, C., Leypold, C., Windischbacher, A., Mijailovic, D., … Freunberger, S. A. (2021). Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation. Nature Chemistry. Springer Nature. https://doi.org/10.1038/s41557-021-00643-z","ieee":"Y. K. Petit et al., “Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation,” Nature Chemistry, vol. 13, no. 5. Springer Nature, pp. 465–471, 2021.","ista":"Petit YK, Mourad E, Prehal C, Leypold C, Windischbacher A, Mijailovic D, Slugovc C, Borisov SM, Zojer E, Brutti S, Fontaine O, Freunberger SA. 2021. Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation. Nature Chemistry. 13(5), 465–471.","ama":"Petit YK, Mourad E, Prehal C, et al. Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation. Nature Chemistry. 2021;13(5):465-471. doi:10.1038/s41557-021-00643-z","chicago":"Petit, Yann K., Eléonore Mourad, Christian Prehal, Christian Leypold, Andreas Windischbacher, Daniel Mijailovic, Christian Slugovc, et al. “Mechanism of Mediated Alkali Peroxide Oxidation and Triplet versus Singlet Oxygen Formation.” Nature Chemistry. Springer Nature, 2021. https://doi.org/10.1038/s41557-021-00643-z.","short":"Y.K. Petit, E. Mourad, C. Prehal, C. Leypold, A. Windischbacher, D. Mijailovic, C. Slugovc, S.M. Borisov, E. Zojer, S. Brutti, O. Fontaine, S.A. Freunberger, Nature Chemistry 13 (2021) 465–471.","mla":"Petit, Yann K., et al. “Mechanism of Mediated Alkali Peroxide Oxidation and Triplet versus Singlet Oxygen Formation.” Nature Chemistry, vol. 13, no. 5, Springer Nature, 2021, pp. 465–71, doi:10.1038/s41557-021-00643-z."},"article_type":"original","page":"465-471","date_published":"2021-03-15T00:00:00Z","file_date_updated":"2021-09-16T22:30:03Z","year":"2021","acknowledgement":"S.A.F. is indebted to the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 636069) as well as IST Austria. O.F thanks the French National Research Agency (STORE-EX Labex Project ANR-10-LABX-76-01). We thank EL-Cell GmbH (Hamburg, Germany) for the pressure test cell. We thank R. Saf for help with the mass spectrometry, J. Schlegl for manufacturing instrumentation, M. Winkler of Acib GmbH, G. Strohmeier and R. Fürst for HPLC measurements and S. Mondal and S. Stadlbauer for kinetic measurements.","pmid":1,"publication_status":"published","department":[{"_id":"StFr"}],"publisher":"Springer Nature","author":[{"full_name":"Petit, Yann K.","last_name":"Petit","first_name":"Yann K."},{"first_name":"Eléonore","last_name":"Mourad","full_name":"Mourad, Eléonore"},{"last_name":"Prehal","first_name":"Christian","full_name":"Prehal, Christian"},{"full_name":"Leypold, Christian","first_name":"Christian","last_name":"Leypold"},{"full_name":"Windischbacher, Andreas","last_name":"Windischbacher","first_name":"Andreas"},{"full_name":"Mijailovic, Daniel","last_name":"Mijailovic","first_name":"Daniel"},{"full_name":"Slugovc, Christian","last_name":"Slugovc","first_name":"Christian"},{"full_name":"Borisov, Sergey M.","first_name":"Sergey M.","last_name":"Borisov"},{"last_name":"Zojer","first_name":"Egbert","full_name":"Zojer, Egbert"},{"last_name":"Brutti","first_name":"Sergio","full_name":"Brutti, Sergio"},{"first_name":"Olivier","last_name":"Fontaine","full_name":"Fontaine, Olivier"},{"first_name":"Stefan Alexander","last_name":"Freunberger","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","orcid":"0000-0003-2902-5319","full_name":"Freunberger, Stefan Alexander"}],"date_updated":"2023-09-05T15:34:44Z","date_created":"2021-03-16T11:12:20Z","volume":13,"month":"03","publication_identifier":{"eissn":["1755-4349"],"issn":["1755-4330"]},"oa":1,"external_id":{"pmid":["33723377"],"isi":["000629296400001"]},"isi":1,"quality_controlled":"1","doi":"10.1038/s41557-021-00643-z","acknowledged_ssus":[{"_id":"M-Shop"}],"language":[{"iso":"eng"}]},{"date_created":"2021-07-01T14:50:17Z","date_updated":"2023-09-07T13:33:27Z","author":[{"id":"2F1E1758-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5223-3346","first_name":"Silvia","last_name":"Caballero Mancebo","full_name":"Caballero Mancebo, Silvia"}],"related_material":{"record":[{"id":"9750","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"9006"}]},"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"CaHe"}],"publisher":"Institute of Science and Technology Austria","year":"2021","file_date_updated":"2022-07-02T22:30:06Z","supervisor":[{"first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"NanoFab"},{"_id":"M-Shop"}],"language":[{"iso":"eng"}],"doi":"10.15479/at:ista:9623","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"month":"07","publication_identifier":{"isbn":["978-3-99078-012-1"],"issn":["2663-337X"]},"file":[{"relation":"source_file","file_id":"9624","checksum":"e039225a47ef32666d59bf35ddd30ecf","date_created":"2021-07-01T14:48:54Z","date_updated":"2022-07-02T22:30:06Z","access_level":"closed","embargo_to":"open_access","file_name":"PhDThesis_SCM.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":131946790,"creator":"scaballe"},{"embargo":"2022-07-01","file_id":"9625","relation":"main_file","checksum":"dd4d78962ea94ad95e97ca7d9af08f4b","date_updated":"2022-07-02T22:30:06Z","date_created":"2021-07-01T14:46:25Z","access_level":"open_access","file_name":"PhDThesis_SCM.pdf","creator":"scaballe","file_size":17094958,"content_type":"application/pdf"}],"oa_version":"Published Version","ddc":["570"],"title":"Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes","status":"public","_id":"9623","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"text":"Cytoplasmic reorganizations are essential for morphogenesis. In large cells like oocytes, these reorganizations become crucial in patterning the oocyte for later stages of embryonic development. Ascidians oocytes reorganize their cytoplasm (ooplasm) in a spectacular manner. Ooplasmic reorganization is initiated at fertilization with the contraction of the actomyosin cortex along the animal-vegetal axis of the oocyte, driving the accumulation of cortical endoplasmic reticulum (cER), maternal mRNAs associated to it and a mitochondria-rich subcortical layer – the myoplasm – in a region of the vegetal pole termed contraction pole (CP). Here we have used the species Phallusia mammillata to investigate the changes in cell shape that accompany these reorganizations and the mechanochemical mechanisms underlining CP formation.\r\nWe report that the length of the animal-vegetal (AV) axis oscillates upon fertilization: it first undergoes a cycle of fast elongation-lengthening followed by a slow expansion of mainly the vegetal pole (VP) of the cell. We show that the fast oscillation corresponds to a dynamic polarization of the actin cortex as a result of a fertilization-induced increase in cortical tension in the oocyte that triggers a rupture of the cortex at the animal pole and the establishment of vegetal-directed cortical flows. These flows are responsible for the vegetal accumulation of actin causing the VP to flatten. \r\nWe find that the slow expansion of the VP, leading to CP formation, correlates with a relaxation of the vegetal cortex and that the myoplasm plays a role in the expansion. We show that the myoplasm is a solid-like layer that buckles under compression forces arising from the contracting actin cortex at the VP. Straightening of the myoplasm when actin flows stops, facilitates the expansion of the VP and the CP. Altogether, our results present a previously unrecognized role for the myoplasm in ascidian ooplasmic segregation. \r\n","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","date_published":"2021-07-01T00:00:00Z","page":"111","citation":{"ama":"Caballero Mancebo S. Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes. 2021. doi:10.15479/at:ista:9623","ista":"Caballero Mancebo S. 2021. Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes. Institute of Science and Technology Austria.","apa":"Caballero Mancebo, S. (2021). Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9623","ieee":"S. Caballero Mancebo, “Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes,” Institute of Science and Technology Austria, 2021.","mla":"Caballero Mancebo, Silvia. Fertilization-Induced Deformations Are Controlled by the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9623.","short":"S. Caballero Mancebo, Fertilization-Induced Deformations Are Controlled by the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes, Institute of Science and Technology Austria, 2021.","chicago":"Caballero Mancebo, Silvia. “Fertilization-Induced Deformations Are Controlled by the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9623."},"article_processing_charge":"No","has_accepted_license":"1"},{"day":"25","article_processing_charge":"No","scopus_import":"1","date_published":"2021-01-25T00:00:00Z","article_type":"original","page":"P213-226","publication":"Developmental Cell","citation":{"mla":"Shamipour, Shayan, et al. “Cytoplasm’s Got Moves.” Developmental Cell, vol. 56, no. 2, Elsevier, 2021, pp. P213-226, doi:10.1016/j.devcel.2020.12.002.","short":"S. Shamipour, S. Caballero Mancebo, C.-P.J. Heisenberg, Developmental Cell 56 (2021) P213-226.","chicago":"Shamipour, Shayan, Silvia Caballero Mancebo, and Carl-Philipp J Heisenberg. “Cytoplasm’s Got Moves.” Developmental Cell. Elsevier, 2021. https://doi.org/10.1016/j.devcel.2020.12.002.","ama":"Shamipour S, Caballero Mancebo S, Heisenberg C-PJ. Cytoplasm’s got moves. Developmental Cell. 2021;56(2):P213-226. doi:10.1016/j.devcel.2020.12.002","ista":"Shamipour S, Caballero Mancebo S, Heisenberg C-PJ. 2021. Cytoplasm’s got moves. Developmental Cell. 56(2), P213-226.","ieee":"S. Shamipour, S. Caballero Mancebo, and C.-P. J. Heisenberg, “Cytoplasm’s got moves,” Developmental Cell, vol. 56, no. 2. Elsevier, pp. P213-226, 2021.","apa":"Shamipour, S., Caballero Mancebo, S., & Heisenberg, C.-P. J. (2021). Cytoplasm’s got moves. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2020.12.002"},"abstract":[{"text":"Cytoplasm is a gel-like crowded environment composed of various macromolecules, organelles, cytoskeletal networks, and cytosol. The structure of the cytoplasm is highly organized and heterogeneous due to the crowding of its constituents and their effective compartmentalization. In such an environment, the diffusive dynamics of the molecules are restricted, an effect that is further amplified by clustering and anchoring of molecules. Despite the crowded nature of the cytoplasm at the microscopic scale, large-scale reorganization of the cytoplasm is essential for important cellular functions, such as cell division and polarization. How such mesoscale reorganization of the cytoplasm is achieved, especially for large cells such as oocytes or syncytial tissues that can span hundreds of micrometers in size, is only beginning to be understood. In this review, we will discuss recent advances in elucidating the molecular, cellular, and biophysical mechanisms by which the cytoskeleton drives cytoplasmic reorganization across different scales, structures, and species.","lang":"eng"}],"issue":"2","type":"journal_article","oa_version":"Published Version","title":"Cytoplasm's got moves","status":"public","intvolume":" 56","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9006","month":"01","publication_identifier":{"issn":["15345807"],"eissn":["18781551"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.devcel.2020.12.002","isi":1,"quality_controlled":"1","external_id":{"pmid":["33321104"],"isi":["000613273900009"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.devcel.2020.12.002"}],"oa":1,"date_created":"2021-01-17T23:01:10Z","date_updated":"2024-03-28T23:30:19Z","volume":56,"author":[{"last_name":"Shamipour","first_name":"Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","full_name":"Shamipour, Shayan"},{"full_name":"Caballero Mancebo, Silvia","orcid":"0000-0002-5223-3346","id":"2F1E1758-F248-11E8-B48F-1D18A9856A87","last_name":"Caballero Mancebo","first_name":"Silvia"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"9623"}]},"publication_status":"published","department":[{"_id":"CaHe"}],"publisher":"Elsevier","acknowledgement":"We would like to thank Justine Renno for illustrations and Edouard Hannezo and members of the Heisenberg group for their comments on previous versions of the manuscript.","year":"2021","pmid":1},{"publication":"Nature Communications","citation":{"ista":"Morandell J, Schwarz LA, Basilico B, Tasciyan S, Dimchev GA, Nicolas A, Sommer CM, Kreuzinger C, Dotter C, Knaus L, Dobler Z, Cacci E, Schur FK, Danzl JG, Novarino G. 2021. Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. Nature Communications. 12(1), 3058.","apa":"Morandell, J., Schwarz, L. A., Basilico, B., Tasciyan, S., Dimchev, G. A., Nicolas, A., … Novarino, G. (2021). Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-23123-x","ieee":"J. Morandell et al., “Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development,” Nature Communications, vol. 12, no. 1. Springer Nature, 2021.","ama":"Morandell J, Schwarz LA, Basilico B, et al. Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-23123-x","chicago":"Morandell, Jasmin, Lena A Schwarz, Bernadette Basilico, Saren Tasciyan, Georgi A Dimchev, Armel Nicolas, Christoph M Sommer, et al. “Cul3 Regulates Cytoskeleton Protein Homeostasis and Cell Migration during a Critical Window of Brain Development.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-23123-x.","mla":"Morandell, Jasmin, et al. “Cul3 Regulates Cytoskeleton Protein Homeostasis and Cell Migration during a Critical Window of Brain Development.” Nature Communications, vol. 12, no. 1, 3058, Springer Nature, 2021, doi:10.1038/s41467-021-23123-x.","short":"J. Morandell, L.A. Schwarz, B. Basilico, S. Tasciyan, G.A. Dimchev, A. Nicolas, C.M. Sommer, C. Kreuzinger, C. Dotter, L. Knaus, Z. Dobler, E. Cacci, F.K. Schur, J.G. Danzl, G. Novarino, Nature Communications 12 (2021)."},"article_type":"original","date_published":"2021-05-24T00:00:00Z","keyword":["General Biochemistry","Genetics and Molecular Biology"],"day":"24","has_accepted_license":"1","article_processing_charge":"No","_id":"9429","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","ddc":["572"],"title":"Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development","intvolume":" 12","file":[{"date_updated":"2021-05-28T12:39:43Z","date_created":"2021-05-28T12:39:43Z","checksum":"337e0f7959c35ec959984cacdcb472ba","success":1,"relation":"main_file","file_id":"9430","content_type":"application/pdf","file_size":9358599,"creator":"kschuh","file_name":"2021_NatureCommunications_Morandell.pdf","access_level":"open_access"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"De novo loss of function mutations in the ubiquitin ligase-encoding gene Cullin3 lead to autism spectrum disorder (ASD). In mouse, constitutive haploinsufficiency leads to motor coordination deficits as well as ASD-relevant social and cognitive impairments. However, induction of Cul3 haploinsufficiency later in life does not lead to ASD-relevant behaviors, pointing to an important role of Cul3 during a critical developmental window. Here we show that Cul3 is essential to regulate neuronal migration and, therefore, constitutive Cul3 heterozygous mutant mice display cortical lamination abnormalities. At the molecular level, we found that Cul3 controls neuronal migration by tightly regulating the amount of Plastin3 (Pls3), a previously unrecognized player of neural migration. Furthermore, we found that Pls3 cell-autonomously regulates cell migration by regulating actin cytoskeleton organization, and its levels are inversely proportional to neural migration speed. Finally, we provide evidence that cellular phenotypes associated with autism-linked gene haploinsufficiency can be rescued by transcriptional activation of the intact allele in vitro, offering a proof of concept for a potential therapeutic approach for ASDs."}],"issue":"1","external_id":{"isi":["000658769900010"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"isi":1,"quality_controlled":"1","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"},{"call_identifier":"H2020","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","_id":"25444568-B435-11E9-9278-68D0E5697425","grant_number":"715508"},{"grant_number":"W1232-B24","_id":"2548AE96-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Molecular Drug Targets"},{"name":"Neural stem cells in autism and epilepsy","grant_number":"F07807","_id":"05A0D778-7A3F-11EA-A408-12923DDC885E"},{"call_identifier":"FWF","name":"Optical control of synaptic function via adhesion molecules","_id":"265CB4D0-B435-11E9-9278-68D0E5697425","grant_number":"I03600"}],"doi":"10.1038/s41467-021-23123-x","acknowledged_ssus":[{"_id":"PreCl"}],"language":[{"iso":"eng"}],"month":"05","publication_identifier":{"eissn":["2041-1723"]},"acknowledgement":"We thank A. Coll Manzano, F. Freeman, M. Ladron de Guevara, and A. Ç. Yahya for technical assistance, S. Deixler, A. Lepold, and A. Schlerka for the management of our animal colony, as well as M. Schunn and the Preclinical Facility team for technical assistance. We thank K. Heesom and her team at the University of Bristol Proteomics Facility for the proteomics sample preparation, data generation, and analysis support. We thank Y. B. Simon for kindly providing the plasmid for lentiviral labeling. Further, we thank M. Sixt for his advice regarding cell migration and the fruitful discussions. This work was supported by the ISTPlus postdoctoral fellowship (Grant Agreement No. 754411) to B.B., by the European Union’s Horizon 2020 research and innovation program (ERC) grant 715508 (REVERSEAUTISM), and by the Austrian Science Fund (FWF) to G.N. (DK W1232-B24 and SFB F7807-B) and to J.G.D (I3600-B27).","year":"2021","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"GaNo"},{"_id":"JoDa"},{"_id":"FlSc"},{"_id":"MiSi"},{"_id":"LifeSc"},{"_id":"Bio"}],"author":[{"first_name":"Jasmin","last_name":"Morandell","id":"4739D480-F248-11E8-B48F-1D18A9856A87","full_name":"Morandell, Jasmin"},{"id":"29A8453C-F248-11E8-B48F-1D18A9856A87","first_name":"Lena A","last_name":"Schwarz","full_name":"Schwarz, Lena A"},{"full_name":"Basilico, Bernadette","id":"36035796-5ACA-11E9-A75E-7AF2E5697425","orcid":"0000-0003-1843-3173","first_name":"Bernadette","last_name":"Basilico"},{"full_name":"Tasciyan, Saren","last_name":"Tasciyan","first_name":"Saren","orcid":"0000-0003-1671-393X","id":"4323B49C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Dimchev, Georgi A","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8370-6161","first_name":"Georgi A","last_name":"Dimchev"},{"last_name":"Nicolas","first_name":"Armel","id":"2A103192-F248-11E8-B48F-1D18A9856A87","full_name":"Nicolas, Armel"},{"last_name":"Sommer","first_name":"Christoph M","orcid":"0000-0003-1216-9105","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","full_name":"Sommer, Christoph M"},{"id":"382077BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kreuzinger","first_name":"Caroline","full_name":"Kreuzinger, Caroline"},{"full_name":"Dotter, Christoph","first_name":"Christoph","last_name":"Dotter","id":"4C66542E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9033-9096"},{"first_name":"Lisa","last_name":"Knaus","id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87","full_name":"Knaus, Lisa"},{"first_name":"Zoe","last_name":"Dobler","id":"D23090A2-9057-11EA-883A-A8396FC7A38F","full_name":"Dobler, Zoe"},{"full_name":"Cacci, Emanuele","first_name":"Emanuele","last_name":"Cacci"},{"full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","first_name":"Florian KM"},{"full_name":"Danzl, Johann G","last_name":"Danzl","first_name":"Johann G","orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia"}],"related_material":{"record":[{"id":"7800","status":"public","relation":"earlier_version"},{"id":"12401","status":"public","relation":"dissertation_contains"}],"link":[{"url":"https://ist.ac.at/en/news/defective-gene-slows-down-brain-cells/","relation":"press_release"}]},"date_created":"2021-05-28T11:49:46Z","date_updated":"2024-03-28T23:30:23Z","volume":12,"article_number":"3058","file_date_updated":"2021-05-28T12:39:43Z","ec_funded":1},{"date_created":"2021-09-30T07:53:49Z","date_updated":"2023-09-08T11:41:08Z","author":[{"last_name":"Jirovec","first_name":"Daniel","orcid":"0000-0002-7197-4801","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","full_name":"Jirovec, Daniel"}],"related_material":{"record":[{"id":"8831","status":"public","relation":"part_of_dissertation"},{"id":"10065","relation":"part_of_dissertation","status":"public"},{"id":"10066","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"8909"},{"status":"public","relation":"part_of_dissertation","id":"5816"}]},"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"GeKa"}],"publisher":"Institute of Science and Technology Austria","year":"2021","acknowledgement":"The author gratefully acknowledges support by the Austrian Science Fund (FWF), grants No P30207, and the Nomis foundation.","file_date_updated":"2022-12-20T23:30:07Z","supervisor":[{"full_name":"Katsaros, Georgios","last_name":"Katsaros","first_name":"Georgios","orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"language":[{"iso":"eng"}],"doi":"10.15479/at:ista:10058","project":[{"call_identifier":"FWF","name":"Hole spin orbit qubits in Ge quantum wells","_id":"2641CE5E-B435-11E9-9278-68D0E5697425","grant_number":"P30207"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"month":"10","publication_identifier":{"issn":["2663-337X"]},"oa_version":"Published Version","file":[{"file_id":"10061","relation":"source_file","checksum":"ad6bcb24083ed7c02baaf1885c9ea3d5","date_created":"2021-09-30T14:29:14Z","date_updated":"2022-12-20T23:30:07Z","access_level":"closed","file_name":"PHD_Thesis_Jirovec_Source.zip","embargo_to":"open_access","creator":"djirovec","content_type":"application/x-zip-compressed","file_size":32397600},{"relation":"main_file","embargo":"2022-10-06","file_id":"10087","date_updated":"2022-12-20T23:30:07Z","date_created":"2021-10-05T07:56:49Z","checksum":"5fbe08d4f66d1153e04c47971538fae8","file_name":"PHD_Thesis_pdfa2b_1.pdf","access_level":"open_access","content_type":"application/pdf","file_size":26910829,"creator":"djirovec"}],"status":"public","title":"Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases","ddc":["621","539"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"10058","abstract":[{"lang":"eng","text":"Quantum information and computation has become a vast field paved with opportunities for researchers and investors. As large multinational companies and international funds are heavily investing in quantum technologies it is still a question which platform is best suited for the task of realizing a scalable quantum processor. In this work we investigate hole spins in Ge quantum wells. These hold great promise as they possess several favorable properties: a small effective mass, a strong spin-orbit coupling, long relaxation time and an inherent immunity to hyperfine noise. All these characteristics helped Ge hole spin qubits to evolve from a single qubit to a fully entangled four qubit processor in only 3 years. Here, we investigated a qubit approach leveraging the large out-of-plane g-factors of heavy hole states in Ge quantum dots. We found this qubit to be reproducibly operable at extremely low magnetic field and at large speeds while maintaining coherence. This was possible because large differences of g-factors in adjacent dots can be achieved in the out-of-plane direction. In the in-plane direction the small g-factors, on the other hand, can be altered very effectively by the confinement potentials. Here, we found that this can even lead to a sign change of the g-factors. The resulting g-factor difference alters the dynamics of the system drastically and produces effects typically attributed to a spin-orbit induced spin-flip term. The investigations carried out in this thesis give further insights into the possibilities of holes in Ge and reveal new physical properties that need to be considered when designing future spin qubit experiments."}],"alternative_title":["ISTA Thesis"],"type":"dissertation","date_published":"2021-10-05T00:00:00Z","page":"151","citation":{"ista":"Jirovec D. 2021. Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases. Institute of Science and Technology Austria.","ieee":"D. Jirovec, “Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases,” Institute of Science and Technology Austria, 2021.","apa":"Jirovec, D. (2021). Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10058","ama":"Jirovec D. Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases. 2021. doi:10.15479/at:ista:10058","chicago":"Jirovec, Daniel. “Singlet-Triplet Qubits and Spin-Orbit Interaction in 2-Dimensional Ge Hole Gases.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10058.","mla":"Jirovec, Daniel. Singlet-Triplet Qubits and Spin-Orbit Interaction in 2-Dimensional Ge Hole Gases. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10058.","short":"D. Jirovec, Singlet-Triplet Qubits and Spin-Orbit Interaction in 2-Dimensional Ge Hole Gases, Institute of Science and Technology Austria, 2021."},"day":"05","article_processing_charge":"No","has_accepted_license":"1","keyword":["qubits","quantum computing","holes"]},{"author":[{"full_name":"Jirovec, Daniel","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7197-4801","first_name":"Daniel","last_name":"Jirovec"},{"last_name":"Hofmann","first_name":"Andrea C","id":"340F461A-F248-11E8-B48F-1D18A9856A87","full_name":"Hofmann, Andrea C"},{"first_name":"Andrea","last_name":"Ballabio","full_name":"Ballabio, Andrea"},{"full_name":"Mutter, Philipp M.","last_name":"Mutter","first_name":"Philipp M."},{"first_name":"Giulio","last_name":"Tavani","full_name":"Tavani, Giulio"},{"first_name":"Marc","last_name":"Botifoll","full_name":"Botifoll, Marc"},{"full_name":"Crippa, Alessandro","last_name":"Crippa","first_name":"Alessandro","orcid":"0000-0002-2968-611X","id":"1F2B21A2-F6E7-11E9-9B82-F7DBE5697425"},{"full_name":"Kukucka, Josip","first_name":"Josip","last_name":"Kukucka","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sagi","first_name":"Oliver","id":"71616374-A8E9-11E9-A7CA-09ECE5697425","full_name":"Sagi, Oliver"},{"full_name":"Martins, Frederico","id":"38F80F9A-1CB8-11EA-BC76-B49B3DDC885E","orcid":"0000-0003-2668-2401","first_name":"Frederico","last_name":"Martins"},{"full_name":"Saez Mollejo, Jaime","id":"e0390f72-f6e0-11ea-865d-862393336714","first_name":"Jaime","last_name":"Saez Mollejo"},{"full_name":"Prieto Gonzalez, Ivan","first_name":"Ivan","last_name":"Prieto Gonzalez","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7370-5357"},{"full_name":"Borovkov, Maksim","last_name":"Borovkov","first_name":"Maksim","id":"2ac7a0a2-3562-11eb-9256-fbd18ea55087"},{"last_name":"Arbiol","first_name":"Jordi","full_name":"Arbiol, Jordi"},{"first_name":"Daniel","last_name":"Chrastina","full_name":"Chrastina, Daniel"},{"last_name":"Isella","first_name":"Giovanni","full_name":"Isella, Giovanni"},{"full_name":"Katsaros, Georgios","last_name":"Katsaros","first_name":"Georgios","orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/quantum-computing-with-holes/"}],"record":[{"status":"public","relation":"research_data","id":"9323"},{"id":"10058","status":"public","relation":"dissertation_contains"}]},"date_updated":"2024-03-28T23:30:27Z","date_created":"2020-12-02T10:50:47Z","volume":20,"acknowledgement":"This research was supported by the Scientific Service Units of Institute of Science and Technology (IST) Austria through resources provided by the Miba Machine Shop and the nanofabrication facility, and was made possible with the support of the NOMIS Foundation. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under Marie Sklodowska-Curie grant agreements no. 844511 and no. 75441, and by the Austrian Science Fund FWF-P 30207 project. A.B. acknowledges support from the European Union Horizon 2020 FET project microSPIRE, no. 766955. M. Botifoll and J.A. acknowledge funding from Generalitat de Catalunya 2017 SGR 327. The Catalan Institute of Nanoscience and Nanotechnology (ICN2) is supported by the Severo Ochoa programme from the Spanish Ministery of Economy (MINECO) (grant no. SEV-2017-0706) and is funded by the Catalonian Research Centre (CERCA) Programme, Generalitat de Catalunya. Part of the present work has been performed within the framework of the Universitat Autónoma de Barcelona Materials Science PhD programme. Part of the HAADF scanning transmission electron microscopy was conducted in the Laboratorio de Microscopias Avanzadas at Instituto de Nanociencia de Aragon, Universidad de Zaragoza. ICN2 acknowledge support from the Spanish Superior Council of Scientific Research (CSIC) Research Platform on Quantum Technologies PTI-001. M.B. acknowledges funding from the Catalan Agency for Management of University and Research Grants (AGAUR) Generalitat de Catalunya formation of investigators (FI) PhD grant.","year":"2021","publication_status":"published","department":[{"_id":"GeKa"},{"_id":"NanoFab"},{"_id":"GradSch"}],"publisher":"Springer Nature","ec_funded":1,"doi":"10.1038/s41563-021-01022-2","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"language":[{"iso":"eng"}],"external_id":{"isi":["000657596400001"],"arxiv":["2011.13755"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/2011.13755","open_access":"1"}],"isi":1,"quality_controlled":"1","project":[{"_id":"26A151DA-B435-11E9-9278-68D0E5697425","grant_number":"844511","call_identifier":"H2020","name":"Majorana bound states in Ge/SiGe heterostructures"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"},{"name":"Hole spin orbit qubits in Ge quantum wells","call_identifier":"FWF","_id":"2641CE5E-B435-11E9-9278-68D0E5697425","grant_number":"P30207"},{"_id":"262116AA-B435-11E9-9278-68D0E5697425","name":"Hybrid Semiconductor - Superconductor Quantum Devices"}],"month":"08","publication_identifier":{"issn":["1476-1122"],"eissn":["1476-4660"]},"oa_version":"Preprint","_id":"8909","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"A singlet triplet hole spin qubit in planar Ge","intvolume":" 20","abstract":[{"lang":"eng","text":"Spin qubits are considered to be among the most promising candidates for building a quantum processor. Group IV hole spin qubits have moved into the focus of interest due to the ease of operation and compatibility with Si technology. In addition, Ge offers the option for monolithic superconductor-semiconductor integration. Here we demonstrate a hole spin qubit operating at fields below 10 mT, the critical field of Al, by exploiting the large out-of-plane hole g-factors in planar Ge and by encoding the qubit into the singlet-triplet states of a double quantum dot. We observe electrically controlled X and Z-rotations with tunable frequencies exceeding 100 MHz and dephasing times of 1μs which we extend beyond 15μs with echo techniques. These results show that Ge hole singlet triplet qubits outperform their electronic Si and GaAs based counterparts in speed and coherence, respectively. In addition, they are on par with Ge single spin qubits, but can be operated at much lower fields underlining their potential for on chip integration with superconducting technologies."}],"issue":"8","type":"journal_article","date_published":"2021-08-01T00:00:00Z","publication":"Nature Materials","citation":{"ista":"Jirovec D, Hofmann AC, Ballabio A, Mutter PM, Tavani G, Botifoll M, Crippa A, Kukucka J, Sagi O, Martins F, Saez Mollejo J, Prieto Gonzalez I, Borovkov M, Arbiol J, Chrastina D, Isella G, Katsaros G. 2021. A singlet triplet hole spin qubit in planar Ge. Nature Materials. 20(8), 1106–1112.","ieee":"D. Jirovec et al., “A singlet triplet hole spin qubit in planar Ge,” Nature Materials, vol. 20, no. 8. Springer Nature, pp. 1106–1112, 2021.","apa":"Jirovec, D., Hofmann, A. C., Ballabio, A., Mutter, P. M., Tavani, G., Botifoll, M., … Katsaros, G. (2021). A singlet triplet hole spin qubit in planar Ge. Nature Materials. Springer Nature. https://doi.org/10.1038/s41563-021-01022-2","ama":"Jirovec D, Hofmann AC, Ballabio A, et al. A singlet triplet hole spin qubit in planar Ge. Nature Materials. 2021;20(8):1106–1112. doi:10.1038/s41563-021-01022-2","chicago":"Jirovec, Daniel, Andrea C Hofmann, Andrea Ballabio, Philipp M. Mutter, Giulio Tavani, Marc Botifoll, Alessandro Crippa, et al. “A Singlet Triplet Hole Spin Qubit in Planar Ge.” Nature Materials. Springer Nature, 2021. https://doi.org/10.1038/s41563-021-01022-2.","mla":"Jirovec, Daniel, et al. “A Singlet Triplet Hole Spin Qubit in Planar Ge.” Nature Materials, vol. 20, no. 8, Springer Nature, 2021, pp. 1106–1112, doi:10.1038/s41563-021-01022-2.","short":"D. Jirovec, A.C. Hofmann, A. Ballabio, P.M. Mutter, G. Tavani, M. Botifoll, A. Crippa, J. Kukucka, O. Sagi, F. Martins, J. Saez Mollejo, I. Prieto Gonzalez, M. Borovkov, J. Arbiol, D. Chrastina, G. Isella, G. Katsaros, Nature Materials 20 (2021) 1106–1112."},"article_type":"original","page":"1106–1112","day":"01","article_processing_charge":"No","scopus_import":"1"},{"file_date_updated":"2022-05-21T22:30:04Z","date_created":"2021-05-17T12:31:30Z","date_updated":"2023-09-07T13:32:32Z","author":[{"full_name":"Huljev, Karla","id":"44C6F6A6-F248-11E8-B48F-1D18A9856A87","last_name":"Huljev","first_name":"Karla"}],"department":[{"_id":"CaHe"},{"_id":"GradSch"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2021","publication_identifier":{"issn":["2663-337X"]},"month":"05","language":[{"iso":"eng"}],"supervisor":[{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J"}],"degree_awarded":"PhD","doi":"10.15479/at:ista:9397","oa":1,"abstract":[{"text":"Accumulation of interstitial fluid (IF) between embryonic cells is a common phenomenon in vertebrate embryogenesis. Unlike other model systems, where these accumulations coalesce into a large central cavity – the blastocoel, in zebrafish, IF is more uniformly distributed between the deep cells (DC) before the onset of gastrulation. This is likely due to the presence of a large extraembryonic structure – the yolk cell (YC) at the position where the blastocoel typically forms in other model organisms. IF has long been speculated to play a role in tissue morphogenesis during embryogenesis, but direct evidence supporting such function is still sparse. Here we show that the relocalization of IF to the interface between the YC and DC/epiblast is critical for axial mesendoderm (ME) cell protrusion formation and migration along this interface, a key process in embryonic axis formation. We further demonstrate that axial ME cell migration and IF relocalization engage in a positive feedback loop, where axial ME migration triggers IF accumulation ahead of the advancing axial ME tissue by mechanically compressing the overlying epiblast cell layer. Upon compression, locally induced flow relocalizes the IF through the porous epiblast tissue resulting in an IF accumulation ahead of the leading axial ME. This IF accumulation, in turn, promotes cell protrusion formation and migration of the leading axial ME cells, thereby facilitating axial ME extension. Our findings reveal a central role of dynamic IF relocalization in orchestrating germ layer morphogenesis during gastrulation.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","oa_version":"Published Version","file":[{"creator":"khuljev","file_size":47799741,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","file_name":"KHuljev_Thesis_corrections.docx","embargo_to":"open_access","checksum":"7f98532f5324a0b2f3fa8de2967baa19","date_created":"2021-05-17T12:29:12Z","date_updated":"2022-05-21T22:30:04Z","file_id":"9398","relation":"source_file"},{"creator":"khuljev","content_type":"application/pdf","file_size":16542131,"access_level":"open_access","file_name":"new_KHuljev_Thesis_corrections.pdf","checksum":"bf512f8a1e572a543778fc4b227c01ba","date_updated":"2022-05-21T22:30:04Z","date_created":"2021-05-18T14:50:28Z","file_id":"9401","embargo":"2022-05-20","relation":"main_file"}],"title":"Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation","status":"public","ddc":["571"],"_id":"9397","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","has_accepted_license":"1","article_processing_charge":"No","day":"18","date_published":"2021-05-18T00:00:00Z","page":"101","citation":{"apa":"Huljev, K. (2021). Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9397","ieee":"K. Huljev, “Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation,” Institute of Science and Technology Austria, 2021.","ista":"Huljev K. 2021. Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation. Institute of Science and Technology Austria.","ama":"Huljev K. Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation. 2021. doi:10.15479/at:ista:9397","chicago":"Huljev, Karla. “Coordinated Spatiotemporal Reorganization of Interstitial Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9397.","short":"K. Huljev, Coordinated Spatiotemporal Reorganization of Interstitial Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation, Institute of Science and Technology Austria, 2021.","mla":"Huljev, Karla. Coordinated Spatiotemporal Reorganization of Interstitial Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9397."}},{"publication":"arXiv","citation":{"ista":"Severin B, Lennon DT, Camenzind LC, Vigneau F, Fedele F, Jirovec D, Ballabio A, Chrastina D, Isella G, Kruijf M de, Carballido MJ, Svab S, Kuhlmann AV, Braakman FR, Geyer S, Froning FNM, Moon H, Osborne MA, Sejdinovic D, Katsaros G, Zumbühl DM, Briggs GAD, Ares N. Cross-architecture tuning of silicon and SiGe-based quantum devices using machine learning. arXiv, 2107.12975.","apa":"Severin, B., Lennon, D. T., Camenzind, L. C., Vigneau, F., Fedele, F., Jirovec, D., … Ares, N. (n.d.). Cross-architecture tuning of silicon and SiGe-based quantum devices using machine learning. arXiv. https://doi.org/10.48550/arXiv.2107.12975","ieee":"B. Severin et al., “Cross-architecture tuning of silicon and SiGe-based quantum devices using machine learning,” arXiv. .","ama":"Severin B, Lennon DT, Camenzind LC, et al. Cross-architecture tuning of silicon and SiGe-based quantum devices using machine learning. arXiv. doi:10.48550/arXiv.2107.12975","chicago":"Severin, B., D. T. Lennon, L. C. Camenzind, F. Vigneau, F. Fedele, Daniel Jirovec, A. Ballabio, et al. “Cross-Architecture Tuning of Silicon and SiGe-Based Quantum Devices Using Machine Learning.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2107.12975.","mla":"Severin, B., et al. “Cross-Architecture Tuning of Silicon and SiGe-Based Quantum Devices Using Machine Learning.” ArXiv, 2107.12975, doi:10.48550/arXiv.2107.12975.","short":"B. Severin, D.T. Lennon, L.C. Camenzind, F. Vigneau, F. Fedele, D. Jirovec, A. Ballabio, D. Chrastina, G. Isella, M. de Kruijf, M.J. Carballido, S. Svab, A.V. Kuhlmann, F.R. Braakman, S. Geyer, F.N.M. Froning, H. Moon, M.A. Osborne, D. Sejdinovic, G. Katsaros, D.M. Zumbühl, G.A.D. Briggs, N. Ares, ArXiv (n.d.)."},"oa":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2107.12975","open_access":"1"}],"external_id":{"arxiv":["2107.12975"]},"project":[{"call_identifier":"FWF","name":"Hole spin orbit qubits in Ge quantum wells","grant_number":"P30207","_id":"2641CE5E-B435-11E9-9278-68D0E5697425"}],"date_published":"2021-07-27T00:00:00Z","doi":"10.48550/arXiv.2107.12975","acknowledged_ssus":[{"_id":"NanoFab"}],"language":[{"iso":"eng"}],"month":"07","day":"27","article_processing_charge":"No","year":"2021","_id":"10066","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"We acknowledge Ang Li, Erik P. A. M. Bakkers (University of Eindhoven) for the fabrication of the Ge/Si nanowire. This work was supported by the Royal Society, the EPSRC National Quantum Technology Hub in Networked Quantum Information Technology (EP/M013243/1), Quantum Technology Capital (EP/N014995/1), EPSRC Platform Grant\r\n(EP/R029229/1), the European Research Council (Grant agreement 948932), the Swiss Nanoscience Institute, the\r\nNCCR SPIN, the EU H2020 European Microkelvin Platform EMP grant No. 824109, the Scientific Service Units\r\nof IST Austria through resources provided by the nanofabrication facility and, the FWF-P30207 project. This publication was also made possible through support from Templeton World Charity Foundation and John Templeton Foundation. The opinions expressed in this publication are those of the authors and do not necessarily reflect the views of the Templeton Foundations.","status":"public","publication_status":"submitted","title":"Cross-architecture tuning of silicon and SiGe-based quantum devices using machine learning","department":[{"_id":"GeKa"}],"author":[{"full_name":"Severin, B.","last_name":"Severin","first_name":"B."},{"full_name":"Lennon, D. T.","first_name":"D. T.","last_name":"Lennon"},{"full_name":"Camenzind, L. C.","last_name":"Camenzind","first_name":"L. C."},{"last_name":"Vigneau","first_name":"F.","full_name":"Vigneau, F."},{"full_name":"Fedele, F.","first_name":"F.","last_name":"Fedele"},{"last_name":"Jirovec","first_name":"Daniel","orcid":"0000-0002-7197-4801","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","full_name":"Jirovec, Daniel"},{"last_name":"Ballabio","first_name":"A.","full_name":"Ballabio, A."},{"last_name":"Chrastina","first_name":"D.","full_name":"Chrastina, D."},{"full_name":"Isella, G.","first_name":"G.","last_name":"Isella"},{"last_name":"Kruijf","first_name":"M. de","full_name":"Kruijf, M. de"},{"first_name":"M. J.","last_name":"Carballido","full_name":"Carballido, M. J."},{"first_name":"S.","last_name":"Svab","full_name":"Svab, S."},{"first_name":"A. V.","last_name":"Kuhlmann","full_name":"Kuhlmann, A. V."},{"full_name":"Braakman, F. R.","first_name":"F. R.","last_name":"Braakman"},{"first_name":"S.","last_name":"Geyer","full_name":"Geyer, S."},{"first_name":"F. N. M.","last_name":"Froning","full_name":"Froning, F. N. M."},{"full_name":"Moon, H.","last_name":"Moon","first_name":"H."},{"first_name":"M. A.","last_name":"Osborne","full_name":"Osborne, M. A."},{"last_name":"Sejdinovic","first_name":"D.","full_name":"Sejdinovic, D."},{"full_name":"Katsaros, Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8342-202X","first_name":"Georgios","last_name":"Katsaros"},{"last_name":"Zumbühl","first_name":"D. M.","full_name":"Zumbühl, D. M."},{"full_name":"Briggs, G. A. D.","last_name":"Briggs","first_name":"G. A. D."},{"first_name":"N.","last_name":"Ares","full_name":"Ares, N."}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10058"}]},"date_created":"2021-10-01T12:40:22Z","date_updated":"2024-03-28T23:30:27Z","oa_version":"Preprint","article_number":"2107.12975","type":"preprint","abstract":[{"lang":"eng","text":"The potential of Si and SiGe-based devices for the scaling of quantum circuits is tainted by device variability. Each device needs to be tuned to operation conditions. We give a key step towards tackling this variability with an algorithm that, without modification, is capable of tuning a 4-gate Si FinFET, a 5-gate GeSi nanowire and a 7-gate SiGe heterostructure double quantum dot device from scratch. We achieve tuning times of 30, 10, and 92 minutes, respectively. The algorithm also provides insight into the parameter space landscape for each of these devices. These results show that overarching solutions for the tuning of quantum devices are enabled by machine learning."}]},{"language":[{"iso":"eng"}],"doi":"10.7554/ELIFE.68274","quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","_id":"25CA28EA-B435-11E9-9278-68D0E5697425","grant_number":"694539"},{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","grant_number":"692692","call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glumatergic synapse"},{"call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000651761700001"]},"month":"04","publication_identifier":{"eissn":["2050-084X"]},"date_updated":"2024-03-28T23:30:31Z","date_created":"2021-05-30T22:01:23Z","volume":10,"author":[{"first_name":"Pradeep","last_name":"Bhandari","id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0863-4481","full_name":"Bhandari, Pradeep"},{"last_name":"Vandael","first_name":"David H","orcid":"0000-0001-7577-1676","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","full_name":"Vandael, David H"},{"first_name":"Diego","last_name":"Fernández-Fernández","full_name":"Fernández-Fernández, Diego"},{"first_name":"Thorsten","last_name":"Fritzius","full_name":"Fritzius, Thorsten"},{"full_name":"Kleindienst, David","id":"42E121A4-F248-11E8-B48F-1D18A9856A87","last_name":"Kleindienst","first_name":"David"},{"full_name":"Önal, Hüseyin C","id":"4659D740-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2771-2011","first_name":"Hüseyin C","last_name":"Önal"},{"id":"3786AB44-F248-11E8-B48F-1D18A9856A87","last_name":"Montanaro-Punzengruber","first_name":"Jacqueline-Claire","full_name":"Montanaro-Punzengruber, Jacqueline-Claire"},{"full_name":"Gassmann, Martin","last_name":"Gassmann","first_name":"Martin"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","first_name":"Peter M","last_name":"Jonas","full_name":"Jonas, Peter M"},{"full_name":"Kulik, Akos","first_name":"Akos","last_name":"Kulik"},{"first_name":"Bernhard","last_name":"Bettler","full_name":"Bettler, Bernhard"},{"orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","first_name":"Ryuichi","full_name":"Shigemoto, Ryuichi"},{"full_name":"Koppensteiner, Peter","orcid":"0000-0002-3509-1948","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","last_name":"Koppensteiner","first_name":"Peter"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"9562"}],"link":[{"relation":"earlier_version","url":"https://doi.org/10.1101/2020.04.16.045112"}]},"publication_status":"published","publisher":"eLife Sciences Publications","department":[{"_id":"RySh"},{"_id":"PeJo"}],"year":"2021","acknowledgement":"We are grateful to Akari Hagiwara and Toshihisa Ohtsuka for CAST antibody, and Masahiko Watanabe for neurexin antibody. We thank David Adams for kindly providing the stable Cav2.3 cell line. Cav2.3 KO mice were kindly provided by Tsutomu Tanabe. This project has received funding from the European Research Council (ERC) and European Commission (EC), under the European Union’s Horizon 2020 research and innovation programme (ERC grant agreement no. 694539 to Ryuichi Shigemoto, no. 692692 to Peter Jonas, and the Marie Skłodowska-Curie grant agreement no. 665385 to Cihan Önal), the Swiss National Science Foundation Grant 31003A-172881 to Bernhard Bettler and Deutsche Forschungsgemeinschaft (For 2143) and BIOSS-2 to Akos Kulik.","file_date_updated":"2021-05-31T09:43:09Z","ec_funded":1,"article_number":"e68274","date_published":"2021-04-29T00:00:00Z","article_type":"original","publication":"eLife","citation":{"mla":"Bhandari, Pradeep, et al. “GABAB Receptor Auxiliary Subunits Modulate Cav2.3-Mediated Release from Medial Habenula Terminals.” ELife, vol. 10, e68274, eLife Sciences Publications, 2021, doi:10.7554/ELIFE.68274.","short":"P. Bhandari, D.H. Vandael, D. Fernández-Fernández, T. Fritzius, D. Kleindienst, H.C. Önal, J.-C. Montanaro-Punzengruber, M. Gassmann, P.M. Jonas, A. Kulik, B. Bettler, R. Shigemoto, P. Koppensteiner, ELife 10 (2021).","chicago":"Bhandari, Pradeep, David H Vandael, Diego Fernández-Fernández, Thorsten Fritzius, David Kleindienst, Hüseyin C Önal, Jacqueline-Claire Montanaro-Punzengruber, et al. “GABAB Receptor Auxiliary Subunits Modulate Cav2.3-Mediated Release from Medial Habenula Terminals.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/ELIFE.68274.","ama":"Bhandari P, Vandael DH, Fernández-Fernández D, et al. GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals. eLife. 2021;10. doi:10.7554/ELIFE.68274","ista":"Bhandari P, Vandael DH, Fernández-Fernández D, Fritzius T, Kleindienst D, Önal HC, Montanaro-Punzengruber J-C, Gassmann M, Jonas PM, Kulik A, Bettler B, Shigemoto R, Koppensteiner P. 2021. GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals. eLife. 10, e68274.","ieee":"P. Bhandari et al., “GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals,” eLife, vol. 10. eLife Sciences Publications, 2021.","apa":"Bhandari, P., Vandael, D. H., Fernández-Fernández, D., Fritzius, T., Kleindienst, D., Önal, H. C., … Koppensteiner, P. (2021). GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals. ELife. eLife Sciences Publications. https://doi.org/10.7554/ELIFE.68274"},"day":"29","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","file":[{"access_level":"open_access","file_name":"2021_eLife_Bhandari.pdf","creator":"cziletti","content_type":"application/pdf","file_size":8174719,"file_id":"9440","relation":"main_file","success":1,"checksum":"6ebcb79999f889766f7cd79ee134ad28","date_updated":"2021-05-31T09:43:09Z","date_created":"2021-05-31T09:43:09Z"}],"oa_version":"Published Version","title":"GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals","status":"public","ddc":["570"],"intvolume":" 10","_id":"9437","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"The synaptic connection from medial habenula (MHb) to interpeduncular nucleus (IPN) is critical for emotion-related behaviors and uniquely expresses R-type Ca2+ channels (Cav2.3) and auxiliary GABAB receptor (GBR) subunits, the K+-channel tetramerization domain-containing proteins (KCTDs). Activation of GBRs facilitates or inhibits transmitter release from MHb terminals depending on the IPN subnucleus, but the role of KCTDs is unknown. We therefore examined the localization and function of Cav2.3, GBRs, and KCTDs in this pathway in mice. We show in heterologous cells that KCTD8 and KCTD12b directly bind to Cav2.3 and that KCTD8 potentiates Cav2.3 currents in the absence of GBRs. In the rostral IPN, KCTD8, KCTD12b, and Cav2.3 co-localize at the presynaptic active zone. Genetic deletion indicated a bidirectional modulation of Cav2.3-mediated release by these KCTDs with a compensatory increase of KCTD8 in the active zone in KCTD12b-deficient mice. The interaction of Cav2.3 with KCTDs therefore scales synaptic strength independent of GBR activation."}],"type":"journal_article"},{"alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"lang":"eng","text":"Left-right asymmetries can be considered a fundamental organizational principle of the vertebrate central nervous system. The hippocampal CA3-CA1 pyramidal cell synaptic connection shows an input-side dependent asymmetry where the hemispheric location of the presynaptic CA3 neuron determines the synaptic properties. Left-input synapses terminating on apical dendrites in stratum radiatum have a higher density of NMDA receptor subunit GluN2B, a lower density of AMPA receptor subunit GluA1 and smaller areas with less often perforated PSDs. On the other hand, left-input synapses terminating on basal dendrites in stratum oriens have lower GluN2B densities than right-input ones. Apical and basal synapses further employ different signaling pathways involved in LTP. SDS-digested freeze-fracture replica labeling can visualize synaptic membrane proteins with high sensitivity and resolution, and has been used to reveal the asymmetry at the electron microscopic level. However, it requires time-consuming manual demarcation of the synaptic surface for quantitative measurements. To facilitate the analysis of replica labeling, I first developed a software named Darea, which utilizes deep-learning to automatize this demarcation. With Darea I characterized the synaptic distribution of NMDA and AMPA receptors as well as the voltage-gated Ca2+ channels in CA1 stratum radiatum and oriens. Second, I explored the role of GluN2B and its carboxy-terminus in the establishment of input-side dependent hippocampal asymmetry. In conditional knock-out mice lacking GluN2B expression in CA1 and GluN2B-2A swap mice, where GluN2B carboxy-terminus was exchanged to that of GluN2A, no significant asymmetries of GluN2B, GluA1 and PSD area were detected. We further discovered a previously unknown functional asymmetry of GluN2A, which was also lost in the swap mouse. These results demonstrate that GluN2B carboxy-terminus plays a critical role in normal formation of input-side dependent asymmetry."}],"ddc":["570"],"title":"2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning","status":"public","_id":"9562","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","file":[{"file_id":"9563","embargo":"2022-07-01","relation":"main_file","checksum":"659df5518db495f679cb1df9e9bd1d94","date_updated":"2022-07-02T22:30:04Z","date_created":"2021-06-17T14:03:14Z","access_level":"open_access","file_name":"Thesis.pdf","creator":"dkleindienst","file_size":77299142,"content_type":"application/pdf"},{"embargo_to":"open_access","file_name":"Thesis_source.zip","access_level":"closed","content_type":"application/zip","file_size":369804895,"creator":"dkleindienst","relation":"source_file","file_id":"9564","date_created":"2021-06-17T14:04:30Z","date_updated":"2022-07-02T22:30:04Z","checksum":"3bcf63a2b19e5b6663be051bea332748"}],"has_accepted_license":"1","article_processing_charge":"No","day":"01","page":"124","citation":{"ama":"Kleindienst D. 2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning. 2021. doi:10.15479/at:ista:9562","apa":"Kleindienst, D. (2021). 2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9562","ieee":"D. Kleindienst, “2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning,” Institute of Science and Technology Austria, 2021.","ista":"Kleindienst D. 2021. 2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning. Institute of Science and Technology Austria.","short":"D. Kleindienst, 2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning, Institute of Science and Technology Austria, 2021.","mla":"Kleindienst, David. 2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9562.","chicago":"Kleindienst, David. “2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9562."},"date_published":"2021-06-01T00:00:00Z","file_date_updated":"2022-07-02T22:30:04Z","department":[{"_id":"GradSch"},{"_id":"RySh"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2021","date_updated":"2023-09-11T12:55:53Z","date_created":"2021-06-17T14:10:47Z","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"9756"},{"relation":"part_of_dissertation","status":"public","id":"9437"},{"id":"8532","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"612"}]},"author":[{"full_name":"Kleindienst, David","first_name":"David","last_name":"Kleindienst","id":"42E121A4-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"issn":["2663-337X"]},"month":"06","oa":1,"language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"first_name":"Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"doi":"10.15479/at:ista:9562"},{"title":"High-Resolution localization and quantitation of membrane proteins by SDS-digested freeze-fracture replica labeling (SDS-FRL)","status":"public","ddc":["573"],"intvolume":" 169","_id":"9756","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","oa_version":"None","alternative_title":["Neuromethods"],"type":"book_chapter","abstract":[{"lang":"eng","text":"High-resolution visualization and quantification of membrane proteins contribute to the understanding of their functions and the roles they play in physiological and pathological conditions. Sodium dodecyl sulfate-digested freeze-fracture replica labeling (SDS-FRL) is a powerful electron microscopy method to study quantitatively the two-dimensional distribution of transmembrane proteins and their tightly associated proteins. During treatment with SDS, intracellular organelles and proteins not anchored to the replica are dissolved, whereas integral membrane proteins captured and stabilized by carbon/platinum deposition remain on the replica. Their intra- and extracellular domains become exposed on the surface of the replica, facilitating the accessibility of antibodies and, therefore, providing higher labeling efficiency than those obtained with other immunoelectron microscopy techniques. In this chapter, we describe the protocols of SDS-FRL adapted for mammalian brain samples, and optimization of the SDS treatment to increase the labeling efficiency for quantification of Cav2.1, the alpha subunit of P/Q-type voltage-dependent calcium channels utilizing deep learning algorithms."}],"page":"267-283","publication":" Receptor and Ion Channel Detection in the Brain","citation":{"chicago":"Kaufmann, Walter, David Kleindienst, Harumi Harada, and Ryuichi Shigemoto. “High-Resolution Localization and Quantitation of Membrane Proteins by SDS-Digested Freeze-Fracture Replica Labeling (SDS-FRL).” In Receptor and Ion Channel Detection in the Brain, 169:267–83. Neuromethods. New York: Humana, 2021. https://doi.org/10.1007/978-1-0716-1522-5_19.","mla":"Kaufmann, Walter, et al. “High-Resolution Localization and Quantitation of Membrane Proteins by SDS-Digested Freeze-Fracture Replica Labeling (SDS-FRL).” Receptor and Ion Channel Detection in the Brain, vol. 169, Humana, 2021, pp. 267–83, doi:10.1007/978-1-0716-1522-5_19.","short":"W. Kaufmann, D. Kleindienst, H. Harada, R. Shigemoto, in:, Receptor and Ion Channel Detection in the Brain, Humana, New York, 2021, pp. 267–283.","ista":"Kaufmann W, Kleindienst D, Harada H, Shigemoto R. 2021.High-Resolution localization and quantitation of membrane proteins by SDS-digested freeze-fracture replica labeling (SDS-FRL). In: Receptor and Ion Channel Detection in the Brain. Neuromethods, vol. 169, 267–283.","ieee":"W. Kaufmann, D. Kleindienst, H. Harada, and R. Shigemoto, “High-Resolution localization and quantitation of membrane proteins by SDS-digested freeze-fracture replica labeling (SDS-FRL),” in Receptor and Ion Channel Detection in the Brain, vol. 169, New York: Humana, 2021, pp. 267–283.","apa":"Kaufmann, W., Kleindienst, D., Harada, H., & Shigemoto, R. (2021). High-Resolution localization and quantitation of membrane proteins by SDS-digested freeze-fracture replica labeling (SDS-FRL). In Receptor and Ion Channel Detection in the Brain (Vol. 169, pp. 267–283). New York: Humana. https://doi.org/10.1007/978-1-0716-1522-5_19","ama":"Kaufmann W, Kleindienst D, Harada H, Shigemoto R. High-Resolution localization and quantitation of membrane proteins by SDS-digested freeze-fracture replica labeling (SDS-FRL). In: Receptor and Ion Channel Detection in the Brain. Vol 169. Neuromethods. New York: Humana; 2021:267-283. doi:10.1007/978-1-0716-1522-5_19"},"date_published":"2021-07-27T00:00:00Z","series_title":"Neuromethods","keyword":["Freeze-fracture replica: Deep learning","Immunogold labeling","Integral membrane protein","Electron microscopy"],"day":"27","article_processing_charge":"No","has_accepted_license":"1","publication_status":"published","publisher":"Humana","department":[{"_id":"RySh"},{"_id":"EM-Fac"}],"year":"2021","acknowledgement":"This work was supported by the European Union (European Research Council Advanced grant no. 694539 and Human Brain Project Ref. 720270 to R. S.) and the Austrian Academy of Sciences (DOC fellowship to D.K.).","date_created":"2021-07-30T09:34:56Z","date_updated":"2024-03-28T23:30:31Z","volume":169,"author":[{"orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","last_name":"Kaufmann","first_name":"Walter","full_name":"Kaufmann, Walter"},{"first_name":"David","last_name":"Kleindienst","id":"42E121A4-F248-11E8-B48F-1D18A9856A87","full_name":"Kleindienst, David"},{"full_name":"Harada, Harumi","first_name":"Harumi","last_name":"Harada","id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7429-7896"},{"full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","first_name":"Ryuichi","last_name":"Shigemoto"}],"related_material":{"record":[{"id":"9562","status":"public","relation":"dissertation_contains"}]},"place":"New York","ec_funded":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"In situ analysis of single channel subunit 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Kafshdar","orcid":"0000-0003-1702-6584","id":"391365CE-F248-11E8-B48F-1D18A9856A87","full_name":"Goharshady, Amir Kafshdar"}],"department":[{"_id":"KrCh"},{"_id":"GradSch"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","acknowledgement":"The research was partially supported by an IBM PhD fellowship, a Facebook PhD fellowship, and DOC fellowship #24956 of the Austrian Academy of Sciences (OeAW).","year":"2021","file_date_updated":"2021-12-23T23:30:04Z","language":[{"iso":"eng"}],"supervisor":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"}],"degree_awarded":"PhD","doi":"10.15479/AT:ISTA:8934","project":[{"_id":"267066CE-B435-11E9-9278-68D0E5697425","name":"Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies"},{"_id":"266EEEC0-B435-11E9-9278-68D0E5697425","name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts"}],"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa":1,"publication_identifier":{"issn":["2663-337X"]},"month":"01","oa_version":"Published 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including invariant generation, reachability analysis, termination analysis of probabilistic programs, data-flow analysis, quantitative analysis of Markov chains and Markov decision processes, and the problem of data packing in cache management.\r\nWe use techniques from parameterized complexity theory, polyhedral geometry, and real algebraic geometry to significantly improve the state-of-the-art, in terms of both scalability and completeness guarantees, for the mentioned problems. In some cases, our results are the first theoretical improvements for the respective problems in two or three decades."}],"alternative_title":["ISTA Thesis"],"type":"dissertation","date_published":"2021-01-01T00:00:00Z","page":"278","citation":{"ista":"Goharshady AK. 2021. Parameterized and algebro-geometric advances in static program analysis. Institute of Science and Technology Austria.","apa":"Goharshady, A. K. (2021). Parameterized and algebro-geometric advances in static program analysis. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8934","ieee":"A. K. Goharshady, “Parameterized and algebro-geometric advances in static program analysis,” Institute of Science and Technology Austria, 2021.","ama":"Goharshady AK. Parameterized and algebro-geometric advances in static program analysis. 2021. doi:10.15479/AT:ISTA:8934","chicago":"Goharshady, Amir Kafshdar. “Parameterized and Algebro-Geometric Advances in Static Program Analysis.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:8934.","mla":"Goharshady, Amir Kafshdar. Parameterized and Algebro-Geometric Advances in Static Program Analysis. Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:8934.","short":"A.K. Goharshady, Parameterized and Algebro-Geometric Advances in Static Program Analysis, Institute of Science and Technology Austria, 2021."},"article_processing_charge":"No","has_accepted_license":"1","day":"01"},{"publication_identifier":{"issn":["2663-337X"]},"month":"11","doi":"10.15479/at:ista:10307","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"supervisor":[{"full_name":"Sixt, Michael K","last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-4561-241X","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","first_name":"Calin C"}],"degree_awarded":"PhD","oa":1,"file_date_updated":"2022-12-20T23:30:05Z","related_material":{"record":[{"id":"10316","status":"public","relation":"part_of_dissertation"}]},"author":[{"last_name":"Tomasek","first_name":"Kathrin","orcid":"0000-0003-3768-877X","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","full_name":"Tomasek, Kathrin"}],"date_updated":"2023-09-07T13:34:38Z","date_created":"2021-11-18T15:05:06Z","year":"2021","publisher":"Institute of Science and Technology Austria","department":[{"_id":"MiSi"},{"_id":"CaGu"},{"_id":"GradSch"}],"publication_status":"published","has_accepted_license":"1","article_processing_charge":"No","day":"18","date_published":"2021-11-18T00:00:00Z","citation":{"chicago":"Tomasek, Kathrin. “Pathogenic Escherichia Coli Hijack the Host Immune Response.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10307.","mla":"Tomasek, Kathrin. Pathogenic Escherichia Coli Hijack the Host Immune Response. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10307.","short":"K. Tomasek, Pathogenic Escherichia Coli Hijack the Host Immune Response, Institute of Science and Technology Austria, 2021.","ista":"Tomasek K. 2021. Pathogenic Escherichia coli hijack the host immune response. Institute of Science and Technology Austria.","apa":"Tomasek, K. (2021). Pathogenic Escherichia coli hijack the host immune response. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10307","ieee":"K. Tomasek, “Pathogenic Escherichia coli hijack the host immune response,” Institute of Science and Technology Austria, 2021.","ama":"Tomasek K. Pathogenic Escherichia coli hijack the host immune response. 2021. doi:10.15479/at:ista:10307"},"page":"73","abstract":[{"lang":"eng","text":"Bacteria-host interactions represent a continuous trade-off between benefit and risk. Thus, the host immune response is faced with a non-trivial problem – accommodate beneficial commensals and remove harmful pathogens. This is especially difficult as molecular patterns, such as lipopolysaccharide or specific surface organelles such as pili, are conserved in both, commensal and pathogenic bacteria. Type 1 pili, tightly regulated by phase variation, are considered an important virulence factor of pathogenic bacteria as they facilitate invasion into host cells. While invasion represents a de facto passive mechanism for pathogens to escape the host immune response, we demonstrate a fundamental role of type 1 pili as active modulators of the innate and adaptive immune response."}],"type":"dissertation","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","file":[{"relation":"main_file","embargo":"2022-11-18","file_id":"10308","checksum":"b39c9e0ef18d0484d537a67551effd02","date_updated":"2022-12-20T23:30:05Z","date_created":"2021-11-18T15:07:31Z","access_level":"open_access","file_name":"ThesisTomasekKathrin.pdf","content_type":"application/pdf","file_size":13266088,"creator":"ktomasek"},{"checksum":"c0c440ee9e5ef1102a518a4f9f023e7c","date_updated":"2022-12-20T23:30:05Z","date_created":"2021-11-18T15:07:46Z","relation":"source_file","file_id":"10309","file_size":7539509,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"ktomasek","access_level":"closed","embargo_to":"open_access","file_name":"ThesisTomasekKathrin.docx"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"10307","ddc":["570"],"status":"public","title":"Pathogenic Escherichia coli hijack the host immune response"},{"abstract":[{"lang":"eng","text":"A key attribute of persistent or recurring bacterial infections is the ability of the pathogen to evade the host’s immune response. Many Enterobacteriaceae express type 1 pili, a pre-adapted virulence trait, to invade host epithelial cells and establish persistent infections. However, the molecular mechanisms and strategies by which bacteria actively circumvent the immune response of the host remain poorly understood. Here, we identified CD14, the major co-receptor for lipopolysaccharide detection, on dendritic cells as a previously undescribed binding partner of FimH, the protein located at the tip of the type 1 pilus of Escherichia coli. The FimH amino acids involved in CD14 binding are highly conserved across pathogenic and non-pathogenic strains. Binding of pathogenic bacteria to CD14 lead to reduced dendritic cell migration and blunted expression of co-stimulatory molecules, both rate-limiting factors of T cell activation. While defining an active molecular mechanism of immune evasion by pathogens, the interaction between FimH and CD14 represents a potential target to interfere with persistent and recurrent infections, such as urinary tract infections or Crohn’s disease."}],"ec_funded":1,"type":"preprint","date_updated":"2024-03-28T23:30:35Z","date_created":"2021-11-19T12:24:16Z","oa_version":"Preprint","author":[{"full_name":"Tomasek, Kathrin","first_name":"Kathrin","last_name":"Tomasek","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3768-877X"},{"full_name":"Leithner, Alexander F","last_name":"Leithner","first_name":"Alexander F","orcid":"0000-0002-1073-744X","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Glatzová, Ivana","first_name":"Ivana","last_name":"Glatzová","id":"727b3c7d-4939-11ec-89b3-b9b0750ab74d"},{"first_name":"Michael S.","last_name":"Lukesch","full_name":"Lukesch, Michael S."},{"last_name":"Guet","first_name":"Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C"},{"last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-4561-241X","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K"}],"related_material":{"record":[{"id":"11843","status":"public","relation":"later_version"},{"status":"public","relation":"dissertation_contains","id":"10307"}]},"status":"public","title":"Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14","publication_status":"submitted","department":[{"_id":"CaGu"},{"_id":"MiSi"}],"publisher":"Cold Spring Harbor Laboratory","_id":"10316","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","acknowledgement":"We thank Ulrich Dobrindt for providing UPEC strain CFT073, Vlad Gavra and Maximilian Götz, Bor Kavčič, Jonna Alanko and Eva Kiermaier for help with experiments and Robert Hauschild, Julian Stopp and Saren Tasciyan for help with data analysis. We thank the IST Austria Scientific Service Units, especially the Bioimaging facility, the Preclinical facility and the Electron microscopy facility for technical support, Jakob Wallner and all members of the Guet and Sixt lab for fruitful discussions and Daria Siekhaus for critically reading the manuscript. This work was supported by grants from the Austrian Research Promotion Agency (FEMtech 868984) to I.G., the European Research Council (CoG 724373) and the Austrian Science Fund (FWF P29911) to M.S.","year":"2021","month":"10","day":"18","article_processing_charge":"No","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"language":[{"iso":"eng"}],"date_published":"2021-10-18T00:00:00Z","doi":"10.1101/2021.10.18.464770","project":[{"call_identifier":"H2020","name":"Cellular navigation along spatial gradients","grant_number":"724373","_id":"25FE9508-B435-11E9-9278-68D0E5697425"},{"grant_number":"P29911","_id":"26018E70-B435-11E9-9278-68D0E5697425","name":"Mechanical adaptation of lamellipodial actin","call_identifier":"FWF"}],"publication":"bioRxiv","oa":1,"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2021.10.18.464770v1","open_access":"1"}],"citation":{"ista":"Tomasek K, Leithner AF, Glatzová I, Lukesch MS, Guet CC, Sixt MK. Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14. bioRxiv, 10.1101/2021.10.18.464770.","apa":"Tomasek, K., Leithner, A. F., Glatzová, I., Lukesch, M. S., Guet, C. C., & Sixt, M. K. (n.d.). Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2021.10.18.464770","ieee":"K. Tomasek, A. F. Leithner, I. Glatzová, M. S. Lukesch, C. C. Guet, and M. K. Sixt, “Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14,” bioRxiv. Cold Spring Harbor Laboratory.","ama":"Tomasek K, Leithner AF, Glatzová I, Lukesch MS, Guet CC, Sixt MK. Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14. bioRxiv. doi:10.1101/2021.10.18.464770","chicago":"Tomasek, Kathrin, Alexander F Leithner, Ivana Glatzová, Michael S. Lukesch, Calin C Guet, and Michael K Sixt. “Type 1 Piliated Uropathogenic Escherichia Coli Hijack the Host Immune Response by Binding to CD14.” BioRxiv. Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/2021.10.18.464770.","mla":"Tomasek, Kathrin, et al. “Type 1 Piliated Uropathogenic Escherichia Coli Hijack the Host Immune Response by Binding to CD14.” BioRxiv, Cold Spring Harbor Laboratory, doi:10.1101/2021.10.18.464770.","short":"K. Tomasek, A.F. Leithner, I. Glatzová, M.S. Lukesch, C.C. Guet, M.K. Sixt, BioRxiv (n.d.)."}},{"type":"journal_article","abstract":[{"lang":"eng","text":"Availability of the essential macronutrient nitrogen in soil plays a critical role in plant growth, development, and impacts agricultural productivity. Plants have evolved different strategies for sensing and responding to heterogeneous nitrogen distribution. Modulation of root system architecture, including primary root growth and branching, is among the most essential plant adaptions to ensure adequate nitrogen acquisition. However, the immediate molecular pathways coordinating the adjustment of root growth in response to distinct nitrogen sources, such as nitrate or ammonium, are poorly understood. Here, we show that growth as manifested by cell division and elongation is synchronized by coordinated auxin flux between two adjacent outer tissue layers of the root. This coordination is achieved by nitrate‐dependent dephosphorylation of the PIN2 auxin efflux carrier at a previously uncharacterized phosphorylation site, leading to subsequent PIN2 lateralization and thereby regulating auxin flow between adjacent tissues. A dynamic computer model based on our experimental data successfully recapitulates experimental observations. Our study provides mechanistic insights broadening our understanding of root growth mechanisms in dynamic environments."}],"issue":"3","_id":"9010","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport","ddc":["580"],"status":"public","intvolume":" 40","file":[{"date_updated":"2021-02-11T12:28:29Z","date_created":"2021-02-11T12:28:29Z","success":1,"checksum":"dc55c900f3b061d6c2790b8813d759a3","file_id":"9110","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":2358617,"file_name":"2021_Embo_Otvos.pdf","access_level":"open_access"}],"oa_version":"Published Version","scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","publication":"EMBO Journal","citation":{"chicago":"Ötvös, Krisztina, Marco Marconi, Andrea Vega, Jose O’Brien, Alexander J Johnson, Rashed Abualia, Livio Antonielli, et al. “Modulation of Plant Root Growth by Nitrogen Source-Defined Regulation of Polar Auxin Transport.” EMBO Journal. Embo Press, 2021. https://doi.org/10.15252/embj.2020106862.","mla":"Ötvös, Krisztina, et al. “Modulation of Plant Root Growth by Nitrogen Source-Defined Regulation of Polar Auxin Transport.” EMBO Journal, vol. 40, no. 3, e106862, Embo Press, 2021, doi:10.15252/embj.2020106862.","short":"K. Ötvös, M. Marconi, A. Vega, J. O’Brien, A.J. Johnson, R. Abualia, L. Antonielli, J.C. Montesinos López, Y. Zhang, S. Tan, C. Cuesta, C. Artner, E. Bouguyon, A. Gojon, J. Friml, R.A. Gutiérrez, K.T. Wabnik, E. Benková, EMBO Journal 40 (2021).","ista":"Ötvös K, Marconi M, Vega A, O’Brien J, Johnson AJ, Abualia R, Antonielli L, Montesinos López JC, Zhang Y, Tan S, Cuesta C, Artner C, Bouguyon E, Gojon A, Friml J, Gutiérrez RA, Wabnik KT, Benková E. 2021. Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport. EMBO Journal. 40(3), e106862.","apa":"Ötvös, K., Marconi, M., Vega, A., O’Brien, J., Johnson, A. J., Abualia, R., … Benková, E. (2021). Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport. EMBO Journal. Embo Press. https://doi.org/10.15252/embj.2020106862","ieee":"K. Ötvös et al., “Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport,” EMBO Journal, vol. 40, no. 3. Embo Press, 2021.","ama":"Ötvös K, Marconi M, Vega A, et al. Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport. EMBO Journal. 2021;40(3). doi:10.15252/embj.2020106862"},"article_type":"original","date_published":"2021-02-01T00:00:00Z","article_number":"e106862","file_date_updated":"2021-02-11T12:28:29Z","year":"2021","acknowledgement":"We acknowledge Gergely Molnar for critical reading of the manuscript, Alexander Johnson for language editing and Yulija Salanenka for technical assistance. Work in the Benkova laboratory was supported by the Austrian Science Fund (FWF01_I1774S) to KO, RA and EB. Work in the Benkova laboratory was supported by the Austrian Science Fund (FWF01_I1774S) to KO, RA and EB and by the DOC Fellowship Programme of the AustrianAcademy of Sciences (25008) to C.A. Work in the Wabnik laboratory was supported by the Programa de Atraccion de Talento 2017 (Comunidad deMadrid, 2017-T1/BIO-5654 to K.W.), Severo Ochoa Programme for Centres of Excellence in R&D from the Agencia Estatal de Investigacion of Spain (grantSEV-2016-0672 (2017-2021) to K.W. via the CBGP) and Programa Estatal de Generacion del Conocimiento y Fortalecimiento Científico y Tecnologico del Sistema de I+D+I 2019 (PGC2018-093387-A-I00) from MICIU (to K.W.). M.M.was supported by a postdoctoral contract associated to SEV-2016-0672.We acknowledge the Bioimaging Facility in IST-Austria and the Advanced Microscopy Facility of the Vienna Bio Center Core Facilities, member of the Vienna Bio Center Austria, for use of the OMX v43D SIM microscope. AJ was supported by the Austrian Science Fund (FWF): I03630 to J.F","pmid":1,"publication_status":"published","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"publisher":"Embo Press","author":[{"full_name":"Ötvös, Krisztina","last_name":"Ötvös","first_name":"Krisztina","orcid":"0000-0002-5503-4983","id":"29B901B0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Marconi, Marco","last_name":"Marconi","first_name":"Marco"},{"full_name":"Vega, Andrea","first_name":"Andrea","last_name":"Vega"},{"first_name":"Jose","last_name":"O’Brien","full_name":"O’Brien, Jose"},{"last_name":"Johnson","first_name":"Alexander J","orcid":"0000-0002-2739-8843","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","full_name":"Johnson, Alexander J"},{"full_name":"Abualia, Rashed","orcid":"0000-0002-9357-9415","id":"4827E134-F248-11E8-B48F-1D18A9856A87","last_name":"Abualia","first_name":"Rashed"},{"full_name":"Antonielli, Livio","last_name":"Antonielli","first_name":"Livio"},{"first_name":"Juan C","last_name":"Montesinos López","id":"310A8E3E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9179-6099","full_name":"Montesinos López, Juan C"},{"full_name":"Zhang, Yuzhou","last_name":"Zhang","first_name":"Yuzhou","orcid":"0000-0003-2627-6956","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tan, Shutang","first_name":"Shutang","last_name":"Tan","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0471-8285"},{"first_name":"Candela","last_name":"Cuesta","id":"33A3C818-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1923-2410","full_name":"Cuesta, Candela"},{"full_name":"Artner, Christina","last_name":"Artner","first_name":"Christina","id":"45DF286A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Bouguyon, Eleonore","first_name":"Eleonore","last_name":"Bouguyon"},{"full_name":"Gojon, Alain","first_name":"Alain","last_name":"Gojon"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří"},{"first_name":"Rodrigo A.","last_name":"Gutiérrez","full_name":"Gutiérrez, Rodrigo A."},{"full_name":"Wabnik, Krzysztof T","first_name":"Krzysztof T","last_name":"Wabnik","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7263-0560"},{"orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","first_name":"Eva","full_name":"Benková, Eva"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10303"}],"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/a-plants-way-to-its-favorite-food/"}]},"date_updated":"2024-03-28T23:30:39Z","date_created":"2021-01-17T23:01:12Z","volume":40,"month":"02","publication_identifier":{"issn":["02614189"],"eissn":["14602075"]},"external_id":{"isi":["000604645600001"],"pmid":[" 33399250"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"isi":1,"quality_controlled":"1","project":[{"_id":"2542D156-B435-11E9-9278-68D0E5697425","grant_number":"I 1774-B16","call_identifier":"FWF","name":"Hormone cross-talk drives nutrient dependent plant development"},{"_id":"2685A872-B435-11E9-9278-68D0E5697425","name":"Hormonal regulation of plant adaptive responses to environmental signals"},{"_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF"}],"doi":"10.15252/embj.2020106862","acknowledged_ssus":[{"_id":"Bio"}],"language":[{"iso":"eng"}]},{"citation":{"mla":"Vega, Andrea, et al. “Nitrate Triggered Phosphoproteome Changes and a PIN2 Phosphosite Modulating Root System Architecture.” EMBO Reports, vol. 22, no. 9, e51813, Wiley, 2021, doi:10.15252/embr.202051813.","short":"A. Vega, I. Fredes, J. O’Brien, Z. Shen, K. Ötvös, R. Abualia, E. Benková, S.P. Briggs, R.A. Gutiérrez, EMBO Reports 22 (2021).","chicago":"Vega, Andrea, Isabel Fredes, José O’Brien, Zhouxin Shen, Krisztina Ötvös, Rashed Abualia, Eva Benková, Steven P. Briggs, and Rodrigo A. Gutiérrez. “Nitrate Triggered Phosphoproteome Changes and a PIN2 Phosphosite Modulating Root System Architecture.” EMBO Reports. Wiley, 2021. https://doi.org/10.15252/embr.202051813.","ama":"Vega A, Fredes I, O’Brien J, et al. Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture. EMBO Reports. 2021;22(9). doi:10.15252/embr.202051813","ista":"Vega A, Fredes I, O’Brien J, Shen Z, Ötvös K, Abualia R, Benková E, Briggs SP, Gutiérrez RA. 2021. Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture. EMBO Reports. 22(9), e51813.","ieee":"A. Vega et al., “Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture,” EMBO Reports, vol. 22, no. 9. Wiley, 2021.","apa":"Vega, A., Fredes, I., O’Brien, J., Shen, Z., Ötvös, K., Abualia, R., … Gutiérrez, R. A. (2021). Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture. EMBO Reports. Wiley. https://doi.org/10.15252/embr.202051813"},"publication":"EMBO Reports","article_type":"original","date_published":"2021-09-06T00:00:00Z","scopus_import":"1","article_processing_charge":"Yes","has_accepted_license":"1","day":"06","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9913","intvolume":" 22","ddc":["580"],"title":"Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture","status":"public","file":[{"relation":"main_file","file_id":"10090","date_updated":"2021-10-05T13:36:42Z","date_created":"2021-10-05T13:36:42Z","checksum":"750de03dc3b715c37090126c1548ba13","success":1,"file_name":"2021_EmboR_Vega.pdf","access_level":"open_access","file_size":3144854,"content_type":"application/pdf","creator":"cchlebak"}],"oa_version":"Published Version","type":"journal_article","issue":"9","abstract":[{"text":"Nitrate commands genome-wide gene expression changes that impact metabolism, physiology, plant growth, and development. In an effort to identify new components involved in nitrate responses in plants, we analyze the Arabidopsis thaliana root phosphoproteome in response to nitrate treatments via liquid chromatography coupled to tandem mass spectrometry. 176 phosphoproteins show significant changes at 5 or 20 min after nitrate treatments. Proteins identified by 5 min include signaling components such as kinases or transcription factors. In contrast, by 20 min, proteins identified were associated with transporter activity or hormone metabolism functions, among others. The phosphorylation profile of NITRATE TRANSPORTER 1.1 (NRT1.1) mutant plants was significantly altered as compared to wild-type plants, confirming its key role in nitrate signaling pathways that involves phosphorylation changes. Integrative bioinformatics analysis highlights auxin transport as an important mechanism modulated by nitrate signaling at the post-translational level. We validated a new phosphorylation site in PIN2 and provide evidence that it functions in primary and lateral root growth responses to nitrate.","lang":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000681754200001"],"pmid":["34357701 "]},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.15252/embr.202051813","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1469-221X"],"eissn":["1469-3178"]},"month":"09","pmid":1,"year":"2021","acknowledgement":"This work was supported by ANID—Millennium Science Initiative Program—ICN17_022, Fondo de Desarrollo de Areas Prioritarias (FONDAP) Center for Genome Regulation (15090007), ANID—Fondo Nacional de Desarrollo Científico y Tecnológico (FONDECYT) 1180759 (to RAG) and 1171631 (to AV). We would like to thank Unidad de Microscopía Avanzada UC (UMA UC).","department":[{"_id":"EvBe"},{"_id":"GradSch"}],"publisher":"Wiley","publication_status":"published","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10303"}]},"author":[{"last_name":"Vega","first_name":"Andrea","full_name":"Vega, Andrea"},{"last_name":"Fredes","first_name":"Isabel","full_name":"Fredes, Isabel"},{"first_name":"José","last_name":"O’Brien","full_name":"O’Brien, José"},{"full_name":"Shen, Zhouxin","last_name":"Shen","first_name":"Zhouxin"},{"first_name":"Krisztina","last_name":"Ötvös","id":"29B901B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5503-4983","full_name":"Ötvös, Krisztina"},{"last_name":"Abualia","first_name":"Rashed","orcid":"0000-0002-9357-9415","id":"4827E134-F248-11E8-B48F-1D18A9856A87","full_name":"Abualia, Rashed"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","first_name":"Eva","last_name":"Benková","full_name":"Benková, Eva"},{"first_name":"Steven P.","last_name":"Briggs","full_name":"Briggs, Steven P."},{"first_name":"Rodrigo A.","last_name":"Gutiérrez","full_name":"Gutiérrez, Rodrigo A."}],"volume":22,"date_created":"2021-08-15T22:01:30Z","date_updated":"2024-03-28T23:30:40Z","article_number":"e51813","file_date_updated":"2021-10-05T13:36:42Z"},{"publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"EvBe"}],"year":"2021","date_updated":"2023-09-19T14:42:45Z","date_created":"2021-11-18T11:20:59Z","author":[{"orcid":"0000-0002-9357-9415","id":"4827E134-F248-11E8-B48F-1D18A9856A87","last_name":"Abualia","first_name":"Rashed","full_name":"Abualia, Rashed"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"9010"},{"relation":"part_of_dissertation","status":"public","id":"9913"},{"relation":"part_of_dissertation","status":"public","id":"47"}]},"file_date_updated":"2022-12-20T23:30:06Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"degree_awarded":"PhD","supervisor":[{"orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","first_name":"Eva","full_name":"Benková, Eva"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"language":[{"iso":"eng"}],"doi":"10.15479/at:ista:10303","month":"11","publication_identifier":{"issn":["2663-337X"]},"status":"public","title":"Role of hormones in nitrate regulated growth","ddc":["580","581"],"_id":"10303","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":28005730,"creator":"rabualia","file_name":"AbualiaPhDthesisfinalv3.pdf","access_level":"open_access","date_updated":"2022-12-20T23:30:06Z","date_created":"2021-11-22T14:48:21Z","checksum":"dea38b98aa4da1cea03dcd0f10862818","relation":"main_file","embargo":"2022-11-23","file_id":"10331"},{"access_level":"closed","file_name":"AbualiaPhDthesisfinalv3.docx","embargo_to":"open_access","creator":"rabualia","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":62841883,"file_id":"10332","relation":"source_file","checksum":"4cd62da5ec5ba4c32e61f0f6d9e61920","date_created":"2021-11-22T14:48:34Z","date_updated":"2022-12-20T23:30:06Z"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"Nitrogen is an essential macronutrient determining plant growth, development and affecting agricultural productivity. Root, as a hub that perceives and integrates local and systemic signals on the plant’s external and endogenous nitrogen resources, communicates with other plant organs to consolidate their physiology and development in accordance with actual nitrogen balance. Over the last years, numerous studies demonstrated that these comprehensive developmental adaptations rely on the interaction between pathways controlling nitrogen homeostasis and hormonal networks acting globally in the plant body. However, molecular insights into how the information about the nitrogen status is translated through hormonal pathways into specific developmental output are lacking. In my work, I addressed so far poorly understood mechanisms underlying root-to-shoot communication that lead to a rapid re-adjustment of shoot growth and development after nitrate provision. Applying a combination of molecular, cell, and developmental biology approaches, genetics and grafting experiments as well as hormonal analytics, I identified and characterized an unknown molecular framework orchestrating shoot development with a root nitrate sensory system. ","lang":"eng"}],"page":"139","citation":{"chicago":"Abualia, Rashed. “Role of Hormones in Nitrate Regulated Growth.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10303.","mla":"Abualia, Rashed. Role of Hormones in Nitrate Regulated Growth. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10303.","short":"R. Abualia, Role of Hormones in Nitrate Regulated Growth, Institute of Science and Technology Austria, 2021.","ista":"Abualia R. 2021. Role of hormones in nitrate regulated growth. Institute of Science and Technology Austria.","apa":"Abualia, R. (2021). Role of hormones in nitrate regulated growth. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10303","ieee":"R. Abualia, “Role of hormones in nitrate regulated growth,” Institute of Science and Technology Austria, 2021.","ama":"Abualia R. Role of hormones in nitrate regulated growth. 2021. doi:10.15479/at:ista:10303"},"date_published":"2021-11-22T00:00:00Z","day":"22","article_processing_charge":"No","has_accepted_license":"1"},{"oa_version":"Published Version","file":[{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":10629190,"creator":"ahansen","embargo_to":"open_access","file_name":"Thesis_Hansen.docx","access_level":"closed","date_updated":"2022-09-03T22:30:04Z","date_created":"2021-08-30T09:17:39Z","checksum":"66b56f5b988b233dc66a4f4b4fb2cdfe","relation":"source_file","file_id":"9971"},{"file_size":13457469,"content_type":"application/pdf","creator":"ahansen","file_name":"Thesis_Hansen_PDFA-1a.pdf","access_level":"open_access","date_created":"2021-08-30T09:29:44Z","date_updated":"2022-09-03T22:30:04Z","checksum":"204fa40321a1c6289b68c473634c4bf3","relation":"main_file","file_id":"9972","embargo":"2022-09-02"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"9962","status":"public","title":"Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration","ddc":["570"],"abstract":[{"lang":"eng","text":"The brain is one of the largest and most complex organs and it is composed of billions of neurons that communicate together enabling e.g. consciousness. The cerebral cortex is the largest site of neural integration in the central nervous system. Concerted radial migration of newly born cortical projection neurons, from their birthplace to their final position, is a key step in the assembly of the cerebral cortex. The cellular and molecular mechanisms regulating radial neuronal migration in vivo are however still unclear. Recent evidence suggests that distinct signaling cues act cell-autonomously but differentially at certain steps during the overall migration process. Moreover, functional analysis of genetic mosaics (mutant neurons present in wild-type/heterozygote environment) using the MADM (Mosaic Analysis with Double Markers) analyses in comparison to global knockout also indicate a significant degree of non-cell-autonomous and/or community effects in the control of cortical neuron migration. The interactions of cell-intrinsic (cell-autonomous) and cell-extrinsic (non-cell-autonomous) components are largely unknown. In part of this thesis work we established a MADM-based experimental strategy for the quantitative analysis of cell-autonomous gene function versus non-cell-autonomous and/or community effects. The direct comparison of mutant neurons from the genetic mosaic (cell-autonomous) to mutant neurons in the conditional and/or global knockout (cell-autonomous + non-cell-autonomous) allows to quantitatively analyze non-cell-autonomous effects. Such analysis enable the high-resolution analysis of projection neuron migration dynamics in distinct environments with concomitant isolation of genomic and proteomic profiles. Using these experimental paradigms and in combination with computational modeling we show and characterize the nature of non-cell-autonomous effects to coordinate radial neuron migration. Furthermore, this thesis discusses recent developments in neurodevelopment with focus on neuronal polarization and non-cell-autonomous mechanisms in neuronal migration."}],"type":"dissertation","alternative_title":["ISTA Thesis"],"date_published":"2021-09-02T00:00:00Z","citation":{"chicago":"Hansen, Andi H. “Cell-Autonomous Gene Function and Non-Cell-Autonomous Effects in Radial Projection Neuron Migration.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9962.","mla":"Hansen, Andi H. Cell-Autonomous Gene Function and Non-Cell-Autonomous Effects in Radial Projection Neuron Migration. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9962.","short":"A.H. Hansen, Cell-Autonomous Gene Function and Non-Cell-Autonomous Effects in Radial Projection Neuron Migration, Institute of Science and Technology Austria, 2021.","ista":"Hansen AH. 2021. Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration. Institute of Science and Technology Austria.","apa":"Hansen, A. H. (2021). Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9962","ieee":"A. H. Hansen, “Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration,” Institute of Science and Technology Austria, 2021.","ama":"Hansen AH. Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration. 2021. doi:10.15479/at:ista:9962"},"page":"182","has_accepted_license":"1","article_processing_charge":"No","day":"02","keyword":["Neuronal migration","Non-cell-autonomous","Cell-autonomous","Neurodevelopmental disease"],"related_material":{"record":[{"id":"8569","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"960"}]},"author":[{"id":"38853E16-F248-11E8-B48F-1D18A9856A87","last_name":"Hansen","first_name":"Andi H","full_name":"Hansen, Andi H"}],"date_created":"2021-08-29T12:36:50Z","date_updated":"2023-09-22T09:58:30Z","year":"2021","department":[{"_id":"GradSch"},{"_id":"SiHi"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","file_date_updated":"2022-09-03T22:30:04Z","doi":"10.15479/at:ista:9962","language":[{"iso":"eng"}],"supervisor":[{"full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","first_name":"Simon","last_name":"Hippenmeyer"}],"degree_awarded":"PhD","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"project":[{"name":"Molecular Mechanisms of Radial Neuronal Migration","grant_number":"24812","_id":"2625A13E-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"issn":["2663-337X"]},"month":"09"},{"file":[{"checksum":"316ed42ea1b42b0f1a3025bb476266fc","date_created":"2021-09-20T09:27:43Z","date_updated":"2021-12-02T23:30:03Z","file_id":"10026","embargo":"2021-12-01","relation":"main_file","creator":"patrickd","file_size":10028836,"content_type":"application/pdf","access_level":"open_access","file_name":"RevisedQMBSreview.pdf"}],"oa_version":"Preprint","intvolume":" 17","ddc":["539"],"status":"public","title":"Quantum many-body scars and weak breaking of ergodicity","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9428","issue":"6","abstract":[{"lang":"eng","text":"Thermalization is the inevitable fate of many complex quantum systems, whose dynamics allow them to fully explore the vast configuration space regardless of the initial state---the behaviour known as quantum ergodicity. In a quest for experimental realizations of coherent long-time dynamics, efforts have focused on ergodicity-breaking mechanisms, such as integrability and localization. The recent discovery of persistent revivals in quantum simulators based on Rydberg atoms have pointed to the existence of a new type of behaviour where the system rapidly relaxes for most initial conditions, while certain initial states give rise to non-ergodic dynamics. This collective effect has been named ”quantum many-body scarring’by analogy with a related form of weak ergodicity breaking that occurs for a single particle inside a stadium billiard potential. In this Review, we provide a pedagogical introduction to quantum many-body scars and highlight the emerging connections with the semiclassical quantization of many-body systems. We discuss the relation between scars and more general routes towards weak violations of ergodicity due to embedded algebras and non-thermal eigenstates, and highlight possible applications of scars in quantum technology."}],"type":"journal_article","date_published":"2021-06-01T00:00:00Z","page":"675–685","article_type":"review","citation":{"chicago":"Serbyn, Maksym, Dmitry A. Abanin, and Zlatko Papić. “Quantum Many-Body Scars and Weak Breaking of Ergodicity.” Nature Physics. Nature Research, 2021. https://doi.org/10.1038/s41567-021-01230-2.","mla":"Serbyn, Maksym, et al. “Quantum Many-Body Scars and Weak Breaking of Ergodicity.” Nature Physics, vol. 17, no. 6, Nature Research, 2021, pp. 675–685, doi:10.1038/s41567-021-01230-2.","short":"M. Serbyn, D.A. Abanin, Z. Papić, Nature Physics 17 (2021) 675–685.","ista":"Serbyn M, Abanin DA, Papić Z. 2021. Quantum many-body scars and weak breaking of ergodicity. Nature Physics. 17(6), 675–685.","apa":"Serbyn, M., Abanin, D. A., & Papić, Z. (2021). Quantum many-body scars and weak breaking of ergodicity. Nature Physics. Nature Research. https://doi.org/10.1038/s41567-021-01230-2","ieee":"M. Serbyn, D. A. Abanin, and Z. Papić, “Quantum many-body scars and weak breaking of ergodicity,” Nature Physics, vol. 17, no. 6. Nature Research, pp. 675–685, 2021.","ama":"Serbyn M, Abanin DA, Papić Z. Quantum many-body scars and weak breaking of ergodicity. Nature Physics. 2021;17(6):675–685. doi:10.1038/s41567-021-01230-2"},"publication":"Nature Physics","has_accepted_license":"1","article_processing_charge":"No","day":"01","volume":17,"date_updated":"2023-10-18T08:20:59Z","date_created":"2021-05-28T09:03:50Z","author":[{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","first_name":"Maksym","last_name":"Serbyn","full_name":"Serbyn, Maksym"},{"full_name":"Abanin, Dmitry A.","first_name":"Dmitry A.","last_name":"Abanin"},{"full_name":"Papić, Zlatko","first_name":"Zlatko","last_name":"Papić"}],"department":[{"_id":"MaSe"}],"publisher":"Nature Research","publication_status":"published","acknowledgement":"We thank our collaborators K. Bull, S. Choi, J.-Y. Desaules, W. W. Ho, A. Hudomal, M. Lukin, I. Martin, H. Pichler, N. Regnault, I. Vasić and in particular A. Michailidis and C. Turner, without whom this work would not have been possible. We also benefited from discussions with E. Altman, B. A. Bernevig, A. Chandran, P. Fendley, V. Khemani and L. Motrunich. M.S. was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 850899). D.A.A. was supported by the Swiss National Science Foundation and by the ERC under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 864597). Z.P. acknowledges support by the Leverhulme Trust Research Leadership Award RL-2019-015.","year":"2021","ec_funded":1,"file_date_updated":"2021-12-02T23:30:03Z","language":[{"iso":"eng"}],"doi":"10.1038/s41567-021-01230-2","project":[{"_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","grant_number":"850899","call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control"}],"quality_controlled":"1","isi":1,"oa":1,"external_id":{"arxiv":["2011.09486"],"isi":["000655563800002"]},"publication_identifier":{"eissn":["1745-2481"]},"month":"06"},{"has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"01","scopus_import":"1","keyword":["Agronomy and Crop Science","Plant Science","Genetics","General Medicine"],"date_published":"2021-02-01T00:00:00Z","citation":{"ama":"Gelová Z, Gallei MC, Pernisová M, et al. Developmental roles of auxin binding protein 1 in Arabidopsis thaliana. Plant Science. 2021;303. doi:10.1016/j.plantsci.2020.110750","ieee":"Z. Gelová et al., “Developmental roles of auxin binding protein 1 in Arabidopsis thaliana,” Plant Science, vol. 303. Elsevier, 2021.","apa":"Gelová, Z., Gallei, M. C., Pernisová, M., Brunoud, G., Zhang, X., Glanc, M., … Friml, J. (2021). Developmental roles of auxin binding protein 1 in Arabidopsis thaliana. Plant Science. Elsevier. https://doi.org/10.1016/j.plantsci.2020.110750","ista":"Gelová Z, Gallei MC, Pernisová M, Brunoud G, Zhang X, Glanc M, Li L, Michalko J, Pavlovicova Z, Verstraeten I, Han H, Hajny J, Hauschild R, Čovanová M, Zwiewka M, Hörmayer L, Fendrych M, Xu T, Vernoux T, Friml J. 2021. Developmental roles of auxin binding protein 1 in Arabidopsis thaliana. Plant Science. 303, 110750.","short":"Z. Gelová, M.C. Gallei, M. Pernisová, G. Brunoud, X. Zhang, M. Glanc, L. Li, J. Michalko, Z. Pavlovicova, I. Verstraeten, H. Han, J. Hajny, R. Hauschild, M. Čovanová, M. Zwiewka, L. Hörmayer, M. Fendrych, T. Xu, T. Vernoux, J. Friml, Plant Science 303 (2021).","mla":"Gelová, Zuzana, et al. “Developmental Roles of Auxin Binding Protein 1 in Arabidopsis Thaliana.” Plant Science, vol. 303, 110750, Elsevier, 2021, doi:10.1016/j.plantsci.2020.110750.","chicago":"Gelová, Zuzana, Michelle C Gallei, Markéta Pernisová, Géraldine Brunoud, Xixi Zhang, Matous Glanc, Lanxin Li, et al. “Developmental Roles of Auxin Binding Protein 1 in Arabidopsis Thaliana.” Plant Science. Elsevier, 2021. https://doi.org/10.1016/j.plantsci.2020.110750."},"publication":"Plant Science","article_type":"original","abstract":[{"lang":"eng","text":"Auxin is a major plant growth regulator, but current models on auxin perception and signaling cannot explain the whole plethora of auxin effects, in particular those associated with rapid responses. A possible candidate for a component of additional auxin perception mechanisms is the AUXIN BINDING PROTEIN 1 (ABP1), whose function in planta remains unclear.\r\nHere we combined expression analysis with gain- and loss-of-function approaches to analyze the role of ABP1 in plant development. ABP1 shows a broad expression largely overlapping with, but not regulated by, transcriptional auxin response activity. Furthermore, ABP1 activity is not essential for the transcriptional auxin signaling. Genetic in planta analysis revealed that abp1 loss-of-function mutants show largely normal development with minor defects in bolting. On the other hand, ABP1 gain-of-function alleles show a broad range of growth and developmental defects, including root and hypocotyl growth and bending, lateral root and leaf development, bolting, as well as response to heat stress. At the cellular level, ABP1 gain-of-function leads to impaired auxin effect on PIN polar distribution and affects BFA-sensitive PIN intracellular aggregation.\r\nThe gain-of-function analysis suggests a broad, but still mechanistically unclear involvement of ABP1 in plant development, possibly masked in abp1 loss-of-function mutants by a functional redundancy."}],"type":"journal_article","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"9083","checksum":"a7f2562bdca62d67dfa88e271b62a629","success":1,"date_created":"2021-02-04T07:49:25Z","date_updated":"2021-02-04T07:49:25Z","access_level":"open_access","file_name":"2021_PlantScience_Gelova.pdf","content_type":"application/pdf","file_size":12563728,"creator":"dernst"}],"_id":"8931","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 303","ddc":["580"],"status":"public","title":"Developmental roles of auxin binding protein 1 in Arabidopsis thaliana","publication_identifier":{"issn":["0168-9452"]},"month":"02","doi":"10.1016/j.plantsci.2020.110750","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["33487339"],"isi":["000614154500001"]},"project":[{"grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020"},{"_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF"},{"grant_number":"25351","_id":"26B4D67E-B435-11E9-9278-68D0E5697425","name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root"}],"isi":1,"quality_controlled":"1","ec_funded":1,"file_date_updated":"2021-02-04T07:49:25Z","article_number":"110750","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"11626"},{"id":"10083","relation":"dissertation_contains","status":"public"}]},"author":[{"orcid":"0000-0003-4783-1752","id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425","last_name":"Gelová","first_name":"Zuzana","full_name":"Gelová, Zuzana"},{"id":"35A03822-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1286-7368","first_name":"Michelle C","last_name":"Gallei","full_name":"Gallei, Michelle C"},{"last_name":"Pernisová","first_name":"Markéta","full_name":"Pernisová, Markéta"},{"full_name":"Brunoud, Géraldine","first_name":"Géraldine","last_name":"Brunoud"},{"last_name":"Zhang","first_name":"Xixi","orcid":"0000-0001-7048-4627","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","full_name":"Zhang, Xixi"},{"full_name":"Glanc, Matous","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","orcid":"0000-0003-0619-7783","first_name":"Matous","last_name":"Glanc"},{"full_name":"Li, Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5607-272X","first_name":"Lanxin","last_name":"Li"},{"full_name":"Michalko, Jaroslav","last_name":"Michalko","first_name":"Jaroslav","id":"483727CA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pavlovicova, Zlata","last_name":"Pavlovicova","first_name":"Zlata"},{"full_name":"Verstraeten, Inge","first_name":"Inge","last_name":"Verstraeten","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7241-2328"},{"first_name":"Huibin","last_name":"Han","id":"31435098-F248-11E8-B48F-1D18A9856A87","full_name":"Han, Huibin"},{"full_name":"Hajny, Jakub","first_name":"Jakub","last_name":"Hajny","id":"4800CC20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2140-7195"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","first_name":"Robert","last_name":"Hauschild","full_name":"Hauschild, Robert"},{"full_name":"Čovanová, Milada","last_name":"Čovanová","first_name":"Milada"},{"last_name":"Zwiewka","first_name":"Marta","full_name":"Zwiewka, Marta"},{"orcid":"0000-0001-8295-2926","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","last_name":"Hörmayer","first_name":"Lukas","full_name":"Hörmayer, Lukas"},{"id":"43905548-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9767-8699","first_name":"Matyas","last_name":"Fendrych","full_name":"Fendrych, Matyas"},{"last_name":"Xu","first_name":"Tongda","full_name":"Xu, Tongda"},{"full_name":"Vernoux, Teva","last_name":"Vernoux","first_name":"Teva"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří"}],"volume":303,"date_created":"2020-12-09T14:48:28Z","date_updated":"2024-03-28T23:30:44Z","pmid":1,"acknowledgement":"We would like to acknowledge Bioimaging and Life Science Facilities at IST Austria for continuous support and also the Plant Sciences Core Facility of CEITEC Masaryk University for their support with obtaining a part of the scientific data. We gratefully acknowledge Lindy Abas for help with ABP1::GFP-ABP1 construct design. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program [grant agreement no. 742985] and Austrian Science Fund (FWF) [I 3630-B25] to J.F.; DOC Fellowship of the Austrian Academy of Sciences to L.L.; the European Structural and Investment Funds, Operational Programme Research, Development and Education - Project „MSCAfellow@MUNI“ [CZ.02.2.69/0.0/0.0/17_050/0008496] to M.P.. This project was also supported by the Czech Science Foundation [GA 20-20860Y] to M.Z and MEYS CR [project no.CZ.02.1.01/0.0/0.0/16_019/0000738] to M. Č.","year":"2021","publisher":"Elsevier","department":[{"_id":"JiFr"},{"_id":"Bio"}],"publication_status":"published"}]