[{"status":"public","day":"30","OA_type":"free access","ec_funded":1,"project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"citation":{"chicago":"Mishra, Nikhil, and Carl-Philipp J Heisenberg. “Dissecting Organismal Morphogenesis by Bridging Genetics and Biophysics.” Annual Review of Genetics. Annual Reviews, 2021. https://doi.org/10.1146/annurev-genet-071819-103748.","apa":"Mishra, N., & Heisenberg, C.-P. J. (2021). Dissecting organismal morphogenesis by bridging genetics and biophysics. Annual Review of Genetics. Annual Reviews. https://doi.org/10.1146/annurev-genet-071819-103748","mla":"Mishra, Nikhil, and Carl-Philipp J. Heisenberg. “Dissecting Organismal Morphogenesis by Bridging Genetics and Biophysics.” Annual Review of Genetics, vol. 55, Annual Reviews, 2021, pp. 209–33, doi:10.1146/annurev-genet-071819-103748.","short":"N. Mishra, C.-P.J. Heisenberg, Annual Review of Genetics 55 (2021) 209–233.","ieee":"N. Mishra and C.-P. J. Heisenberg, “Dissecting organismal morphogenesis by bridging genetics and biophysics,” Annual Review of Genetics, vol. 55. Annual Reviews, pp. 209–233, 2021.","ama":"Mishra N, Heisenberg C-PJ. Dissecting organismal morphogenesis by bridging genetics and biophysics. Annual Review of Genetics. 2021;55:209-233. doi:10.1146/annurev-genet-071819-103748","ista":"Mishra N, Heisenberg C-PJ. 2021. Dissecting organismal morphogenesis by bridging genetics and biophysics. Annual Review of Genetics. 55, 209–233."},"scopus_import":"1","_id":"10406","acknowledgement":"The authors would like to thank Feyza Nur Arslan, Suyash Naik, Diana Pinheiro, Alexandra Schauer, and Shayan Shamipour for their comments on the draft. N.M. is supported by an ISTplus postdoctoral fellowship (H2020 Marie-Sklodowska-Curie COFUND Action).","type":"journal_article","oa_version":"Published Version","intvolume":" 55","article_type":"original","date_updated":"2026-06-18T08:39:48Z","publisher":"Annual Reviews","department":[{"_id":"CaHe"}],"date_published":"2021-08-30T00:00:00Z","month":"08","language":[{"iso":"eng"}],"oa":1,"isi":1,"publication":"Annual Review of Genetics","doi":"10.1146/annurev-genet-071819-103748","publication_identifier":{"issn":["0066-4197"],"eissn":["1545-2948"]},"date_created":"2021-12-05T23:01:41Z","year":"2021","ddc":["570"],"main_file_link":[{"url":"https://doi.org/10.1146/annurev-genet-071819-103748","open_access":"1"}],"quality_controlled":"1","corr_author":"1","pmid":1,"OA_place":"publisher","volume":55,"author":[{"full_name":"Mishra, Nikhil","orcid":"0000-0002-6425-5788","id":"C4D70E82-1081-11EA-B3ED-9A4C3DDC885E","first_name":"Nikhil","last_name":"Mishra"},{"first_name":"Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","keyword":["morphogenesis","forward genetics","high-resolution microscopy","biophysics","biochemistry","patterning"],"title":"Dissecting organismal morphogenesis by bridging genetics and biophysics","publication_status":"published","external_id":{"isi":["000747220900010"],"pmid":["34460295"]},"abstract":[{"lang":"eng","text":"Multicellular organisms develop complex shapes from much simpler, single-celled zygotes through a process commonly called morphogenesis. Morphogenesis involves an interplay between several factors, ranging from the gene regulatory networks determining cell fate and differentiation to the mechanical processes underlying cell and tissue shape changes. Thus, the study of morphogenesis has historically been based on multidisciplinary approaches at the interface of biology with physics and mathematics. Recent technological advances have further improved our ability to study morphogenesis by bridging the gap between the genetic and biophysical factors through the development of new tools for visualizing, analyzing, and perturbing these factors and their biochemical intermediaries. Here, we review how a combination of genetic, microscopic, biophysical, and biochemical approaches has aided our attempts to understand morphogenesis and discuss potential approaches that may be beneficial to such an inquiry in the future."}],"article_processing_charge":"No","page":"209-233"},{"doi":"10.1007/978-3-030-90453-1_14","publication_identifier":{"eissn":["1611-3349"],"isbn":["9-783-0309-0452-4"],"issn":["0302-9743"]},"date_created":"2021-12-05T23:01:42Z","year":"2021","main_file_link":[{"url":"https://eprint.iacr.org/2021/1224","open_access":"1"}],"conference":{"location":"Raleigh, NC, United States","end_date":"2021-11-11","name":"TCC: Theory of Cryptography Conference","start_date":"2021-11-08"},"quality_controlled":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Chakraborty, Suvradip","id":"B9CD0494-D033-11E9-B219-A439E6697425","first_name":"Suvradip","last_name":"Chakraborty"},{"full_name":"Dziembowski, Stefan","last_name":"Dziembowski","first_name":"Stefan"},{"last_name":"Gałązka","first_name":"Małgorzata","full_name":"Gałązka, Małgorzata"},{"first_name":"Tomasz","last_name":"Lizurej","full_name":"Lizurej, Tomasz"},{"full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z","last_name":"Pietrzak"},{"first_name":"Michelle X","last_name":"Yeo","orcid":"0009-0001-3676-4809","id":"2D82B818-F248-11E8-B48F-1D18A9856A87","full_name":"Yeo, Michelle X"}],"volume":13043,"title":"Trojan-resilience without cryptography","article_processing_charge":"No","page":"397-428","publication_status":"published","external_id":{"isi":["000728364000014"]},"abstract":[{"lang":"eng","text":"Digital hardware Trojans are integrated circuits whose implementation differ from the specification in an arbitrary and malicious way. For example, the circuit can differ from its specified input/output behavior after some fixed number of queries (known as “time bombs”) or on some particular input (known as “cheat codes”). To detect such Trojans, countermeasures using multiparty computation (MPC) or verifiable computation (VC) have been proposed. On a high level, to realize a circuit with specification F one has more sophisticated circuits F⋄ manufactured (where F⋄ specifies a MPC or VC of F ), and then embeds these F⋄ ’s into a master circuit which must be trusted but is relatively simple compared to F . Those solutions impose a significant overhead as F⋄ is much more complex than F , also the master circuits are not exactly trivial. In this work, we show that in restricted settings, where F has no evolving state and is queried on independent inputs, we can achieve a relaxed security notion using very simple constructions. In particular, we do not change the specification of the circuit at all (i.e., F=F⋄ ). Moreover the master circuit basically just queries a subset of its manufactured circuits and checks if they’re all the same. The security we achieve guarantees that, if the manufactured circuits are initially tested on up to T inputs, the master circuit will catch Trojans that try to deviate on significantly more than a 1/T fraction of the inputs. This bound is optimal for the type of construction considered, and we provably achieve it using a construction where 12 instantiations of F need to be embedded into the master. We also discuss an extremely simple construction with just 2 instantiations for which we conjecture that it already achieves the optimal bound."}],"alternative_title":["LNCS"],"status":"public","day":"04","ec_funded":1,"citation":{"ama":"Chakraborty S, Dziembowski S, Gałązka M, Lizurej T, Pietrzak KZ, Yeo MX. Trojan-resilience without cryptography. In: Vol 13043. Springer Nature; 2021:397-428. doi:10.1007/978-3-030-90453-1_14","ista":"Chakraborty S, Dziembowski S, Gałązka M, Lizurej T, Pietrzak KZ, Yeo MX. 2021. Trojan-resilience without cryptography. TCC: Theory of Cryptography Conference, LNCS, vol. 13043, 397–428.","short":"S. Chakraborty, S. Dziembowski, M. Gałązka, T. Lizurej, K.Z. Pietrzak, M.X. Yeo, in:, Springer Nature, 2021, pp. 397–428.","ieee":"S. Chakraborty, S. Dziembowski, M. Gałązka, T. Lizurej, K. Z. Pietrzak, and M. X. Yeo, “Trojan-resilience without cryptography,” presented at the TCC: Theory of Cryptography Conference, Raleigh, NC, United States, 2021, vol. 13043, pp. 397–428.","mla":"Chakraborty, Suvradip, et al. Trojan-Resilience without Cryptography. Vol. 13043, Springer Nature, 2021, pp. 397–428, doi:10.1007/978-3-030-90453-1_14.","chicago":"Chakraborty, Suvradip, Stefan Dziembowski, Małgorzata Gałązka, Tomasz Lizurej, Krzysztof Z Pietrzak, and Michelle X Yeo. “Trojan-Resilience without Cryptography,” 13043:397–428. Springer Nature, 2021. https://doi.org/10.1007/978-3-030-90453-1_14.","apa":"Chakraborty, S., Dziembowski, S., Gałązka, M., Lizurej, T., Pietrzak, K. Z., & Yeo, M. X. (2021). Trojan-resilience without cryptography (Vol. 13043, pp. 397–428). Presented at the TCC: Theory of Cryptography Conference, Raleigh, NC, United States: Springer Nature. https://doi.org/10.1007/978-3-030-90453-1_14"},"project":[{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815","call_identifier":"H2020","name":"Teaching Old Crypto New Tricks"}],"scopus_import":"1","_id":"10407","intvolume":" 13043","oa_version":"Preprint","type":"conference","date_published":"2021-11-04T00:00:00Z","language":[{"iso":"eng"}],"month":"11","date_updated":"2025-04-14T07:22:05Z","department":[{"_id":"KrPi"}],"publisher":"Springer Nature","isi":1,"oa":1},{"project":[{"name":"Teaching Old Crypto New Tricks","call_identifier":"H2020","grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"},{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020"}],"citation":{"ieee":"J. F. Alwen et al., “Grafting key trees: Efficient key management for overlapping groups,” in 19th International Conference, Raleigh, NC, United States, 2021, vol. 13044, pp. 222–253.","short":"J.F. Alwen, B. Auerbach, M.A. Baig, M. Cueto Noval, K. Klein, G. Pascual Perez, K.Z. Pietrzak, M. Walter, in:, 19th International Conference, Springer Nature, 2021, pp. 222–253.","ama":"Alwen JF, Auerbach B, Baig MA, et al. Grafting key trees: Efficient key management for overlapping groups. In: 19th International Conference. Vol 13044. Springer Nature; 2021:222-253. doi:10.1007/978-3-030-90456-2_8","ista":"Alwen JF, Auerbach B, Baig MA, Cueto Noval M, Klein K, Pascual Perez G, Pietrzak KZ, Walter M. 2021. Grafting key trees: Efficient key management for overlapping groups. 19th International Conference. TCC: Theory of Cryptography, LNCS, vol. 13044, 222–253.","apa":"Alwen, J. F., Auerbach, B., Baig, M. A., Cueto Noval, M., Klein, K., Pascual Perez, G., … Walter, M. (2021). Grafting key trees: Efficient key management for overlapping groups. In 19th International Conference (Vol. 13044, pp. 222–253). Raleigh, NC, United States: Springer Nature. https://doi.org/10.1007/978-3-030-90456-2_8","chicago":"Alwen, Joel F, Benedikt Auerbach, Mirza Ahad Baig, Miguel Cueto Noval, Karen Klein, Guillermo Pascual Perez, Krzysztof Z Pietrzak, and Michael Walter. “Grafting Key Trees: Efficient Key Management for Overlapping Groups.” In 19th International Conference, 13044:222–53. Springer Nature, 2021. https://doi.org/10.1007/978-3-030-90456-2_8.","mla":"Alwen, Joel F., et al. “Grafting Key Trees: Efficient Key Management for Overlapping Groups.” 19th International Conference, vol. 13044, Springer Nature, 2021, pp. 222–53, doi:10.1007/978-3-030-90456-2_8."},"ec_funded":1,"status":"public","day":"04","alternative_title":["LNCS"],"oa":1,"isi":1,"department":[{"_id":"KrPi"}],"publisher":"Springer Nature","date_updated":"2026-04-07T13:01:26Z","month":"11","language":[{"iso":"eng"}],"date_published":"2021-11-04T00:00:00Z","type":"conference","acknowledgement":"B. Auerbach, M.A. Baig and K. Pietrzak—received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (682815 - TOCNeT); Karen Klein was supported in part by ERC CoG grant 724307 and conducted part of this work at IST Austria, funded by the ERC under the European Union’s Horizon 2020 research and innovation programme (682815 - TOCNeT); Guillermo Pascual-Perez was funded by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385; Michael Walter conducted part of this work at IST Austria, funded by the ERC under the European Union’s Horizon 2020 research and innovation programme (682815 - TOCNeT).","intvolume":" 13044","oa_version":"Preprint","_id":"10408","scopus_import":"1","quality_controlled":"1","conference":{"end_date":"2021-11-11","location":"Raleigh, NC, United States","start_date":"2021-11-08","name":"TCC: Theory of Cryptography"},"main_file_link":[{"url":"https://eprint.iacr.org/2021/1158","open_access":"1"}],"year":"2021","date_created":"2021-12-05T23:01:42Z","publication":"19th International Conference","publication_identifier":{"eissn":["1611-3349"],"isbn":["9-783-0309-0455-5"],"issn":["0302-9743"],"eisbn":["978-3-030-90456-2"]},"doi":"10.1007/978-3-030-90456-2_8","abstract":[{"lang":"eng","text":"Key trees are often the best solution in terms of transmission cost and storage requirements for managing keys in a setting where a group needs to share a secret key, while being able to efficiently rotate the key material of users (in order to recover from a potential compromise, or to add or remove users). Applications include multicast encryption protocols like LKH (Logical Key Hierarchies) or group messaging like the current IETF proposal TreeKEM. A key tree is a (typically balanced) binary tree, where each node is identified with a key: leaf nodes hold users’ secret keys while the root is the shared group key. For a group of size N, each user just holds log(N) keys (the keys on the path from its leaf to the root) and its entire key material can be rotated by broadcasting 2log(N) ciphertexts (encrypting each fresh key on the path under the keys of its parents). In this work we consider the natural setting where we have many groups with partially overlapping sets of users, and ask if we can find solutions where the cost of rotating a key is better than in the trivial one where we have a separate key tree for each group. We show that in an asymptotic setting (where the number m of groups is fixed while the number N of users grows) there exist more general key graphs whose cost converges to the cost of a single group, thus saving a factor linear in the number of groups over the trivial solution. As our asymptotic “solution” converges very slowly and performs poorly on concrete examples, we propose an algorithm that uses a natural heuristic to compute a key graph for any given group structure. Our algorithm combines two greedy algorithms, and is thus very efficient: it first converts the group structure into a “lattice graph”, which is then turned into a key graph by repeatedly applying the algorithm for constructing a Huffman code. To better understand how far our proposal is from an optimal solution, we prove lower bounds on the update cost of continuous group-key agreement and multicast encryption in a symbolic model admitting (asymmetric) encryption, pseudorandom generators, and secret sharing as building blocks."}],"external_id":{"isi":["000728363700008"]},"publication_status":"published","page":"222-253","article_processing_charge":"No","title":"Grafting key trees: Efficient key management for overlapping groups","volume":13044,"author":[{"full_name":"Alwen, Joel F","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","last_name":"Alwen","first_name":"Joel F"},{"full_name":"Auerbach, Benedikt","id":"D33D2B18-E445-11E9-ABB7-15F4E5697425","orcid":"0000-0002-7553-6606","last_name":"Auerbach","first_name":"Benedikt"},{"first_name":"Mirza Ahad","last_name":"Baig","full_name":"Baig, Mirza Ahad","id":"3EDE6DE4-AA5A-11E9-986D-341CE6697425"},{"orcid":"0000-0002-2505-4246","id":"ffc563a3-f6e0-11ea-865d-e3cce03d17cc","full_name":"Cueto Noval, Miguel","first_name":"Miguel","last_name":"Cueto Noval"},{"full_name":"Klein, Karen","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87","first_name":"Karen","last_name":"Klein"},{"last_name":"Pascual Perez","first_name":"Guillermo","full_name":"Pascual Perez, Guillermo","id":"2D7ABD02-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8630-415X"},{"full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","last_name":"Pietrzak","first_name":"Krzysztof Z"},{"id":"488F98B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3186-2482","full_name":"Walter, Michael","last_name":"Walter","first_name":"Michael"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","related_material":{"record":[{"relation":"dissertation_contains","id":"18088","status":"public"}]}},{"year":"2021","date_created":"2021-12-05T23:01:45Z","doi":"10.1007/978-3-030-90870-6_33","publication_identifier":{"issn":["0302-9743"],"eisbn":["978-3-030-90870-6"],"isbn":["9-783-0309-0869-0"],"eissn":["1611-3349"]},"publication":"24th International Symposium on Formal Methods","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2108.02188"}],"conference":{"start_date":"2021-11-20","name":"FM: Formal Methods","location":"Virtual","end_date":"2021-11-26"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ehsan","last_name":"Kafshdar Goharshadi","id":"103b4fa0-896a-11ed-bdf8-87b697bef40d","orcid":"0000-0002-8595-0587","full_name":"Kafshdar Goharshadi, Ehsan"},{"first_name":"Petr","last_name":"Novotný","full_name":"Novotný, Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jiří","last_name":"Zárevúcky","full_name":"Zárevúcky, Jiří"},{"full_name":"Zikelic, Dorde","orcid":"0000-0002-4681-1699","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","first_name":"Dorde","last_name":"Zikelic"}],"volume":13047,"related_material":{"record":[{"status":"public","relation":"later_version","id":"14778"},{"relation":"dissertation_contains","id":"14539","status":"public"}]},"page":"619-639","article_processing_charge":"No","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"}],"publication_status":"published","external_id":{"arxiv":["2108.02188"],"isi":["000758218600033"]},"title":"On lexicographic proof rules for probabilistic termination","ec_funded":1,"alternative_title":["LNCS"],"status":"public","day":"10","citation":{"mla":"Chatterjee, Krishnendu, et al. “On Lexicographic Proof Rules for Probabilistic Termination.” 24th International Symposium on Formal Methods, vol. 13047, Springer Nature, 2021, pp. 619–39, doi:10.1007/978-3-030-90870-6_33.","apa":"Chatterjee, K., Goharshady, E., 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","chicago":"Chatterjee, Krishnendu, Ehsan 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.","ama":"Chatterjee K, Goharshady E, 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","ista":"Chatterjee K, Goharshady E, 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. Goharshady, P. Novotný, J. Zárevúcky, D. Zikelic, in:, 24th International Symposium on Formal Methods, Springer Nature, 2021, pp. 619–639.","ieee":"K. Chatterjee, E. 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."},"project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program"}],"intvolume":" 13047","oa_version":"Preprint","type":"conference","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.","_id":"10414","scopus_import":"1","isi":1,"oa":1,"month":"11","language":[{"iso":"eng"}],"date_published":"2021-11-10T00:00:00Z","arxiv":1,"publisher":"Springer Nature","department":[{"_id":"KrCh"}],"date_updated":"2026-04-07T13:27:55Z"},{"day":"01","status":"public","alternative_title":["Progress in Mathematics"],"place":"Cham","doi":"10.1007/978-3-030-86872-7","publication_identifier":{"eissn":["2296-505X"],"issn":["0743-1643"],"eisbn":["978-3-030-86872-7"],"isbn":["978-3-030-86871-0"]},"year":"2021","date_created":"2021-12-05T23:01:46Z","quality_controlled":"1","corr_author":"1","citation":{"mla":"Browning, Timothy D. Cubic Forms and the Circle Method. Vol. 343, Springer Nature, 2021, doi:10.1007/978-3-030-86872-7.","apa":"Browning, T. D. (2021). Cubic Forms and the Circle Method (Vol. 343). Cham: Springer Nature. https://doi.org/10.1007/978-3-030-86872-7","chicago":"Browning, Timothy D. Cubic Forms and the Circle Method. Vol. 343. Cham: Springer Nature, 2021. https://doi.org/10.1007/978-3-030-86872-7.","ama":"Browning TD. Cubic Forms and the Circle Method. Vol 343. Cham: Springer Nature; 2021. doi:10.1007/978-3-030-86872-7","ista":"Browning TD. 2021. Cubic Forms and the Circle Method, Cham: Springer Nature, XIV, 166p.","ieee":"T. D. Browning, Cubic Forms and the Circle Method, vol. 343. Cham: Springer Nature, 2021.","short":"T.D. Browning, Cubic Forms and the Circle Method, Springer Nature, Cham, 2021."},"_id":"10415","scopus_import":"1","type":"book","volume":343,"intvolume":" 343","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","author":[{"orcid":"0000-0002-8314-0177","id":"35827D50-F248-11E8-B48F-1D18A9856A87","full_name":"Browning, Timothy D","last_name":"Browning","first_name":"Timothy D"}],"publisher":"Springer Nature","department":[{"_id":"TiBr"}],"date_updated":"2024-10-09T21:01:16Z","month":"12","title":"Cubic Forms and the Circle Method","language":[{"iso":"eng"}],"date_published":"2021-12-01T00:00:00Z","abstract":[{"lang":"eng","text":"The Hardy–Littlewood circle method was invented over a century ago to study integer solutions to special Diophantine equations, but it has since proven to be one of the most successful all-purpose tools available to number theorists. Not only is it capable of handling remarkably general systems of polynomial equations defined over arbitrary global fields, but it can also shed light on the space of rational curves that lie on algebraic varieties. This book, in which the arithmetic of cubic polynomials takes centre stage, is aimed at bringing beginning graduate students into contact with some of the many facets of the circle method, both classical and modern. This monograph is the winner of the 2021 Ferran Sunyer i Balaguer Prize, a prestigious award for books of expository nature presenting the latest developments in an active area of research in mathematics."}],"publication_status":"published","page":"XIV, 166","article_processing_charge":"No"},{"citation":{"ieee":"A. Piankov, “Towards designer materials using customizable particle shape,” Institute of Science and Technology Austria, 2021.","short":"A. Piankov, Towards Designer Materials Using Customizable Particle Shape, Institute of Science and Technology Austria, 2021.","ama":"Piankov A. Towards designer materials using customizable particle shape. 2021. doi:10.15479/at:ista:10422","ista":"Piankov A. 2021. Towards designer materials using customizable particle shape. Institute of Science and Technology Austria.","chicago":"Piankov, Anton. “Towards Designer Materials Using Customizable Particle Shape.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10422.","apa":"Piankov, A. (2021). Towards designer materials using customizable particle shape. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10422","mla":"Piankov, Anton. Towards Designer Materials Using Customizable Particle Shape. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10422."},"day":"07","status":"public","alternative_title":["ISTA Master's Thesis"],"date_updated":"2026-04-08T06:58:55Z","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"CaGo"}],"date_published":"2021-12-07T00:00:00Z","language":[{"iso":"eng"}],"month":"12","file_date_updated":"2022-03-10T12:10:25Z","oa":1,"_id":"10422","type":"dissertation","oa_version":"Published Version","ddc":["530"],"has_accepted_license":"1","file":[{"file_size":394018,"date_updated":"2022-03-10T12:10:25Z","access_level":"closed","relation":"source_file","checksum":"114e8f4b2c002c6c352416c12de2c695","file_id":"10424","creator":"cchlebak","file_name":"Thesis.zip","content_type":"application/x-zip-compressed","date_created":"2021-12-07T11:13:52Z"},{"file_id":"10425","relation":"source_file","checksum":"cd15ae991ced352a9959815f794e657c","access_level":"closed","date_updated":"2022-03-10T12:10:25Z","file_size":47638,"date_created":"2021-12-07T11:14:01Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"Preliminary_pages_Piankov.docx","creator":"cchlebak"},{"success":1,"creator":"cchlebak","content_type":"application/pdf","file_name":"2021_Piankov_combined.pdf","date_created":"2021-12-07T11:20:35Z","file_size":484965,"date_updated":"2021-12-07T11:20:35Z","access_level":"open_access","checksum":"e6899c798b75ba42fab9822bce309050","relation":"main_file","file_id":"10426"}],"corr_author":"1","publication_identifier":{"issn":["2791-4585"]},"doi":"10.15479/at:ista:10422","date_created":"2021-12-07T10:48:06Z","year":"2021","supervisor":[{"first_name":"Carl Peter","last_name":"Goodrich","full_name":"Goodrich, Carl Peter","orcid":"0000-0002-1307-5074","id":"EB352CD2-F68A-11E9-89C5-A432E6697425"}],"degree_awarded":"MS","title":"Towards designer materials using customizable particle shape","publication_status":"published","abstract":[{"text":"Those who aim to devise new materials with desirable properties usually examine present methods first. However, they will find out that some approaches can exist only conceptually without high chances to become practically useful. It seems that a numerical technique called automatic differentiation together with increasing supply of computational accelerators will soon shift many methods of the material design from the category ”unimaginable” to the category ”expensive but possible”. Approach we suggest is not an exception. Our overall goal is to have an efficient and generalizable approach allowing to solve inverse design problems. In this thesis we scratch its surface. We consider jammed systems of identical particles. And ask ourselves how the shape of those particles (or the parameters codifying it) may affect mechanical properties of the system. An indispensable part of reaching the answer is an appropriate particle parametrization. We come up with a simple, yet generalizable and purposeful scheme for it. Using our generalizable shape parameterization, we simulate the formation of a solid composed of pentagonal-like particles and measure anisotropy in the resulting elastic response. Through automatic differentiation techniques, we directly connect the shape parameters with the elastic response. Interestingly, for our system we find that less isotropic particles lead to a more isotropic elastic response. Together with other results known about our method it seems that it can be successfully generalized for different inverse design problems.","lang":"eng"}],"article_processing_charge":"No","OA_place":"publisher","author":[{"last_name":"Piankov","first_name":"Anton","id":"865E3C26-AA8C-11E9-A409-C4C4E5697425","full_name":"Piankov, Anton"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd"},{"type":"conference","acknowledgement":"We gratefully acknowledge funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 805223 ScaleML). PD partly conducted this work while at IST Austria and was supported by the European Union’s Horizon 2020 programme under the Marie Skłodowska-Curie grant agreement No. 754411. SL was funded in part by European Research Council (ERC) under the European Union’s Horizon 2020 programme (grant agreement DAPP, No. 678880, and EPiGRAM-HS, No. 801039).\r\n","oa_version":"Published Version","_id":"10435","oa":1,"date_updated":"2026-06-18T08:41:40Z","department":[{"_id":"DaAl"}],"publisher":"Neural Information Processing Systems Foundation","arxiv":1,"date_published":"2021-12-01T00:00:00Z","month":"12","language":[{"iso":"eng"}],"ec_funded":1,"status":"public","day":"01","project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"},{"name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020","grant_number":"805223","_id":"268A44D6-B435-11E9-9278-68D0E5697425"}],"citation":{"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.","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.","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.","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.","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.","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.","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."},"author":[{"orcid":"0000-0001-5634-0731","id":"3279A00C-F248-11E8-B48F-1D18A9856A87","full_name":"Nadiradze, Giorgi","last_name":"Nadiradze","first_name":"Giorgi"},{"first_name":"Amirmojtaba","last_name":"Sabour","id":"bcc145fd-e77f-11ea-ae8b-80d661dbff67","full_name":"Sabour, Amirmojtaba"},{"last_name":"Davies","first_name":"Peter","full_name":"Davies, Peter","id":"11396234-BB50-11E9-B24C-90FCE5697425","orcid":"0000-0002-5646-9524"},{"first_name":"Shigang","last_name":"Li","full_name":"Li, Shigang"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","last_name":"Alistarh"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"relation":"dissertation_contains","id":"10429","status":"public"}]},"external_id":{"arxiv":["1910.12308"]},"publication_status":"published","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"}],"article_processing_charge":"No","title":"Asynchronous decentralized SGD with quantized and local updates","date_created":"2021-12-09T10:59:12Z","year":"2021","publication":"35th Conference on Neural Information Processing Systems","quality_controlled":"1","conference":{"name":"NeurIPS: Neural Information Processing Systems","start_date":"2021-12-06","end_date":"2021-12-14","location":"Sydney, Australia"},"ddc":["000"],"main_file_link":[{"url":"https://papers.nips.cc/paper/2021/hash/362c99307cdc3f2d8b410652386a9dd1-Abstract.html","open_access":"1"}]},{"volume":127,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"orcid":"0000-0001-9666-3543","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","full_name":"Ghazaryan, Areg","first_name":"Areg","last_name":"Ghazaryan"},{"last_name":"Holder","first_name":"Tobias","full_name":"Holder, Tobias"},{"full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym","last_name":"Serbyn"},{"first_name":"Erez","last_name":"Berg","full_name":"Berg, Erez"}],"related_material":{"link":[{"description":"News on IST Webpage","url":"https://ist.ac.at/en/news/resolving-the-puzzles-of-graphene-superconductivity/","relation":"press_release"}]},"external_id":{"arxiv":["2109.00011"],"isi":["000923819400004"]},"publication_status":"published","abstract":[{"lang":"eng","text":"We show that in a two-dimensional electron gas with an annular Fermi surface, long-range Coulomb interactions can lead to unconventional superconductivity by the Kohn-Luttinger mechanism. Superconductivity is strongly enhanced when the inner and outer Fermi surfaces are close to each other. The most prevalent state has chiral p-wave symmetry, but d-wave and extended s-wave pairing are also possible. We discuss these results in the context of rhombohedral trilayer graphene, where superconductivity was recently discovered in regimes where the normal state has an annular Fermi surface. Using realistic parameters, our mechanism can account for the order of magnitude of Tc, as well as its trends as a function of electron density and perpendicular displacement field. Moreover, it naturally explains some of the outstanding puzzles in this material, that include the weak temperature dependence of the resistivity above Tc, and the proximity of spin singlet superconductivity to the ferromagnetic phase."}],"article_processing_charge":"No","keyword":["general physics and astronomy"],"title":"Unconventional superconductivity in systems with annular Fermi surfaces: Application to rhombohedral trilayer graphene","article_number":"247001","date_created":"2021-12-10T07:51:33Z","year":"2021","publication":"Physical Review Letters","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"doi":"10.1103/physrevlett.127.247001","issue":"24","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/2109.00011","open_access":"1"}],"type":"journal_article","acknowledgement":"We thank Yang-Zhi Chou, Andrey Chubukov, Johannes Hofmann, Steve Kivelson, Sri Raghu, and Sankar das Sarma, Jay Sau, Fengcheng Wu, and Andrea Young for many stimulating discussions and for their comments on the manuscript. E.B. thanks S. Chatterjee, T. Wang, and M. Zaletel for a collaboration on a related topic. A.G. acknowledges support by the European Unions Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement No. 754411. E.B. and T.H. were supported by the European Research Council (ERC) under grant HQMAT (Grant Agreement No. 817799), by the Israel-USA Binational Science Foundation (BSF), and by a Research grant from Irving and Cherna Moskowitz.","intvolume":" 127","oa_version":"Preprint","article_type":"original","scopus_import":"1","_id":"10527","oa":1,"isi":1,"date_updated":"2025-04-14T07:43:47Z","department":[{"_id":"MaSe"}],"arxiv":1,"publisher":"American Physical Society","date_published":"2021-12-09T00:00:00Z","month":"12","language":[{"iso":"eng"}],"ec_funded":1,"day":"09","status":"public","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"citation":{"mla":"Ghazaryan, Areg, et al. “Unconventional Superconductivity in Systems with Annular Fermi Surfaces: Application to Rhombohedral Trilayer Graphene.” Physical Review Letters, vol. 127, no. 24, 247001, American Physical Society, 2021, doi:10.1103/physrevlett.127.247001.","apa":"Ghazaryan, A., Holder, T., Serbyn, M., & Berg, E. (2021). Unconventional superconductivity in systems with annular Fermi surfaces: Application to rhombohedral trilayer graphene. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.127.247001","chicago":"Ghazaryan, Areg, Tobias Holder, Maksym Serbyn, and Erez Berg. “Unconventional Superconductivity in Systems with Annular Fermi Surfaces: Application to Rhombohedral Trilayer Graphene.” Physical Review Letters. American Physical Society, 2021. https://doi.org/10.1103/physrevlett.127.247001.","ama":"Ghazaryan A, Holder T, Serbyn M, Berg E. Unconventional superconductivity in systems with annular Fermi surfaces: Application to rhombohedral trilayer graphene. Physical Review Letters. 2021;127(24). doi:10.1103/physrevlett.127.247001","ista":"Ghazaryan A, Holder T, Serbyn M, Berg E. 2021. Unconventional superconductivity in systems with annular Fermi surfaces: Application to rhombohedral trilayer graphene. Physical Review Letters. 127(24), 247001.","short":"A. Ghazaryan, T. Holder, M. Serbyn, E. Berg, Physical Review Letters 127 (2021).","ieee":"A. Ghazaryan, T. Holder, M. Serbyn, and E. Berg, “Unconventional superconductivity in systems with annular Fermi surfaces: Application to rhombohedral trilayer graphene,” Physical Review Letters, vol. 127, no. 24. American Physical Society, 2021."}},{"article_number":"e72676","year":"2021","date_created":"2021-12-10T13:12:08Z","publication":"eLife","doi":"10.7554/elife.72676","publication_identifier":{"issn":["2050-084X"]},"quality_controlled":"1","file":[{"date_created":"2022-05-16T10:42:22Z","content_type":"application/pdf","file_name":"2021_eLife_Choi.pdf","creator":"dernst","success":1,"file_id":"11384","checksum":"22ed4c55fb550f6da02ae55c359be651","relation":"main_file","access_level":"open_access","file_size":2715200,"date_updated":"2022-05-16T10:42:22Z"}],"corr_author":"1","ddc":["570"],"has_accepted_license":"1","volume":10,"author":[{"first_name":"Jaemyung","last_name":"Choi","full_name":"Choi, Jaemyung"},{"full_name":"Lyons, David B","last_name":"Lyons","first_name":"David B"},{"first_name":"Daniel","last_name":"Zilberman","full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","pmid":1,"abstract":[{"text":"Flowering plants utilize small RNA molecules to guide DNA methyltransferases to genomic sequences. This RNA-directed DNA methylation (RdDM) pathway preferentially targets euchromatic transposable elements. However, RdDM is thought to be recruited by methylation of histone H3 at lysine 9 (H3K9me), a hallmark of heterochromatin. How RdDM is targeted to euchromatin despite an affinity for H3K9me is unclear. Here we show that loss of histone H1 enhances heterochromatic RdDM, preferentially at nucleosome linker DNA. Surprisingly, this does not require SHH1, the RdDM component that binds H3K9me. Furthermore, H3K9me is dispensable for RdDM, as is CG DNA methylation. Instead, we find that non-CG methylation is specifically associated with small RNA biogenesis, and without H1 small RNA production quantitatively expands to non-CG methylated loci. Our results demonstrate that H1 enforces the separation of euchromatic and heterochromatic DNA methylation pathways by excluding the small RNA-generating branch of RdDM from non-CG methylated heterochromatin.","lang":"eng"}],"external_id":{"pmid":["34850679"],"isi":["000754832000001"]},"publication_status":"published","article_processing_charge":"No","title":"Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin","keyword":["genetics and molecular biology"],"ec_funded":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"day":"01","status":"public","project":[{"grant_number":"725746","_id":"62935a00-2b32-11ec-9570-eff30fa39068","name":"Quantitative analysis of DNA methylation maintenance with chromatin","call_identifier":"H2020"}],"citation":{"chicago":"Choi, Jaemyung, David B Lyons, and Daniel Zilberman. “Histone H1 Prevents Non-CG Methylation-Mediated Small RNA Biogenesis in Arabidopsis Heterochromatin.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/elife.72676.","apa":"Choi, J., Lyons, D. B., & Zilberman, D. (2021). Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.72676","mla":"Choi, Jaemyung, et al. “Histone H1 Prevents Non-CG Methylation-Mediated Small RNA Biogenesis in Arabidopsis Heterochromatin.” ELife, vol. 10, e72676, eLife Sciences Publications, 2021, doi:10.7554/elife.72676.","short":"J. Choi, D.B. Lyons, D. Zilberman, ELife 10 (2021).","ieee":"J. Choi, D. B. Lyons, and D. Zilberman, “Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin,” eLife, vol. 10. eLife Sciences Publications, 2021.","ama":"Choi J, Lyons DB, Zilberman D. Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin. eLife. 2021;10. doi:10.7554/elife.72676","ista":"Choi J, Lyons DB, Zilberman D. 2021. Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin. eLife. 10, e72676."},"acknowledgement":"We thank X Feng for helpful comments on the manuscript. This work was supported by a European Research Council grant MaintainMeth (725746) to DZ.","type":"journal_article","article_type":"original","intvolume":" 10","oa_version":"Published Version","_id":"10533","scopus_import":"1","oa":1,"file_date_updated":"2022-05-16T10:42:22Z","isi":1,"publisher":"eLife Sciences Publications","department":[{"_id":"DaZi"}],"date_updated":"2025-04-14T07:57:42Z","language":[{"iso":"eng"}],"month":"12","date_published":"2021-12-01T00:00:00Z"},{"quality_controlled":"1","file":[{"file_id":"10538","checksum":"6b73c214ce54a6894a5854b4364413d7","relation":"main_file","access_level":"open_access","file_size":4979390,"date_updated":"2021-12-13T09:24:42Z","date_created":"2021-12-13T09:24:42Z","content_type":"application/pdf","file_name":"2021_JMaterChemC_Dong.pdf","creator":"cchlebak","success":1}],"has_accepted_license":"1","ddc":["540"],"year":"2021","date_created":"2021-12-12T23:01:27Z","issue":"45","doi":"10.1039/d1tc02753k","publication_identifier":{"eissn":["2050-7526"],"issn":["2050-7534"]},"publication":"Journal of Materials Chemistry C","page":"16217-16225","article_processing_charge":"No","abstract":[{"lang":"eng","text":"For many years, fullerene derivatives have been the main n-type material of organic electronics and optoelectronics. Recently, fullerene derivatives functionalized with ethylene glycol (EG) side chains have been showing important properties such as enhanced dielectric constants, facile doping and enhanced self-assembly capabilities. Here, we have prepared field-effect transistors using a series of these fullerene derivatives equipped with EG side chains of different lengths. Transport data show the beneficial effect of increasing the EG side chain. In order to understand the material properties, full structural determination of these fullerene derivatives has been achieved by coupling the X-ray data with molecular dynamics (MD) simulations. The increase in transport properties is paired with the formation of extended layered structures, efficient molecular packing and an increase in the crystallite alignment. The layer-like structure is composed of conducting layers, containing of closely packed C60 balls approaching the inter-distance of 1 nm, that are separated by well-defined EG layers, where the EG chains are rather splayed with the chain direction almost perpendicular to the layer normal. Such a layered structure appears highly ordered and highly aligned with the C60 planes oriented parallel to the substrate in the thin film configuration. The order inside the thin film increases with the EG chain length, allowing the systems to achieve mobilities as high as 0.053 cm2 V−1 s−1. Our work elucidates the structure of these interesting semiconducting organic molecules and shows that the synergistic use of X-ray structural analysis and MD simulations is a powerful tool to identify the structure of thin organic films for optoelectronic applications."}],"external_id":{"isi":["000688135700001"]},"publication_status":"published","title":"Fullerene derivatives with oligoethylene-glycol side chains: An investigation on the origin of their outstanding transport properties","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Dong, Jingjin","last_name":"Dong","first_name":"Jingjin"},{"first_name":"Selim","last_name":"Sami","full_name":"Sami, Selim"},{"orcid":"0000-0001-7597-043X","id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E","full_name":"Balazs, Daniel","last_name":"Balazs","first_name":"Daniel"},{"first_name":"Riccardo","last_name":"Alessandri","full_name":"Alessandri, Riccardo"},{"first_name":"Fatimeh","last_name":"Jahani","full_name":"Jahani, Fatimeh"},{"full_name":"Qiu, Li","first_name":"Li","last_name":"Qiu"},{"full_name":"Marrink, Siewert J.","last_name":"Marrink","first_name":"Siewert J."},{"last_name":"Havenith","first_name":"Remco W.A.","full_name":"Havenith, Remco W.A."},{"full_name":"Hummelen, Jan C.","first_name":"Jan C.","last_name":"Hummelen"},{"full_name":"Loi, Maria A.","first_name":"Maria A.","last_name":"Loi"},{"full_name":"Portale, Giuseppe","last_name":"Portale","first_name":"Giuseppe"}],"volume":9,"citation":{"short":"J. Dong, S. Sami, D. Balazs, R. Alessandri, F. Jahani, L. Qiu, S.J. Marrink, R.W.A. Havenith, J.C. Hummelen, M.A. Loi, G. Portale, Journal of Materials Chemistry C 9 (2021) 16217–16225.","ieee":"J. Dong et al., “Fullerene derivatives with oligoethylene-glycol side chains: An investigation on the origin of their outstanding transport properties,” Journal of Materials Chemistry C, vol. 9, no. 45. Royal Society of Chemistry, pp. 16217–16225, 2021.","ama":"Dong J, Sami S, Balazs D, et al. Fullerene derivatives with oligoethylene-glycol side chains: An investigation on the origin of their outstanding transport properties. Journal of Materials Chemistry C. 2021;9(45):16217-16225. doi:10.1039/d1tc02753k","ista":"Dong J, Sami S, Balazs D, Alessandri R, Jahani F, Qiu L, Marrink SJ, Havenith RWA, Hummelen JC, Loi MA, Portale G. 2021. Fullerene derivatives with oligoethylene-glycol side chains: An investigation on the origin of their outstanding transport properties. Journal of Materials Chemistry C. 9(45), 16217–16225.","chicago":"Dong, Jingjin, Selim Sami, Daniel Balazs, Riccardo Alessandri, Fatimeh Jahani, Li Qiu, Siewert J. Marrink, et al. “Fullerene Derivatives with Oligoethylene-Glycol Side Chains: An Investigation on the Origin of Their Outstanding Transport Properties.” Journal of Materials Chemistry C. Royal Society of Chemistry, 2021. https://doi.org/10.1039/d1tc02753k.","apa":"Dong, J., Sami, S., Balazs, D., Alessandri, R., Jahani, F., Qiu, L., … Portale, G. (2021). Fullerene derivatives with oligoethylene-glycol side chains: An investigation on the origin of their outstanding transport properties. Journal of Materials Chemistry C. Royal Society of Chemistry. https://doi.org/10.1039/d1tc02753k","mla":"Dong, Jingjin, et al. “Fullerene Derivatives with Oligoethylene-Glycol Side Chains: An Investigation on the Origin of Their Outstanding Transport Properties.” Journal of Materials Chemistry C, vol. 9, no. 45, Royal Society of Chemistry, 2021, pp. 16217–25, doi:10.1039/d1tc02753k."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"day":"07","status":"public","isi":1,"oa":1,"file_date_updated":"2021-12-13T09:24:42Z","language":[{"iso":"eng"}],"month":"12","date_published":"2021-12-07T00:00:00Z","department":[{"_id":"MaIb"}],"publisher":"Royal Society of Chemistry","date_updated":"2023-08-17T06:18:44Z","article_type":"original","oa_version":"Published Version","intvolume":" 9","type":"journal_article","acknowledgement":"J. D. gratefully acknowledges the China Scholarship Council (CSC No. 201606340158) for supporting his PhD studies. S. S. thanks J. Antoja-Lleonart for insightful discussions on simulating the X-ray diffraction patterns. Part of the work was sponsored by NWO Exact and Natural Sciences for the use of supercomputer facilities (Contract no. 17197 7095). Regarding S. S., R. A., R. W. A. H., J. C. H., and M. A. L., this is a publication by the FOM Focus Group “Next Generation Organic Photovoltaics”, participating in the Dutch Institute for Fundamental Energy Research (DIFFER). The ESRF is acknowledged for providing the beamtime. J. D. and G. P. are grateful to the BM26B staff for their great support during the beamtime. M. A. L., D. M. B. are grateful for the financial support of the European Research Council via a Starting Grant (HySPOD, No. 306983).","_id":"10534","scopus_import":"1"},{"date_updated":"2024-10-09T21:01:16Z","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"arxiv":1,"publisher":"Public Library of Science","date_published":"2021-12-01T00:00:00Z","language":[{"iso":"eng"}],"month":"12","file_date_updated":"2022-05-16T08:53:11Z","oa":1,"scopus_import":"1","_id":"10535","acknowledgement":"Computational resources for the study were provided by the Institute of Science and Technology, Austria.\r\nKB received funding from the Scientific Grant Agency of the Slovak Republic under the Grants Nos. 1/0755/19 and 1/0521/20.","type":"journal_article","intvolume":" 17","oa_version":"Published Version","article_type":"original","citation":{"ista":"Bodova K, Szep E, Barton NH. 2021. Dynamic maximum entropy provides accurate approximation of structured population dynamics. PLoS Computational Biology. 17(12), e1009661.","ama":"Bodova K, Szep E, Barton NH. Dynamic maximum entropy provides accurate approximation of structured population dynamics. PLoS Computational Biology. 2021;17(12). doi:10.1371/journal.pcbi.1009661","ieee":"K. Bodova, E. Szep, and N. H. Barton, “Dynamic maximum entropy provides accurate approximation of structured population dynamics,” PLoS Computational Biology, vol. 17, no. 12. Public Library of Science, 2021.","short":"K. Bodova, E. Szep, N.H. Barton, PLoS Computational Biology 17 (2021).","mla":"Bodova, Katarina, et al. “Dynamic Maximum Entropy Provides Accurate Approximation of Structured Population Dynamics.” PLoS Computational Biology, vol. 17, no. 12, e1009661, Public Library of Science, 2021, doi:10.1371/journal.pcbi.1009661.","apa":"Bodova, K., Szep, E., & Barton, N. H. (2021). Dynamic maximum entropy provides accurate approximation of structured population dynamics. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1009661","chicago":"Bodova, Katarina, Eniko Szep, and Nicholas H Barton. “Dynamic Maximum Entropy Provides Accurate Approximation of Structured Population Dynamics.” PLoS Computational Biology. Public Library of Science, 2021. https://doi.org/10.1371/journal.pcbi.1009661."},"day":"01","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"title":"Dynamic maximum entropy provides accurate approximation of structured population dynamics","publication_status":"published","external_id":{"arxiv":["2102.03669"],"pmid":["34851948"]},"abstract":[{"lang":"eng","text":"Realistic models of biological processes typically involve interacting components on multiple scales, driven by changing environment and inherent stochasticity. Such models are often analytically and numerically intractable. We revisit a dynamic maximum entropy method that combines a static maximum entropy with a quasi-stationary approximation. This allows us to reduce stochastic non-equilibrium dynamics expressed by the Fokker-Planck equation to a simpler low-dimensional deterministic dynamics, without the need to track microscopic details. Although the method has been previously applied to a few (rather complicated) applications in population genetics, our main goal here is to explain and to better understand how the method works. We demonstrate the usefulness of the method for two widely studied stochastic problems, highlighting its accuracy in capturing important macroscopic quantities even in rapidly changing non-stationary conditions. For the Ornstein-Uhlenbeck process, the method recovers the exact dynamics whilst for a stochastic island model with migration from other habitats, the approximation retains high macroscopic accuracy under a wide range of scenarios in a dynamic environment."}],"article_processing_charge":"No","pmid":1,"acknowledged_ssus":[{"_id":"ScienComp"}],"volume":17,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Katarína","last_name":"Bod'ová","full_name":"Bod'ová, Katarína","orcid":"0000-0002-7214-0171","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87"},{"id":"485BB5A4-F248-11E8-B48F-1D18A9856A87","full_name":"Szep, Eniko","first_name":"Eniko","last_name":"Szep"},{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H"}],"ddc":["570"],"has_accepted_license":"1","quality_controlled":"1","file":[{"date_created":"2022-05-16T08:53:11Z","content_type":"application/pdf","file_name":"2021_PLOsComBio_Bodova.pdf","success":1,"creator":"dernst","file_id":"11383","access_level":"open_access","relation":"main_file","checksum":"dcd185d4f7e0acee25edf1d6537f447e","file_size":2299486,"date_updated":"2022-05-16T08:53:11Z"}],"corr_author":"1","publication":"PLoS Computational Biology","doi":"10.1371/journal.pcbi.1009661","publication_identifier":{"issn":["1553-734X"],"eissn":["1553-7358"]},"issue":"12","article_number":"e1009661","date_created":"2021-12-12T23:01:27Z","year":"2021"},{"article_type":"original","intvolume":" 11","oa_version":"Published Version","type":"journal_article","acknowledgement":"The authors acknowledge the assistance of the Laboratory Animal Services Center (LASC) – UZH, Center for Microscopy and Image Analysis, and the Flow Cytometry Center of the University of Zurich.","_id":"10536","scopus_import":"1","isi":1,"oa":1,"file_date_updated":"2021-12-13T13:32:37Z","language":[{"iso":"eng"}],"month":"11","date_published":"2021-11-18T00:00:00Z","department":[{"_id":"DaSi"}],"publisher":"Frontiers","date_updated":"2023-08-17T06:20:32Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","day":"18","citation":{"ama":"Stefanescu C, Van Gogh M, Roblek M, Heikenwalder M, Borsig L. TGFβ signaling in myeloid cells promotes lung and liver metastasis through different mechanisms. Frontiers in Oncology. 2021;11. doi:10.3389/fonc.2021.765151","ista":"Stefanescu C, Van Gogh M, Roblek M, Heikenwalder M, Borsig L. 2021. TGFβ signaling in myeloid cells promotes lung and liver metastasis through different mechanisms. Frontiers in Oncology. 11, 765151.","ieee":"C. Stefanescu, M. Van Gogh, M. Roblek, M. Heikenwalder, and L. Borsig, “TGFβ signaling in myeloid cells promotes lung and liver metastasis through different mechanisms,” Frontiers in Oncology, vol. 11. Frontiers, 2021.","short":"C. Stefanescu, M. Van Gogh, M. Roblek, M. Heikenwalder, L. Borsig, Frontiers in Oncology 11 (2021).","mla":"Stefanescu, Cristina, et al. “TGFβ Signaling in Myeloid Cells Promotes Lung and Liver Metastasis through Different Mechanisms.” Frontiers in Oncology, vol. 11, 765151, Frontiers, 2021, doi:10.3389/fonc.2021.765151.","apa":"Stefanescu, C., Van Gogh, M., Roblek, M., Heikenwalder, M., & Borsig, L. (2021). TGFβ signaling in myeloid cells promotes lung and liver metastasis through different mechanisms. Frontiers in Oncology. Frontiers. https://doi.org/10.3389/fonc.2021.765151","chicago":"Stefanescu, Cristina, Merel Van Gogh, Marko Roblek, Mathias Heikenwalder, and Lubor Borsig. “TGFβ Signaling in Myeloid Cells Promotes Lung and Liver Metastasis through Different Mechanisms.” Frontiers in Oncology. Frontiers, 2021. https://doi.org/10.3389/fonc.2021.765151."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Stefanescu","first_name":"Cristina","full_name":"Stefanescu, Cristina"},{"full_name":"Van Gogh, Merel","last_name":"Van Gogh","first_name":"Merel"},{"last_name":"Roblek","first_name":"Marko","orcid":"0000-0001-9588-1389","id":"3047D808-F248-11E8-B48F-1D18A9856A87","full_name":"Roblek, Marko"},{"first_name":"Mathias","last_name":"Heikenwalder","full_name":"Heikenwalder, Mathias"},{"full_name":"Borsig, Lubor","last_name":"Borsig","first_name":"Lubor"}],"volume":11,"pmid":1,"article_processing_charge":"No","abstract":[{"text":"TGFβ overexpression is commonly detected in cancer patients and correlates with poor prognosis and metastasis. Cancer progression is often associated with an enhanced recruitment of myeloid-derived cells to the tumor microenvironment. Here we show that functional TGFβ-signaling in myeloid cells is required for metastasis to the lungs and the liver. Myeloid-specific deletion of Tgfbr2 resulted in reduced spontaneous lung metastasis, which was associated with a reduction of proinflammatory cytokines in the metastatic microenvironment. Notably, CD8+ T cell depletion in myeloid-specific Tgfbr2-deficient mice rescued lung metastasis. Myeloid-specific Tgfbr2-deficiency resulted in reduced liver metastasis with an almost complete absence of myeloid cells within metastatic foci. On contrary, an accumulation of Tgfβ-responsive myeloid cells was associated with an increased recruitment of monocytes and granulocytes and higher proinflammatory cytokine levels in control mice. Monocytic cells isolated from metastatic livers of Tgfbr2-deficient mice showed increased polarization towards the M1 phenotype, Tnfα and Il-1β expression, reduced levels of M2 markers and reduced production of chemokines responsible for myeloid-cell recruitment. No significant differences in Tgfβ levels were observed at metastatic sites of any model. These data demonstrate that Tgfβ signaling in monocytic myeloid cells suppresses CD8+ T cell activity during lung metastasis, while these cells actively contribute to tumor growth during liver metastasis. Thus, myeloid cells modulate metastasis through different mechanisms in a tissue-specific manner.","lang":"eng"}],"publication_status":"published","external_id":{"isi":["000726603400001"],"pmid":["34868988"]},"title":"TGFβ signaling in myeloid cells promotes lung and liver metastasis through different mechanisms","year":"2021","date_created":"2021-12-12T23:01:27Z","article_number":"765151","doi":"10.3389/fonc.2021.765151","publication_identifier":{"eissn":["2234-943X"]},"publication":"Frontiers in Oncology","quality_controlled":"1","file":[{"file_id":"10539","access_level":"open_access","relation":"main_file","checksum":"56cbac80e6891ce750511a30161b7792","date_updated":"2021-12-13T13:32:37Z","file_size":9245199,"date_created":"2021-12-13T13:32:37Z","content_type":"application/pdf","file_name":"2021_Frontiers_Stefanescu.pdf","success":1,"creator":"alisjak"}],"has_accepted_license":"1","ddc":["610"]},{"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"17208"}]},"volume":104,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"id":"CE680B90-D85A-11E9-B684-C920E6697425","orcid":"0000-0002-5383-2869","full_name":"Medina Ramos, Raimel A","first_name":"Raimel A","last_name":"Medina Ramos"},{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym","first_name":"Maksym","last_name":"Serbyn"}],"title":"Duality approach to quantum annealing of the 3-variable exclusive-or satisfiability problem (3-XORSAT)","external_id":{"isi":["000753659200004"],"arxiv":["2106.06344"]},"publication_status":"published","abstract":[{"lang":"eng","text":"Classical models with complex energy landscapes represent a perspective avenue for the near-term application of quantum simulators. Until now, many theoretical works studied the performance of quantum algorithms for models with a unique ground state. However, when the classical problem is in a so-called clustering phase, the ground state manifold is highly degenerate. As an example, we consider a 3-XORSAT model defined on simple hypergraphs. The degeneracy of classical ground state manifold translates into the emergence of an extensive number of Z2 symmetries, which remain intact even in the presence of a quantum transverse magnetic field. We establish a general duality approach that restricts the quantum problem to a given sector of conserved Z2 charges and use it to study how the outcome of the quantum adiabatic algorithm depends on the hypergraph geometry. We show that the tree hypergraph which corresponds to a classically solvable instance of the 3-XORSAT problem features a constant gap, whereas the closed hypergraph encounters a second-order phase transition with a gap vanishing as a power-law in the problem size. The duality developed in this work provides a practical tool for studies of quantum models with classically degenerate energy manifold and reveals potential connections between glasses and gauge theories."}],"article_processing_charge":"No","publication":"Physical Review A","doi":"10.1103/physreva.104.062423","publication_identifier":{"eissn":["2469-9934"],"issn":["2469-9926"]},"issue":"6","article_number":"062423","date_created":"2021-12-14T20:46:07Z","year":"2021","main_file_link":[{"url":"https://arxiv.org/abs/2106.06344","open_access":"1"}],"quality_controlled":"1","scopus_import":"1","_id":"10545","acknowledgement":"We would like to thank S. De Nicola, A. Michaidilis, T. Gulden, Y. Nez-Fernndez, P. Brighi, and S. Sack for fruitful discussions and valuable feedback on the manuscript. M.S. acknowledges useful discussions with E. Altman, L. Cugliandolo, and C. Laumann. We acknowledge support from the European Research Council (ERC) under the European Union's Horizon 2020 Research and Innovation Programme Grant Agreement No. 850899.","type":"journal_article","oa_version":"Preprint","intvolume":" 104","article_type":"original","date_updated":"2026-04-07T12:43:22Z","arxiv":1,"department":[{"_id":"MaSe"}],"publisher":"American Physical Society","date_published":"2021-12-14T00:00:00Z","month":"12","language":[{"iso":"eng"}],"oa":1,"isi":1,"day":"14","status":"public","ec_funded":1,"project":[{"call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","grant_number":"850899"}],"citation":{"chicago":"Medina Ramos, Raimel A, and Maksym Serbyn. “Duality Approach to Quantum Annealing of the 3-Variable Exclusive-or Satisfiability Problem (3-XORSAT).” Physical Review A. American Physical Society, 2021. https://doi.org/10.1103/physreva.104.062423.","apa":"Medina Ramos, R. A., & Serbyn, M. (2021). Duality approach to quantum annealing of the 3-variable exclusive-or satisfiability problem (3-XORSAT). Physical Review A. American Physical Society. https://doi.org/10.1103/physreva.104.062423","mla":"Medina Ramos, Raimel A., and Maksym Serbyn. “Duality Approach to Quantum Annealing of the 3-Variable Exclusive-or Satisfiability Problem (3-XORSAT).” Physical Review A, vol. 104, no. 6, 062423, American Physical Society, 2021, doi:10.1103/physreva.104.062423.","short":"R.A. Medina Ramos, M. Serbyn, Physical Review A 104 (2021).","ieee":"R. A. Medina Ramos and M. Serbyn, “Duality approach to quantum annealing of the 3-variable exclusive-or satisfiability problem (3-XORSAT),” Physical Review A, vol. 104, no. 6. American Physical Society, 2021.","ista":"Medina Ramos RA, Serbyn M. 2021. Duality approach to quantum annealing of the 3-variable exclusive-or satisfiability problem (3-XORSAT). Physical Review A. 104(6), 062423.","ama":"Medina Ramos RA, Serbyn M. Duality approach to quantum annealing of the 3-variable exclusive-or satisfiability problem (3-XORSAT). Physical Review A. 2021;104(6). doi:10.1103/physreva.104.062423"}},{"author":[{"orcid":"0000-0002-0479-558X","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","full_name":"Fischer, Julian L","last_name":"Fischer","first_name":"Julian L"},{"last_name":"Neukamm","first_name":"Stefan","full_name":"Neukamm, Stefan"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":242,"page":"343-452","article_processing_charge":"Yes (via OA deal)","abstract":[{"lang":"eng","text":"We derive optimal-order homogenization rates for random nonlinear elliptic PDEs with monotone nonlinearity in the uniformly elliptic case. More precisely, for a random monotone operator on \\mathbb {R}^d with stationary law (that is spatially homogeneous statistics) and fast decay of correlations on scales larger than the microscale \\varepsilon >0, we establish homogenization error estimates of the order \\varepsilon in case d\\geqq 3, and of the order \\varepsilon |\\log \\varepsilon |^{1/2} in case d=2. Previous results in nonlinear stochastic homogenization have been limited to a small algebraic rate of convergence \\varepsilon ^\\delta . We also establish error estimates for the approximation of the homogenized operator by the method of representative volumes of the order (L/\\varepsilon )^{-d/2} for a representative volume of size L. Our results also hold in the case of systems for which a (small-scale) C^{1,\\alpha } regularity theory is available."}],"publication_status":"published","external_id":{"arxiv":["1908.02273"],"isi":["000668431200001"]},"title":"Optimal homogenization rates in stochastic homogenization of nonlinear uniformly elliptic equations and systems","keyword":["Mechanical Engineering","Mathematics (miscellaneous)","Analysis"],"year":"2021","date_created":"2021-12-16T12:12:33Z","issue":"1","doi":"10.1007/s00205-021-01686-9","publication_identifier":{"issn":["0003-9527"],"eissn":["1432-0673"]},"publication":"Archive for Rational Mechanics and Analysis","file":[{"file_id":"10558","file_size":1640121,"date_updated":"2021-12-16T14:58:08Z","access_level":"open_access","checksum":"cc830b739aed83ca2e32c4e0ce266a4c","relation":"main_file","file_name":"2021_ArchRatMechAnalysis_Fischer.pdf","content_type":"application/pdf","date_created":"2021-12-16T14:58:08Z","success":1,"creator":"cchlebak"}],"quality_controlled":"1","has_accepted_license":"1","ddc":["530"],"article_type":"original","intvolume":" 242","oa_version":"Published Version","type":"journal_article","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). SN acknowledges partial support by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – project number 405009441.","_id":"10549","scopus_import":"1","isi":1,"oa":1,"file_date_updated":"2021-12-16T14:58:08Z","language":[{"iso":"eng"}],"month":"06","date_published":"2021-06-30T00:00:00Z","publisher":"Springer Nature","arxiv":1,"department":[{"_id":"JuFi"}],"date_updated":"2023-08-17T06:23:21Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"day":"30","status":"public","citation":{"ista":"Fischer JL, Neukamm S. 2021. Optimal homogenization rates in stochastic homogenization of nonlinear uniformly elliptic equations and systems. Archive for Rational Mechanics and Analysis. 242(1), 343–452.","ama":"Fischer JL, Neukamm S. Optimal homogenization rates in stochastic homogenization of nonlinear uniformly elliptic equations and systems. Archive for Rational Mechanics and Analysis. 2021;242(1):343-452. doi:10.1007/s00205-021-01686-9","short":"J.L. Fischer, S. Neukamm, Archive for Rational Mechanics and Analysis 242 (2021) 343–452.","ieee":"J. L. Fischer and S. Neukamm, “Optimal homogenization rates in stochastic homogenization of nonlinear uniformly elliptic equations and systems,” Archive for Rational Mechanics and Analysis, vol. 242, no. 1. Springer Nature, pp. 343–452, 2021.","mla":"Fischer, Julian L., and Stefan Neukamm. “Optimal Homogenization Rates in Stochastic Homogenization of Nonlinear Uniformly Elliptic Equations and Systems.” Archive for Rational Mechanics and Analysis, vol. 242, no. 1, Springer Nature, 2021, pp. 343–452, doi:10.1007/s00205-021-01686-9.","apa":"Fischer, J. L., & Neukamm, S. (2021). Optimal homogenization rates in stochastic homogenization of nonlinear uniformly elliptic equations and systems. Archive for Rational Mechanics and Analysis. Springer Nature. https://doi.org/10.1007/s00205-021-01686-9","chicago":"Fischer, Julian L, and Stefan Neukamm. “Optimal Homogenization Rates in Stochastic Homogenization of Nonlinear Uniformly Elliptic Equations and Systems.” Archive for Rational Mechanics and Analysis. Springer Nature, 2021. https://doi.org/10.1007/s00205-021-01686-9."}},{"author":[{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kolmogorov, Vladimir","last_name":"Kolmogorov","first_name":"Vladimir"},{"last_name":"Pock","first_name":"Thomas","full_name":"Pock, Thomas"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","publication_status":"published","external_id":{"arxiv":["2101.12617"]},"abstract":[{"text":"We study a class of convex-concave saddle-point problems of the form minxmaxy⟨Kx,y⟩+fP(x)−h∗(y) where K is a linear operator, fP is the sum of a convex function f with a Lipschitz-continuous gradient and the indicator function of a bounded convex polytope P, and h∗ is a convex (possibly nonsmooth) function. Such problem arises, for example, as a Lagrangian relaxation of various discrete optimization problems. Our main assumptions are the existence of an efficient linear minimization oracle (lmo) for fP and an efficient proximal map for h∗ which motivate the solution via a blend of proximal primal-dual algorithms and Frank-Wolfe algorithms. In case h∗ is the indicator function of a linear constraint and function f is quadratic, we show a O(1/n2) convergence rate on the dual objective, requiring O(nlogn) calls of lmo. If the problem comes from the constrained optimization problem minx∈Rd{fP(x)|Ax−b=0} then we additionally get bound O(1/n2) both on the primal gap and on the infeasibility gap. In the most general case, we show a O(1/n) convergence rate of the primal-dual gap again requiring O(nlogn) calls of lmo. To the best of our knowledge, this improves on the known convergence rates for the considered class of saddle-point problems. We show applications to labeling problems frequently appearing in machine learning and computer vision.","lang":"eng"}],"title":"One-sided Frank-Wolfe algorithms for saddle problems","date_created":"2021-12-16T12:41:20Z","year":"2021","publication":"38th International Conference on Machine Learning","corr_author":"1","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/2101.12617","open_access":"1"}],"conference":{"location":"Virtual","end_date":"2021-07-24","start_date":"2021-07-18","name":"ICML: International Conference on Machine Learning"},"oa_version":"Preprint","acknowledgement":"Vladimir Kolmogorov was supported by the European Research Council under the European Unions Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement no 616160. Thomas Pock acknowledges support by an ERC grant HOMOVIS, no 640156.","type":"conference","scopus_import":"1","_id":"10552","oa":1,"date_published":"2021-07-01T00:00:00Z","language":[{"iso":"eng"}],"month":"07","date_updated":"2025-07-16T08:04:23Z","department":[{"_id":"VlKo"}],"arxiv":1,"ec_funded":1,"day":"01","status":"public","citation":{"mla":"Kolmogorov, Vladimir, and Thomas Pock. “One-Sided Frank-Wolfe Algorithms for Saddle Problems.” 38th International Conference on Machine Learning, 2021.","chicago":"Kolmogorov, Vladimir, and Thomas Pock. “One-Sided Frank-Wolfe Algorithms for Saddle Problems.” In 38th International Conference on Machine Learning, 2021.","apa":"Kolmogorov, V., & Pock, T. (2021). One-sided Frank-Wolfe algorithms for saddle problems. In 38th International Conference on Machine Learning. Virtual.","ama":"Kolmogorov V, Pock T. One-sided Frank-Wolfe algorithms for saddle problems. In: 38th International Conference on Machine Learning. ; 2021.","ista":"Kolmogorov V, Pock T. 2021. One-sided Frank-Wolfe algorithms for saddle problems. 38th International Conference on Machine Learning. ICML: International Conference on Machine Learning.","ieee":"V. Kolmogorov and T. Pock, “One-sided Frank-Wolfe algorithms for saddle problems,” in 38th International Conference on Machine Learning, Virtual, 2021.","short":"V. Kolmogorov, T. Pock, in:, 38th International Conference on Machine Learning, 2021."},"project":[{"name":"Discrete Optimization in Computer Vision: Theory and Practice","call_identifier":"FP7","grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425"}]},{"publication_identifier":{"isbn":["9-781-4503-8548-0"]},"doi":"10.1145/3465084.3467941","publication":"Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing","year":"2021","date_created":"2021-12-16T13:20:19Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2103.03181"}],"conference":{"start_date":"2021-07-26","name":"PODC: Principles of Distributed Computing","end_date":"2021-07-30","location":"Virtual, Italy"},"quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Gelashvili","first_name":"Rati","full_name":"Gelashvili, Rati"},{"id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","full_name":"Kokoris Kogias, Eleftherios","first_name":"Eleftherios","last_name":"Kokoris Kogias"},{"last_name":"Spiegelman","first_name":"Alexander","full_name":"Spiegelman, Alexander"},{"full_name":"Xiang, Zhuolun","first_name":"Zhuolun","last_name":"Xiang"}],"title":"Brief announcement: Be prepared when network goes bad: An asynchronous view-change protocol","keyword":["optimal","state machine replication","fallback","asynchrony","byzantine faults"],"page":"187-190","article_processing_charge":"No","abstract":[{"lang":"eng","text":"The popularity of permissioned blockchain systems demands BFT SMR protocols that are efficient under good network conditions (synchrony) and robust under bad network conditions (asynchrony). The state-of-the-art partially synchronous BFT SMR protocols provide optimal linear communication cost per decision under synchrony and good leaders, but lose liveness under asynchrony. On the other hand, the state-of-the-art asynchronous BFT SMR protocols are live even under asynchrony, but always pay quadratic cost even under synchrony. In this paper, we propose a BFT SMR protocol that achieves the best of both worlds -- optimal linear cost per decision under good networks and leaders, optimal quadratic cost per decision under bad networks, and remains always live."}],"external_id":{"isi":["000744439800018"],"arxiv":["2103.03181"]},"publication_status":"published","status":"public","day":"21","citation":{"short":"R. Gelashvili, E. Kokoris Kogias, A. Spiegelman, Z. Xiang, in:, Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2021, pp. 187–190.","ieee":"R. Gelashvili, E. Kokoris Kogias, A. Spiegelman, and Z. Xiang, “Brief announcement: Be prepared when network goes bad: An asynchronous view-change protocol,” in Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, Virtual, Italy, 2021, pp. 187–190.","ama":"Gelashvili R, Kokoris Kogias E, Spiegelman A, Xiang Z. Brief announcement: Be prepared when network goes bad: An asynchronous view-change protocol. In: Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing. Association for Computing Machinery; 2021:187-190. doi:10.1145/3465084.3467941","ista":"Gelashvili R, Kokoris Kogias E, Spiegelman A, Xiang Z. 2021. Brief announcement: Be prepared when network goes bad: An asynchronous view-change protocol. Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing. PODC: Principles of Distributed Computing, 187–190.","chicago":"Gelashvili, Rati, Eleftherios Kokoris Kogias, Alexander Spiegelman, and Zhuolun Xiang. “Brief Announcement: Be Prepared When Network Goes Bad: An Asynchronous View-Change Protocol.” In Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, 187–90. Association for Computing Machinery, 2021. https://doi.org/10.1145/3465084.3467941.","apa":"Gelashvili, R., Kokoris Kogias, E., Spiegelman, A., & Xiang, Z. (2021). Brief announcement: Be prepared when network goes bad: An asynchronous view-change protocol. In Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing (pp. 187–190). Virtual, Italy: Association for Computing Machinery. https://doi.org/10.1145/3465084.3467941","mla":"Gelashvili, Rati, et al. “Brief Announcement: Be Prepared When Network Goes Bad: An Asynchronous View-Change Protocol.” Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2021, pp. 187–90, doi:10.1145/3465084.3467941."},"_id":"10553","scopus_import":"1","oa_version":"Preprint","type":"conference","language":[{"iso":"eng"}],"month":"07","date_published":"2021-07-21T00:00:00Z","publisher":"Association for Computing Machinery","arxiv":1,"department":[{"_id":"ElKo"}],"date_updated":"2023-09-04T11:42:10Z","isi":1,"oa":1},{"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2102.08325"}],"conference":{"end_date":"2021-07-30","location":"Virtual, Italy","name":"PODC: Principles of Distributed Computing","start_date":"2021-07-26"},"date_created":"2021-12-16T13:21:13Z","year":"2021","doi":"10.1145/3465084.3467905","publication_identifier":{"isbn":["978-1-4503-8548-0"]},"publication":"Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing","article_processing_charge":"No","page":"165-175","external_id":{"isi":["000744439800016"],"arxiv":["2102.08325"]},"publication_status":"published","abstract":[{"lang":"eng","text":"We present DAG-Rider, the first asynchronous Byzantine Atomic Broadcast protocol that achieves optimal resilience, optimal amortized communication complexity, and optimal time complexity. DAG-Rider is post-quantum safe and ensures that all values proposed by correct processes eventually get delivered. We construct DAG-Rider in two layers: In the first layer, processes reliably broadcast their proposals and build a structured Directed Acyclic Graph (DAG) of the communication among them. In the second layer, processes locally observe their DAGs and totally order all proposals with no extra communication."}],"title":"All You Need is DAG","author":[{"full_name":"Keidar, Idit","first_name":"Idit","last_name":"Keidar"},{"last_name":"Kokoris Kogias","first_name":"Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","full_name":"Kokoris Kogias, Eleftherios"},{"full_name":"Naor, Oded","last_name":"Naor","first_name":"Oded"},{"full_name":"Spiegelman, Alexander","first_name":"Alexander","last_name":"Spiegelman"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"apa":"Keidar, I., Kokoris Kogias, E., Naor, O., & Spiegelman, A. (2021). All You Need is DAG. In Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing (pp. 165–175). Virtual, Italy: Association for Computing Machinery. https://doi.org/10.1145/3465084.3467905","chicago":"Keidar, Idit, Eleftherios Kokoris Kogias, Oded Naor, and Alexander Spiegelman. “All You Need Is DAG.” In Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, 165–75. Association for Computing Machinery, 2021. https://doi.org/10.1145/3465084.3467905.","mla":"Keidar, Idit, et al. “All You Need Is DAG.” Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2021, pp. 165–75, doi:10.1145/3465084.3467905.","short":"I. Keidar, E. Kokoris Kogias, O. Naor, A. Spiegelman, in:, Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2021, pp. 165–175.","ieee":"I. Keidar, E. Kokoris Kogias, O. Naor, and A. Spiegelman, “All You Need is DAG,” in Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, Virtual, Italy, 2021, pp. 165–175.","ista":"Keidar I, Kokoris Kogias E, Naor O, Spiegelman A. 2021. All You Need is DAG. Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing. PODC: Principles of Distributed Computing, 165–175.","ama":"Keidar I, Kokoris Kogias E, Naor O, Spiegelman A. All You Need is DAG. In: Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing. Association for Computing Machinery; 2021:165-175. doi:10.1145/3465084.3467905"},"status":"public","day":"21","isi":1,"oa":1,"date_published":"2021-07-21T00:00:00Z","month":"07","language":[{"iso":"eng"}],"date_updated":"2023-08-17T06:24:44Z","arxiv":1,"department":[{"_id":"ElKo"}],"publisher":"Association for Computing Machinery","oa_version":"Preprint","acknowledgement":"Oded Naor is grateful to the Technion Hiroshi Fujiwara Cyber-Security Research Center for providing a research grant. Part of Oded’s work was done while at Novi Research. This work was funded by the Novi team at Facebook. We also wish to thank the Novi Research team for valuable feedback, and in particular George Danezis, Alberto Sonnino, and Dahlia Malkhi.\r\n","type":"conference","scopus_import":"1","_id":"10554"},{"day":"15","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ec_funded":1,"project":[{"name":"Majorana bound states in Ge/SiGe heterostructures","call_identifier":"H2020","grant_number":"844511","_id":"26A151DA-B435-11E9-9278-68D0E5697425"},{"_id":"237E5020-32DE-11EA-91FC-C7463DDC885E","grant_number":"862046","call_identifier":"H2020","name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS"}],"citation":{"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.","chicago":"Aggarwal, Kushagra, Andrea C Hofmann, Daniel Jirovec, Ivan Prieto Gonzalez, Amir Sammak, Marc Botifoll, Sara Martí-Sánchez, et al. “Enhancement of Proximity-Induced Superconductivity in a Planar Ge Hole Gas.” Physical Review Research. American Physical Society, 2021. https://doi.org/10.1103/physrevresearch.3.l022005.","apa":"Aggarwal, K., Hofmann, A. C., Jirovec, D., Prieto Gonzalez, I., Sammak, A., Botifoll, M., … Katsaros, G. (2021). Enhancement of proximity-induced superconductivity in a planar Ge hole gas. Physical Review Research. American Physical Society. https://doi.org/10.1103/physrevresearch.3.l022005","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.","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","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.","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)."},"scopus_import":"1","_id":"10559","type":"journal_article","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.","intvolume":" 3","oa_version":"Published Version","article_type":"original","date_updated":"2025-04-15T08:38:16Z","department":[{"_id":"GeKa"}],"arxiv":1,"publisher":"American Physical Society","date_published":"2021-04-15T00:00:00Z","language":[{"iso":"eng"}],"month":"04","file_date_updated":"2021-12-17T08:12:37Z","oa":1,"publication":"Physical Review Research","publication_identifier":{"issn":["2643-1564"]},"doi":"10.1103/physrevresearch.3.l022005","issue":"2","article_number":"L022005","date_created":"2021-12-16T18:50:57Z","year":"2021","ddc":["620"],"has_accepted_license":"1","file":[{"file_size":1917512,"date_updated":"2021-12-17T08:12:37Z","access_level":"open_access","relation":"main_file","checksum":"60a1bc9c9b616b1b155044bb8cfc6484","file_id":"10561","success":1,"creator":"cchlebak","content_type":"application/pdf","file_name":"2021_PhysRevResearch_Aggarwal.pdf","date_created":"2021-12-17T08:12:37Z"}],"quality_controlled":"1","corr_author":"1","related_material":{"record":[{"status":"public","id":"8834","relation":"research_data"},{"relation":"earlier_version","id":"8831","status":"public"}]},"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"volume":3,"author":[{"full_name":"Aggarwal, Kushagra","id":"b22ab905-3539-11eb-84c3-fc159dcd79cb","orcid":"0000-0001-9985-9293","first_name":"Kushagra","last_name":"Aggarwal"},{"first_name":"Andrea C","last_name":"Hofmann","full_name":"Hofmann, Andrea C","id":"340F461A-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-7197-4801","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","full_name":"Jirovec, Daniel","last_name":"Jirovec","first_name":"Daniel"},{"full_name":"Prieto Gonzalez, Ivan","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7370-5357","first_name":"Ivan","last_name":"Prieto Gonzalez"},{"first_name":"Amir","last_name":"Sammak","full_name":"Sammak, Amir"},{"full_name":"Botifoll, Marc","first_name":"Marc","last_name":"Botifoll"},{"first_name":"Sara","last_name":"Martí-Sánchez","full_name":"Martí-Sánchez, Sara"},{"first_name":"Menno","last_name":"Veldhorst","full_name":"Veldhorst, Menno"},{"full_name":"Arbiol, Jordi","last_name":"Arbiol","first_name":"Jordi"},{"first_name":"Giordano","last_name":"Scappucci","full_name":"Scappucci, Giordano"},{"first_name":"Jeroen","last_name":"Danon","full_name":"Danon, Jeroen"},{"last_name":"Katsaros","first_name":"Georgios","orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","full_name":"Katsaros, Georgios"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","keyword":["general engineering"],"title":"Enhancement of proximity-induced superconductivity in a planar Ge hole gas","external_id":{"arxiv":["2012.00322"]},"publication_status":"published","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"}],"article_processing_charge":"No"},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ec_funded":1,"status":"public","day":"17","citation":{"short":"A. Venturino, S. Siegert, STAR Protocols 2 (2021).","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, 2021.","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","ista":"Venturino A, Siegert S. 2021. Minimally invasive protocols and quantification for microglia-mediated perineuronal net disassembly in mouse brain. STAR Protocols. 2(4), 101012.","chicago":"Venturino, Alessandro, and Sandra Siegert. “Minimally Invasive Protocols and Quantification for Microglia-Mediated Perineuronal Net Disassembly in Mouse Brain.” STAR Protocols. Elsevier, 2021. https://doi.org/10.1016/j.xpro.2021.101012.","apa":"Venturino, A., & Siegert, S. (2021). Minimally invasive protocols and quantification for microglia-mediated perineuronal net disassembly in mouse brain. STAR Protocols. Elsevier. https://doi.org/10.1016/j.xpro.2021.101012","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, 2021, doi:10.1016/j.xpro.2021.101012."},"project":[{"_id":"25D4A630-B435-11E9-9278-68D0E5697425","grant_number":"715571","call_identifier":"H2020","name":"Microglia action towards neuronal circuit formation and function in health and disease"}],"oa_version":"Published Version","intvolume":" 2","article_type":"original","type":"journal_article","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.","scopus_import":"1","_id":"10565","file_date_updated":"2021-12-20T08:58:40Z","oa":1,"date_published":"2021-12-17T00:00:00Z","month":"12","language":[{"iso":"eng"}],"date_updated":"2025-05-14T11:26:30Z","publisher":"Elsevier","department":[{"_id":"SaSi"}],"date_created":"2021-12-19T23:01:32Z","year":"2021","article_number":"101012","publication_identifier":{"eissn":["2666-1667"]},"doi":"10.1016/j.xpro.2021.101012","issue":"4","publication":"STAR Protocols","quality_controlled":"1","file":[{"access_level":"open_access","checksum":"9ea2501056c5df99e84726b845e9b976","relation":"main_file","file_size":6207060,"date_updated":"2021-12-20T08:58:40Z","file_id":"10570","success":1,"creator":"cchlebak","date_created":"2021-12-20T08:58:40Z","content_type":"application/pdf","file_name":"2021_STARProt_Venturino.pdf"}],"has_accepted_license":"1","ddc":["573"],"author":[{"id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2356-9403","full_name":"Venturino, Alessandro","last_name":"Venturino","first_name":"Alessandro"},{"orcid":"0000-0001-8635-0877","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","full_name":"Siegert, Sandra","last_name":"Siegert","first_name":"Sandra"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":2,"acknowledged_ssus":[{"_id":"Bio"}],"article_processing_charge":"Yes","publication_status":"published","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)."}],"title":"Minimally invasive protocols and quantification for microglia-mediated perineuronal net disassembly in mouse brain"},{"scopus_import":"1","_id":"10568","acknowledgement":"We are grateful for the help of Kristina Dauven, Andreas Ebner, Janina Röckner, and Paulina Urban for fish collection in the field and fish maintenance. Furthermore, we thank Fabian Wendt for setting up the aquaria system and Tatjana Liese, Paulina Urban, Jakob Gismann, and Thorsten Reusch for support with DNA extraction and analysis of pipefish population structure. The authors acknowledge support of Isabel Tanger, Agnes Piecyk, Jonas Müller, Grace Walls, Sebastian Albrecht, Julia Böge, and Julia Stefanschitz for their support in preparing cDNA and running of Fluidigm chips. A special thank goes to Diana Gill for general lab support, ordering materials and just being the good spirit of our molecular lab, to Till Bayer for bioinformatics support and to Melanie Heckwolf for fruitful discussion and feedback on the manuscript. HG is very grateful for inspirational office space with ocean view provided by Lisa Hentschel and family. This manuscript has been released as a pre-print at BIORXIV.","type":"journal_article","intvolume":" 9","oa_version":"Published Version","article_type":"original","date_updated":"2023-08-17T06:27:22Z","publisher":"Frontiers Media","department":[{"_id":"SyCr"}],"date_published":"2021-03-25T00:00:00Z","language":[{"iso":"eng"}],"month":"03","file_date_updated":"2021-12-20T10:44:20Z","oa":1,"isi":1,"day":"25","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"citation":{"short":"H. Goehlich, L. Sartoris, K.-S. Wagner, C.C. Wendling, O. Roth, Frontiers in Ecology and Evolution 9 (2021).","ieee":"H. Goehlich, L. Sartoris, K.-S. Wagner, C. C. Wendling, and O. Roth, “Pipefish locally adapted to low salinity in the Baltic Sea retain phenotypic plasticity to cope with ancestral salinity levels,” Frontiers in Ecology and Evolution, vol. 9. Frontiers Media, 2021.","ama":"Goehlich H, Sartoris L, Wagner K-S, Wendling CC, Roth O. Pipefish locally adapted to low salinity in the Baltic Sea retain phenotypic plasticity to cope with ancestral salinity levels. Frontiers in Ecology and Evolution. 2021;9. doi:10.3389/fevo.2021.626442","ista":"Goehlich H, Sartoris L, Wagner K-S, Wendling CC, Roth O. 2021. Pipefish locally adapted to low salinity in the Baltic Sea retain phenotypic plasticity to cope with ancestral salinity levels. Frontiers in Ecology and Evolution. 9, 626442.","apa":"Goehlich, H., Sartoris, L., Wagner, K.-S., Wendling, C. C., & Roth, O. (2021). Pipefish locally adapted to low salinity in the Baltic Sea retain phenotypic plasticity to cope with ancestral salinity levels. Frontiers in Ecology and Evolution. Frontiers Media. https://doi.org/10.3389/fevo.2021.626442","chicago":"Goehlich, Henry, Linda Sartoris, Kim-Sara Wagner, Carolin C. Wendling, and Olivia Roth. “Pipefish Locally Adapted to Low Salinity in the Baltic Sea Retain Phenotypic Plasticity to Cope with Ancestral Salinity Levels.” Frontiers in Ecology and Evolution. Frontiers Media, 2021. https://doi.org/10.3389/fevo.2021.626442.","mla":"Goehlich, Henry, et al. “Pipefish Locally Adapted to Low Salinity in the Baltic Sea Retain Phenotypic Plasticity to Cope with Ancestral Salinity Levels.” Frontiers in Ecology and Evolution, vol. 9, 626442, Frontiers Media, 2021, doi:10.3389/fevo.2021.626442."},"volume":9,"author":[{"full_name":"Goehlich, Henry","first_name":"Henry","last_name":"Goehlich"},{"first_name":"Linda","last_name":"Sartoris","id":"2B9284CA-F248-11E8-B48F-1D18A9856A87","full_name":"Sartoris, Linda"},{"first_name":"Kim-Sara","last_name":"Wagner","full_name":"Wagner, Kim-Sara"},{"first_name":"Carolin C.","last_name":"Wendling","full_name":"Wendling, Carolin C."},{"last_name":"Roth","first_name":"Olivia","full_name":"Roth, Olivia"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","keyword":["ecology","evolution","behavior and systematics","trans-generational plasticity","genetic adaptation","local adaptation","phenotypic plasticity","Baltic Sea","climate change","salinity","syngnathids"],"title":"Pipefish locally adapted to low salinity in the Baltic Sea retain phenotypic plasticity to cope with ancestral salinity levels","external_id":{"isi":["000637736300001"]},"publication_status":"published","abstract":[{"text":"Genetic adaptation and phenotypic plasticity facilitate the migration into new habitats and enable organisms to cope with a rapidly changing environment. In contrast to genetic adaptation that spans multiple generations as an evolutionary process, phenotypic plasticity allows acclimation within the life-time of an organism. Genetic adaptation and phenotypic plasticity are usually studied in isolation, however, only by including their interactive impact, we can understand acclimation and adaptation in nature. We aimed to explore the contribution of adaptation and plasticity in coping with an abiotic (salinity) and a biotic (Vibrio bacteria) stressor using six different populations of the broad-nosed pipefish Syngnathus typhle that originated from either high [14–17 Practical Salinity Unit (PSU)] or low (7–11 PSU) saline environments along the German coastline of the Baltic Sea. We exposed wild caught animals, to either high (15 PSU) or low (7 PSU) salinity, representing native and novel salinity conditions and allowed animals to mate. After male pregnancy, offspring was split and each half was exposed to one of the two salinities and infected with Vibrio alginolyticus bacteria that were evolved at either of the two salinities in a fully reciprocal design. We investigated life-history traits of fathers and expression of 47 target genes in mothers and offspring. Pregnant males originating from high salinity exposed to low salinity were highly susceptible to opportunistic fungi infections resulting in decreased offspring size and number. In contrast, no signs of fungal infection were identified in fathers originating from low saline conditions suggesting that genetic adaptation has the potential to overcome the challenges encountered at low salinity. Offspring from parents with low saline origin survived better at low salinity suggesting genetic adaptation to low salinity. In addition, gene expression analyses of juveniles indicated patterns of local adaptation, trans-generational plasticity and developmental plasticity. In conclusion, our study suggests that pipefish are locally adapted to the low salinity in their environment, however, they are retaining phenotypic plasticity, which allows them to also cope with ancestral salinity levels and prevailing pathogens.","lang":"eng"}],"article_processing_charge":"No","publication":"Frontiers in Ecology and Evolution","doi":"10.3389/fevo.2021.626442","publication_identifier":{"issn":["2296-701X"]},"article_number":"626442","date_created":"2021-12-20T07:53:19Z","year":"2021","ddc":["597"],"has_accepted_license":"1","quality_controlled":"1","file":[{"file_name":"2021_Frontiers_Goehlich.pdf","content_type":"application/pdf","date_created":"2021-12-20T10:44:20Z","success":1,"creator":"alisjak","file_id":"10572","date_updated":"2021-12-20T10:44:20Z","file_size":3175085,"access_level":"open_access","checksum":"8d6e2b767bb0240a9b5a3a3555be51fd","relation":"main_file"}]}]