[{"project":[{"name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","grant_number":"F6504"},{"grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics","_id":"256E75B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"publication":"Journal of Functional Analysis","arxiv":1,"article_number":"109234","publication_identifier":{"eissn":["1096-0783"],"issn":["0022-1236"]},"year":"2021","acknowledgement":"The authors are grateful to Professor Kazuhiro Kuwae for kindly providing a copy of [49]. They are also grateful to Dr. Bang-Xian Han for helpful discussions on the Sobolev-to-Lipschitz property on metric measure spaces. They wish to express their deepest gratitude to an anonymous Reviewer, whose punctual remarks and comments greatly improved the accessibility and overall quality of the initial submission. This work was completed while L.D.S. was a member of the Institut für Angewandte Mathematik of the University of Bonn. He acknowledges funding of his position at that time by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) through the Sonderforschungsbereich (Sfb, Collaborative Research Center) 1060 - project number 211504053. He also acknowledges funding of his current position by the Austrian Science Fund (FWF) grant F65, and by the European Research Council (ERC, grant No. 716117, awarded to Prof. Dr. Jan Maas). K.S. gratefully acknowledges funding by: the JSPS Overseas Research Fellowships, Grant Nr. 290142; World Premier International Research Center Initiative (WPI), MEXT, Japan; and JSPS Grant-in-Aid for Scientific Research on Innovative Areas “Discrete Geometric Analysis for Materials Design”, Grant Number 17H06465.","article_type":"original","ec_funded":1,"oa":1,"day":"15","doi":"10.1016/j.jfa.2021.109234","date_published":"2021-09-15T00:00:00Z","intvolume":"       281","language":[{"iso":"eng"}],"status":"public","article_processing_charge":"No","author":[{"orcid":"0000-0002-9881-6870","id":"ECEBF480-9E4F-11EA-B557-B0823DDC885E","last_name":"Dello Schiavo","full_name":"Dello Schiavo, Lorenzo","first_name":"Lorenzo"},{"first_name":"Kohei","last_name":"Suzuki","full_name":"Suzuki, Kohei"}],"title":"Rademacher-type theorems and Sobolev-to-Lipschitz properties for strongly local Dirichlet spaces","date_updated":"2025-04-14T07:27:45Z","oa_version":"Preprint","corr_author":"1","publisher":"Elsevier","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2008.01492","open_access":"1"}],"volume":281,"department":[{"_id":"JaMa"}],"citation":{"short":"L. Dello Schiavo, K. Suzuki, Journal of Functional Analysis 281 (2021).","ieee":"L. Dello Schiavo and K. Suzuki, “Rademacher-type theorems and Sobolev-to-Lipschitz properties for strongly local Dirichlet spaces,” <i>Journal of Functional Analysis</i>, vol. 281, no. 11. Elsevier, 2021.","ama":"Dello Schiavo L, Suzuki K. Rademacher-type theorems and Sobolev-to-Lipschitz properties for strongly local Dirichlet spaces. <i>Journal of Functional Analysis</i>. 2021;281(11). doi:<a href=\"https://doi.org/10.1016/j.jfa.2021.109234\">10.1016/j.jfa.2021.109234</a>","apa":"Dello Schiavo, L., &#38; Suzuki, K. (2021). Rademacher-type theorems and Sobolev-to-Lipschitz properties for strongly local Dirichlet spaces. <i>Journal of Functional Analysis</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jfa.2021.109234\">https://doi.org/10.1016/j.jfa.2021.109234</a>","ista":"Dello Schiavo L, Suzuki K. 2021. Rademacher-type theorems and Sobolev-to-Lipschitz properties for strongly local Dirichlet spaces. Journal of Functional Analysis. 281(11), 109234.","chicago":"Dello Schiavo, Lorenzo, and Kohei Suzuki. “Rademacher-Type Theorems and Sobolev-to-Lipschitz Properties for Strongly Local Dirichlet Spaces.” <i>Journal of Functional Analysis</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.jfa.2021.109234\">https://doi.org/10.1016/j.jfa.2021.109234</a>.","mla":"Dello Schiavo, Lorenzo, and Kohei Suzuki. “Rademacher-Type Theorems and Sobolev-to-Lipschitz Properties for Strongly Local Dirichlet Spaces.” <i>Journal of Functional Analysis</i>, vol. 281, no. 11, 109234, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.jfa.2021.109234\">10.1016/j.jfa.2021.109234</a>."},"abstract":[{"text":"We extensively discuss the Rademacher and Sobolev-to-Lipschitz properties for generalized intrinsic distances on strongly local Dirichlet spaces possibly without square field operator. We present many non-smooth and infinite-dimensional examples. As an application, we prove the integral Varadhan short-time asymptotic with respect to a given distance function for a large class of strongly local Dirichlet forms.","lang":"eng"}],"type":"journal_article","quality_controlled":"1","month":"09","scopus_import":"1","issue":"11","_id":"10070","external_id":{"isi":["000703896600005"],"arxiv":["2008.01492"]},"publication_status":"published","date_created":"2021-10-03T22:01:21Z"},{"oa_version":"Published Version","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","title":"How to tutorial-a-thon","author":[{"first_name":"Henry","full_name":"Adams, Henry","last_name":"Adams"},{"first_name":"Hana","id":"D9B8E14C-3C26-11EA-98F5-1F833DDC885E","full_name":"Kourimska, Hana","last_name":"Kourimska"},{"first_name":"Teresa","last_name":"Heiss","full_name":"Heiss, Teresa","id":"4879BB4E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1780-2689"},{"first_name":"Sarah","full_name":"Percival, Sarah","last_name":"Percival"},{"first_name":"Lori","last_name":"Ziegelmeier","full_name":"Ziegelmeier, Lori"}],"page":"1511-1514","date_updated":"2021-12-03T07:31:26Z","year":"2021","publication_identifier":{"eissn":["1088-9477"],"issn":["0002-9920"]},"article_type":"letter_note","day":"01","doi":"10.1090/noti2349","oa":1,"intvolume":"        68","date_published":"2021-10-01T00:00:00Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication":"Notices of the American Mathematical Society","alternative_title":["Early Career"],"publication_status":"published","date_created":"2021-10-03T22:01:22Z","month":"10","issue":"9","scopus_import":"1","_id":"10071","type":"journal_article","citation":{"short":"H. Adams, H. Kourimska, T. Heiss, S. Percival, L. Ziegelmeier, Notices of the American Mathematical Society 68 (2021) 1511–1514.","chicago":"Adams, Henry, Hana Kourimska, Teresa Heiss, Sarah Percival, and Lori Ziegelmeier. “How to Tutorial-a-Thon.” <i>Notices of the American Mathematical Society</i>. American Mathematical Society, 2021. <a href=\"https://doi.org/10.1090/noti2349\">https://doi.org/10.1090/noti2349</a>.","ista":"Adams H, Kourimska H, Heiss T, Percival S, Ziegelmeier L. 2021. How to tutorial-a-thon. Notices of the American Mathematical Society. 68(9), 1511–1514.","mla":"Adams, Henry, et al. “How to Tutorial-a-Thon.” <i>Notices of the American Mathematical Society</i>, vol. 68, no. 9, American Mathematical Society, 2021, pp. 1511–14, doi:<a href=\"https://doi.org/10.1090/noti2349\">10.1090/noti2349</a>.","ama":"Adams H, Kourimska H, Heiss T, Percival S, Ziegelmeier L. How to tutorial-a-thon. <i>Notices of the American Mathematical Society</i>. 2021;68(9):1511-1514. doi:<a href=\"https://doi.org/10.1090/noti2349\">10.1090/noti2349</a>","apa":"Adams, H., Kourimska, H., Heiss, T., Percival, S., &#38; Ziegelmeier, L. (2021). How to tutorial-a-thon. <i>Notices of the American Mathematical Society</i>. American Mathematical Society. <a href=\"https://doi.org/10.1090/noti2349\">https://doi.org/10.1090/noti2349</a>","ieee":"H. Adams, H. Kourimska, T. Heiss, S. Percival, and L. Ziegelmeier, “How to tutorial-a-thon,” <i>Notices of the American Mathematical Society</i>, vol. 68, no. 9. American Mathematical Society, pp. 1511–1514, 2021."},"quality_controlled":"1","publisher":"American Mathematical Society","main_file_link":[{"url":"http://www.ams.org/notices/","open_access":"1"}],"volume":68,"department":[{"_id":"HeEd"}]},{"month":"09","scopus_import":"1","_id":"10072","conference":{"name":"APPROX/RANDOM: Approximation Algorithms for Combinatorial Optimization Problems/ Randomization and Computation","location":"Virtual","start_date":"2021-08-16","end_date":"2021-08-18"},"alternative_title":["LIPIcs"],"external_id":{"arxiv":["2008.05569"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"published","date_created":"2021-10-03T22:01:22Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","volume":207,"department":[{"_id":"VlKo"}],"citation":{"short":"D.G. Harris, F. Iliopoulos, V. Kolmogorov, in:, Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021.","ieee":"D. G. Harris, F. Iliopoulos, and V. Kolmogorov, “A new notion of commutativity for the algorithmic Lovász Local Lemma,” in <i>Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques</i>, Virtual, 2021, vol. 207.","apa":"Harris, D. G., Iliopoulos, F., &#38; Kolmogorov, V. (2021). A new notion of commutativity for the algorithmic Lovász Local Lemma. In <i>Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques</i> (Vol. 207). Virtual: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.APPROX/RANDOM.2021.31\">https://doi.org/10.4230/LIPIcs.APPROX/RANDOM.2021.31</a>","ama":"Harris DG, Iliopoulos F, Kolmogorov V. A new notion of commutativity for the algorithmic Lovász Local Lemma. In: <i>Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques</i>. Vol 207. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2021. doi:<a href=\"https://doi.org/10.4230/LIPIcs.APPROX/RANDOM.2021.31\">10.4230/LIPIcs.APPROX/RANDOM.2021.31</a>","ista":"Harris DG, Iliopoulos F, Kolmogorov V. 2021. A new notion of commutativity for the algorithmic Lovász Local Lemma. Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques. APPROX/RANDOM: Approximation Algorithms for Combinatorial Optimization Problems/ Randomization and Computation, LIPIcs, vol. 207, 31.","chicago":"Harris, David G., Fotis Iliopoulos, and Vladimir Kolmogorov. “A New Notion of Commutativity for the Algorithmic Lovász Local Lemma.” In <i>Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques</i>, Vol. 207. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021. <a href=\"https://doi.org/10.4230/LIPIcs.APPROX/RANDOM.2021.31\">https://doi.org/10.4230/LIPIcs.APPROX/RANDOM.2021.31</a>.","mla":"Harris, David G., et al. “A New Notion of Commutativity for the Algorithmic Lovász Local Lemma.” <i>Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques</i>, vol. 207, 31, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021, doi:<a href=\"https://doi.org/10.4230/LIPIcs.APPROX/RANDOM.2021.31\">10.4230/LIPIcs.APPROX/RANDOM.2021.31</a>."},"type":"conference","abstract":[{"lang":"eng","text":"The Lovász Local Lemma (LLL) is a powerful tool in probabilistic combinatorics which can be used to establish the existence of objects that satisfy certain properties. The breakthrough paper of Moser and Tardos and follow-up works revealed that the LLL has intimate connections with a class of stochastic local search algorithms for finding such desirable objects. In particular, it can be seen as a sufficient condition for this type of algorithms to converge fast. Besides conditions for existence of and fast convergence to desirable objects, one may naturally ask further questions regarding properties of these algorithms. For instance, \"are they parallelizable?\", \"how many solutions can they output?\", \"what is the expected \"weight\" of a solution?\", etc. These questions and more have been answered for a class of LLL-inspired algorithms called commutative. In this paper we introduce a new, very natural and more general notion of commutativity (essentially matrix commutativity) which allows us to show a number of new refined properties of LLL-inspired local search algorithms with significantly simpler proofs."}],"quality_controlled":"1","language":[{"iso":"eng"}],"status":"public","has_accepted_license":"1","article_processing_charge":"Yes","file_date_updated":"2021-10-06T13:51:54Z","author":[{"full_name":"Harris, David G.","last_name":"Harris","first_name":"David G."},{"full_name":"Iliopoulos, Fotis","last_name":"Iliopoulos","first_name":"Fotis"},{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kolmogorov, Vladimir","last_name":"Kolmogorov","first_name":"Vladimir"}],"title":"A new notion of commutativity for the algorithmic Lovász Local Lemma","date_updated":"2026-02-10T09:59:59Z","related_material":{"record":[{"relation":"later_version","id":"21143","status":"public"}]},"oa_version":"Published Version","project":[{"name":"Discrete Optimization in Computer Vision: Theory and Practice","_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160","call_identifier":"FP7"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"arxiv":1,"publication":"Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques","article_number":"31","publication_identifier":{"issn":["1868-8969"],"isbn":["978-3-9597-7207-5"]},"acknowledgement":"Fotis Iliopoulos: This material is based upon work directly supported by the IAS Fund for Math and indirectly supported by the National Science Foundation Grant No. CCF-1900460. Any opinions, findings and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation. This work is also supported by the National Science Foundation Grant No. CCF-1815328.\r\nVladimir Kolmogorov: Supported by the European Research Council under the European Unions Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement no 616160.","year":"2021","ec_funded":1,"file":[{"file_id":"10098","date_updated":"2021-10-06T13:51:54Z","relation":"main_file","checksum":"9d2544d53aa5b01565c6891d97a4d765","content_type":"application/pdf","file_size":804472,"creator":"cchlebak","date_created":"2021-10-06T13:51:54Z","file_name":"2021_LIPIcs_Harris.pdf","success":1,"access_level":"open_access"}],"oa":1,"doi":"10.4230/LIPIcs.APPROX/RANDOM.2021.31","day":"15","date_published":"2021-09-15T00:00:00Z","intvolume":"       207"},{"volume":14,"department":[{"_id":"MaIb"}],"publisher":"MDPI","corr_author":"1","pmid":1,"abstract":[{"lang":"eng","text":"Thermoelectric materials enable the direct conversion between heat and electricity. SnTe is a promising candidate due to its high charge transport performance. Here, we prepared SnTe nanocomposites by employing an aqueous method to synthetize SnTe nanoparticles (NP), followed by a unique surface treatment prior NP consolidation. This synthetic approach allowed optimizing the charge and phonon transport synergistically. The novelty of this strategy was the use of a soluble PbS molecular complex prepared using a thiol-amine solvent mixture that upon blending is adsorbed on the SnTe NP surface. Upon consolidation with spark plasma sintering, SnTe-PbS nanocomposite is formed. The presence of PbS complexes significantly compensates for the Sn vacancy and increases the average grain size of the nanocomposite, thus improving the carrier mobility. Moreover, lattice thermal conductivity is also reduced by the Pb and S-induced mass and strain fluctuation. As a result, an enhanced ZT of ca. 0.8 is reached at 873 K. Our finding provides a novel strategy to conduct rational surface treatment on NP-based thermoelectrics."}],"type":"journal_article","citation":{"short":"C. Chang, M. Ibáñez, Materials 14 (2021).","ama":"Chang C, Ibáñez M. Enhanced thermoelectric performance by surface engineering in SnTe-PbS nanocomposites. <i>Materials</i>. 2021;14(18). doi:<a href=\"https://doi.org/10.3390/ma14185416\">10.3390/ma14185416</a>","ieee":"C. Chang and M. Ibáñez, “Enhanced thermoelectric performance by surface engineering in SnTe-PbS nanocomposites,” <i>Materials</i>, vol. 14, no. 18. MDPI, 2021.","apa":"Chang, C., &#38; Ibáñez, M. (2021). Enhanced thermoelectric performance by surface engineering in SnTe-PbS nanocomposites. <i>Materials</i>. MDPI. <a href=\"https://doi.org/10.3390/ma14185416\">https://doi.org/10.3390/ma14185416</a>","mla":"Chang, Cheng, and Maria Ibáñez. “Enhanced Thermoelectric Performance by Surface Engineering in SnTe-PbS Nanocomposites.” <i>Materials</i>, vol. 14, no. 18, 5416, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/ma14185416\">10.3390/ma14185416</a>.","ista":"Chang C, Ibáñez M. 2021. Enhanced thermoelectric performance by surface engineering in SnTe-PbS nanocomposites. Materials. 14(18), 5416.","chicago":"Chang, Cheng, and Maria Ibáñez. “Enhanced Thermoelectric Performance by Surface Engineering in SnTe-PbS Nanocomposites.” <i>Materials</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/ma14185416\">https://doi.org/10.3390/ma14185416</a>."},"quality_controlled":"1","_id":"10073","month":"09","scopus_import":"1","issue":"18","publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_created":"2021-10-03T22:01:23Z","external_id":{"isi":["000700689400001"],"pmid":["34576640"]},"publication":"Materials","isi":1,"project":[{"name":"Bottom-up Engineering for Thermoelectric Applications","_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A","grant_number":"M02889"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["540"],"doi":"10.3390/ma14185416","day":"19","oa":1,"file":[{"access_level":"open_access","date_created":"2021-10-14T11:56:39Z","success":1,"file_name":"2021_Materials_Chang.pdf","file_size":4404141,"creator":"cchlebak","relation":"main_file","content_type":"application/pdf","checksum":"4929dfc673a3ae77c010b6174279cc1d","file_id":"10140","date_updated":"2021-10-14T11:56:39Z"}],"intvolume":"        14","date_published":"2021-09-19T00:00:00Z","acknowledged_ssus":[{"_id":"EM-Fac"}],"article_number":"5416","year":"2021","article_type":"original","publication_identifier":{"eissn":["1996-1944"]},"acknowledgement":"The authors thank the EMF facility in IST Austria for providing SEM and EDX measurements.\r\n","title":"Enhanced thermoelectric performance by surface engineering in SnTe-PbS nanocomposites","author":[{"id":"9E331C2E-9F27-11E9-AE48-5033E6697425","full_name":"Chang, Cheng","last_name":"Chang","orcid":"0000-0002-9515-4277","first_name":"Cheng"},{"first_name":"Maria","orcid":"0000-0001-5013-2843","last_name":"Ibáñez","full_name":"Ibáñez, Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2025-04-14T09:29:32Z","status":"public","language":[{"iso":"eng"}],"file_date_updated":"2021-10-14T11:56:39Z","article_processing_charge":"Yes","has_accepted_license":"1","oa_version":"Published Version"},{"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"KrCh"}],"volume":202,"quality_controlled":"1","type":"conference","abstract":[{"lang":"eng","text":"We study the expressiveness and succinctness of good-for-games pushdown automata (GFG-PDA) over finite words, that is, pushdown automata whose nondeterminism can be resolved based on the run constructed so far, but independently of the remainder of the input word. We prove that GFG-PDA recognise more languages than deterministic PDA (DPDA) but not all context-free languages (CFL). This class is orthogonal to unambiguous CFL. We further show that GFG-PDA can be exponentially more succinct than DPDA, while PDA can be double-exponentially more succinct than GFG-PDA. We also study GFGness in visibly pushdown automata (VPA), which enjoy better closure properties than PDA, and for which we show GFGness to be ExpTime-complete. GFG-VPA can be exponentially more succinct than deterministic VPA, while VPA can be exponentially more succinct than GFG-VPA. Both of these lower bounds are tight. Finally, we study the complexity of resolving nondeterminism in GFG-PDA. Every GFG-PDA has a positional resolver, a function that resolves nondeterminism and that is only dependant on the current configuration. Pushdown transducers are sufficient to implement the resolvers of GFG-VPA, but not those of GFG-PDA. GFG-PDA with finite-state resolvers are determinisable."}],"citation":{"short":"S. Guha, I.R. Jecker, K. Lehtinen, M. Zimmermann, in:, 46th International Symposium on Mathematical Foundations of Computer Science, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021.","chicago":"Guha, Shibashis, Ismael R Jecker, Karoliina Lehtinen, and Martin Zimmermann. “A Bit of Nondeterminism Makes Pushdown Automata Expressive and Succinct.” In <i>46th International Symposium on Mathematical Foundations of Computer Science</i>, Vol. 202. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021. <a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2021.53\">https://doi.org/10.4230/LIPIcs.MFCS.2021.53</a>.","ista":"Guha S, Jecker IR, Lehtinen K, Zimmermann M. 2021. A bit of nondeterminism makes pushdown automata expressive and succinct. 46th International Symposium on Mathematical Foundations of Computer Science. MFCS: Mathematical Foundations of Computer Science, LIPIcs, vol. 202, 53.","mla":"Guha, Shibashis, et al. “A Bit of Nondeterminism Makes Pushdown Automata Expressive and Succinct.” <i>46th International Symposium on Mathematical Foundations of Computer Science</i>, vol. 202, 53, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021, doi:<a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2021.53\">10.4230/LIPIcs.MFCS.2021.53</a>.","ieee":"S. Guha, I. R. Jecker, K. Lehtinen, and M. Zimmermann, “A bit of nondeterminism makes pushdown automata expressive and succinct,” in <i>46th International Symposium on Mathematical Foundations of Computer Science</i>, Tallinn, Estonia, 2021, vol. 202.","apa":"Guha, S., Jecker, I. R., Lehtinen, K., &#38; Zimmermann, M. (2021). A bit of nondeterminism makes pushdown automata expressive and succinct. In <i>46th International Symposium on Mathematical Foundations of Computer Science</i> (Vol. 202). Tallinn, Estonia: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2021.53\">https://doi.org/10.4230/LIPIcs.MFCS.2021.53</a>","ama":"Guha S, Jecker IR, Lehtinen K, Zimmermann M. A bit of nondeterminism makes pushdown automata expressive and succinct. In: <i>46th International Symposium on Mathematical Foundations of Computer Science</i>. Vol 202. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2021. doi:<a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2021.53\">10.4230/LIPIcs.MFCS.2021.53</a>"},"scopus_import":"1","month":"08","_id":"10075","alternative_title":["LIPIcs"],"external_id":{"arxiv":["2105.02611"]},"conference":{"start_date":"2021-08-23","name":"MFCS: Mathematical Foundations of Computer Science","location":"Tallinn, Estonia","end_date":"2021-08-27"},"date_created":"2021-10-03T22:01:23Z","publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"ddc":["000"],"project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"46th International Symposium on Mathematical Foundations of Computer Science","arxiv":1,"ec_funded":1,"year":"2021","acknowledgement":"Ismaël Jecker: Funded by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 754411. Karoliina Lehtinen: Funded by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 892704.","publication_identifier":{"isbn":["978-3-9597-7201-3"],"issn":["1868-8969"]},"article_number":"53","intvolume":"       202","date_published":"2021-08-18T00:00:00Z","day":"18","doi":"10.4230/LIPIcs.MFCS.2021.53","oa":1,"file":[{"file_id":"10097","date_updated":"2021-10-06T12:44:05Z","relation":"main_file","checksum":"f4d407d43a97330c3fb11e6a7a6fbfb2","content_type":"application/pdf","file_size":825567,"creator":"cchlebak","success":1,"date_created":"2021-10-06T12:44:05Z","file_name":"2021_LIPIcs_Guha.pdf","access_level":"open_access"}],"file_date_updated":"2021-10-06T12:44:05Z","has_accepted_license":"1","article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","date_updated":"2025-05-14T10:54:50Z","author":[{"first_name":"Shibashis","full_name":"Guha, Shibashis","last_name":"Guha"},{"first_name":"Ismael R","id":"85D7C63E-7D5D-11E9-9C0F-98C4E5697425","full_name":"Jecker, Ismael R","last_name":"Jecker"},{"last_name":"Lehtinen","full_name":"Lehtinen, Karoliina","first_name":"Karoliina"},{"full_name":"Zimmermann, Martin","last_name":"Zimmermann","first_name":"Martin"}],"title":"A bit of nondeterminism makes pushdown automata expressive and succinct","oa_version":"Published Version"},{"oa_version":"Preprint","article_processing_charge":"No","status":"public","language":[{"iso":"eng"}],"date_updated":"2025-07-10T11:49:40Z","page":"431-450","author":[{"last_name":"Blackshear","full_name":"Blackshear, Sam","first_name":"Sam"},{"last_name":"Chalkias","full_name":"Chalkias, Konstantinos","first_name":"Konstantinos"},{"first_name":"Panagiotis","full_name":"Chatzigiannis, Panagiotis","last_name":"Chatzigiannis"},{"full_name":"Faizullabhoy, Riyaz","last_name":"Faizullabhoy","first_name":"Riyaz"},{"last_name":"Khaburzaniya","full_name":"Khaburzaniya, Irakliy","first_name":"Irakliy"},{"last_name":"Kokoris Kogias","full_name":"Kokoris Kogias, Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","first_name":"Eleftherios"},{"first_name":"Joshua","last_name":"Lind","full_name":"Lind, Joshua"},{"full_name":"Wong, David","last_name":"Wong","first_name":"David"},{"first_name":"Tim","full_name":"Zakian, Tim","last_name":"Zakian"}],"title":"Reactive key-loss protection in blockchains","publication_identifier":{"eissn":["1611-3349"],"eisbn":["978-3-662-63958-0"],"isbn":["978-3-6626-3957-3"],"issn":["0302-9743"]},"acknowledgement":"The authors would like to thank all anonymous reviewers of FC21 WTSC workshop for comments and suggestions that greatly improved the quality of this paper.","year":"2021","date_published":"2021-09-17T00:00:00Z","oa":1,"doi":"10.1007/978-3-662-63958-0_34","day":"17","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"publication":"FC 2021 Workshops","external_id":{"isi":["000713005000034"]},"alternative_title":["LNCS"],"conference":{"end_date":"2021-03-05","start_date":"2021-03-01","location":"Virtual","name":"FC: Financial Cryptography and Data Security"},"date_created":"2021-10-03T22:01:24Z","publication_status":"published","scopus_import":"1","month":"09","_id":"10076","quality_controlled":"1","citation":{"short":"S. Blackshear, K. Chalkias, P. Chatzigiannis, R. Faizullabhoy, I. Khaburzaniya, E. Kokoris Kogias, J. Lind, D. Wong, T. Zakian, in:, FC 2021 Workshops, Springer Nature, 2021, pp. 431–450.","ama":"Blackshear S, Chalkias K, Chatzigiannis P, et al. Reactive key-loss protection in blockchains. In: <i>FC 2021 Workshops</i>. Vol 12676. Springer Nature; 2021:431-450. doi:<a href=\"https://doi.org/10.1007/978-3-662-63958-0_34\">10.1007/978-3-662-63958-0_34</a>","ieee":"S. Blackshear <i>et al.</i>, “Reactive key-loss protection in blockchains,” in <i>FC 2021 Workshops</i>, Virtual, 2021, vol. 12676, pp. 431–450.","apa":"Blackshear, S., Chalkias, K., Chatzigiannis, P., Faizullabhoy, R., Khaburzaniya, I., Kokoris Kogias, E., … Zakian, T. (2021). Reactive key-loss protection in blockchains. In <i>FC 2021 Workshops</i> (Vol. 12676, pp. 431–450). Virtual: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-662-63958-0_34\">https://doi.org/10.1007/978-3-662-63958-0_34</a>","chicago":"Blackshear, Sam, Konstantinos Chalkias, Panagiotis Chatzigiannis, Riyaz Faizullabhoy, Irakliy Khaburzaniya, Eleftherios Kokoris Kogias, Joshua Lind, David Wong, and Tim Zakian. “Reactive Key-Loss Protection in Blockchains.” In <i>FC 2021 Workshops</i>, 12676:431–50. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/978-3-662-63958-0_34\">https://doi.org/10.1007/978-3-662-63958-0_34</a>.","ista":"Blackshear S, Chalkias K, Chatzigiannis P, Faizullabhoy R, Khaburzaniya I, Kokoris Kogias E, Lind J, Wong D, Zakian T. 2021. Reactive key-loss protection in blockchains. FC 2021 Workshops. FC: Financial Cryptography and Data Security, LNCS, vol. 12676, 431–450.","mla":"Blackshear, Sam, et al. “Reactive Key-Loss Protection in Blockchains.” <i>FC 2021 Workshops</i>, vol. 12676, Springer Nature, 2021, pp. 431–50, doi:<a href=\"https://doi.org/10.1007/978-3-662-63958-0_34\">10.1007/978-3-662-63958-0_34</a>."},"abstract":[{"lang":"eng","text":"We present a novel approach for blockchain asset owners to reclaim their funds in case of accidental private-key loss or transfer to a mistyped address. Our solution can be deployed upon failure or absence of proactively implemented backup mechanisms, such as secret sharing and cold storage. The main advantages against previous proposals is it does not require any prior action from users and works with both single-key and multi-sig accounts. We achieve this by a 3-phase   Commit()→Reveal()→Claim()−or−Challenge()  smart contract that enables accessing funds of addresses for which the spending key is not available. We provide an analysis of the threat and incentive models and formalize the concept of reactive KEy-Loss Protection (KELP)."}],"type":"conference","main_file_link":[{"url":"https://research.fb.com/publications/reactive-key-loss-protection-in-blockchains/","open_access":"1"}],"publisher":"Springer Nature","department":[{"_id":"ElKo"}],"volume":"12676 "},{"ec_funded":1,"acknowledgement":"We thank Federico Stella for invaluable suggestions and discussions. We thank Yosman BapatDhar and Andrea Cumpelik for comments, help and suggestions on the exposure of the text. We thank Predrag Živadinović and Juliana Couras for comments on the text and the figures. This work was supported by the EU-FP7 MC-ITN IN-SENS (grant 607616).","year":"2021","abstract":[{"text":"Hippocampal and neocortical neural activity is modulated by the position of the individual in space. While hippocampal neurons provide the basis for a spatial map, prefrontal cortical neurons generalize over environmental features. Whether these generalized representations result from a bidirectional interaction with, or are mainly derived from hippocampal spatial representations is not known. By examining simultaneously recorded hippocampal and medial prefrontal neurons, we observed that prefrontal spatial representations show a delayed coherence with hippocampal ones. We also identified subpopulations of cells in the hippocampus and medial prefrontal cortex that formed functional cross-area couplings; these resembled the optimal connections predicted by a probabilistic model of spatial information transfer and generalization. Moreover, cross-area couplings were strongest and had the shortest delay preceding spatial decision-making. Our results suggest that generalized spatial coding in the medial prefrontal cortex is inherited from spatial representations in the hippocampus, and that the routing of information can change dynamically with behavioral demands.","lang":"eng"}],"doi":"10.1101/2021.09.30.462269","type":"preprint","day":"02","oa":1,"citation":{"ieee":"M. Nardin, K. Käfer, and J. L. Csicsvari, “The generalized spatial representation in the prefrontal cortex is inherited from the hippocampus,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory.","apa":"Nardin, M., Käfer, K., &#38; Csicsvari, J. L. (n.d.). The generalized spatial representation in the prefrontal cortex is inherited from the hippocampus. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/2021.09.30.462269\">https://doi.org/10.1101/2021.09.30.462269</a>","ama":"Nardin M, Käfer K, Csicsvari JL. The generalized spatial representation in the prefrontal cortex is inherited from the hippocampus. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2021.09.30.462269\">10.1101/2021.09.30.462269</a>","ista":"Nardin M, Käfer K, Csicsvari JL. The generalized spatial representation in the prefrontal cortex is inherited from the hippocampus. bioRxiv, <a href=\"https://doi.org/10.1101/2021.09.30.462269\">10.1101/2021.09.30.462269</a>.","chicago":"Nardin, Michele, Karola Käfer, and Jozsef L Csicsvari. “The Generalized Spatial Representation in the Prefrontal Cortex Is Inherited from the Hippocampus.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, n.d. <a href=\"https://doi.org/10.1101/2021.09.30.462269\">https://doi.org/10.1101/2021.09.30.462269</a>.","mla":"Nardin, Michele, et al. “The Generalized Spatial Representation in the Prefrontal Cortex Is Inherited from the Hippocampus.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, doi:<a href=\"https://doi.org/10.1101/2021.09.30.462269\">10.1101/2021.09.30.462269</a>.","short":"M. Nardin, K. Käfer, J.L. Csicsvari, BioRxiv (n.d.)."},"date_published":"2021-10-02T00:00:00Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","project":[{"grant_number":"607616","_id":"257BBB4C-B435-11E9-9278-68D0E5697425","name":"inter-and intracellular signalling in schizophrenia","call_identifier":"FP7"}],"publisher":"Cold Spring Harbor Laboratory","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2021.09.30.462269","open_access":"1"}],"publication":"bioRxiv","department":[{"_id":"GradSch"},{"_id":"JoCs"}],"publication_status":"submitted","date_created":"2021-10-04T06:28:32Z","oa_version":"Preprint","status":"public","month":"10","language":[{"iso":"eng"}],"article_processing_charge":"No","title":"The generalized spatial representation in the prefrontal cortex is inherited from the hippocampus","author":[{"last_name":"Nardin","full_name":"Nardin, Michele","id":"30BD0376-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8849-6570","first_name":"Michele"},{"last_name":"Käfer","full_name":"Käfer, Karola","id":"2DAA49AA-F248-11E8-B48F-1D18A9856A87","first_name":"Karola"},{"first_name":"Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari","full_name":"Csicsvari, Jozsef L","orcid":"0000-0002-5193-4036"}],"_id":"10080","date_updated":"2025-04-15T06:48:21Z"},{"isi":1,"publication":"Viruses","ddc":["616"],"project":[{"grant_number":"P31445","name":"Structural conservation and diversity in retroviral capsid","_id":"26736D6A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2021-09-17T00:00:00Z","intvolume":"        13","oa":1,"file":[{"date_created":"2021-10-08T10:38:15Z","success":1,"file_name":"2021_Viruses_Obr.pdf","creator":"cchlebak","file_size":4146796,"access_level":"open_access","date_updated":"2021-10-08T10:38:15Z","file_id":"10115","checksum":"bcfd72a12977d48e22df3d0cc55aacf1","content_type":"application/pdf","relation":"main_file"}],"day":"17","doi":"10.3390/v13091853","publication_identifier":{"issn":["1999-4915"]},"year":"2021","acknowledgement":"We thank Volker M. Vogt for his critical comments in preparation of the review.","article_type":"original","article_number":"1853","date_updated":"2025-04-15T08:24:49Z","title":"A structural perspective of the role of IP6 in immature and mature retroviral assembly","author":[{"full_name":"Obr, Martin","last_name":"Obr","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1756-6564","first_name":"Martin"},{"full_name":"Schur, Florian KM","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","first_name":"Florian KM"},{"first_name":"Robert A.","last_name":"Dick","full_name":"Dick, Robert A."}],"has_accepted_license":"1","article_processing_charge":"Yes","file_date_updated":"2021-10-08T10:38:15Z","language":[{"iso":"eng"}],"status":"public","oa_version":"Published Version","keyword":["virology","infectious diseases"],"department":[{"_id":"FlSc"}],"volume":13,"publisher":"MDPI","corr_author":"1","quality_controlled":"1","citation":{"mla":"Obr, Martin, et al. “A Structural Perspective of the Role of IP6 in Immature and Mature Retroviral Assembly.” <i>Viruses</i>, vol. 13, no. 9, 1853, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/v13091853\">10.3390/v13091853</a>.","chicago":"Obr, Martin, Florian KM Schur, and Robert A. Dick. “A Structural Perspective of the Role of IP6 in Immature and Mature Retroviral Assembly.” <i>Viruses</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/v13091853\">https://doi.org/10.3390/v13091853</a>.","ista":"Obr M, Schur FK, Dick RA. 2021. A structural perspective of the role of IP6 in immature and mature retroviral assembly. Viruses. 13(9), 1853.","ieee":"M. Obr, F. K. Schur, and R. A. Dick, “A structural perspective of the role of IP6 in immature and mature retroviral assembly,” <i>Viruses</i>, vol. 13, no. 9. MDPI, 2021.","apa":"Obr, M., Schur, F. K., &#38; Dick, R. A. (2021). A structural perspective of the role of IP6 in immature and mature retroviral assembly. <i>Viruses</i>. MDPI. <a href=\"https://doi.org/10.3390/v13091853\">https://doi.org/10.3390/v13091853</a>","ama":"Obr M, Schur FK, Dick RA. A structural perspective of the role of IP6 in immature and mature retroviral assembly. <i>Viruses</i>. 2021;13(9). doi:<a href=\"https://doi.org/10.3390/v13091853\">10.3390/v13091853</a>","short":"M. Obr, F.K. Schur, R.A. Dick, Viruses 13 (2021)."},"abstract":[{"text":"The small cellular molecule inositol hexakisphosphate (IP6) has been known for ~20 years to promote the in vitro assembly of HIV-1 into immature virus-like particles. However, the molecular details underlying this effect have been determined only recently, with the identification of the IP6 binding site in the immature Gag lattice. IP6 also promotes formation of the mature capsid protein (CA) lattice via a second IP6 binding site, and enhances core stability, creating a favorable environment for reverse transcription. IP6 also enhances assembly of other retroviruses, from both the Lentivirus and the Alpharetrovirus genera. These findings suggest that IP6 may have a conserved function throughout the family Retroviridae. Here, we discuss the different steps in the viral life cycle that are influenced by IP6, and describe in detail how IP6 interacts with the immature and mature lattices of different retroviruses.","lang":"eng"}],"pmid":1,"type":"journal_article","_id":"10103","scopus_import":"1","issue":"9","month":"09","date_created":"2021-10-07T09:13:29Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"published","external_id":{"pmid":["34578434"],"isi":["000699841100001"]}},{"type":"conference","abstract":[{"text":"We argue that the time is ripe to investigate differential monitoring, in which the specification of a program's behavior is implicitly given by a second program implementing the same informal specification. Similar ideas have been proposed before, and are currently implemented in restricted form for testing and specialized run-time analyses, aspects of which we combine. We discuss the challenges of implementing differential monitoring as a general-purpose, black-box run-time monitoring framework, and present promising results of a preliminary implementation, showing low monitoring overheads for diverse programs.","lang":"eng"}],"citation":{"chicago":"Mühlböck, Fabian, and Thomas A Henzinger. “Differential Monitoring.” In <i>International Conference on Runtime Verification</i>, 12974:231–43. Cham: Springer Nature, 2021. <a href=\"https://doi.org/10.1007/978-3-030-88494-9_12\">https://doi.org/10.1007/978-3-030-88494-9_12</a>.","ista":"Mühlböck F, Henzinger TA. 2021. Differential monitoring. International Conference on Runtime Verification. RV: Runtime Verification, LNCS, vol. 12974, 231–243.","mla":"Mühlböck, Fabian, and Thomas A. Henzinger. “Differential Monitoring.” <i>International Conference on Runtime Verification</i>, vol. 12974, Springer Nature, 2021, pp. 231–43, doi:<a href=\"https://doi.org/10.1007/978-3-030-88494-9_12\">10.1007/978-3-030-88494-9_12</a>.","ieee":"F. Mühlböck and T. A. Henzinger, “Differential monitoring,” in <i>International Conference on Runtime Verification</i>, Virtual, 2021, vol. 12974, pp. 231–243.","apa":"Mühlböck, F., &#38; Henzinger, T. A. (2021). Differential monitoring. In <i>International Conference on Runtime Verification</i> (Vol. 12974, pp. 231–243). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-88494-9_12\">https://doi.org/10.1007/978-3-030-88494-9_12</a>","ama":"Mühlböck F, Henzinger TA. Differential monitoring. In: <i>International Conference on Runtime Verification</i>. Vol 12974. Cham: Springer Nature; 2021:231-243. doi:<a href=\"https://doi.org/10.1007/978-3-030-88494-9_12\">10.1007/978-3-030-88494-9_12</a>","short":"F. Mühlböck, T.A. Henzinger, in:, International Conference on Runtime Verification, Springer Nature, Cham, 2021, pp. 231–243."},"quality_controlled":"1","volume":12974,"department":[{"_id":"ToHe"}],"publisher":"Springer Nature","corr_author":"1","publication_status":"published","date_created":"2021-10-07T23:30:10Z","conference":{"end_date":"2021-10-14","location":"Virtual","name":"RV: Runtime Verification","start_date":"2021-10-11"},"alternative_title":["LNCS"],"external_id":{"isi":["000719383800012"]},"_id":"10108","month":"10","scopus_import":"1","place":"Cham","doi":"10.1007/978-3-030-88494-9_12","day":"06","oa":1,"file":[{"file_id":"10109","date_updated":"2021-10-07T23:32:18Z","relation":"main_file","checksum":"554c7fdb259eda703a8b6328a6dad55a","content_type":"application/pdf","file_size":350632,"creator":"fmuehlbo","file_name":"differentialmonitoring-cameraready-openaccess.pdf","success":1,"date_created":"2021-10-07T23:32:18Z","access_level":"open_access"}],"intvolume":"     12974","date_published":"2021-10-06T00:00:00Z","publication_identifier":{"isbn":["978-3-030-88493-2"],"eisbn":["978-3-030-88494-9"],"eissn":["1611-3349"],"issn":["0302-9743"]},"acknowledgement":"The authors would like to thank Borzoo Bonakdarpour, Derek Dreyer, Adrian Francalanza, Owolabi Legunsen, Mae Milano, Manuel Rigger, Cesar Sanchez, and the members of the IST Verification Seminar for their helpful comments and insights on various stages of this work, as well as the reviewers of RV’21 for their helpful suggestions on the actual paper.","year":"2021","publication":"International Conference on Runtime Verification","isi":1,"project":[{"call_identifier":"FWF","name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["005"],"oa_version":"Preprint","keyword":["run-time verification","software engineering","implicit specification"],"title":"Differential monitoring","author":[{"orcid":"0000-0003-1548-0177","last_name":"Mühlböck","full_name":"Mühlböck, Fabian","id":"6395C5F6-89DF-11E9-9C97-6BDFE5697425","first_name":"Fabian"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724"}],"related_material":{"record":[{"relation":"extended_version","id":"9946","status":"public"}]},"date_updated":"2025-04-15T06:26:12Z","page":"231-243","language":[{"iso":"eng"}],"status":"public","file_date_updated":"2021-10-07T23:32:18Z","has_accepted_license":"1","article_processing_charge":"No"},{"_id":"10116","month":"09","scopus_import":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"published","date_created":"2021-10-10T22:01:22Z","external_id":{"pmid":["34499028"],"isi":["000695716100001"]},"volume":10,"department":[{"_id":"MaDe"}],"publisher":"eLife Sciences Publications","citation":{"ista":"Vuong-Brender T, Flynn S, Vallis Y, de Bono M. 2021. Neuronal calmodulin levels are controlled by CAMTA transcription factors. eLife. 10, e68238.","chicago":"Vuong-Brender, Thanh, Sean Flynn, Yvonne Vallis, and Mario de Bono. “Neuronal Calmodulin Levels Are Controlled by CAMTA Transcription Factors.” <i>ELife</i>. eLife Sciences Publications, 2021. <a href=\"https://doi.org/10.7554/eLife.68238\">https://doi.org/10.7554/eLife.68238</a>.","mla":"Vuong-Brender, Thanh, et al. “Neuronal Calmodulin Levels Are Controlled by CAMTA Transcription Factors.” <i>ELife</i>, vol. 10, e68238, eLife Sciences Publications, 2021, doi:<a href=\"https://doi.org/10.7554/eLife.68238\">10.7554/eLife.68238</a>.","ama":"Vuong-Brender T, Flynn S, Vallis Y, de Bono M. Neuronal calmodulin levels are controlled by CAMTA transcription factors. <i>eLife</i>. 2021;10. doi:<a href=\"https://doi.org/10.7554/eLife.68238\">10.7554/eLife.68238</a>","ieee":"T. Vuong-Brender, S. Flynn, Y. Vallis, and M. de Bono, “Neuronal calmodulin levels are controlled by CAMTA transcription factors,” <i>eLife</i>, vol. 10. eLife Sciences Publications, 2021.","apa":"Vuong-Brender, T., Flynn, S., Vallis, Y., &#38; de Bono, M. (2021). Neuronal calmodulin levels are controlled by CAMTA transcription factors. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.68238\">https://doi.org/10.7554/eLife.68238</a>","short":"T. Vuong-Brender, S. Flynn, Y. Vallis, M. de Bono, ELife 10 (2021)."},"abstract":[{"text":"The ubiquitous Ca2+ sensor calmodulin (CaM) binds and regulates many proteins, including ion channels, CaM kinases, and calcineurin, according to Ca2+-CaM levels. What regulates neuronal CaM levels, is, however, unclear. CaM-binding transcription activators (CAMTAs) are ancient proteins expressed broadly in nervous systems and whose loss confers pleiotropic behavioral defects in flies, mice, and humans. Using Caenorhabditis elegans and Drosophila, we show that CAMTAs control neuronal CaM levels. The behavioral and neuronal Ca2+ signaling defects in mutants lacking camt-1, the sole C. elegans CAMTA, can be rescued by supplementing neuronal CaM. CAMT-1 binds multiple sites in the CaM promoter and deleting these sites phenocopies camt-1. Our data suggest CAMTAs mediate a conserved and general mechanism that controls neuronal CaM levels, thereby regulating Ca2+ signaling, physiology, and behavior.","lang":"eng"}],"type":"journal_article","pmid":1,"quality_controlled":"1","title":"Neuronal calmodulin levels are controlled by CAMTA transcription factors","author":[{"id":"D389312E-10C4-11EA-ABF4-A4B43DDC885E","full_name":"Vuong-Brender, Thanh","last_name":"Vuong-Brender","first_name":"Thanh"},{"last_name":"Flynn","full_name":"Flynn, Sean","first_name":"Sean"},{"last_name":"Vallis","full_name":"Vallis, Yvonne","id":"05A2795C-31B5-11EA-83A7-7DA23DDC885E","first_name":"Yvonne"},{"id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","full_name":"De Bono, Mario","last_name":"De Bono","orcid":"0000-0001-8347-0443","first_name":"Mario"}],"date_updated":"2025-04-14T07:43:46Z","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","has_accepted_license":"1","file_date_updated":"2021-10-11T14:15:07Z","oa_version":"Published Version","isi":1,"publication":"eLife","project":[{"call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["610"],"oa":1,"file":[{"file_size":1774624,"creator":"cchlebak","date_created":"2021-10-11T14:15:07Z","file_name":"2021_eLife_VuongBrender.pdf","success":1,"access_level":"open_access","file_id":"10122","date_updated":"2021-10-11T14:15:07Z","relation":"main_file","content_type":"application/pdf","checksum":"b465e172d2b1f57aa26a2571a085d052"}],"doi":"10.7554/eLife.68238","day":"17","date_published":"2021-09-17T00:00:00Z","intvolume":"        10","article_number":"e68238","publication_identifier":{"eissn":["2050-084X"]},"year":"2021","article_type":"original","acknowledgement":"The authors thank the MRC-LMB Flow Cytometry facility and Imaging Service for support, the Cancer Research UK Cambridge Institute Genomics Core for Next Generation Sequencing, Julie Ahringer and Alex Appert for advice and technical help for ChIP-seq experiments, Paula Freire-Pritchett, Tim Stevens, and Gurpreet Ghattaoraya for RNA-seq and ChIP-seq analyses, Nikos Chronis for the TN-XL plasmid, Hong-Sheng Li and Daisuke Yamamoto for generously sending the tes2 and cro mutants, Daria Siekhaus for hosting the fly work, Michaela Misova for technical assistance. The authors are very grateful to Salihah Ece Sönmez for teaching us how to dissect, mount and stain Drosophila retinae. This work was supported by an Advanced ERC grant (269058 ACMO) and a Wellcome Investigator Award (209504/Z/17/Z) to MdB, and an IST Plus Fellowship to TV-B (Marie Sklodowska-Curie Agreement no 754411).","ec_funded":1},{"project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["612"],"isi":1,"publication":"Journal of Biological Chemistry","article_number":"101094","publication_identifier":{"eissn":["1083-351X"],"issn":["0021-9258"]},"year":"2021","article_type":"original","acknowledgement":"We thank de Bono lab members for helpful comments on the manuscript, IST Austria and University of Vienna Mass Spec Facilities for invaluable discussions and comments for the optimization of mass spec analyses of worm samples. The biotin auxotropic E. coli strain MG1655bioB:kan was gift from John Cronan (University of Illinois) and was kindly sent to us by Jessica Feldman and Ariana Sanchez (Stanford University). dg398 pEntryslot2_mNeongreen::3XFLAG::stop and dg397 pEntryslot3_mNeongreen::3XFLAG::stop::unc-54 3′UTR entry vector were kindly shared by Dr Dominique Glauser (University of Fribourg). Codon-optimized mScarlet vector was a generous gift from Dr Manuel Zimmer (University of Vienna).","ec_funded":1,"oa":1,"file":[{"relation":"main_file","checksum":"19e39d36c5b9387c6dc0e89c9ae856ab","content_type":"application/pdf","file_id":"10121","date_updated":"2021-10-11T12:20:58Z","access_level":"open_access","file_size":1680010,"creator":"cchlebak","date_created":"2021-10-11T12:20:58Z","file_name":"2021_JBC_Artan.pdf","success":1}],"doi":"10.1016/J.JBC.2021.101094","day":"01","date_published":"2021-09-01T00:00:00Z","intvolume":"       297","language":[{"iso":"eng"}],"status":"public","has_accepted_license":"1","article_processing_charge":"Yes","file_date_updated":"2021-10-11T12:20:58Z","author":[{"first_name":"Murat","id":"C407B586-6052-11E9-B3AE-7006E6697425","last_name":"Artan","full_name":"Artan, Murat","orcid":"0000-0001-8945-6992"},{"last_name":"Barratt","full_name":"Barratt, Stephen","id":"57740d2b-2a88-11ec-97cf-d9e6d1b39677","first_name":"Stephen"},{"first_name":"Sean M.","last_name":"Flynn","full_name":"Flynn, Sean M."},{"first_name":"Farida","last_name":"Begum","full_name":"Begum, Farida"},{"last_name":"Skehel","full_name":"Skehel, Mark","first_name":"Mark"},{"full_name":"Nicolas, Armel","last_name":"Nicolas","id":"2A103192-F248-11E8-B48F-1D18A9856A87","first_name":"Armel"},{"first_name":"Mario","orcid":"0000-0001-8347-0443","last_name":"De Bono","full_name":"De Bono, Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87"}],"title":"Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling","date_updated":"2025-04-14T07:43:46Z","oa_version":"Published Version","publisher":"Elsevier","volume":297,"department":[{"_id":"MaDe"},{"_id":"LifeSc"}],"citation":{"short":"M. Artan, S. Barratt, S.M. Flynn, F. Begum, M. Skehel, A. Nicolas, M. de Bono, Journal of Biological Chemistry 297 (2021).","ama":"Artan M, Barratt S, Flynn SM, et al. Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling. <i>Journal of Biological Chemistry</i>. 2021;297(3). doi:<a href=\"https://doi.org/10.1016/J.JBC.2021.101094\">10.1016/J.JBC.2021.101094</a>","apa":"Artan, M., Barratt, S., Flynn, S. M., Begum, F., Skehel, M., Nicolas, A., &#38; de Bono, M. (2021). Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling. <i>Journal of Biological Chemistry</i>. Elsevier. <a href=\"https://doi.org/10.1016/J.JBC.2021.101094\">https://doi.org/10.1016/J.JBC.2021.101094</a>","ieee":"M. Artan <i>et al.</i>, “Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling,” <i>Journal of Biological Chemistry</i>, vol. 297, no. 3. Elsevier, 2021.","mla":"Artan, Murat, et al. “Interactome Analysis of Caenorhabditis Elegans Synapses by TurboID-Based Proximity Labeling.” <i>Journal of Biological Chemistry</i>, vol. 297, no. 3, 101094, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/J.JBC.2021.101094\">10.1016/J.JBC.2021.101094</a>.","ista":"Artan M, Barratt S, Flynn SM, Begum F, Skehel M, Nicolas A, de Bono M. 2021. Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling. Journal of Biological Chemistry. 297(3), 101094.","chicago":"Artan, Murat, Stephen Barratt, Sean M. Flynn, Farida Begum, Mark Skehel, Armel Nicolas, and Mario de Bono. “Interactome Analysis of Caenorhabditis Elegans Synapses by TurboID-Based Proximity Labeling.” <i>Journal of Biological Chemistry</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/J.JBC.2021.101094\">https://doi.org/10.1016/J.JBC.2021.101094</a>."},"abstract":[{"text":"Proximity labeling provides a powerful in vivo tool to characterize the proteome of subcellular structures and the interactome of specific proteins. The nematode Caenorhabditis elegans is one of the most intensely studied organisms in biology, offering many advantages for biochemistry. Using the highly active biotin ligase TurboID, we optimize here a proximity labeling protocol for C. elegans. An advantage of TurboID is that biotin's high affinity for streptavidin means biotin-labeled proteins can be affinity-purified under harsh denaturing conditions. By combining extensive sonication with aggressive denaturation using SDS and urea, we achieved near-complete solubilization of worm proteins. We then used this protocol to characterize the proteomes of the worm gut, muscle, skin, and nervous system. Neurons are among the smallest C. elegans cells. To probe the method's sensitivity, we expressed TurboID exclusively in the two AFD neurons and showed that the protocol could identify known and previously unknown proteins expressed selectively in AFD. The active zones of synapses are composed of a protein matrix that is difficult to solubilize and purify. To test if our protocol could solubilize active zone proteins, we knocked TurboID into the endogenous elks-1 gene, which encodes a presynaptic active zone protein. We identified many known ELKS-1-interacting active zone proteins, as well as previously uncharacterized synaptic proteins. Versatile vectors and the inherent advantages of using C. elegans, including fast growth and the ability to rapidly make and functionally test knock-ins, make proximity labeling a valuable addition to the armory of this model organism.","lang":"eng"}],"type":"journal_article","quality_controlled":"1","month":"09","scopus_import":"1","issue":"3","_id":"10117","external_id":{"isi":["000706409200006"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"published","date_created":"2021-10-10T22:01:23Z"},{"external_id":{"pmid":["34550677 "]},"date_created":"2021-10-12T07:31:21Z","oa_version":"Preprint","publication_status":"published","article_processing_charge":"No","month":"09","language":[{"iso":"eng"}],"status":"public","date_updated":"2021-10-12T09:50:19Z","_id":"10124","author":[{"last_name":"Palaia","full_name":"Palaia, Ivan","first_name":"Ivan"},{"full_name":"Paraschiv, Alexandru","last_name":"Paraschiv","first_name":"Alexandru"},{"first_name":"Vincent","full_name":"Debets, Vincent","last_name":"Debets"},{"last_name":"Storm","full_name":"Storm, Cornelis","first_name":"Cornelis"},{"first_name":"Anđela","full_name":"Šarić, Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139"}],"title":"Durotaxis of passive nanoparticles on elastic membranes","article_type":"original","year":"2021","acknowledgement":"We acknowledge support from the Engineering and Physical Sciences Research Council (A.P. and A.Š.), the Royal Society (A.Š.) and the European Research Council (I.P. and A.Š.).","quality_controlled":"1","date_published":"2021-09-22T00:00:00Z","abstract":[{"text":"The transport of macromolecules and nanoscopic particles to a target cellular site is a crucial aspect in many physiological processes. This directional motion is generally controlled via active mechanical and chemical processes. Here we show, by means of molecular dynamics simulations and an analytical theory, that completely passive nanoparticles can exhibit directional motion when embedded in non-uniform mechanical environments. Specifically, we study the motion of a passive nanoparticle adhering to a mechanically non-uniform elastic membrane. We observe a non-monotonic affinity of the particle to the membrane as a function of the membrane’s rigidity, which results in the particle transport. This transport can be both up or down the rigidity gradient, depending on the absolute values of the rigidities that the gradient spans across. We conclude that rigidity gradients can be used to direct average motion of passive macromolecules and nanoparticles on deformable membranes, resulting in the preferential accumulation of the macromolecules in regions of certain mechanical properties.","lang":"eng"}],"extern":"1","day":"22","doi":"10.1021/acsnano.1c02777 ","pmid":1,"type":"journal_article","oa":1,"citation":{"short":"I. Palaia, A. Paraschiv, V. Debets, C. Storm, A. Šarić, ACS Nano (2021).","ista":"Palaia I, Paraschiv A, Debets V, Storm C, Šarić A. 2021. Durotaxis of passive nanoparticles on elastic membranes. ACS Nano.","chicago":"Palaia, Ivan, Alexandru Paraschiv, Vincent Debets, Cornelis Storm, and Anđela Šarić. “Durotaxis of Passive Nanoparticles on Elastic Membranes.” <i>ACS Nano</i>. American Chemical Society, 2021. <a href=\"https://doi.org/10.1021/acsnano.1c02777 \">https://doi.org/10.1021/acsnano.1c02777 </a>.","mla":"Palaia, Ivan, et al. “Durotaxis of Passive Nanoparticles on Elastic Membranes.” <i>ACS Nano</i>, American Chemical Society, 2021, doi:<a href=\"https://doi.org/10.1021/acsnano.1c02777 \">10.1021/acsnano.1c02777 </a>.","apa":"Palaia, I., Paraschiv, A., Debets, V., Storm, C., &#38; Šarić, A. (2021). Durotaxis of passive nanoparticles on elastic membranes. <i>ACS Nano</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acsnano.1c02777 \">https://doi.org/10.1021/acsnano.1c02777 </a>","ama":"Palaia I, Paraschiv A, Debets V, Storm C, Šarić A. Durotaxis of passive nanoparticles on elastic membranes. <i>ACS Nano</i>. 2021. doi:<a href=\"https://doi.org/10.1021/acsnano.1c02777 \">10.1021/acsnano.1c02777 </a>","ieee":"I. Palaia, A. Paraschiv, V. Debets, C. Storm, and A. Šarić, “Durotaxis of passive nanoparticles on elastic membranes,” <i>ACS Nano</i>. American Chemical Society, 2021."},"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2021.04.01.438065"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publisher":"American Chemical Society","publication":"ACS Nano"},{"publication_status":"submitted","date_created":"2021-10-12T07:45:07Z","oa_version":"Preprint","language":[{"iso":"eng"}],"month":"03","status":"public","article_processing_charge":"No","title":"Physical mechanisms of ESCRT-III-driven cell division in archaea","author":[{"full_name":"Harker-Kirschneck, L.","last_name":"Harker-Kirschneck","first_name":"L."},{"full_name":"Hafner, A. E.","last_name":"Hafner","first_name":"A. E."},{"first_name":"T.","last_name":"Yao","full_name":"Yao, T."},{"last_name":"Pulschen","full_name":"Pulschen, A.","first_name":"A."},{"full_name":"Hurtig, F.","last_name":"Hurtig","first_name":"F."},{"first_name":"C.","full_name":"Vanhille-Campos, C.","last_name":"Vanhille-Campos"},{"full_name":"Hryniuk, D.","last_name":"Hryniuk","first_name":"D."},{"first_name":"S.","last_name":"Culley","full_name":"Culley, S."},{"first_name":"R.","last_name":"Henriques","full_name":"Henriques, R."},{"last_name":"Baum","full_name":"Baum, B.","first_name":"B."},{"first_name":"Anđela","last_name":"Šarić","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139"}],"date_updated":"2021-10-12T09:50:26Z","_id":"10125","acknowledgement":"We acknowledge support from the Biotechnology and Biological Sciences Research Council (L.H.K.), EPSRC (A.E.H), UCL IPLS (T.Y and D. H.), Wellcome Trust (203276/Z/16/Z, A.P., S.C., R. H., B.B.), Volkswagen Foundation (Az 96727, A.P., B.B., A.Š.), MRC (MC CF1226, R.H., B.B., A.Š.), the ERC grant (”NEPA” 802960, A.Š.), the Royal Society (C.V.-H., A.Š.), the UK Materials and Molecular Modelling Hub for computational resources (EP/P020194/1).","year":"2021","abstract":[{"text":"Living systems propagate by undergoing rounds of cell growth and division. Cell division is at heart a physical process that requires mechanical forces, usually exerted by protein assemblies. Here we developed the first physical model for the division of archaeal cells, which despite their structural simplicity share machinery and evolutionary origins with eukaryotes. We show how active geometry changes of elastic ESCRT-III filaments, coupled to filament disassembly, are sufficient to efficiently split the cell. We explore how the non-equilibrium processes that govern the filament behaviour impact the resulting cell division. We show how a quantitative comparison between our simulations and dynamic data for ESCRTIII-mediated division in Sulfolobus acidocaldarius, the closest archaeal relative to eukaryotic cells that can currently be cultured in the lab, and reveal the most likely physical mechanism behind its division.","lang":"eng"}],"type":"preprint","doi":"10.1101/2021.03.23.436559","day":"23","extern":"1","oa":1,"citation":{"short":"L. Harker-Kirschneck, A.E. Hafner, T. Yao, A. Pulschen, F. Hurtig, C. Vanhille-Campos, D. Hryniuk, S. Culley, R. Henriques, B. Baum, A. Šarić, BioRxiv (n.d.).","ista":"Harker-Kirschneck L, Hafner AE, Yao T, Pulschen A, Hurtig F, Vanhille-Campos C, Hryniuk D, Culley S, Henriques R, Baum B, Šarić A. Physical mechanisms of ESCRT-III-driven cell division in archaea. bioRxiv, <a href=\"https://doi.org/10.1101/2021.03.23.436559\">10.1101/2021.03.23.436559</a>.","chicago":"Harker-Kirschneck, L., A. E. Hafner, T. Yao, A. Pulschen, F. Hurtig, C. Vanhille-Campos, D. Hryniuk, et al. “Physical Mechanisms of ESCRT-III-Driven Cell Division in Archaea.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, n.d. <a href=\"https://doi.org/10.1101/2021.03.23.436559\">https://doi.org/10.1101/2021.03.23.436559</a>.","mla":"Harker-Kirschneck, L., et al. “Physical Mechanisms of ESCRT-III-Driven Cell Division in Archaea.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, doi:<a href=\"https://doi.org/10.1101/2021.03.23.436559\">10.1101/2021.03.23.436559</a>.","ieee":"L. Harker-Kirschneck <i>et al.</i>, “Physical mechanisms of ESCRT-III-driven cell division in archaea,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory.","ama":"Harker-Kirschneck L, Hafner AE, Yao T, et al. Physical mechanisms of ESCRT-III-driven cell division in archaea. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2021.03.23.436559\">10.1101/2021.03.23.436559</a>","apa":"Harker-Kirschneck, L., Hafner, A. E., Yao, T., Pulschen, A., Hurtig, F., Vanhille-Campos, C., … Šarić, A. (n.d.). Physical mechanisms of ESCRT-III-driven cell division in archaea. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/2021.03.23.436559\">https://doi.org/10.1101/2021.03.23.436559</a>"},"date_published":"2021-03-23T00:00:00Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publisher":"Cold Spring Harbor Laboratory","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2021.03.23.436559"}],"publication":"bioRxiv"},{"date_updated":"2025-04-14T07:43:46Z","author":[{"first_name":"Fumika","orcid":"0000-0003-4982-5970","id":"650C99FC-1079-11EA-A3C0-73AE3DDC885E","last_name":"Suzuki","full_name":"Suzuki, Fumika"},{"first_name":"Mikhail","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Wojciech H.","last_name":"Zurek","full_name":"Zurek, Wojciech H."},{"first_name":"Roman V.","last_name":"Krems","full_name":"Krems, Roman V."}],"title":"Anderson localization of composite particles","article_processing_charge":"No","status":"public","language":[{"iso":"eng"}],"oa_version":"Preprint","keyword":["General Physics and Astronomy"],"arxiv":1,"publication":"Physical Review Letters","isi":1,"project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"},{"name":"Angulon: physics and applications of a new quasiparticle","_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770","call_identifier":"H2020"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":"       127","date_published":"2021-10-12T00:00:00Z","doi":"10.1103/physrevlett.127.160602","day":"12","oa":1,"ec_funded":1,"acknowledgement":"We acknowledge helpful discussions with W. G. Unruh and A. Rodriguez. F. S. is supported by European Union’s\r\nHorizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant No. 754411. M. L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). W. H. Z. is\r\nsupported by Department of Energy under the Los\r\nAlamos National Laboratory LDRD Program as well as by the U.S. Department of Energy, Office of Science, Basic\r\nEnergy Sciences, Materials Sciences and Engineering Division, Condensed Matter Theory Program. R. V. K. is supported by NSERC of Canada.\r\n","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"article_type":"original","year":"2021","article_number":"160602","_id":"10134","issue":"16","scopus_import":"1","month":"10","date_created":"2021-10-13T09:21:33Z","publication_status":"published","external_id":{"isi":["000707495700001"],"arxiv":["2011.06279"]},"department":[{"_id":"MiLe"}],"volume":127,"main_file_link":[{"url":"https://arxiv.org/abs/2011.06279","open_access":"1"}],"corr_author":"1","publisher":"American Physical Society ","quality_controlled":"1","type":"journal_article","abstract":[{"lang":"eng","text":"We investigate the effect of coupling between translational and internal degrees of freedom of composite quantum particles on their localization in a random potential. We show that entanglement between the two degrees of freedom weakens localization due to the upper bound imposed on the inverse participation ratio by purity of a quantum state. We perform numerical calculations for a two-particle system bound by a harmonic force in a 1D disordered lattice and a rigid rotor in a 2D disordered lattice. We illustrate that the coupling has a dramatic effect on localization properties, even with a small number of internal states participating in quantum dynamics."}],"citation":{"mla":"Suzuki, Fumika, et al. “Anderson Localization of Composite Particles.” <i>Physical Review Letters</i>, vol. 127, no. 16, 160602, American Physical Society , 2021, doi:<a href=\"https://doi.org/10.1103/physrevlett.127.160602\">10.1103/physrevlett.127.160602</a>.","ista":"Suzuki F, Lemeshko M, Zurek WH, Krems RV. 2021. Anderson localization of composite particles. Physical Review Letters. 127(16), 160602.","chicago":"Suzuki, Fumika, Mikhail Lemeshko, Wojciech H. Zurek, and Roman V. Krems. “Anderson Localization of Composite Particles.” <i>Physical Review Letters</i>. American Physical Society , 2021. <a href=\"https://doi.org/10.1103/physrevlett.127.160602\">https://doi.org/10.1103/physrevlett.127.160602</a>.","ama":"Suzuki F, Lemeshko M, Zurek WH, Krems RV. Anderson localization of composite particles. <i>Physical Review Letters</i>. 2021;127(16). doi:<a href=\"https://doi.org/10.1103/physrevlett.127.160602\">10.1103/physrevlett.127.160602</a>","ieee":"F. Suzuki, M. Lemeshko, W. H. Zurek, and R. V. Krems, “Anderson localization of composite particles,” <i>Physical Review Letters</i>, vol. 127, no. 16. American Physical Society , 2021.","apa":"Suzuki, F., Lemeshko, M., Zurek, W. H., &#38; Krems, R. V. (2021). Anderson localization of composite particles. <i>Physical Review Letters</i>. American Physical Society . <a href=\"https://doi.org/10.1103/physrevlett.127.160602\">https://doi.org/10.1103/physrevlett.127.160602</a>","short":"F. Suzuki, M. Lemeshko, W.H. Zurek, R.V. Krems, Physical Review Letters 127 (2021)."}},{"ddc":["576"],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication":"Life Science Alliance","acknowledgement":"We thank Connor Richterich and Patricia Reinert, ETH Zurich, for invaluable experimental help; Manuela Pérez Berlanga, University Zurich, for help with the confocal imaging; Lukas Fischer for help with electrical engineering; Thomas Hennek, Sol Taguinod, and Dr. Stephan Sonntag, EPIC Phenomics Center, ETH Zürich, for the generation and maintenance of K14-OptoR2 mice; and Dr. Petra Boukamp, Leibniz Institute, Düsseldorf, Germany, for early-passage HaCaT keratinocytes. This work was supported by the ETH Zurich (grant ETH-06 15-1 to S Werner and L Maddaluno), the Swiss National Science Foundation (grant 31003B-189364 to S Werner), and a Marie Curie postdoctoral fellowship from the European Union (to L Maddaluno).","year":"2021","publication_identifier":{"eissn":["2575-1077"]},"article_type":"original","article_number":"e202101100","date_published":"2021-09-21T00:00:00Z","intvolume":"         4","oa":1,"file":[{"relation":"main_file","content_type":"application/pdf","checksum":"89fb95b211dbe8678809e7cca4626952","file_id":"10152","date_updated":"2021-10-18T14:48:06Z","access_level":"open_access","file_name":"2021_LifeScAlliance_Rauschendorfer.pdf","date_created":"2021-10-18T14:48:06Z","success":1,"file_size":2055981,"creator":"cchlebak"}],"doi":"10.26508/lsa.202101100","day":"21","article_processing_charge":"Yes","has_accepted_license":"1","file_date_updated":"2021-10-18T14:48:06Z","language":[{"iso":"eng"}],"status":"public","date_updated":"2024-10-09T21:01:02Z","author":[{"first_name":"Theresa","full_name":"Rauschendorfer, Theresa","last_name":"Rauschendorfer"},{"full_name":"Gurri, Selina","last_name":"Gurri","first_name":"Selina"},{"first_name":"Irina","full_name":"Heggli, Irina","last_name":"Heggli"},{"last_name":"Maddaluno","full_name":"Maddaluno, Luigi","first_name":"Luigi"},{"first_name":"Michael","last_name":"Meyer","full_name":"Meyer, Michael"},{"first_name":"Álvaro","id":"2A9DB292-F248-11E8-B48F-1D18A9856A87","full_name":"Inglés Prieto, Álvaro","last_name":"Inglés Prieto","orcid":"0000-0002-5409-8571"},{"orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","last_name":"Janovjak","full_name":"Janovjak, Harald L","first_name":"Harald L"},{"full_name":"Werner, Sabine","last_name":"Werner","first_name":"Sabine"}],"title":"Acute and chronic effects of a light-activated FGF receptor in keratinocytes in vitro and in mice","oa_version":"Published Version","corr_author":"1","publisher":"Life Science Alliance","volume":4,"quality_controlled":"1","citation":{"ieee":"T. Rauschendorfer <i>et al.</i>, “Acute and chronic effects of a light-activated FGF receptor in keratinocytes in vitro and in mice,” <i>Life Science Alliance</i>, vol. 4, no. 11. Life Science Alliance, 2021.","ama":"Rauschendorfer T, Gurri S, Heggli I, et al. Acute and chronic effects of a light-activated FGF receptor in keratinocytes in vitro and in mice. <i>Life Science Alliance</i>. 2021;4(11). doi:<a href=\"https://doi.org/10.26508/lsa.202101100\">10.26508/lsa.202101100</a>","apa":"Rauschendorfer, T., Gurri, S., Heggli, I., Maddaluno, L., Meyer, M., Inglés Prieto, Á., … Werner, S. (2021). Acute and chronic effects of a light-activated FGF receptor in keratinocytes in vitro and in mice. <i>Life Science Alliance</i>. Life Science Alliance. <a href=\"https://doi.org/10.26508/lsa.202101100\">https://doi.org/10.26508/lsa.202101100</a>","mla":"Rauschendorfer, Theresa, et al. “Acute and Chronic Effects of a Light-Activated FGF Receptor in Keratinocytes in Vitro and in Mice.” <i>Life Science Alliance</i>, vol. 4, no. 11, e202101100, Life Science Alliance, 2021, doi:<a href=\"https://doi.org/10.26508/lsa.202101100\">10.26508/lsa.202101100</a>.","ista":"Rauschendorfer T, Gurri S, Heggli I, Maddaluno L, Meyer M, Inglés Prieto Á, Janovjak HL, Werner S. 2021. Acute and chronic effects of a light-activated FGF receptor in keratinocytes in vitro and in mice. Life Science Alliance. 4(11), e202101100.","chicago":"Rauschendorfer, Theresa, Selina Gurri, Irina Heggli, Luigi Maddaluno, Michael Meyer, Álvaro Inglés Prieto, Harald L Janovjak, and Sabine Werner. “Acute and Chronic Effects of a Light-Activated FGF Receptor in Keratinocytes in Vitro and in Mice.” <i>Life Science Alliance</i>. Life Science Alliance, 2021. <a href=\"https://doi.org/10.26508/lsa.202101100\">https://doi.org/10.26508/lsa.202101100</a>.","short":"T. Rauschendorfer, S. Gurri, I. Heggli, L. Maddaluno, M. Meyer, Á. Inglés Prieto, H.L. Janovjak, S. Werner, Life Science Alliance 4 (2021)."},"pmid":1,"abstract":[{"text":"FGFs and their high-affinity receptors (FGFRs) play key roles in development, tissue repair, and disease. Because FGFRs bind overlapping sets of ligands, their individual functions cannot be determined using ligand stimulation. Here, we generated a light-activated FGFR2 variant (OptoR2) to selectively activate signaling by the major FGFR in keratinocytes. Illumination of OptoR2-expressing HEK 293T cells activated FGFR signaling with remarkable temporal precision and promoted cell migration and proliferation. In murine and human keratinocytes, OptoR2 activation rapidly induced the classical FGFR signaling pathways and expression of FGF target genes. Surprisingly, multi-level counter-regulation occurred in keratinocytes in vitro and in transgenic mice in vivo, including OptoR2 down-regulation and loss of responsiveness to light activation. These results demonstrate unexpected cell type-specific limitations of optogenetic FGFRs in long-term in vitro and in vivo settings and highlight the complex consequences of transferring optogenetic cell signaling tools into their relevant cellular contexts.","lang":"eng"}],"type":"journal_article","extern":"1","scopus_import":"1","issue":"11","month":"09","_id":"10144","external_id":{"pmid":["34548382"]},"date_created":"2021-10-17T22:01:16Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"published"},{"status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","author":[{"id":"3ED6AF16-F248-11E8-B48F-1D18A9856A87","full_name":"Vercellino, Irene","last_name":"Vercellino","orcid":"0000-0001-5618-3449","first_name":"Irene"},{"first_name":"Leonid A","full_name":"Sazanov, Leonid A","last_name":"Sazanov","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989"}],"title":"Structure and assembly of the mammalian mitochondrial supercomplex CIII<sub>2</sub>CIV","page":"364-367","related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/boosting-the-cells-power-house/","description":"News on IST Webpage"}]},"date_updated":"2025-04-14T07:43:46Z","oa_version":"None","project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication":"Nature","isi":1,"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"EM-Fac"},{"_id":"ScienComp"}],"ec_funded":1,"publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"year":"2021","article_type":"original","acknowledgement":"We thank the pre-clinical facility of the IST Austria and A. Venturino for assistance with the animals; and V.-V. Hodirnau for assistance during the Titan Krios data collection, performed at the IST Austria. The data processing was performed at the IST high-performance computing cluster. This project has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement no. 754411.","day":"14","doi":"10.1038/s41586-021-03927-z","intvolume":"       598","date_published":"2021-10-14T00:00:00Z","month":"10","scopus_import":"1","issue":"7880","_id":"10146","external_id":{"isi":["000704581600001"],"pmid":["34616041"]},"publication_status":"published","date_created":"2021-10-17T22:01:17Z","publisher":"Springer Nature","corr_author":"1","volume":598,"department":[{"_id":"LeSa"}],"abstract":[{"text":"The enzymes of the mitochondrial electron transport chain are key players of cell metabolism. Despite being active when isolated, in vivo they associate into supercomplexes1, whose precise role is debated. Supercomplexes CIII2CIV1-2 (refs. 2,3), CICIII2 (ref. 4) and CICIII2CIV (respirasome)5,6,7,8,9,10 exist in mammals, but in contrast to CICIII2 and the respirasome, to date the only known eukaryotic structures of CIII2CIV1-2 come from Saccharomyces cerevisiae11,12 and plants13, which have different organization. Here we present the first, to our knowledge, structures of mammalian (mouse and ovine) CIII2CIV and its assembly intermediates, in different conformations. We describe the assembly of CIII2CIV from the CIII2 precursor to the final CIII2CIV conformation, driven by the insertion of the N terminus of the assembly factor SCAF1 (ref. 14) deep into CIII2, while its C terminus is integrated into CIV. Our structures (which include CICIII2 and the respirasome) also confirm that SCAF1 is exclusively required for the assembly of CIII2CIV and has no role in the assembly of the respirasome. We show that CIII2 is asymmetric due to the presence of only one copy of subunit 9, which straddles both monomers and prevents the attachment of a second copy of SCAF1 to CIII2, explaining the presence of one copy of CIV in CIII2CIV in mammals. Finally, we show that CIII2 and CIV gain catalytic advantage when assembled into the supercomplex and propose a role for CIII2CIV in fine tuning the efficiency of electron transfer in the electron transport chain.","lang":"eng"}],"type":"journal_article","pmid":1,"citation":{"chicago":"Vercellino, Irene, and Leonid A Sazanov. “Structure and Assembly of the Mammalian Mitochondrial Supercomplex CIII<sub>2</sub>CIV.” <i>Nature</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41586-021-03927-z\">https://doi.org/10.1038/s41586-021-03927-z</a>.","ista":"Vercellino I, Sazanov LA. 2021. Structure and assembly of the mammalian mitochondrial supercomplex CIII<sub>2</sub>CIV. Nature. 598(7880), 364–367.","mla":"Vercellino, Irene, and Leonid A. Sazanov. “Structure and Assembly of the Mammalian Mitochondrial Supercomplex CIII<sub>2</sub>CIV.” <i>Nature</i>, vol. 598, no. 7880, Springer Nature, 2021, pp. 364–67, doi:<a href=\"https://doi.org/10.1038/s41586-021-03927-z\">10.1038/s41586-021-03927-z</a>.","apa":"Vercellino, I., &#38; Sazanov, L. A. (2021). Structure and assembly of the mammalian mitochondrial supercomplex CIII<sub>2</sub>CIV. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-021-03927-z\">https://doi.org/10.1038/s41586-021-03927-z</a>","ama":"Vercellino I, Sazanov LA. Structure and assembly of the mammalian mitochondrial supercomplex CIII<sub>2</sub>CIV. <i>Nature</i>. 2021;598(7880):364-367. doi:<a href=\"https://doi.org/10.1038/s41586-021-03927-z\">10.1038/s41586-021-03927-z</a>","ieee":"I. Vercellino and L. A. Sazanov, “Structure and assembly of the mammalian mitochondrial supercomplex CIII<sub>2</sub>CIV,” <i>Nature</i>, vol. 598, no. 7880. Springer Nature, pp. 364–367, 2021.","short":"I. Vercellino, L.A. Sazanov, Nature 598 (2021) 364–367."},"quality_controlled":"1"},{"quality_controlled":"1","type":"conference","abstract":[{"lang":"eng","text":"Tactile feedback of an object’s surface enables us to discern its material properties and affordances. This understanding is used in digital fabrication processes by creating objects with high-resolution surface variations to influence a user’s tactile perception. As the design of such surface haptics commonly relies on knowledge from real-life experiences, it is unclear how to adapt this information for digital design methods. In this work, we investigate replicating the haptics of real materials. Using an existing process for capturing an object’s microgeometry, we digitize and reproduce the stable surface information of a set of 15 fabric samples. In a psychophysical experiment, we evaluate the tactile qualities of our set of original samples and their replicas. From our results, we see that direct reproduction of surface variations is able to influence different psychophysical dimensions of the tactile perception of surface textures. While the fabrication process did not preserve all properties, our approach underlines that replication of surface microgeometries benefits fabrication methods in terms of haptic perception by covering a large range of tactile variations. Moreover, by changing the surface structure of a single fabricated material, its material perception can be influenced. We conclude by proposing strategies for capturing and reproducing digitized textures to better resemble the perceived haptics of the originals."}],"citation":{"short":"D. Degraen, M. Piovarci, B. Bickel, A. Kruger, in:, 34th Annual ACM Symposium, Association for Computing Machinery, 2021, pp. 954–971.","mla":"Degraen, Donald, et al. “Capturing Tactile Properties of Real Surfaces for Haptic Reproduction.” <i>34th Annual ACM Symposium</i>, Association for Computing Machinery, 2021, pp. 954–71, doi:<a href=\"https://doi.org/10.1145/3472749.3474798\">10.1145/3472749.3474798</a>.","chicago":"Degraen, Donald, Michael Piovarci, Bernd Bickel, and Antonio Kruger. “Capturing Tactile Properties of Real Surfaces for Haptic Reproduction.” In <i>34th Annual ACM Symposium</i>, 954–71. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3472749.3474798\">https://doi.org/10.1145/3472749.3474798</a>.","ista":"Degraen D, Piovarci M, Bickel B, Kruger A. 2021. Capturing tactile properties of real surfaces for haptic reproduction. 34th Annual ACM Symposium. UIST: User Interface Software and Technology, 954–971.","ama":"Degraen D, Piovarci M, Bickel B, Kruger A. Capturing tactile properties of real surfaces for haptic reproduction. In: <i>34th Annual ACM Symposium</i>. Association for Computing Machinery; 2021:954-971. doi:<a href=\"https://doi.org/10.1145/3472749.3474798\">10.1145/3472749.3474798</a>","ieee":"D. Degraen, M. Piovarci, B. Bickel, and A. Kruger, “Capturing tactile properties of real surfaces for haptic reproduction,” in <i>34th Annual ACM Symposium</i>, Virtual, 2021, pp. 954–971.","apa":"Degraen, D., Piovarci, M., Bickel, B., &#38; Kruger, A. (2021). Capturing tactile properties of real surfaces for haptic reproduction. In <i>34th Annual ACM Symposium</i> (pp. 954–971). Virtual: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3472749.3474798\">https://doi.org/10.1145/3472749.3474798</a>"},"department":[{"_id":"BeBi"}],"publisher":"Association for Computing Machinery","date_created":"2021-10-18T07:36:11Z","publication_status":"published","conference":{"end_date":"2021-10-14","start_date":"2021-10-10","name":"UIST: User Interface Software and Technology","location":"Virtual"},"_id":"10148","scopus_import":"1","month":"10","date_published":"2021-10-10T00:00:00Z","day":"10","doi":"10.1145/3472749.3474798","oa":1,"file":[{"content_type":"application/pdf","checksum":"b0b26464df79b3a59e8ed82e4e19ab15","relation":"main_file","date_updated":"2021-10-18T07:36:03Z","file_id":"10149","access_level":"open_access","date_created":"2021-10-18T07:36:03Z","file_name":"degraen-UIST2021_Texture_Appropriation_CR_preprint.pdf","creator":"bbickel","file_size":29796364}],"ec_funded":1,"acknowledgement":"Our gratitude goes out to Kamila Mushkina, Akhmajon Makhsadov, Jordan Espenshade, Bruno Fruchard, Roland Bennewitz, and Robert Drumm. This project has received funding from the EU’s Horizon 2020 research and innovation programme, under the Marie Skłodowska-Curie grant agreement No 642841 (DISTRO).","year":"2021","publication_identifier":{"isbn":["978-1-4503-8635-7"]},"publication":"34th Annual ACM Symposium","ddc":["000"],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","project":[{"name":"Distributed 3D Object Design","_id":"2508E324-B435-11E9-9278-68D0E5697425","grant_number":"642841","call_identifier":"H2020"}],"oa_version":"Preprint","date_updated":"2025-03-31T15:58:15Z","page":"954-971","title":"Capturing tactile properties of real surfaces for haptic reproduction","author":[{"last_name":"Degraen","full_name":"Degraen, Donald","first_name":"Donald"},{"id":"62E473F4-5C99-11EA-A40E-AF823DDC885E","full_name":"Piovarci, Michael","last_name":"Piovarci","orcid":"0000-0002-5062-4474","first_name":"Michael"},{"first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385"},{"first_name":"Antonio","last_name":"Kruger","full_name":"Kruger, Antonio"}],"file_date_updated":"2021-10-18T07:36:03Z","has_accepted_license":"1","article_processing_charge":"No","status":"public","language":[{"iso":"eng"}]},{"department":[{"_id":"ToHe"}],"volume":5,"publisher":"Association for Computing Machinery","quality_controlled":"1","citation":{"mla":"Mühlböck, Fabian, and Ross Tate. “Transitioning from Structural to Nominal Code with Efficient Gradual Typing.” <i>Proceedings of the ACM on Programming Languages</i>, vol. 5, 127, Association for Computing Machinery, 2021, doi:<a href=\"https://doi.org/10.1145/3485504\">10.1145/3485504</a>.","ista":"Mühlböck F, Tate R. 2021. Transitioning from structural to nominal code with efficient gradual typing. Proceedings of the ACM on Programming Languages. 5, 127.","chicago":"Mühlböck, Fabian, and Ross Tate. “Transitioning from Structural to Nominal Code with Efficient Gradual Typing.” <i>Proceedings of the ACM on Programming Languages</i>. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3485504\">https://doi.org/10.1145/3485504</a>.","apa":"Mühlböck, F., &#38; Tate, R. (2021). Transitioning from structural to nominal code with efficient gradual typing. <i>Proceedings of the ACM on Programming Languages</i>. Chicago, IL, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3485504\">https://doi.org/10.1145/3485504</a>","ama":"Mühlböck F, Tate R. Transitioning from structural to nominal code with efficient gradual typing. <i>Proceedings of the ACM on Programming Languages</i>. 2021;5. doi:<a href=\"https://doi.org/10.1145/3485504\">10.1145/3485504</a>","ieee":"F. Mühlböck and R. Tate, “Transitioning from structural to nominal code with efficient gradual typing,” <i>Proceedings of the ACM on Programming Languages</i>, vol. 5. Association for Computing Machinery, 2021.","short":"F. Mühlböck, R. Tate, Proceedings of the ACM on Programming Languages 5 (2021)."},"type":"journal_article","abstract":[{"lang":"eng","text":"Gradual typing is a principled means for mixing typed and untyped code. But typed and untyped code often exhibit different programming patterns. There is already substantial research investigating gradually giving types to code exhibiting typical untyped patterns, and some research investigating gradually removing types from code exhibiting typical typed patterns. This paper investigates how to extend these established gradual-typing concepts to give formal guarantees not only about how to change types as code evolves but also about how to change such programming patterns as well.\r\n\r\nIn particular, we explore mixing untyped \"structural\" code with typed \"nominal\" code in an object-oriented language. But whereas previous work only allowed \"nominal\" objects to be treated as \"structural\" objects, we also allow \"structural\" objects to dynamically acquire certain nominal types, namely interfaces. We present a calculus that supports such \"cross-paradigm\" code migration and interoperation in a manner satisfying both the static and dynamic gradual guarantees, and demonstrate that the calculus can be implemented efficiently."}],"_id":"10153","scopus_import":"1","month":"10","date_created":"2021-10-19T12:48:44Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","short":"CC BY-ND (4.0)","image":"/image/cc_by_nd.png"},"publication_status":"published","conference":{"location":"Chicago, IL, United States","name":"OOPSLA: Object-Oriented Programming, Systems, Languages, and Applications","start_date":"2021-10-17","end_date":"2021-10-23"},"publication":"Proceedings of the ACM on Programming Languages","ddc":["005"],"license":"https://creativecommons.org/licenses/by-nd/4.0/","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","project":[{"call_identifier":"FWF","grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"date_published":"2021-10-15T00:00:00Z","intvolume":"         5","oa":1,"file":[{"access_level":"open_access","file_size":770269,"creator":"fmuehlbo","success":1,"date_created":"2021-10-19T12:52:23Z","file_name":"monnom-oopsla21.pdf","relation":"main_file","checksum":"71011efd2da771cafdec7f0d9693f8c1","content_type":"application/pdf","file_id":"10154","date_updated":"2021-10-19T12:52:23Z"}],"doi":"10.1145/3485504","day":"15","acknowledgement":"We thank the reviewers for their valuable suggestions towards improving the paper. We also \r\nthank Mae Milano and Adrian Sampson, as well as the members of the Programming Languages Discussion Group at Cornell University and of the Programming Research Laboratory at Northeastern University, for their helpful feedback on preliminary findings of this work.\r\n\r\nThis material is based upon work supported in part by the National Science Foundation (NSF) through grant CCF-1350182 and the Austrian Science Fund (FWF) through grant Z211-N23 (Wittgenstein~Award).\r\nAny opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the NSF or the FWF.","article_type":"original","year":"2021","publication_identifier":{"eissn":["2475-1421"]},"article_number":"127","date_updated":"2025-04-15T06:25:55Z","author":[{"last_name":"Mühlböck","full_name":"Mühlböck, Fabian","id":"6395C5F6-89DF-11E9-9C97-6BDFE5697425","orcid":"0000-0003-1548-0177","first_name":"Fabian"},{"full_name":"Tate, Ross","last_name":"Tate","first_name":"Ross"}],"title":"Transitioning from structural to nominal code with efficient gradual typing","has_accepted_license":"1","article_processing_charge":"No","file_date_updated":"2021-10-19T12:52:23Z","language":[{"iso":"eng"}],"status":"public","oa_version":"Published Version","keyword":["gradual typing","gradual guarantee","nominal","structural","call tags"]},{"volume":12,"department":[{"_id":"CaBe"}],"publisher":"Springer Nature","citation":{"short":"L.-M. Appel, V. Franke, M. Bruno, I. Grishkovskaya, A. Kasiliauskaite, T. Kaufmann, U.E. Schoeberl, M.G. Puchinger, S. Kostrhon, C. Ebenwaldner, M. Sebesta, E. Beltzung, K. Mechtler, G. Lin, A. Vlasova, M. Leeb, R. Pavri, A. Stark, A. Akalin, R. Stefl, C. Bernecky, K. Djinovic-Carugo, D. Slade, Nature Communications 12 (2021).","apa":"Appel, L.-M., Franke, V., Bruno, M., Grishkovskaya, I., Kasiliauskaite, A., Kaufmann, T., … Slade, D. (2021). PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-021-26360-2\">https://doi.org/10.1038/s41467-021-26360-2</a>","ieee":"L.-M. Appel <i>et al.</i>, “PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC,” <i>Nature Communications</i>, vol. 12, no. 1. Springer Nature, 2021.","ama":"Appel L-M, Franke V, Bruno M, et al. PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC. <i>Nature Communications</i>. 2021;12(1). doi:<a href=\"https://doi.org/10.1038/s41467-021-26360-2\">10.1038/s41467-021-26360-2</a>","mla":"Appel, Lisa-Marie, et al. “PHF3 Regulates Neuronal Gene Expression through the Pol II CTD Reader Domain SPOC.” <i>Nature Communications</i>, vol. 12, no. 1, 6078, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-26360-2\">10.1038/s41467-021-26360-2</a>.","ista":"Appel L-M, Franke V, Bruno M, Grishkovskaya I, Kasiliauskaite A, Kaufmann T, Schoeberl UE, Puchinger MG, Kostrhon S, Ebenwaldner C, Sebesta M, Beltzung E, Mechtler K, Lin G, Vlasova A, Leeb M, Pavri R, Stark A, Akalin A, Stefl R, Bernecky C, Djinovic-Carugo K, Slade D. 2021. PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC. Nature Communications. 12(1), 6078.","chicago":"Appel, Lisa-Marie, Vedran Franke, Melania Bruno, Irina Grishkovskaya, Aiste Kasiliauskaite, Tanja Kaufmann, Ursula E. Schoeberl, et al. “PHF3 Regulates Neuronal Gene Expression through the Pol II CTD Reader Domain SPOC.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-021-26360-2\">https://doi.org/10.1038/s41467-021-26360-2</a>."},"type":"journal_article","abstract":[{"lang":"eng","text":"The C-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol II) is a regulatory hub for transcription and RNA processing. Here, we identify PHD-finger protein 3 (PHF3) as a regulator of transcription and mRNA stability that docks onto Pol II CTD through its SPOC domain. We characterize SPOC as a CTD reader domain that preferentially binds two phosphorylated Serine-2 marks in adjacent CTD repeats. PHF3 drives liquid-liquid phase separation of phosphorylated Pol II, colocalizes with Pol II clusters and tracks with Pol II across the length of genes. PHF3 knock-out or SPOC deletion in human cells results in increased Pol II stalling, reduced elongation rate and an increase in mRNA stability, with marked derepression of neuronal genes. Key neuronal genes are aberrantly expressed in Phf3 knock-out mouse embryonic stem cells, resulting in impaired neuronal differentiation. Our data suggest that PHF3 acts as a prominent effector of neuronal gene regulation by bridging transcription with mRNA decay."}],"quality_controlled":"1","_id":"10163","month":"10","issue":"1","scopus_import":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"published","date_created":"2021-10-20T14:40:32Z","external_id":{"isi":["000709050300001"]},"isi":1,"publication":"Nature Communications","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["610"],"file":[{"file_id":"10169","date_updated":"2021-10-21T13:51:49Z","relation":"main_file","content_type":"application/pdf","checksum":"d99fcd51aebde19c21314e3de0148007","success":1,"file_name":"2021_NatComm_Appel.pdf","date_created":"2021-10-21T13:51:49Z","file_size":5111706,"creator":"cchlebak","access_level":"open_access"}],"oa":1,"day":"19","doi":"10.1038/s41467-021-26360-2","date_published":"2021-10-19T00:00:00Z","intvolume":"        12","article_number":"6078","acknowledgement":"D.S. thanks Claudine Kraft, Renée Schroeder, Verena Jantsch, Franz Klein and Peter Schlögelhofer for support. We thank Anita Testa Salmazo for help with purifying Pol II; Matthias Geyer and Robert Düster for sharing DYRK1A kinase; Felix Hartmann and Clemens Plaschka for help with mass photometry; Goran Kokic for design of the arrest assay sequences; Petra van der Lelij for help with generating mESC KO; Maximilian Freilinger for help with the purification of mEGFP-CTD; Stefan Ameres, Nina Fasching and Brian Reichholf for advice on SLAM-seq and for sharing reagents; Laura Gallego Valle for advice regarding LLPS assays; Krzysztof Chylinski for advice regarding CRISPR/Cas9 methodology; VBCF Protein Technologies facility for purifying PHF3 and providing gRNAs and Cas9; VBCF NGS facility for sequencing; Monoclonal antibody facility at the Helmholtz center for Pol II antibodies; Friedrich Propst and Elzbieta Kowalska for advice and for sharing materials; Egon Ogris for sharing materials; Martin Eilers for recommending a ChIP-grade TFIIS antibody; Susanne Opravil, Otto Hudecz, Markus Hartl and Natascha Hartl for mass spectrometry analysis; staff of the X-ray beamlines at the ESRF in Grenoble for their excellent support; Christa Bücker, Anton Meinhart, Clemens Plaschka and members of the Slade lab for critical comments on the manuscript; Life Science Editors for editing assistance. M.B. and D.S. acknowledge support by the FWF-funded DK ‘Chromosome Dynamics’. T.K. is a recipient of the DOC fellowship from the Austrian Academy of Sciences. U.S. is supported by the L’Oreal for Women in Science Austria Fellowship and the Austrian Science Fund (FWF T 795-B30). M.L is supported by the Vienna Science and Technology Fund (WWTF, VRG14-006). R.S. is supported by the Czech Science Foundation (15-17670 S and 21-24460 S), Ministry of Education, Youths and Sports of the Czech Republic (CEITEC 2020 project (LQ1601)), and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant agreement no. 649030); this publication reflects only the author’s view and the Research Executive Agency is not responsible for any use that may be made of the information it contains. M.S. is supported by the Czech Science Foundation (GJ20-21581Y). K.D.C. research is supported by the Austrian Science Fund (FWF) Projects I525 and I1593, P22276, P19060, and W1221, Federal Ministry of Economy, Family and Youth through the initiative ‘Laura Bassi Centres of Expertise’, funding from the Centre of Optimized Structural Studies No. 253275, the Wellcome Trust Collaborative Award (201543/Z/16), COST action BM1405 Non-globular proteins - from sequence to structure, function and application in molecular physiopathology (NGP-NET), the Vienna Science and Technology Fund (WWTF LS17-008), and by the University of Vienna. This project was funded by the MFPL start-up grant, the Vienna Science and Technology Fund (WWTF LS14-001), and the Austrian Science Fund (P31546-B28 and W1258 “DK: Integrative Structural Biology”) to D.S.","publication_identifier":{"eissn":["2041-1723"]},"year":"2021","article_type":"original","title":"PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC","author":[{"first_name":"Lisa-Marie","last_name":"Appel","full_name":"Appel, Lisa-Marie"},{"first_name":"Vedran","full_name":"Franke, Vedran","last_name":"Franke"},{"first_name":"Melania","last_name":"Bruno","full_name":"Bruno, Melania"},{"first_name":"Irina","last_name":"Grishkovskaya","full_name":"Grishkovskaya, Irina"},{"last_name":"Kasiliauskaite","full_name":"Kasiliauskaite, Aiste","first_name":"Aiste"},{"first_name":"Tanja","last_name":"Kaufmann","full_name":"Kaufmann, Tanja"},{"last_name":"Schoeberl","full_name":"Schoeberl, Ursula E.","first_name":"Ursula E."},{"first_name":"Martin G.","last_name":"Puchinger","full_name":"Puchinger, Martin G."},{"first_name":"Sebastian","last_name":"Kostrhon","full_name":"Kostrhon, Sebastian"},{"last_name":"Ebenwaldner","full_name":"Ebenwaldner, Carmen","first_name":"Carmen"},{"first_name":"Marek","last_name":"Sebesta","full_name":"Sebesta, Marek"},{"full_name":"Beltzung, Etienne","last_name":"Beltzung","first_name":"Etienne"},{"full_name":"Mechtler, Karl","last_name":"Mechtler","first_name":"Karl"},{"full_name":"Lin, Gen","last_name":"Lin","first_name":"Gen"},{"first_name":"Anna","full_name":"Vlasova, Anna","last_name":"Vlasova"},{"last_name":"Leeb","full_name":"Leeb, Martin","first_name":"Martin"},{"first_name":"Rushad","full_name":"Pavri, Rushad","last_name":"Pavri"},{"first_name":"Alexander","last_name":"Stark","full_name":"Stark, Alexander"},{"first_name":"Altuna","full_name":"Akalin, Altuna","last_name":"Akalin"},{"last_name":"Stefl","full_name":"Stefl, Richard","first_name":"Richard"},{"orcid":"0000-0003-0893-7036","last_name":"Bernecky","full_name":"Bernecky, Carrie A","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","first_name":"Carrie A"},{"last_name":"Djinovic-Carugo","full_name":"Djinovic-Carugo, Kristina","first_name":"Kristina"},{"last_name":"Slade","full_name":"Slade, Dea","first_name":"Dea"}],"date_updated":"2024-10-21T06:02:05Z","related_material":{"link":[{"description":"Preprint ","url":"https://www.biorxiv.org/content/10.1101/2020.02.11.943159","relation":"earlier_version"}]},"status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","has_accepted_license":"1","file_date_updated":"2021-10-21T13:51:49Z","oa_version":"Published Version","keyword":["general physics and astronomy","general biochemistry","genetics and molecular biology","general chemistry"]},{"external_id":{"pmid":["34547909"],"isi":["000697643700001"]},"publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_created":"2021-10-21T07:46:06Z","month":"09","scopus_import":"1","issue":"1959","_id":"10166","abstract":[{"lang":"eng","text":"While sexual reproduction is widespread among many taxa, asexual lineages have repeatedly evolved from sexual ancestors. Despite extensive research on the evolution of sex, it is still unclear whether this switch represents a major transition requiring major molecular reorganization, and how convergent the changes involved are. In this study, we investigated the phylogenetic relationship and patterns of gene expression of sexual and asexual lineages of Eurasian Artemia brine shrimp, to assess how gene expression patterns are affected by the transition to asexuality. We find only a few genes that are consistently associated with the evolution of asexuality, suggesting that this shift may not require an extensive overhauling of the meiotic machinery. While genes with sex-biased expression have high rates of expression divergence within Eurasian Artemia, neither female- nor male-biased genes appear to show unusual evolutionary patterns after sexuality is lost, contrary to theoretical expectations."}],"type":"journal_article","pmid":1,"citation":{"short":"A.K. Huylmans, A. Macon, F. Hontoria, B. Vicoso, Proceedings of the Royal Society B: Biological Sciences 288 (2021).","apa":"Huylmans, A. K., Macon, A., Hontoria, F., &#38; Vicoso, B. (2021). Transitions to asexuality and evolution of gene expression in Artemia brine shrimp. <i>Proceedings of the Royal Society B: Biological Sciences</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rspb.2021.1720\">https://doi.org/10.1098/rspb.2021.1720</a>","ama":"Huylmans AK, Macon A, Hontoria F, Vicoso B. Transitions to asexuality and evolution of gene expression in Artemia brine shrimp. <i>Proceedings of the Royal Society B: Biological Sciences</i>. 2021;288(1959). doi:<a href=\"https://doi.org/10.1098/rspb.2021.1720\">10.1098/rspb.2021.1720</a>","ieee":"A. K. Huylmans, A. Macon, F. Hontoria, and B. Vicoso, “Transitions to asexuality and evolution of gene expression in Artemia brine shrimp,” <i>Proceedings of the Royal Society B: Biological Sciences</i>, vol. 288, no. 1959. The Royal Society, 2021.","mla":"Huylmans, Ann K., et al. “Transitions to Asexuality and Evolution of Gene Expression in Artemia Brine Shrimp.” <i>Proceedings of the Royal Society B: Biological Sciences</i>, vol. 288, no. 1959, 20211720, The Royal Society, 2021, doi:<a href=\"https://doi.org/10.1098/rspb.2021.1720\">10.1098/rspb.2021.1720</a>.","ista":"Huylmans AK, Macon A, Hontoria F, Vicoso B. 2021. Transitions to asexuality and evolution of gene expression in Artemia brine shrimp. Proceedings of the Royal Society B: Biological Sciences. 288(1959), 20211720.","chicago":"Huylmans, Ann K, Ariana Macon, Francisco Hontoria, and Beatriz Vicoso. “Transitions to Asexuality and Evolution of Gene Expression in Artemia Brine Shrimp.” <i>Proceedings of the Royal Society B: Biological Sciences</i>. The Royal Society, 2021. <a href=\"https://doi.org/10.1098/rspb.2021.1720\">https://doi.org/10.1098/rspb.2021.1720</a>."},"quality_controlled":"1","publisher":"The Royal Society","volume":288,"department":[{"_id":"BeVi"}],"keyword":["asexual reproduction","parthenogenesis","sex-biased genes","sexual conflict","automixis","crustaceans"],"oa_version":"Published Version","status":"public","language":[{"iso":"eng"}],"file_date_updated":"2021-10-22T11:48:02Z","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","author":[{"orcid":"0000-0001-8871-4961","last_name":"Huylmans","full_name":"Huylmans, Ann K","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","first_name":"Ann K"},{"last_name":"Macon","full_name":"Macon, Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","first_name":"Ariana"},{"full_name":"Hontoria, Francisco","last_name":"Hontoria","first_name":"Francisco"},{"first_name":"Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz","last_name":"Vicoso"}],"title":"Transitions to asexuality and evolution of gene expression in Artemia brine shrimp","related_material":{"link":[{"url":"https://doi.org/10.6084/m9.figshare.c.5615488.v1","relation":"supplementary_material"}],"record":[{"status":"public","relation":"research_data","id":"9949"}]},"date_updated":"2025-04-14T07:41:20Z","acknowledged_ssus":[{"_id":"ScienComp"}],"article_number":"20211720","ec_funded":1,"publication_identifier":{"issn":["0962-8452"],"eissn":["1471-2954"]},"acknowledgement":"We thank the Vicoso laboratory, Thomas Lenormand and Tanja Schwander for helpful discussions, the group of Gonzalo Gajardo, especially Cristian Gallardo-Escárate and Margarita Parraguez Donoso, for sequencing data and advice, and the IST Scientific Computing Group for their support. This work was supported by the European Research Council under the European Union's Horizon 2020 research and innovation program (grant agreement no. 715257).","year":"2021","article_type":"original","day":"22","doi":"10.1098/rspb.2021.1720","file":[{"relation":"main_file","checksum":"76e7f253b7040bca2ad76f82bd7c45c0","content_type":"application/pdf","file_id":"10172","date_updated":"2021-10-22T11:48:02Z","access_level":"open_access","success":1,"date_created":"2021-10-22T11:48:02Z","file_name":"2021_ProRoSocBBioSci_Huylmans.pdf","file_size":995806,"creator":"cchlebak"}],"oa":1,"intvolume":"       288","date_published":"2021-09-22T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"grant_number":"715257","_id":"250BDE62-B435-11E9-9278-68D0E5697425","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","call_identifier":"H2020"}],"ddc":["595"],"publication":"Proceedings of the Royal Society B: Biological Sciences","isi":1}]