[{"citation":{"ieee":"V. Kaloshin and E. Koudjinan, “Non co-preservation of the 1/2 and 1/(2l+1)-rational caustics along deformations of circles.” 2021.","ama":"Kaloshin V, Koudjinan E. Non co-preservation of the 1/2 and 1/(2l+1)-rational caustics along deformations of circles. 2021.","short":"V. Kaloshin, E. Koudjinan, (2021).","chicago":"Kaloshin, Vadim, and Edmond Koudjinan. “Non Co-Preservation of the 1/2 and 1/(2l+1)-Rational Caustics along Deformations of Circles,” 2021.","mla":"Kaloshin, Vadim, and Edmond Koudjinan. Non Co-Preservation of the 1/2 and 1/(2l+1)-Rational Caustics along Deformations of Circles. 2021.","apa":"Kaloshin, V., & Koudjinan, E. (2021). Non co-preservation of the 1/2 and 1/(2l+1)-rational caustics along deformations of circles.","ista":"Kaloshin V, Koudjinan E. 2021. Non co-preservation of the 1/2 and 1/(2l+1)-rational caustics along deformations of circles."},"ddc":["500"],"file_date_updated":"2021-05-30T13:57:37Z","article_processing_charge":"No","language":[{"iso":"eng"}],"department":[{"_id":"VaKa"}],"date_published":"2021-01-01T00:00:00Z","oa_version":"Submitted Version","type":"preprint","date_created":"2021-05-30T13:58:13Z","has_accepted_license":"1","title":"Non co-preservation of the 1/2 and 1/(2l+1)-rational caustics along deformations of circles","oa":1,"status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","file":[{"file_size":353431,"content_type":"application/pdf","relation":"main_file","date_created":"2021-05-30T13:57:37Z","file_name":"CoExistence 2&3 caustics 3_17_6_2_3.pdf","date_updated":"2021-05-30T13:57:37Z","access_level":"open_access","creator":"ekoudjin","checksum":"b281b5c2e3e90de0646c3eafcb2c6c25","file_id":"9436"}],"_id":"9435","author":[{"id":"FE553552-CDE8-11E9-B324-C0EBE5697425","last_name":"Kaloshin","first_name":"Vadim","orcid":"0000-0002-6051-2628","full_name":"Kaloshin, Vadim"},{"id":"52DF3E68-AEFA-11EA-95A4-124A3DDC885E","last_name":"Koudjinan","first_name":"Edmond","orcid":"0000-0003-2640-4049","full_name":"Koudjinan, Edmond"}],"year":"2021","date_updated":"2021-06-01T09:10:22Z","abstract":[{"text":"For any given positive integer l, we prove that every plane deformation of a circlewhich preserves the 1/2and 1/ (2l + 1) -rational caustics is trivial i.e. the deformationconsists only of similarities (rescalings and isometries).","lang":"eng"}]},{"has_accepted_license":"1","publication":"eLife","date_created":"2021-05-30T22:01:23Z","type":"journal_article","department":[{"_id":"RySh"},{"_id":"PeJo"}],"language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","volume":10,"quality_controlled":"1","external_id":{"isi":["000651761700001"]},"related_material":{"record":[{"id":"9562","status":"public","relation":"dissertation_contains"}],"link":[{"relation":"earlier_version","url":"https://doi.org/10.1101/2020.04.16.045112"}]},"acknowledgement":"We are grateful to Akari Hagiwara and Toshihisa Ohtsuka for CAST antibody, and Masahiko Watanabe for neurexin antibody. We thank David Adams for kindly providing the stable Cav2.3 cell line. Cav2.3 KO mice were kindly provided by Tsutomu Tanabe. This project has received funding from the European Research Council (ERC) and European Commission (EC), under the European Union’s Horizon 2020 research and innovation programme (ERC grant agreement no. 694539 to Ryuichi Shigemoto, no. 692692 to Peter Jonas, and the Marie Skłodowska-Curie grant agreement no. 665385 to Cihan Önal), the Swiss National Science Foundation Grant 31003A-172881 to Bernhard Bettler and Deutsche Forschungsgemeinschaft (For 2143) and BIOSS-2 to Akos Kulik.","day":"29","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"first_name":"Pradeep","orcid":"0000-0003-0863-4481","last_name":"Bhandari","id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87","full_name":"Bhandari, Pradeep"},{"last_name":"Vandael","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","first_name":"David H","orcid":"0000-0001-7577-1676","full_name":"Vandael, David H"},{"full_name":"Fernández-Fernández, Diego","last_name":"Fernández-Fernández","first_name":"Diego"},{"full_name":"Fritzius, Thorsten","last_name":"Fritzius","first_name":"Thorsten"},{"first_name":"David","last_name":"Kleindienst","id":"42E121A4-F248-11E8-B48F-1D18A9856A87","full_name":"Kleindienst, David"},{"full_name":"Önal, Hüseyin C","orcid":"0000-0002-2771-2011","first_name":"Hüseyin C","id":"4659D740-F248-11E8-B48F-1D18A9856A87","last_name":"Önal"},{"full_name":"Montanaro-Punzengruber, Jacqueline-Claire","first_name":"Jacqueline-Claire","id":"3786AB44-F248-11E8-B48F-1D18A9856A87","last_name":"Montanaro-Punzengruber"},{"last_name":"Gassmann","first_name":"Martin","full_name":"Gassmann, Martin"},{"first_name":"Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Jonas, Peter M"},{"last_name":"Kulik","first_name":"Akos","full_name":"Kulik, Akos"},{"full_name":"Bettler, Bernhard","first_name":"Bernhard","last_name":"Bettler"},{"first_name":"Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi"},{"id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","last_name":"Koppensteiner","first_name":"Peter","orcid":"0000-0002-3509-1948","full_name":"Koppensteiner, Peter"}],"isi":1,"project":[{"call_identifier":"H2020","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","grant_number":"694539","_id":"25CA28EA-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","grant_number":"692692","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020"}],"file":[{"relation":"main_file","content_type":"application/pdf","success":1,"file_size":8174719,"file_name":"2021_eLife_Bhandari.pdf","date_updated":"2021-05-31T09:43:09Z","date_created":"2021-05-31T09:43:09Z","creator":"cziletti","file_id":"9440","checksum":"6ebcb79999f889766f7cd79ee134ad28","access_level":"open_access"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"eLife Sciences Publications","title":"GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals","doi":"10.7554/ELIFE.68274","publication_status":"published","oa_version":"Published Version","date_published":"2021-04-29T00:00:00Z","scopus_import":"1","file_date_updated":"2021-05-31T09:43:09Z","ddc":["570"],"citation":{"short":"P. Bhandari, D.H. Vandael, D. Fernández-Fernández, T. Fritzius, D. Kleindienst, H.C. Önal, J.-C. Montanaro-Punzengruber, M. Gassmann, P.M. Jonas, A. Kulik, B. Bettler, R. Shigemoto, P. Koppensteiner, ELife 10 (2021).","ama":"Bhandari P, Vandael DH, Fernández-Fernández D, et al. GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals. eLife. 2021;10. doi:10.7554/ELIFE.68274","ieee":"P. Bhandari et al., “GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals,” eLife, vol. 10. eLife Sciences Publications, 2021.","chicago":"Bhandari, Pradeep, David H Vandael, Diego Fernández-Fernández, Thorsten Fritzius, David Kleindienst, Hüseyin C Önal, Jacqueline-Claire Montanaro-Punzengruber, et al. “GABAB Receptor Auxiliary Subunits Modulate Cav2.3-Mediated Release from Medial Habenula Terminals.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/ELIFE.68274.","ista":"Bhandari P, Vandael DH, Fernández-Fernández D, Fritzius T, Kleindienst D, Önal HC, Montanaro-Punzengruber J-C, Gassmann M, Jonas PM, Kulik A, Bettler B, Shigemoto R, Koppensteiner P. 2021. GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals. eLife. 10, e68274.","apa":"Bhandari, P., Vandael, D. H., Fernández-Fernández, D., Fritzius, T., Kleindienst, D., Önal, H. C., … Koppensteiner, P. (2021). GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals. ELife. eLife Sciences Publications. https://doi.org/10.7554/ELIFE.68274","mla":"Bhandari, Pradeep, et al. “GABAB Receptor Auxiliary Subunits Modulate Cav2.3-Mediated Release from Medial Habenula Terminals.” ELife, vol. 10, e68274, eLife Sciences Publications, 2021, doi:10.7554/ELIFE.68274."},"intvolume":" 10","abstract":[{"lang":"eng","text":"The synaptic connection from medial habenula (MHb) to interpeduncular nucleus (IPN) is critical for emotion-related behaviors and uniquely expresses R-type Ca2+ channels (Cav2.3) and auxiliary GABAB receptor (GBR) subunits, the K+-channel tetramerization domain-containing proteins (KCTDs). Activation of GBRs facilitates or inhibits transmitter release from MHb terminals depending on the IPN subnucleus, but the role of KCTDs is unknown. We therefore examined the localization and function of Cav2.3, GBRs, and KCTDs in this pathway in mice. We show in heterologous cells that KCTD8 and KCTD12b directly bind to Cav2.3 and that KCTD8 potentiates Cav2.3 currents in the absence of GBRs. In the rostral IPN, KCTD8, KCTD12b, and Cav2.3 co-localize at the presynaptic active zone. Genetic deletion indicated a bidirectional modulation of Cav2.3-mediated release by these KCTDs with a compensatory increase of KCTD8 in the active zone in KCTD12b-deficient mice. The interaction of Cav2.3 with KCTDs therefore scales synaptic strength independent of GBR activation."}],"date_updated":"2024-03-25T23:30:16Z","year":"2021","article_number":"e68274","_id":"9437","status":"public","publication_identifier":{"eissn":["2050-084X"]},"oa":1,"month":"04","ec_funded":1},{"citation":{"ama":"Vandael DH, Okamoto Y, Borges Merjane C, Vargas Barroso VM, Suter B, Jonas PM. Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses. Nature Protocols. 2021;16(6):2947–2967. doi:10.1038/s41596-021-00526-0","ieee":"D. H. Vandael, Y. Okamoto, C. Borges Merjane, V. M. Vargas Barroso, B. Suter, and P. M. Jonas, “Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses,” Nature Protocols, vol. 16, no. 6. Springer Nature, pp. 2947–2967, 2021.","short":"D.H. Vandael, Y. Okamoto, C. Borges Merjane, V.M. Vargas Barroso, B. Suter, P.M. Jonas, Nature Protocols 16 (2021) 2947–2967.","chicago":"Vandael, David H, Yuji Okamoto, Carolina Borges Merjane, Victor M Vargas Barroso, Benjamin Suter, and Peter M Jonas. “Subcellular Patch-Clamp Techniques for Single-Bouton Stimulation and Simultaneous Pre- and Postsynaptic Recording at Cortical Synapses.” Nature Protocols. Springer Nature, 2021. https://doi.org/10.1038/s41596-021-00526-0.","apa":"Vandael, D. H., Okamoto, Y., Borges Merjane, C., Vargas Barroso, V. M., Suter, B., & Jonas, P. M. (2021). Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses. Nature Protocols. Springer Nature. https://doi.org/10.1038/s41596-021-00526-0","ista":"Vandael DH, Okamoto Y, Borges Merjane C, Vargas Barroso VM, Suter B, Jonas PM. 2021. Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses. Nature Protocols. 16(6), 2947–2967.","mla":"Vandael, David H., et al. “Subcellular Patch-Clamp Techniques for Single-Bouton Stimulation and Simultaneous Pre- and Postsynaptic Recording at Cortical Synapses.” Nature Protocols, vol. 16, no. 6, Springer Nature, 2021, pp. 2947–2967, doi:10.1038/s41596-021-00526-0."},"intvolume":" 16","ddc":["570"],"scopus_import":"1","file_date_updated":"2021-12-02T23:30:05Z","date_published":"2021-06-01T00:00:00Z","oa_version":"Submitted Version","doi":"10.1038/s41596-021-00526-0","publication_status":"published","ec_funded":1,"month":"06","oa":1,"publication_identifier":{"eissn":["17502799"],"issn":["17542189"]},"status":"public","_id":"9438","acknowledged_ssus":[{"_id":"M-Shop"}],"year":"2021","issue":"6","abstract":[{"text":"Rigorous investigation of synaptic transmission requires analysis of unitary synaptic events by simultaneous recording from presynaptic terminals and postsynaptic target neurons. However, this has been achieved at only a limited number of model synapses, including the squid giant synapse and the mammalian calyx of Held. Cortical presynaptic terminals have been largely inaccessible to direct presynaptic recording, due to their small size. Here, we describe a protocol for improved subcellular patch-clamp recording in rat and mouse brain slices, with the synapse in a largely intact environment. Slice preparation takes ~2 h, recording ~3 h and post hoc morphological analysis 2 d. Single presynaptic hippocampal mossy fiber terminals are stimulated minimally invasively in the bouton-attached configuration, in which the cytoplasmic content remains unperturbed, or in the whole-bouton configuration, in which the cytoplasmic composition can be precisely controlled. Paired pre–postsynaptic recordings can be integrated with biocytin labeling and morphological analysis, allowing correlative investigation of synapse structure and function. Paired recordings can be obtained from mossy fiber terminals in slices from both rats and mice, implying applicability to genetically modified synapses. Paired recordings can also be performed together with axon tract stimulation or optogenetic activation, allowing comparison of unitary and compound synaptic events in the same target cell. Finally, paired recordings can be combined with spontaneous event analysis, permitting collection of miniature events generated at a single identified synapse. In conclusion, the subcellular patch-clamp techniques detailed here should facilitate analysis of biophysics, plasticity and circuit function of cortical synapses in the mammalian central nervous system.","lang":"eng"}],"date_updated":"2023-08-10T22:30:51Z","quality_controlled":"1","volume":16,"external_id":{"pmid":["33990799"],"isi":["000650528700003"]},"article_type":"original","article_processing_charge":"No","department":[{"_id":"PeJo"}],"language":[{"iso":"eng"}],"type":"journal_article","publication":"Nature Protocols","date_created":"2021-05-30T22:01:24Z","page":"2947–2967","has_accepted_license":"1","title":"Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Springer Nature","file":[{"embargo":"2021-12-01","file_size":38574802,"content_type":"application/pdf","relation":"main_file","date_created":"2021-07-08T12:27:55Z","date_updated":"2021-12-02T23:30:05Z","file_name":"VandaeletalAuthorVersion2021.pdf","access_level":"open_access","file_id":"9639","creator":"cziletti","checksum":"7eb580abd8893cdb0b410cf41bc8c263"}],"author":[{"full_name":"Vandael, David H","orcid":"0000-0001-7577-1676","first_name":"David H","last_name":"Vandael","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-0408-6094","first_name":"Yuji","id":"3337E116-F248-11E8-B48F-1D18A9856A87","last_name":"Okamoto","full_name":"Okamoto, Yuji"},{"orcid":"0000-0003-0005-401X","first_name":"Carolina","id":"4305C450-F248-11E8-B48F-1D18A9856A87","last_name":"Borges Merjane","full_name":"Borges Merjane, Carolina"},{"first_name":"Victor M","last_name":"Vargas Barroso","id":"2F55A9DE-F248-11E8-B48F-1D18A9856A87","full_name":"Vargas Barroso, Victor M"},{"full_name":"Suter, Benjamin","first_name":"Benjamin","orcid":"0000-0002-9885-6936","last_name":"Suter","id":"4952F31E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Jonas, Peter M","first_name":"Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas"}],"isi":1,"project":[{"call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","grant_number":"692692","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize"},{"grant_number":"V00739","_id":"2696E7FE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Structural plasticity at mossy fiber-CA3 synapses"}],"day":"01","acknowledgement":"This project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 692692 to P.J.) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award to P.J., V 739-B27 to C.B.M.). We are grateful to F. Marr and C. Altmutter for excellent technical assistance and cell reconstruction, E. Kralli-Beller for manuscript editing, and the Scientific Service Units of IST Austria, especially T. Asenov and Miba machine shop, for maximally efficient support.","pmid":1},{"type":"journal_article","department":[{"_id":"GaTk"}],"language":[{"iso":"eng"}],"publication":"Nature Neuroscience","page":"998-1009","date_created":"2021-05-30T22:01:24Z","quality_controlled":"1","volume":24,"external_id":{"isi":["000652577300003"]},"article_type":"original","article_processing_charge":"No","author":[{"first_name":"Wiktor F","last_name":"Mlynarski","id":"358A453A-F248-11E8-B48F-1D18A9856A87","full_name":"Mlynarski, Wiktor F"},{"last_name":"Hermundstad","first_name":"Ann M.","full_name":"Hermundstad, Ann M."}],"isi":1,"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"acknowledgement":"We thank D. Kastner and T. Münch for generously providing figures from their work. We also thank V. Jayaraman, M. Noorman, T. Ma, and K. Krishnamurthy for useful discussions and feedback on the manuscript. W.F.M. was funded by the European Union’s Horizon 2020 Research and Innovation Programme under Marie Skłodowska-Curie Grant Agreement No. 754411. A.M.H. was supported by the Howard Hughes Medical Institute.","day":"20","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Springer Nature","title":"Efficient and adaptive sensory codes","oa_version":"Preprint","date_published":"2021-05-20T00:00:00Z","doi":"10.1038/s41593-021-00846-0","publication_status":"published","citation":{"chicago":"Mlynarski, Wiktor F, and Ann M. Hermundstad. “Efficient and Adaptive Sensory Codes.” Nature Neuroscience. Springer Nature, 2021. https://doi.org/10.1038/s41593-021-00846-0.","apa":"Mlynarski, W. F., & Hermundstad, A. M. (2021). Efficient and adaptive sensory codes. Nature Neuroscience. Springer Nature. https://doi.org/10.1038/s41593-021-00846-0","ista":"Mlynarski WF, Hermundstad AM. 2021. Efficient and adaptive sensory codes. Nature Neuroscience. 24, 998–1009.","mla":"Mlynarski, Wiktor F., and Ann M. Hermundstad. “Efficient and Adaptive Sensory Codes.” Nature Neuroscience, vol. 24, Springer Nature, 2021, pp. 998–1009, doi:10.1038/s41593-021-00846-0.","short":"W.F. Mlynarski, A.M. Hermundstad, Nature Neuroscience 24 (2021) 998–1009.","ieee":"W. F. Mlynarski and A. M. Hermundstad, “Efficient and adaptive sensory codes,” Nature Neuroscience, vol. 24. Springer Nature, pp. 998–1009, 2021.","ama":"Mlynarski WF, Hermundstad AM. Efficient and adaptive sensory codes. Nature Neuroscience. 2021;24:998-1009. doi:10.1038/s41593-021-00846-0"},"intvolume":" 24","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1101/669200 ","open_access":"1"}],"_id":"9439","abstract":[{"lang":"eng","text":"The ability to adapt to changes in stimulus statistics is a hallmark of sensory systems. Here, we developed a theoretical framework that can account for the dynamics of adaptation from an information processing perspective. We use this framework to optimize and analyze adaptive sensory codes, and we show that codes optimized for stationary environments can suffer from prolonged periods of poor performance when the environment changes. To mitigate the adversarial effects of these environmental changes, sensory systems must navigate tradeoffs between the ability to accurately encode incoming stimuli and the ability to rapidly detect and adapt to changes in the distribution of these stimuli. We derive families of codes that balance these objectives, and we demonstrate their close match to experimentally observed neural dynamics during mean and variance adaptation. Our results provide a unifying perspective on adaptation across a range of sensory systems, environments, and sensory tasks."}],"date_updated":"2023-08-08T13:51:14Z","year":"2021","month":"05","ec_funded":1,"status":"public","publication_identifier":{"issn":["1097-6256"],"eissn":["1546-1726"]},"oa":1},{"month":"06","ec_funded":1,"status":"public","publication_identifier":{"issn":["1868-8969"],"isbn":["978-3-95977-184-9"]},"oa":1,"place":"Dagstuhl, Germany","_id":"9441","date_updated":"2023-10-10T07:34:34Z","abstract":[{"lang":"eng","text":"Isomanifolds are the generalization of isosurfaces to arbitrary dimension and codimension, i.e. submanifolds of ℝ^d defined as the zero set of some multivariate multivalued smooth function f: ℝ^d → ℝ^{d-n}, where n is the intrinsic dimension of the manifold. A natural way to approximate a smooth isomanifold M is to consider its Piecewise-Linear (PL) approximation M̂ based on a triangulation 𝒯 of the ambient space ℝ^d. In this paper, we describe a simple algorithm to trace isomanifolds from a given starting point. The algorithm works for arbitrary dimensions n and d, and any precision D. Our main result is that, when f (or M) has bounded complexity, the complexity of the algorithm is polynomial in d and δ = 1/D (and unavoidably exponential in n). Since it is known that for δ = Ω (d^{2.5}), M̂ is O(D²)-close and isotopic to M, our algorithm produces a faithful PL-approximation of isomanifolds of bounded complexity in time polynomial in d. Combining this algorithm with dimensionality reduction techniques, the dependency on d in the size of M̂ can be completely removed with high probability. We also show that the algorithm can handle isomanifolds with boundary and, more generally, isostratifolds. The algorithm for isomanifolds with boundary has been implemented and experimental results are reported, showing that it is practical and can handle cases that are far ahead of the state-of-the-art. "}],"year":"2021","intvolume":" 189","citation":{"ieee":"J.-D. Boissonnat, S. Kachanovich, and M. Wintraecken, “Tracing isomanifolds in Rd in time polynomial in d using Coxeter-Freudenthal-Kuhn triangulations,” in 37th International Symposium on Computational Geometry (SoCG 2021), Virtual, 2021, vol. 189, p. 17:1-17:16.","ama":"Boissonnat J-D, Kachanovich S, Wintraecken M. Tracing isomanifolds in Rd in time polynomial in d using Coxeter-Freudenthal-Kuhn triangulations. In: 37th International Symposium on Computational Geometry (SoCG 2021). Vol 189. Leibniz International Proceedings in Informatics (LIPIcs). Dagstuhl, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2021:17:1-17:16. doi:10.4230/LIPIcs.SoCG.2021.17","short":"J.-D. Boissonnat, S. Kachanovich, M. Wintraecken, in:, 37th International Symposium on Computational Geometry (SoCG 2021), Schloss Dagstuhl - Leibniz-Zentrum für Informatik, Dagstuhl, Germany, 2021, p. 17:1-17:16.","chicago":"Boissonnat, Jean-Daniel, Siargey Kachanovich, and Mathijs Wintraecken. “Tracing Isomanifolds in Rd in Time Polynomial in d Using Coxeter-Freudenthal-Kuhn Triangulations.” In 37th International Symposium on Computational Geometry (SoCG 2021), 189:17:1-17:16. Leibniz International Proceedings in Informatics (LIPIcs). Dagstuhl, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021. https://doi.org/10.4230/LIPIcs.SoCG.2021.17.","mla":"Boissonnat, Jean-Daniel, et al. “Tracing Isomanifolds in Rd in Time Polynomial in d Using Coxeter-Freudenthal-Kuhn Triangulations.” 37th International Symposium on Computational Geometry (SoCG 2021), vol. 189, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021, p. 17:1-17:16, doi:10.4230/LIPIcs.SoCG.2021.17.","apa":"Boissonnat, J.-D., Kachanovich, S., & Wintraecken, M. (2021). Tracing isomanifolds in Rd in time polynomial in d using Coxeter-Freudenthal-Kuhn triangulations. In 37th International Symposium on Computational Geometry (SoCG 2021) (Vol. 189, p. 17:1-17:16). Dagstuhl, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2021.17","ista":"Boissonnat J-D, Kachanovich S, Wintraecken M. 2021. Tracing isomanifolds in Rd in time polynomial in d using Coxeter-Freudenthal-Kuhn triangulations. 37th International Symposium on Computational Geometry (SoCG 2021). SoCG: Symposium on Computational GeometryLeibniz International Proceedings in Informatics (LIPIcs), LIPIcs, vol. 189, 17:1-17:16."},"file_date_updated":"2021-06-02T10:22:33Z","ddc":["005","516","514"],"oa_version":"Published Version","date_published":"2021-06-02T00:00:00Z","conference":{"name":"SoCG: Symposium on Computational Geometry","start_date":"2021-06-07","location":"Virtual","end_date":"2021-06-11"},"publication_status":"published","doi":"10.4230/LIPIcs.SoCG.2021.17","alternative_title":["LIPIcs"],"series_title":"Leibniz International Proceedings in Informatics (LIPIcs)","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","title":"Tracing isomanifolds in Rd in time polynomial in d using Coxeter-Freudenthal-Kuhn triangulations","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"author":[{"full_name":"Boissonnat, Jean-Daniel","last_name":"Boissonnat","first_name":"Jean-Daniel"},{"last_name":"Kachanovich","first_name":"Siargey","full_name":"Kachanovich, Siargey"},{"full_name":"Wintraecken, Mathijs","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","last_name":"Wintraecken","orcid":"0000-0002-7472-2220","first_name":"Mathijs"}],"file":[{"access_level":"open_access","file_id":"9442","checksum":"c322aa48d5d35a35877896cc565705b6","creator":"mwintrae","date_created":"2021-06-02T10:22:33Z","date_updated":"2021-06-02T10:22:33Z","file_name":"LIPIcs-SoCG-2021-17.pdf","success":1,"file_size":1972902,"content_type":"application/pdf","relation":"main_file"}],"acknowledgement":"We thank Dominique Attali, Guilherme de Fonseca, Arijit Ghosh, Vincent Pilaud and Aurélien Alvarez for their comments and suggestions. We also acknowledge the reviewers.","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"02","volume":189,"quality_controlled":"1","related_material":{"record":[{"id":"12960","relation":"later_version","status":"public"}]},"article_processing_charge":"No","type":"conference","language":[{"iso":"eng"}],"department":[{"_id":"HeEd"}],"has_accepted_license":"1","date_created":"2021-06-02T10:10:55Z","page":"17:1-17:16","publication":"37th International Symposium on Computational Geometry (SoCG 2021)"},{"oa_version":"Published Version","date_published":"2021-07-01T00:00:00Z","publication_status":"published","doi":"10.1093/plcell/koab122","intvolume":" 33","citation":{"chicago":"Ruiz-Lopez, N, J Pérez-Sancho, A Esteban Del Valle, RP Haslam, S Vanneste, R Catalá, C Perea-Resa, et al. “Synaptotagmins at the Endoplasmic Reticulum-Plasma Membrane Contact Sites Maintain Diacylglycerol Homeostasis during Abiotic Stress.” Plant Cell. American Society of Plant Biologists, 2021. https://doi.org/10.1093/plcell/koab122.","apa":"Ruiz-Lopez, N., Pérez-Sancho, J., Esteban Del Valle, A., Haslam, R., Vanneste, S., Catalá, R., … Botella, M. (2021). Synaptotagmins at the endoplasmic reticulum-plasma membrane contact sites maintain diacylglycerol homeostasis during abiotic stress. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1093/plcell/koab122","ista":"Ruiz-Lopez N, Pérez-Sancho J, Esteban Del Valle A, Haslam R, Vanneste S, Catalá R, Perea-Resa C, Van Damme D, García-Hernández S, Albert A, Vallarino J, Lin J, Friml J, Macho A, Salinas J, Rosado A, Napier J, Amorim-Silva V, Botella M. 2021. Synaptotagmins at the endoplasmic reticulum-plasma membrane contact sites maintain diacylglycerol homeostasis during abiotic stress. Plant Cell. 33(7), 2431–2453.","mla":"Ruiz-Lopez, N., et al. “Synaptotagmins at the Endoplasmic Reticulum-Plasma Membrane Contact Sites Maintain Diacylglycerol Homeostasis during Abiotic Stress.” Plant Cell, vol. 33, no. 7, American Society of Plant Biologists, 2021, pp. 2431–53, doi:10.1093/plcell/koab122.","ama":"Ruiz-Lopez N, Pérez-Sancho J, Esteban Del Valle A, et al. Synaptotagmins at the endoplasmic reticulum-plasma membrane contact sites maintain diacylglycerol homeostasis during abiotic stress. Plant Cell. 2021;33(7):2431-2453. doi:10.1093/plcell/koab122","ieee":"N. Ruiz-Lopez et al., “Synaptotagmins at the endoplasmic reticulum-plasma membrane contact sites maintain diacylglycerol homeostasis during abiotic stress,” Plant Cell, vol. 33, no. 7. American Society of Plant Biologists, pp. 2431–2453, 2021.","short":"N. Ruiz-Lopez, J. Pérez-Sancho, A. Esteban Del Valle, R. Haslam, S. Vanneste, R. Catalá, C. Perea-Resa, D. Van Damme, S. García-Hernández, A. Albert, J. Vallarino, J. Lin, J. Friml, A. Macho, J. Salinas, A. Rosado, J. Napier, V. Amorim-Silva, M. Botella, Plant Cell 33 (2021) 2431–2453."},"scopus_import":"1","file_date_updated":"2021-10-14T13:36:38Z","ddc":["580"],"_id":"9443","date_updated":"2023-08-08T13:54:32Z","issue":"7","abstract":[{"text":"Endoplasmic reticulum–plasma membrane contact sites (ER–PM CS) play fundamental roles in all eukaryotic cells. Arabidopsis thaliana mutants lacking the ER–PM protein tether synaptotagmin1 (SYT1) exhibit decreased PM integrity under multiple abiotic stresses, such as freezing, high salt, osmotic stress, and mechanical damage. Here, we show that, together with SYT1, the stress-induced SYT3 is an ER–PM tether that also functions in maintaining PM integrity. The ER–PM CS localization of SYT1 and SYT3 is dependent on PM phosphatidylinositol-4-phosphate and is regulated by abiotic stress. Lipidomic analysis revealed that cold stress increased the accumulation of diacylglycerol at the PM in a syt1/3 double mutant relative to wild-type while the levels of most glycerolipid species remain unchanged. In addition, the SYT1-green fluorescent protein fusion preferentially binds diacylglycerol in vivo with little affinity for polar glycerolipids. Our work uncovers a SYT-dependent mechanism of stress adaptation counteracting the detrimental accumulation of diacylglycerol at the PM produced during episodes of abiotic stress.","lang":"eng"}],"year":"2021","month":"07","ec_funded":1,"status":"public","publication_identifier":{"eissn":["1532-298x"],"issn":["1040-4651"]},"oa":1,"type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"JiFr"}],"has_accepted_license":"1","page":"2431-2453","date_created":"2021-06-02T13:13:58Z","publication":"Plant Cell","external_id":{"isi":["000703938100026"],"pmid":["33944955"]},"volume":33,"quality_controlled":"1","article_processing_charge":"No","article_type":"original","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"author":[{"full_name":"Ruiz-Lopez, N","first_name":"N","last_name":"Ruiz-Lopez"},{"last_name":"Pérez-Sancho","first_name":"J","full_name":"Pérez-Sancho, J"},{"full_name":"Esteban Del Valle, A","last_name":"Esteban Del Valle","first_name":"A"},{"last_name":"Haslam","first_name":"RP","full_name":"Haslam, RP"},{"full_name":"Vanneste, S","last_name":"Vanneste","first_name":"S"},{"full_name":"Catalá, R","last_name":"Catalá","first_name":"R"},{"full_name":"Perea-Resa, C","last_name":"Perea-Resa","first_name":"C"},{"full_name":"Van Damme, D","first_name":"D","last_name":"Van Damme"},{"full_name":"García-Hernández, S","last_name":"García-Hernández","first_name":"S"},{"last_name":"Albert","first_name":"A","full_name":"Albert, A"},{"first_name":"J","last_name":"Vallarino","full_name":"Vallarino, J"},{"last_name":"Lin","first_name":"J","full_name":"Lin, J"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"AP","last_name":"Macho","full_name":"Macho, AP"},{"full_name":"Salinas, J","last_name":"Salinas","first_name":"J"},{"full_name":"Rosado, A","first_name":"A","last_name":"Rosado"},{"full_name":"Napier, JA","last_name":"Napier","first_name":"JA"},{"first_name":"V","last_name":"Amorim-Silva","full_name":"Amorim-Silva, V"},{"full_name":"Botella, MA","last_name":"Botella","first_name":"MA"}],"isi":1,"file":[{"relation":"main_file","content_type":"application/pdf","success":1,"file_size":2952028,"date_updated":"2021-10-14T13:36:38Z","file_name":"2021_PlantCell_RuizLopez.pdf","date_created":"2021-10-14T13:36:38Z","file_id":"10141","checksum":"22d596678d00310d793611864a6d0fcd","creator":"cchlebak","access_level":"open_access"}],"acknowledgement":"We would also like to thank Lothar Willmitzer for the lipidomic analysis at the Max Planck Institute of Molecular Plant Physiology (Potsdam, Germany). We thank Manuela Vega from SCI for her technical assistance in image analysis. We thank John R. Pearson and the Bionand Nanoimaging Unit, F. David Navas Fernández and the SCAI Imaging Facility and The Plant Cell Biology facility at the Shanghai Center for Plant Stress Biology for assistance with confocal microscopy. The FaFAH1 clone was a gift from Iraida Amaya Saavedra (IFAPA-Centro de Churriana, Málaga, Spain). The AHA3 antibody against the H+-ATPase was a gift from Ramón Serrano Salom (Instituto de Biología Molecular y Celular de Plantas, Valencia, Spain). The MAP-mTU2-SAC1 construct was provided by Yvon Jaillais (Laboratoire Reproduction et Développement des Plantes, Univ Lyon, France). The pGWB5 from the pGWB vector series, was provided by Tsuyoshi Nakagawa (Department of Molecular and Functional Genomics, Shimane University). We thank Plan Propio from the University of Málaga for financial support.\r\nFunding","pmid":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"day":"01","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","publisher":"American Society of Plant Biologists","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Synaptotagmins at the endoplasmic reticulum-plasma membrane contact sites maintain diacylglycerol homeostasis during abiotic stress"},{"publication":"Journal of Functional Analysis","date_created":"2021-06-06T22:01:28Z","type":"journal_article","department":[{"_id":"RoSe"}],"language":[{"iso":"eng"}],"article_processing_charge":"No","article_type":"original","quality_controlled":"1","volume":281,"external_id":{"isi":["000656508600008"],"arxiv":["2009.00992"]},"acknowledgement":"Funding from the European Union's Horizon 2020 research and innovation programme under the ERC grant agreement No 694227 (R.S.) and under the Marie Sklodowska-Curie grant agreement No 836146 (A.D.) is gratefully acknowledged. A.D. acknowledges support of the Swiss National Science Foundation through the Ambizione grant PZ00P2 185851.","day":"15","author":[{"full_name":"Deuchert, Andreas","last_name":"Deuchert","first_name":"Andreas"},{"last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","first_name":"Robert","full_name":"Seiringer, Robert"}],"isi":1,"project":[{"grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Analysis of quantum many-body systems"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Elsevier","title":"Semiclassical approximation and critical temperature shift for weakly interacting trapped bosons","doi":"10.1016/j.jfa.2021.109096","publication_status":"published","oa_version":"Preprint","date_published":"2021-09-15T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2009.00992"}],"scopus_import":"1","citation":{"ama":"Deuchert A, Seiringer R. Semiclassical approximation and critical temperature shift for weakly interacting trapped bosons. Journal of Functional Analysis. 2021;281(6). doi:10.1016/j.jfa.2021.109096","ieee":"A. Deuchert and R. Seiringer, “Semiclassical approximation and critical temperature shift for weakly interacting trapped bosons,” Journal of Functional Analysis, vol. 281, no. 6. Elsevier, 2021.","short":"A. Deuchert, R. Seiringer, Journal of Functional Analysis 281 (2021).","chicago":"Deuchert, Andreas, and Robert Seiringer. “Semiclassical Approximation and Critical Temperature Shift for Weakly Interacting Trapped Bosons.” Journal of Functional Analysis. Elsevier, 2021. https://doi.org/10.1016/j.jfa.2021.109096.","apa":"Deuchert, A., & Seiringer, R. (2021). Semiclassical approximation and critical temperature shift for weakly interacting trapped bosons. Journal of Functional Analysis. Elsevier. https://doi.org/10.1016/j.jfa.2021.109096","ista":"Deuchert A, Seiringer R. 2021. Semiclassical approximation and critical temperature shift for weakly interacting trapped bosons. Journal of Functional Analysis. 281(6), 109096.","mla":"Deuchert, Andreas, and Robert Seiringer. “Semiclassical Approximation and Critical Temperature Shift for Weakly Interacting Trapped Bosons.” Journal of Functional Analysis, vol. 281, no. 6, 109096, Elsevier, 2021, doi:10.1016/j.jfa.2021.109096."},"intvolume":" 281","arxiv":1,"issue":"6","abstract":[{"lang":"eng","text":"We consider a system of N trapped bosons with repulsive interactions in a combined semiclassical mean-field limit at positive temperature. We show that the free energy is well approximated by the minimum of the Hartree free energy functional – a natural extension of the Hartree energy functional to positive temperatures. The Hartree free energy functional converges in the same limit to a semiclassical free energy functional, and we show that the system displays Bose–Einstein condensation if and only if it occurs in the semiclassical free energy functional. This allows us to show that for weak coupling the critical temperature decreases due to the repulsive interactions."}],"date_updated":"2023-08-08T13:56:27Z","year":"2021","article_number":"109096","_id":"9462","status":"public","publication_identifier":{"issn":["0022-1236"],"eissn":["1096-0783"]},"oa":1,"month":"09","ec_funded":1},{"date_published":"2021-04-01T00:00:00Z","oa_version":"Published Version","doi":"10.1007/s00022-021-00577-4","publication_status":"published","intvolume":" 112","citation":{"ieee":"H. Edelsbrunner, A. Nikitenko, and G. F. Osang, “A step in the Delaunay mosaic of order k,” Journal of Geometry, vol. 112, no. 1. Springer Nature, 2021.","ama":"Edelsbrunner H, Nikitenko A, Osang GF. A step in the Delaunay mosaic of order k. Journal of Geometry. 2021;112(1). doi:10.1007/s00022-021-00577-4","short":"H. Edelsbrunner, A. Nikitenko, G.F. Osang, Journal of Geometry 112 (2021).","apa":"Edelsbrunner, H., Nikitenko, A., & Osang, G. F. (2021). A step in the Delaunay mosaic of order k. Journal of Geometry. Springer Nature. https://doi.org/10.1007/s00022-021-00577-4","ista":"Edelsbrunner H, Nikitenko A, Osang GF. 2021. A step in the Delaunay mosaic of order k. Journal of Geometry. 112(1), 15.","mla":"Edelsbrunner, Herbert, et al. “A Step in the Delaunay Mosaic of Order K.” Journal of Geometry, vol. 112, no. 1, 15, Springer Nature, 2021, doi:10.1007/s00022-021-00577-4.","chicago":"Edelsbrunner, Herbert, Anton Nikitenko, and Georg F Osang. “A Step in the Delaunay Mosaic of Order K.” Journal of Geometry. Springer Nature, 2021. https://doi.org/10.1007/s00022-021-00577-4."},"ddc":["510"],"scopus_import":"1","file_date_updated":"2021-06-11T13:16:26Z","_id":"9465","article_number":"15","year":"2021","issue":"1","abstract":[{"text":"Given a locally finite set 𝑋⊆ℝ𝑑 and an integer 𝑘≥0, we consider the function 𝐰𝑘:Del𝑘(𝑋)→ℝ on the dual of the order-k Voronoi tessellation, whose sublevel sets generalize the notion of alpha shapes from order-1 to order-k (Edelsbrunner et al. in IEEE Trans Inf Theory IT-29:551–559, 1983; Krasnoshchekov and Polishchuk in Inf Process Lett 114:76–83, 2014). While this function is not necessarily generalized discrete Morse, in the sense of Forman (Adv Math 134:90–145, 1998) and Freij (Discrete Math 309:3821–3829, 2009), we prove that it satisfies similar properties so that its increments can be meaningfully classified into critical and non-critical steps. This result extends to the case of weighted points and sheds light on k-fold covers with balls in Euclidean space.","lang":"eng"}],"date_updated":"2022-05-12T11:41:45Z","month":"04","oa":1,"publication_identifier":{"issn":["00472468"],"eissn":["14208997"]},"status":"public","department":[{"_id":"HeEd"}],"language":[{"iso":"eng"}],"type":"journal_article","publication":"Journal of Geometry","date_created":"2021-06-06T22:01:29Z","has_accepted_license":"1","quality_controlled":"1","volume":112,"article_type":"original","article_processing_charge":"Yes (via OA deal)","file":[{"file_name":"2021_Geometry_Edelsbrunner.pdf","date_updated":"2021-06-11T13:16:26Z","date_created":"2021-06-11T13:16:26Z","checksum":"e52a832f1def52a2b23d21bcc09e646f","file_id":"9544","creator":"kschuh","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_size":694706,"success":1}],"author":[{"full_name":"Edelsbrunner, Herbert","first_name":"Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner"},{"full_name":"Nikitenko, Anton","last_name":"Nikitenko","id":"3E4FF1BA-F248-11E8-B48F-1D18A9856A87","first_name":"Anton"},{"full_name":"Osang, Georg F","last_name":"Osang","id":"464B40D6-F248-11E8-B48F-1D18A9856A87","first_name":"Georg F"}],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"01","title":"A step in the Delaunay mosaic of order k","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer Nature"},{"year":"2021","date_updated":"2023-02-23T13:58:47Z","abstract":[{"lang":"eng","text":"In this work, we apply the dynamical systems analysis of Hanrot et al. (CRYPTO’11) to a class of lattice block reduction algorithms that includes (natural variants of) slide reduction and block-Rankin reduction. This implies sharper bounds on the polynomial running times (in the query model) for these algorithms and opens the door to faster practical variants of slide reduction. We give heuristic arguments showing that such variants can indeed speed up slide reduction significantly in practice. This is confirmed by experimental evidence, which also shows that our variants are competitive with state-of-the-art reduction algorithms."}],"_id":"9466","oa":1,"publication_identifier":{"isbn":["9783030752446"],"eissn":["16113349"],"issn":["03029743"]},"status":"public","ec_funded":1,"month":"05","conference":{"start_date":"2021-05-10","name":"PKC: IACR International Conference on Practice and Theory of Public Key Cryptography","end_date":"2021-05-13","location":"Virtual"},"publication_status":"published","doi":"10.1007/978-3-030-75245-3_3","date_published":"2021-05-01T00:00:00Z","oa_version":"Published Version","ddc":["000"],"file_date_updated":"2022-05-27T09:48:31Z","scopus_import":"1","intvolume":" 12710","citation":{"short":"M. Walter, in:, Public-Key Cryptography – PKC 2021, Springer Nature, 2021, pp. 45–67.","ama":"Walter M. The convergence of slide-type reductions. In: Public-Key Cryptography – PKC 2021. Vol 12710. Springer Nature; 2021:45-67. doi:10.1007/978-3-030-75245-3_3","ieee":"M. Walter, “The convergence of slide-type reductions,” in Public-Key Cryptography – PKC 2021, Virtual, 2021, vol. 12710, pp. 45–67.","chicago":"Walter, Michael. “The Convergence of Slide-Type Reductions.” In Public-Key Cryptography – PKC 2021, 12710:45–67. Springer Nature, 2021. https://doi.org/10.1007/978-3-030-75245-3_3.","apa":"Walter, M. (2021). The convergence of slide-type reductions. In Public-Key Cryptography – PKC 2021 (Vol. 12710, pp. 45–67). Virtual: Springer Nature. https://doi.org/10.1007/978-3-030-75245-3_3","ista":"Walter M. 2021. The convergence of slide-type reductions. Public-Key Cryptography – PKC 2021. PKC: IACR International Conference on Practice and Theory of Public Key Cryptography, LNCS, vol. 12710, 45–67.","mla":"Walter, Michael. “The Convergence of Slide-Type Reductions.” Public-Key Cryptography – PKC 2021, vol. 12710, Springer Nature, 2021, pp. 45–67, doi:10.1007/978-3-030-75245-3_3."},"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"01","acknowledgement":"This work was initiated in discussions with Léo Ducas, when the author was visiting the Simons Institute for the Theory of Computation during the program “Lattices: Algorithms, Complexity, and Cryptography”. We thank Thomas Espitau for pointing out a bug in a proof in an earlier version of this manuscript.","file":[{"date_updated":"2022-05-27T09:48:31Z","file_name":"2021_PKC_Walter.pdf","date_created":"2022-05-27T09:48:31Z","checksum":"413e564d645ed93d7318672361d9d470","creator":"dernst","file_id":"11416","access_level":"open_access","content_type":"application/pdf","relation":"main_file","success":1,"file_size":489017}],"project":[{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815","call_identifier":"H2020","name":"Teaching Old Crypto New Tricks"}],"author":[{"last_name":"Walter","id":"488F98B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3186-2482","first_name":"Michael","full_name":"Walter, Michael"}],"title":"The convergence of slide-type reductions","publisher":"Springer Nature","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","alternative_title":["LNCS"],"page":"45-67","date_created":"2021-06-06T22:01:29Z","publication":"Public-Key Cryptography – PKC 2021","has_accepted_license":"1","language":[{"iso":"eng"}],"department":[{"_id":"KrPi"}],"type":"conference","article_processing_charge":"No","volume":12710,"quality_controlled":"1"},{"article_number":"A17","_id":"9467","arxiv":1,"abstract":[{"lang":"eng","text":"Turbulence in the flow of fluid through a pipe can be suppressed by buoyancy forces. As the suppression of turbulence leads to severe heat transfer deterioration, this is an important and undesirable phenomenon in both heating and cooling applications. Vertical flow is often considered, as the axial buoyancy force can help drive the flow. With heating measured by the buoyancy parameter 𝐶, our direct numerical simulations show that shear-driven turbulence may either be completely laminarised or it transitions to a relatively quiescent convection-driven state. Buoyancy forces cause a flattening of the base flow profile, which in isothermal pipe flow has recently been linked to complete suppression of turbulence (Kühnen et al., Nat. Phys., vol. 14, 2018, pp. 386–390), and the flattened laminar base profile has enhanced nonlinear stability (Marensi et al., J. Fluid Mech., vol. 863, 2019, pp. 50–875). In agreement with these findings, the nonlinear lower-branch travelling-wave solution analysed here, which is believed to mediate transition to turbulence in isothermal pipe flow, is shown to be suppressed by buoyancy. A linear instability of the laminar base flow is responsible for the appearance of the relatively quiescent convection driven state for 𝐶≳4 across the range of Reynolds numbers considered. In the suppression of turbulence, however, i.e. in the transition from turbulence, we find clearer association with the analysis of He et al. (J. Fluid Mech., vol. 809, 2016, pp. 31–71) than with the above dynamical systems approach, which describes better the transition to turbulence. The laminarisation criterion He et al. propose, based on an apparent Reynolds number of the flow as measured by its driving pressure gradient, is found to capture the critical 𝐶=𝐶𝑐𝑟(𝑅𝑒) above which the flow will be laminarised or switch to the convection-driven type. Our analysis suggests that it is the weakened rolls, rather than the streaks, which appear to be critical for laminarisation."}],"date_updated":"2023-08-08T13:58:41Z","year":"2021","month":"07","status":"public","publication_identifier":{"issn":["00221120"],"eissn":["14697645"]},"oa":1,"oa_version":"Published Version","date_published":"2021-07-25T00:00:00Z","doi":"10.1017/jfm.2021.371","publication_status":"published","citation":{"short":"E. Marensi, S. He, A.P. Willis, Journal of Fluid Mechanics 919 (2021).","ieee":"E. Marensi, S. He, and A. P. Willis, “Suppression of turbulence and travelling waves in a vertical heated pipe,” Journal of Fluid Mechanics, vol. 919. Cambridge University Press, 2021.","ama":"Marensi E, He S, Willis AP. Suppression of turbulence and travelling waves in a vertical heated pipe. Journal of Fluid Mechanics. 2021;919. doi:10.1017/jfm.2021.371","chicago":"Marensi, Elena, Shuisheng He, and Ashley P. Willis. “Suppression of Turbulence and Travelling Waves in a Vertical Heated Pipe.” Journal of Fluid Mechanics. Cambridge University Press, 2021. https://doi.org/10.1017/jfm.2021.371.","ista":"Marensi E, He S, Willis AP. 2021. Suppression of turbulence and travelling waves in a vertical heated pipe. Journal of Fluid Mechanics. 919, A17.","apa":"Marensi, E., He, S., & Willis, A. P. (2021). Suppression of turbulence and travelling waves in a vertical heated pipe. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2021.371","mla":"Marensi, Elena, et al. “Suppression of Turbulence and Travelling Waves in a Vertical Heated Pipe.” Journal of Fluid Mechanics, vol. 919, A17, Cambridge University Press, 2021, doi:10.1017/jfm.2021.371."},"intvolume":" 919","file_date_updated":"2021-08-03T09:53:28Z","scopus_import":"1","ddc":["530"],"author":[{"full_name":"Marensi, Elena","last_name":"Marensi","id":"0BE7553A-1004-11EA-B805-18983DDC885E","first_name":"Elena"},{"full_name":"He, Shuisheng","first_name":"Shuisheng","last_name":"He"},{"full_name":"Willis, Ashley P.","first_name":"Ashley P.","last_name":"Willis"}],"isi":1,"file":[{"access_level":"open_access","checksum":"867ad077e45c181c2c5ec1311ba27c41","creator":"kschuh","file_id":"9766","date_created":"2021-08-03T09:53:28Z","date_updated":"2021-08-03T09:53:28Z","file_name":"2021_JournalFluidMechanics_Marensi.pdf","success":1,"file_size":4087358,"relation":"main_file","content_type":"application/pdf"}],"acknowledgement":"The anonymous referees are kindly acknowledged for their useful suggestions andcomments.","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"25","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Cambridge University Press","title":"Suppression of turbulence and travelling waves in a vertical heated pipe","type":"journal_article","department":[{"_id":"BjHo"}],"language":[{"iso":"eng"}],"has_accepted_license":"1","publication":"Journal of Fluid Mechanics","date_created":"2021-06-06T22:01:30Z","volume":919,"quality_controlled":"1","external_id":{"arxiv":["2008.13486"],"isi":["000653785000001"]},"article_type":"original","article_processing_charge":"Yes (via OA deal)"},{"author":[{"full_name":"Arroyo Guevara, Alan M","first_name":"Alan M","orcid":"0000-0003-2401-8670","last_name":"Arroyo Guevara","id":"3207FDC6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"R. Bruce","last_name":"Richter","full_name":"Richter, R. Bruce"},{"full_name":"Sunohara, Matthew","last_name":"Sunohara","first_name":"Matthew"}],"isi":1,"project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"day":"20","title":"Extending drawings of complete graphs into arrangements of pseudocircles","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Society for Industrial and Applied Mathematics","department":[{"_id":"UlWa"}],"language":[{"iso":"eng"}],"type":"journal_article","publication":"SIAM Journal on Discrete Mathematics","page":"1050-1076","date_created":"2021-06-06T22:01:30Z","volume":35,"quality_controlled":"1","external_id":{"arxiv":["2001.06053"],"isi":["000674142200022"]},"article_processing_charge":"No","article_type":"original","_id":"9468","year":"2021","abstract":[{"lang":"eng","text":"Motivated by the successful application of geometry to proving the Harary--Hill conjecture for “pseudolinear” drawings of $K_n$, we introduce “pseudospherical” drawings of graphs. A spherical drawing of a graph $G$ is a drawing in the unit sphere $\\mathbb{S}^2$ in which the vertices of $G$ are represented as points---no three on a great circle---and the edges of $G$ are shortest-arcs in $\\mathbb{S}^2$ connecting pairs of vertices. Such a drawing has three properties: (1) every edge $e$ is contained in a simple closed curve $\\gamma_e$ such that the only vertices in $\\gamma_e$ are the ends of $e$; (2) if $e\\ne f$, then $\\gamma_e\\cap\\gamma_f$ has precisely two crossings; and (3) if $e\\ne f$, then $e$ intersects $\\gamma_f$ at most once, in either a crossing or an end of $e$. We use properties (1)--(3) to define a pseudospherical drawing of $G$. Our main result is that for the complete graph, properties (1)--(3) are equivalent to the same three properties but with “precisely two crossings” in (2) replaced by “at most two crossings.” The proof requires a result in the geometric transversal theory of arrangements of pseudocircles. This is proved using the surprising result that the absence of special arcs (coherent spirals) in an arrangement of simple closed curves characterizes the fact that any two curves in the arrangement have at most two crossings. Our studies provide the necessary ideas for exhibiting a drawing of $K_{10}$ that has no extension to an arrangement of pseudocircles and a drawing of $K_9$ that does extend to an arrangement of pseudocircles, but no such extension has all pairs of pseudocircles crossing twice.\r\n"}],"arxiv":1,"issue":"2","date_updated":"2023-08-08T13:58:12Z","ec_funded":1,"month":"05","publication_identifier":{"issn":["08954801"]},"oa":1,"status":"public","date_published":"2021-05-20T00:00:00Z","oa_version":"Preprint","doi":"10.1137/20M1313234","publication_status":"published","intvolume":" 35","citation":{"short":"A.M. Arroyo Guevara, R.B. Richter, M. Sunohara, SIAM Journal on Discrete Mathematics 35 (2021) 1050–1076.","ama":"Arroyo Guevara AM, Richter RB, Sunohara M. Extending drawings of complete graphs into arrangements of pseudocircles. SIAM Journal on Discrete Mathematics. 2021;35(2):1050-1076. doi:10.1137/20M1313234","ieee":"A. M. Arroyo Guevara, R. B. Richter, and M. Sunohara, “Extending drawings of complete graphs into arrangements of pseudocircles,” SIAM Journal on Discrete Mathematics, vol. 35, no. 2. Society for Industrial and Applied Mathematics, pp. 1050–1076, 2021.","chicago":"Arroyo Guevara, Alan M, R. Bruce Richter, and Matthew Sunohara. “Extending Drawings of Complete Graphs into Arrangements of Pseudocircles.” SIAM Journal on Discrete Mathematics. Society for Industrial and Applied Mathematics, 2021. https://doi.org/10.1137/20M1313234.","ista":"Arroyo Guevara AM, Richter RB, Sunohara M. 2021. Extending drawings of complete graphs into arrangements of pseudocircles. SIAM Journal on Discrete Mathematics. 35(2), 1050–1076.","apa":"Arroyo Guevara, A. M., Richter, R. B., & Sunohara, M. (2021). Extending drawings of complete graphs into arrangements of pseudocircles. SIAM Journal on Discrete Mathematics. Society for Industrial and Applied Mathematics. https://doi.org/10.1137/20M1313234","mla":"Arroyo Guevara, Alan M., et al. “Extending Drawings of Complete Graphs into Arrangements of Pseudocircles.” SIAM Journal on Discrete Mathematics, vol. 35, no. 2, Society for Industrial and Applied Mathematics, 2021, pp. 1050–76, doi:10.1137/20M1313234."},"main_file_link":[{"url":"https://arxiv.org/abs/2001.06053","open_access":"1"}],"scopus_import":"1"},{"tmp":{"image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"day":"01","acknowledgement":"We thank the editor, two helpful reviewers, Roger Butlin, Kerstin Johannesson, Valentina Peona, Rike Stelkens, Julie Blommaert, Nick Barton, and João Alpedrinha for helpful comments that improved the manuscript. The authors acknowledge funding from the Swedish Research Council Formas (2017-01597 to AS), the Swedish Research Council Vetenskapsrådet (2016-05139 to AS, 2019-04452 to TS) and from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 757451 to TS). ELB was funded by a Carl Tryggers grant awarded to Tanja Slotte. Anja M. Westram was funded by the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 797747. Inês Fragata was funded by a Junior Researcher contract from FCT (CEECIND/02616/2018).","file":[{"relation":"main_file","content_type":"application/pdf","success":1,"file_size":1031978,"creator":"kschuh","file_id":"9545","checksum":"e6f4731365bde2614b333040a08265d8","access_level":"open_access","file_name":"2021_MolecularEcology_Berdan.pdf","date_updated":"2021-06-11T15:34:53Z","date_created":"2021-06-11T15:34:53Z"}],"project":[{"_id":"265B41B8-B435-11E9-9278-68D0E5697425","grant_number":"797747","call_identifier":"H2020","name":"Theoretical and empirical approaches to understanding Parallel Adaptation"}],"author":[{"full_name":"Berdan, Emma L.","last_name":"Berdan","first_name":"Emma L."},{"first_name":"Alexandre","last_name":"Blanckaert","full_name":"Blanckaert, Alexandre"},{"last_name":"Slotte","first_name":"Tanja","full_name":"Slotte, Tanja"},{"full_name":"Suh, Alexander","first_name":"Alexander","last_name":"Suh"},{"last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M"},{"full_name":"Fragata, Inês","last_name":"Fragata","first_name":"Inês"}],"isi":1,"title":"Unboxing mutations: Connecting mutation types with evolutionary consequences","publisher":"Wiley","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","page":"2710-2723","date_created":"2021-06-06T22:01:31Z","publication":"Molecular Ecology","has_accepted_license":"1","language":[{"iso":"eng"}],"department":[{"_id":"NiBa"}],"type":"journal_article","article_processing_charge":"No","external_id":{"isi":["000652056400001"]},"volume":30,"quality_controlled":"1","year":"2021","date_updated":"2023-08-08T13:59:18Z","issue":"12","abstract":[{"lang":"eng","text":"A key step in understanding the genetic basis of different evolutionary outcomes (e.g., adaptation) is to determine the roles played by different mutation types (e.g., SNPs, translocations and inversions). To do this we must simultaneously consider different mutation types in an evolutionary framework. Here, we propose a research framework that directly utilizes the most important characteristics of mutations, their population genetic effects, to determine their relative evolutionary significance in a given scenario. We review known population genetic effects of different mutation types and show how these may be connected to different evolutionary outcomes. We provide examples of how to implement this framework and pinpoint areas where more data, theory and synthesis are needed. Linking experimental and theoretical approaches to examine different mutation types simultaneously is a critical step towards understanding their evolutionary significance."}],"_id":"9470","oa":1,"publication_identifier":{"eissn":["1365294X"],"issn":["09621083"]},"status":"public","ec_funded":1,"month":"06","publication_status":"published","doi":"10.1111/mec.15936","date_published":"2021-06-01T00:00:00Z","oa_version":"Published Version","ddc":["570"],"scopus_import":"1","file_date_updated":"2021-06-11T15:34:53Z","citation":{"chicago":"Berdan, Emma L., Alexandre Blanckaert, Tanja Slotte, Alexander Suh, Anja M Westram, and Inês Fragata. “Unboxing Mutations: Connecting Mutation Types with Evolutionary Consequences.” Molecular Ecology. Wiley, 2021. https://doi.org/10.1111/mec.15936.","ista":"Berdan EL, Blanckaert A, Slotte T, Suh A, Westram AM, Fragata I. 2021. Unboxing mutations: Connecting mutation types with evolutionary consequences. Molecular Ecology. 30(12), 2710–2723.","apa":"Berdan, E. L., Blanckaert, A., Slotte, T., Suh, A., Westram, A. M., & Fragata, I. (2021). Unboxing mutations: Connecting mutation types with evolutionary consequences. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.15936","mla":"Berdan, Emma L., et al. “Unboxing Mutations: Connecting Mutation Types with Evolutionary Consequences.” Molecular Ecology, vol. 30, no. 12, Wiley, 2021, pp. 2710–23, doi:10.1111/mec.15936.","ama":"Berdan EL, Blanckaert A, Slotte T, Suh A, Westram AM, Fragata I. Unboxing mutations: Connecting mutation types with evolutionary consequences. Molecular Ecology. 2021;30(12):2710-2723. doi:10.1111/mec.15936","ieee":"E. L. Berdan, A. Blanckaert, T. Slotte, A. Suh, A. M. Westram, and I. Fragata, “Unboxing mutations: Connecting mutation types with evolutionary consequences,” Molecular Ecology, vol. 30, no. 12. Wiley, pp. 2710–2723, 2021.","short":"E.L. Berdan, A. Blanckaert, T. Slotte, A. Suh, A.M. Westram, I. Fragata, Molecular Ecology 30 (2021) 2710–2723."},"intvolume":" 30"},{"month":"06","status":"public","publication_identifier":{"eissn":["2041-1723"]},"oa":1,"acknowledged_ssus":[{"_id":"EM-Fac"}],"article_number":"3483","_id":"9540","issue":"1","abstract":[{"text":"The hexameric AAA-ATPase Drg1 is a key factor in eukaryotic ribosome biogenesis and initiates cytoplasmic maturation of the large ribosomal subunit by releasing the shuttling maturation factor Rlp24. Drg1 monomers contain two AAA-domains (D1 and D2) that act in a concerted manner. Rlp24 release is inhibited by the drug diazaborine which blocks ATP hydrolysis in D2. The mode of inhibition was unknown. Here we show the first cryo-EM structure of Drg1 revealing the inhibitory mechanism. Diazaborine forms a covalent bond to the 2′-OH of the nucleotide in D2, explaining its specificity for this site. As a consequence, the D2 domain is locked in a rigid, inactive state, stalling the whole Drg1 hexamer. Resistance mechanisms identified include abolished drug binding and altered positioning of the nucleotide. Our results suggest nucleotide-modifying compounds as potential novel inhibitors for AAA-ATPases.","lang":"eng"}],"date_updated":"2023-08-08T14:05:26Z","year":"2021","citation":{"short":"M. Prattes, I. Grishkovskaya, V.-V. Hodirnau, I. Rössler, I. Klein, C. Hetzmannseder, G. Zisser, C.C. Gruber, K. Gruber, D. Haselbach, H. Bergler, Nature Communications 12 (2021).","ama":"Prattes M, Grishkovskaya I, Hodirnau V-V, et al. Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-23854-x","ieee":"M. Prattes et al., “Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine,” Nature Communications, vol. 12, no. 1. Springer Nature, 2021.","chicago":"Prattes, Michael, Irina Grishkovskaya, Victor-Valentin Hodirnau, Ingrid Rössler, Isabella Klein, Christina Hetzmannseder, Gertrude Zisser, et al. “Structural Basis for Inhibition of the AAA-ATPase Drg1 by Diazaborine.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-23854-x.","mla":"Prattes, Michael, et al. “Structural Basis for Inhibition of the AAA-ATPase Drg1 by Diazaborine.” Nature Communications, vol. 12, no. 1, 3483, Springer Nature, 2021, doi:10.1038/s41467-021-23854-x.","ista":"Prattes M, Grishkovskaya I, Hodirnau V-V, Rössler I, Klein I, Hetzmannseder C, Zisser G, Gruber CC, Gruber K, Haselbach D, Bergler H. 2021. Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine. Nature Communications. 12(1), 3483.","apa":"Prattes, M., Grishkovskaya, I., Hodirnau, V.-V., Rössler, I., Klein, I., Hetzmannseder, C., … Bergler, H. (2021). Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-23854-x"},"intvolume":" 12","file_date_updated":"2021-06-15T18:55:59Z","ddc":["570"],"oa_version":"Published Version","date_published":"2021-06-09T00:00:00Z","doi":"10.1038/s41467-021-23854-x","publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Springer Nature","title":"Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine","author":[{"full_name":"Prattes, Michael","last_name":"Prattes","first_name":"Michael"},{"full_name":"Grishkovskaya, Irina","first_name":"Irina","last_name":"Grishkovskaya"},{"full_name":"Hodirnau, Victor-Valentin","first_name":"Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87","last_name":"Hodirnau"},{"first_name":"Ingrid","last_name":"Rössler","full_name":"Rössler, Ingrid"},{"full_name":"Klein, Isabella","last_name":"Klein","first_name":"Isabella"},{"full_name":"Hetzmannseder, Christina","last_name":"Hetzmannseder","first_name":"Christina"},{"full_name":"Zisser, Gertrude","last_name":"Zisser","first_name":"Gertrude"},{"last_name":"Gruber","first_name":"Christian C.","full_name":"Gruber, Christian C."},{"full_name":"Gruber, Karl","first_name":"Karl","last_name":"Gruber"},{"full_name":"Haselbach, David","first_name":"David","last_name":"Haselbach"},{"first_name":"Helmut","last_name":"Bergler","full_name":"Bergler, Helmut"}],"isi":1,"file":[{"date_created":"2021-06-15T18:55:59Z","date_updated":"2021-06-15T18:55:59Z","file_name":"2021_NatureComm_Prattes.pdf","access_level":"open_access","checksum":"40fc24c1310930990b52a8ad1142ee97","file_id":"9556","creator":"cziletti","file_size":3397292,"success":1,"relation":"main_file","content_type":"application/pdf"}],"pmid":1,"acknowledgement":"We are deeply grateful to the late Gregor Högenauer who built the foundation for this study with his visionary work on the inhibitor diazaborine and its bacterial target. We thank Rolf Breinbauer for insightful discussions on boron chemistry. We thank Anton Meinhart and Tim Clausen for the valuable discussion of the manuscript. We are indebted to Thomas Köcher for the MS measurement of the diazaborine-ATPγS adduct. We thank the team of the VBCF for support during early phases of this work and the IST Austria Electron Microscopy Facility for providing equipment. The lab of D.H. is supported by Boehringer Ingelheim. The work was funded by FWF projects P32536 and P32977 (to H.B.).","day":"09","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":12,"keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"quality_controlled":"1","external_id":{"pmid":["34108481"],"isi":["000664874700014"]},"article_type":"original","article_processing_charge":"No","type":"journal_article","department":[{"_id":"EM-Fac"}],"language":[{"iso":"eng"}],"has_accepted_license":"1","publication":"Nature Communications","date_created":"2021-06-10T14:57:45Z"},{"department":[{"_id":"DaAl"}],"language":[{"iso":"eng"}],"type":"journal_article","publication":"ACM Transactions on Algorithms","date_created":"2021-06-10T19:31:05Z","has_accepted_license":"1","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"7802"}]},"volume":17,"quality_controlled":"1","external_id":{"isi":["000661311300006"],"arxiv":["1912.05390"]},"article_processing_charge":"No","article_type":"original","file":[{"content_type":"application/pdf","relation":"main_file","success":1,"file_size":587404,"file_name":"MISMM-arxiv.pdf","date_updated":"2021-06-10T19:33:56Z","date_created":"2021-06-10T19:33:56Z","checksum":"a21c627683890c309a68f6389302c408","creator":"pdavies","file_id":"9542","access_level":"open_access"}],"author":[{"first_name":"Artur","last_name":"Czumaj","full_name":"Czumaj, Artur"},{"full_name":"Davies, Peter","last_name":"Davies","id":"11396234-BB50-11E9-B24C-90FCE5697425","orcid":"0000-0002-5646-9524","first_name":"Peter"},{"first_name":"Merav","last_name":"Parter","full_name":"Parter, Merav"}],"isi":1,"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"day":"01","acknowledgement":"Institute of Science and Technology Austria (IST Austria). Email: peter.davies@ist.ac.at. Work partially\r\ndone at the Department of Computer Science and Centre for Discrete Mathematics and its Applications (DIMAP),University of Warwick. Research partially supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 754411, the Centre for Discrete Mathematics and its Applications, a Weizmann-UK Making Connections Grant, and EPSRC award EP/N011163/1.","title":"Graph sparsification for derandomizing massively parallel computation with low space","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Association for Computing Machinery","date_published":"2021-06-01T00:00:00Z","oa_version":"Submitted Version","doi":"10.1145/3451992","publication_status":"published","citation":{"short":"A. Czumaj, P. Davies, M. Parter, ACM Transactions on Algorithms 17 (2021).","ama":"Czumaj A, Davies P, Parter M. Graph sparsification for derandomizing massively parallel computation with low space. ACM Transactions on Algorithms. 2021;17(2). doi:10.1145/3451992","ieee":"A. Czumaj, P. Davies, and M. Parter, “Graph sparsification for derandomizing massively parallel computation with low space,” ACM Transactions on Algorithms, vol. 17, no. 2. Association for Computing Machinery, 2021.","chicago":"Czumaj, Artur, Peter Davies, and Merav Parter. “Graph Sparsification for Derandomizing Massively Parallel Computation with Low Space.” ACM Transactions on Algorithms. Association for Computing Machinery, 2021. https://doi.org/10.1145/3451992.","apa":"Czumaj, A., Davies, P., & Parter, M. (2021). Graph sparsification for derandomizing massively parallel computation with low space. ACM Transactions on Algorithms. Association for Computing Machinery. https://doi.org/10.1145/3451992","mla":"Czumaj, Artur, et al. “Graph Sparsification for Derandomizing Massively Parallel Computation with Low Space.” ACM Transactions on Algorithms, vol. 17, no. 2, 16, Association for Computing Machinery, 2021, doi:10.1145/3451992.","ista":"Czumaj A, Davies P, Parter M. 2021. Graph sparsification for derandomizing massively parallel computation with low space. ACM Transactions on Algorithms. 17(2), 16."},"intvolume":" 17","ddc":["000"],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1912.05390"}],"file_date_updated":"2021-06-10T19:33:56Z","_id":"9541","article_number":"16","year":"2021","abstract":[{"text":"The Massively Parallel Computation (MPC) model is an emerging model that distills core aspects of distributed and parallel computation, developed as a tool to solve combinatorial (typically graph) problems in systems of many machines with limited space. Recent work has focused on the regime in which machines have sublinear (in n, the number of nodes in the input graph) space, with randomized algorithms presented for the fundamental problems of Maximal Matching and Maximal Independent Set. However, there have been no prior corresponding deterministic algorithms. A major challenge underlying the sublinear space setting is that the local space of each machine might be too small to store all edges incident to a single node. This poses a considerable obstacle compared to classical models in which each node is assumed to know and have easy access to its incident edges. To overcome this barrier, we introduce a new graph sparsification technique that deterministically computes a low-degree subgraph, with the additional property that solving the problem on this subgraph provides significant progress towards solving the problem for the original input graph. Using this framework to derandomize the well-known algorithm of Luby [SICOMP’86], we obtain O(log Δ + log log n)-round deterministic MPC algorithms for solving the problems of Maximal Matching and Maximal Independent Set with O(nɛ) space on each machine for any constant ɛ > 0. These algorithms also run in O(log Δ) rounds in the closely related model of CONGESTED CLIQUE, improving upon the state-of-the-art bound of O(log 2Δ) rounds by Censor-Hillel et al. [DISC’17].","lang":"eng"}],"arxiv":1,"issue":"2","date_updated":"2024-02-28T12:53:09Z","ec_funded":1,"month":"06","publication_identifier":{"issn":["1549-6325"],"eissn":["1549-6333"]},"oa":1,"status":"public"},{"external_id":{"arxiv":["2002.09268"]},"quality_controlled":"1","citation":{"apa":"Davies, P., Gurunanthan, V., Moshrefi, N., Ashkboos, S., & Alistarh, D.-A. (2021). New bounds for distributed mean estimation and variance reduction. In 9th International Conference on Learning Representations. Virtual.","ista":"Davies P, Gurunanthan V, Moshrefi N, Ashkboos S, Alistarh D-A. 2021. New bounds for distributed mean estimation and variance reduction. 9th International Conference on Learning Representations. ICLR: International Conference on Learning Representations.","mla":"Davies, Peter, et al. “New Bounds for Distributed Mean Estimation and Variance Reduction.” 9th International Conference on Learning Representations, 2021.","chicago":"Davies, Peter, Vijaykrishna Gurunanthan, Niusha Moshrefi, Saleh Ashkboos, and Dan-Adrian Alistarh. “New Bounds for Distributed Mean Estimation and Variance Reduction.” In 9th International Conference on Learning Representations, 2021.","short":"P. Davies, V. Gurunanthan, N. Moshrefi, S. Ashkboos, D.-A. Alistarh, in:, 9th International Conference on Learning Representations, 2021.","ama":"Davies P, Gurunanthan V, Moshrefi N, Ashkboos S, Alistarh D-A. New bounds for distributed mean estimation and variance reduction. In: 9th International Conference on Learning Representations. ; 2021.","ieee":"P. Davies, V. Gurunanthan, N. Moshrefi, S. Ashkboos, and D.-A. Alistarh, “New bounds for distributed mean estimation and variance reduction,” in 9th International Conference on Learning Representations, Virtual, 2021."},"main_file_link":[{"url":"https://openreview.net/pdf?id=t86MwoUCCNe","open_access":"1"}],"article_processing_charge":"No","language":[{"iso":"eng"}],"date_published":"2021-05-01T00:00:00Z","department":[{"_id":"DaAl"}],"type":"conference","oa_version":"Published Version","date_created":"2021-06-10T19:46:08Z","publication":"9th International Conference on Learning Representations","publication_status":"published","conference":{"start_date":"2021-05-03","name":" ICLR: International Conference on Learning Representations","end_date":"2021-05-07","location":"Virtual"},"ec_funded":1,"month":"05","title":"New bounds for distributed mean estimation and variance reduction","oa":1,"status":"public","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","_id":"9543","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"author":[{"full_name":"Davies, Peter","first_name":"Peter","orcid":"0000-0002-5646-9524","id":"11396234-BB50-11E9-B24C-90FCE5697425","last_name":"Davies"},{"last_name":"Gurunanthan","first_name":"Vijaykrishna","full_name":"Gurunanthan, Vijaykrishna"},{"first_name":"Niusha ","id":"4db776ff-ce15-11eb-96e3-bc2b90b01c16","last_name":"Moshrefi","full_name":"Moshrefi, Niusha "},{"full_name":"Ashkboos, Saleh","first_name":"Saleh","id":"0D0A9058-257B-11EA-A937-9341C3D8BC8A","last_name":"Ashkboos"},{"full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh"}],"day":"01","year":"2021","date_updated":"2023-02-23T14:00:40Z","abstract":[{"text":"We consider the problem ofdistributed mean estimation (DME), in which n machines are each given a local d-dimensional vector xv∈Rd, and must cooperate to estimate the mean of their inputs μ=1n∑nv=1xv, while minimizing total communication cost. DME is a fundamental construct in distributed machine learning, and there has been considerable work on variants of this problem, especially in the context of distributed variance reduction for stochastic gradients in parallel SGD. Previous work typically assumes an upper bound on the norm of the input vectors, and achieves an error bound in terms of this norm. However, in many real applications, the input vectors are concentrated around the correct output μ, but μ itself has large norm. In such cases, previous output error bounds perform poorly. In this paper, we show that output error bounds need not depend on input norm. We provide a method of quantization which allows distributed mean estimation to be performed with solution quality dependent only on the distance between inputs, not on input norm, and show an analogous result for distributed variance reduction. The technique is based on a new connection with lattice theory. We also provide lower bounds showing that the communication to error trade-off of our algorithms is asymptotically optimal. As the lattices achieving optimal bounds under l2-norm can be computationally impractical, we also present an extension which leverages easy-to-use cubic lattices, and is loose only up to a logarithmic factor ind. We show experimentally that our method yields practical improvements for common applications, relative to prior approaches.","lang":"eng"}],"arxiv":1},{"oa_version":"Submitted Version","date_published":"2021-05-01T00:00:00Z","publication_status":"published","doi":"10.1111/cgf.142626","citation":{"mla":"Rittig, Tobias, et al. “Neural Acceleration of Scattering-Aware Color 3D Printing.” Computer Graphics Forum, vol. 40, no. 2, Wiley, 2021, pp. 205–19, doi:10.1111/cgf.142626.","apa":"Rittig, T., Sumin, D., Babaei, V., Didyk, P., Voloboy, A., Wilkie, A., … Křivánek, J. (2021). Neural acceleration of scattering-aware color 3D printing. Computer Graphics Forum. Wiley. https://doi.org/10.1111/cgf.142626","ista":"Rittig T, Sumin D, Babaei V, Didyk P, Voloboy A, Wilkie A, Bickel B, Myszkowski K, Weyrich T, Křivánek J. 2021. Neural acceleration of scattering-aware color 3D printing. Computer Graphics Forum. 40(2), 205–219.","chicago":"Rittig, Tobias, Denis Sumin, Vahid Babaei, Piotr Didyk, Alexey Voloboy, Alexander Wilkie, Bernd Bickel, Karol Myszkowski, Tim Weyrich, and Jaroslav Křivánek. “Neural Acceleration of Scattering-Aware Color 3D Printing.” Computer Graphics Forum. Wiley, 2021. https://doi.org/10.1111/cgf.142626.","ama":"Rittig T, Sumin D, Babaei V, et al. Neural acceleration of scattering-aware color 3D printing. Computer Graphics Forum. 2021;40(2):205-219. doi:10.1111/cgf.142626","ieee":"T. Rittig et al., “Neural acceleration of scattering-aware color 3D printing,” Computer Graphics Forum, vol. 40, no. 2. Wiley, pp. 205–219, 2021.","short":"T. Rittig, D. Sumin, V. Babaei, P. Didyk, A. Voloboy, A. Wilkie, B. Bickel, K. Myszkowski, T. Weyrich, J. Křivánek, Computer Graphics Forum 40 (2021) 205–219."},"intvolume":" 40","file_date_updated":"2021-10-11T12:06:50Z","scopus_import":"1","ddc":["004"],"_id":"9547","date_updated":"2023-08-14T08:01:50Z","issue":"2","abstract":[{"lang":"eng","text":"With the wider availability of full-color 3D printers, color-accurate 3D-print preparation has received increased attention. A key challenge lies in the inherent translucency of commonly used print materials that blurs out details of the color texture. Previous work tries to compensate for these scattering effects through strategic assignment of colored primary materials to printer voxels. To date, the highest-quality approach uses iterative optimization that relies on computationally expensive Monte Carlo light transport simulation to predict the surface appearance from subsurface scattering within a given print material distribution; that optimization, however, takes in the order of days on a single machine. In our work, we dramatically speed up the process by replacing the light transport simulation with a data-driven approach. Leveraging a deep neural network to predict the scattering within a highly heterogeneous medium, our method performs around two orders of magnitude faster than Monte Carlo rendering while yielding optimization results of similar quality level. The network is based on an established method from atmospheric cloud rendering, adapted to our domain and extended by a physically motivated weight sharing scheme that substantially reduces the network size. We analyze its performance in an end-to-end print preparation pipeline and compare quality and runtime to alternative approaches, and demonstrate its generalization to unseen geometry and material values. This for the first time enables full heterogenous material optimization for 3D-print preparation within time frames in the order of the actual printing time."}],"year":"2021","month":"05","ec_funded":1,"status":"public","publication_identifier":{"eissn":["1467-8659"],"issn":["0167-7055"]},"oa":1,"type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"BeBi"}],"has_accepted_license":"1","date_created":"2021-06-13T22:01:32Z","page":"205-219","publication":"Computer Graphics Forum","external_id":{"isi":["000657959600017"]},"quality_controlled":"1","volume":40,"article_type":"original","article_processing_charge":"No","project":[{"grant_number":"642841","_id":"2508E324-B435-11E9-9278-68D0E5697425","name":"Distributed 3D Object Design","call_identifier":"H2020"},{"_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020"}],"author":[{"first_name":"Tobias","last_name":"Rittig","full_name":"Rittig, Tobias"},{"full_name":"Sumin, Denis","first_name":"Denis","last_name":"Sumin"},{"last_name":"Babaei","first_name":"Vahid","full_name":"Babaei, Vahid"},{"full_name":"Didyk, Piotr","first_name":"Piotr","last_name":"Didyk"},{"first_name":"Alexey","last_name":"Voloboy","full_name":"Voloboy, Alexey"},{"full_name":"Wilkie, Alexander","last_name":"Wilkie","first_name":"Alexander"},{"full_name":"Bickel, Bernd","first_name":"Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel"},{"full_name":"Myszkowski, Karol","first_name":"Karol","last_name":"Myszkowski"},{"last_name":"Weyrich","first_name":"Tim","full_name":"Weyrich, Tim"},{"last_name":"Křivánek","first_name":"Jaroslav","full_name":"Křivánek, Jaroslav"}],"isi":1,"file":[{"content_type":"application/pdf","relation":"main_file","success":1,"file_size":26026501,"file_id":"10120","checksum":"33271724215f54a75c39d2ed40f2c502","creator":"bbickel","access_level":"open_access","date_updated":"2021-10-11T12:06:50Z","file_name":"ScatteringAwareColor3DPrinting_authorVersion.pdf","date_created":"2021-10-11T12:06:50Z"}],"acknowledgement":"We thank Sebastian Cucerca for processing and capturing the phys-cal printouts. This work was supported by the Charles University grant SVV-260588 and Czech Science Foundation grant 19-07626S. This project has received funding from the European Union’s Horizon 2020 research and innovation programme, under the Marie Skłodowska Curie grant agreements No 642841 (DISTRO) and No765911 (RealVision), and under the European Research Council grant agreement No 715767 (MATERIALIZABLE).","day":"01","publisher":"Wiley","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Neural acceleration of scattering-aware color 3D printing"},{"quality_controlled":"1","volume":31,"external_id":{"arxiv":["2008.09543"],"isi":["000656507500001"]},"article_processing_charge":"No","article_type":"original","department":[{"_id":"UlWa"}],"language":[{"iso":"eng"}],"type":"journal_article","publication":"Journal of Geometric Analysis","date_created":"2021-06-13T22:01:32Z","page":"11493-11528","title":"Functional Löwner ellipsoids","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Springer","author":[{"full_name":"Ivanov, Grigory","id":"87744F66-5C6F-11EA-AFE0-D16B3DDC885E","last_name":"Ivanov","first_name":"Grigory"},{"last_name":"Tsiutsiurupa","first_name":"Igor","full_name":"Tsiutsiurupa, Igor"}],"isi":1,"day":"31","acknowledgement":"The authors acknowledge the support of the grant of the Russian Government N 075-15-2019-1926.","citation":{"ista":"Ivanov G, Tsiutsiurupa I. 2021. Functional Löwner ellipsoids. Journal of Geometric Analysis. 31, 11493–11528.","apa":"Ivanov, G., & Tsiutsiurupa, I. (2021). Functional Löwner ellipsoids. Journal of Geometric Analysis. Springer. https://doi.org/10.1007/s12220-021-00691-4","mla":"Ivanov, Grigory, and Igor Tsiutsiurupa. “Functional Löwner Ellipsoids.” Journal of Geometric Analysis, vol. 31, Springer, 2021, pp. 11493–528, doi:10.1007/s12220-021-00691-4.","chicago":"Ivanov, Grigory, and Igor Tsiutsiurupa. “Functional Löwner Ellipsoids.” Journal of Geometric Analysis. Springer, 2021. https://doi.org/10.1007/s12220-021-00691-4.","short":"G. Ivanov, I. Tsiutsiurupa, Journal of Geometric Analysis 31 (2021) 11493–11528.","ama":"Ivanov G, Tsiutsiurupa I. Functional Löwner ellipsoids. Journal of Geometric Analysis. 2021;31:11493-11528. doi:10.1007/s12220-021-00691-4","ieee":"G. Ivanov and I. Tsiutsiurupa, “Functional Löwner ellipsoids,” Journal of Geometric Analysis, vol. 31. Springer, pp. 11493–11528, 2021."},"intvolume":" 31","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2008.09543"}],"scopus_import":"1","date_published":"2021-05-31T00:00:00Z","oa_version":"Preprint","doi":"10.1007/s12220-021-00691-4","publication_status":"published","month":"05","oa":1,"publication_identifier":{"eissn":["1559-002X"],"issn":["1050-6926"]},"status":"public","_id":"9548","year":"2021","arxiv":1,"abstract":[{"lang":"eng","text":"We extend the notion of the minimal volume ellipsoid containing a convex body in Rd to the setting of logarithmically concave functions. We consider a vast class of logarithmically concave functions whose superlevel sets are concentric ellipsoids. For a fixed function from this class, we consider the set of all its “affine” positions. For any log-concave function f on Rd, we consider functions belonging to this set of “affine” positions, and find the one with the minimal integral under the condition that it is pointwise greater than or equal to f. We study the properties of existence and uniqueness of the solution to this problem. For any s∈[0,+∞), we consider the construction dual to the recently defined John s-function (Ivanov and Naszódi in Functional John ellipsoids. arXiv preprint: arXiv:2006.09934, 2020). We prove that such a construction determines a unique function and call it the Löwner s-function of f. We study the Löwner s-functions as s tends to zero and to infinity. Finally, extending the notion of the outer volume ratio, we define the outer integral ratio of a log-concave function and give an asymptotically tight bound on it."}],"date_updated":"2023-08-08T14:04:49Z"},{"external_id":{"isi":["000657238100003"],"pmid":["34079129"]},"volume":594,"quality_controlled":"1","article_type":"original","article_processing_charge":"No","language":[{"iso":"eng"}],"department":[{"_id":"PeJo"}],"type":"journal_article","page":"454-458","date_created":"2021-06-13T22:01:33Z","publication":"Nature","title":"Gating and modulation of a hetero-octameric AMPA glutamate receptor","publisher":"Springer Nature","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"author":[{"first_name":"Danyang","last_name":"Zhang","full_name":"Zhang, Danyang"},{"full_name":"Watson, Jake","id":"63836096-4690-11EA-BD4E-32803DDC885E","last_name":"Watson","first_name":"Jake","orcid":"0000-0002-8698-3823"},{"first_name":"Peter M.","last_name":"Matthews","full_name":"Matthews, Peter M."},{"full_name":"Cais, Ondrej","first_name":"Ondrej","last_name":"Cais"},{"last_name":"Greger","first_name":"Ingo H.","full_name":"Greger, Ingo H."}],"day":"02","pmid":1,"acknowledgement":"We thank members of the Greger laboratory, B. Herguedas, J. Krieger and J.-N. Dohrke for comments on the manuscript; J. Krieger and J.-N. Dohrke for discussion, J. Krieger for help with the normal mode analysis, B. Köhegyi for help with cryo-EM imaging, V. Chang and K. Suzuki for helping to generate the CNIH2-1D4-HA stable cell line, M. Carvalho for assistance at early stages of this project, the LMB scientific computing and the cryo-EM facility for support, P. Emsley for help with model building, T. Nakane for helpful comments with RELION 3.1 and R. Warshamanage for helping with EMDA cryo-EM-map processing. We acknowledge the Diamond Light Source for access and support of the Cryo-EM facilities at the UK national electron bio10 imaging centre (eBIC), proposal EM17434, funded by the Wellcome Trust, MRC and BBSRC. This work was supported by grants from the Medical Research Council, as part of United Kingdom Research and Innovation (also known as UK Research and Innovation) (MC_U105174197) and BBSRC (BB/N002113/1) to I.H.G.","intvolume":" 594","citation":{"ista":"Zhang D, Watson J, Matthews PM, Cais O, Greger IH. 2021. Gating and modulation of a hetero-octameric AMPA glutamate receptor. Nature. 594, 454–458.","apa":"Zhang, D., Watson, J., Matthews, P. M., Cais, O., & Greger, I. H. (2021). Gating and modulation of a hetero-octameric AMPA glutamate receptor. Nature. Springer Nature. https://doi.org/10.1038/s41586-021-03613-0","mla":"Zhang, Danyang, et al. “Gating and Modulation of a Hetero-Octameric AMPA Glutamate Receptor.” Nature, vol. 594, Springer Nature, 2021, pp. 454–58, doi:10.1038/s41586-021-03613-0.","chicago":"Zhang, Danyang, Jake Watson, Peter M. Matthews, Ondrej Cais, and Ingo H. Greger. “Gating and Modulation of a Hetero-Octameric AMPA Glutamate Receptor.” Nature. Springer Nature, 2021. https://doi.org/10.1038/s41586-021-03613-0.","short":"D. Zhang, J. Watson, P.M. Matthews, O. Cais, I.H. Greger, Nature 594 (2021) 454–458.","ama":"Zhang D, Watson J, Matthews PM, Cais O, Greger IH. Gating and modulation of a hetero-octameric AMPA glutamate receptor. Nature. 2021;594:454-458. doi:10.1038/s41586-021-03613-0","ieee":"D. Zhang, J. Watson, P. M. Matthews, O. Cais, and I. H. Greger, “Gating and modulation of a hetero-octameric AMPA glutamate receptor,” Nature, vol. 594. Springer Nature, pp. 454–458, 2021."},"main_file_link":[{"url":"https://doi.org/10.1038/s41586-021-03613-0","open_access":"1"}],"scopus_import":"1","date_published":"2021-06-02T00:00:00Z","oa_version":"Published Version","publication_status":"published","doi":"10.1038/s41586-021-03613-0","month":"06","oa":1,"publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"status":"public","_id":"9549","year":"2021","date_updated":"2023-08-08T13:59:51Z","abstract":[{"text":"AMPA receptors (AMPARs) mediate the majority of excitatory transmission in the brain and enable the synaptic plasticity that underlies learning1. A diverse array of AMPAR signalling complexes are established by receptor auxiliary subunits, which associate with the AMPAR in various combinations to modulate trafficking, gating and synaptic strength2. However, their mechanisms of action are poorly understood. Here we determine cryo-electron microscopy structures of the heteromeric GluA1–GluA2 receptor assembled with both TARP-γ8 and CNIH2, the predominant AMPAR complex in the forebrain, in both resting and active states. Two TARP-γ8 and two CNIH2 subunits insert at distinct sites beneath the ligand-binding domains of the receptor, with site-specific lipids shaping each interaction and affecting the gating regulation of the AMPARs. Activation of the receptor leads to asymmetry between GluA1 and GluA2 along the ion conduction path and an outward expansion of the channel triggers counter-rotations of both auxiliary subunit pairs, promoting the active-state conformation. In addition, both TARP-γ8 and CNIH2 pivot towards the pore exit upon activation, extending their reach for cytoplasmic receptor elements. CNIH2 achieves this through its uniquely extended M2 helix, which has transformed this endoplasmic reticulum-export factor into a powerful AMPAR modulator that is capable of providing hippocampal pyramidal neurons with their integrative synaptic properties. ","lang":"eng"}]},{"publication_status":"published","doi":"10.1017/fms.2021.38","date_published":"2021-05-27T00:00:00Z","oa_version":"Published Version","ddc":["510"],"scopus_import":"1","file_date_updated":"2021-06-15T14:40:45Z","intvolume":" 9","citation":{"short":"Z. Bao, L. Erdös, K. Schnelli, Forum of Mathematics, Sigma 9 (2021).","ama":"Bao Z, Erdös L, Schnelli K. Equipartition principle for Wigner matrices. Forum of Mathematics, Sigma. 2021;9. doi:10.1017/fms.2021.38","ieee":"Z. Bao, L. Erdös, and K. Schnelli, “Equipartition principle for Wigner matrices,” Forum of Mathematics, Sigma, vol. 9. Cambridge University Press, 2021.","mla":"Bao, Zhigang, et al. “Equipartition Principle for Wigner Matrices.” Forum of Mathematics, Sigma, vol. 9, e44, Cambridge University Press, 2021, doi:10.1017/fms.2021.38.","apa":"Bao, Z., Erdös, L., & Schnelli, K. (2021). Equipartition principle for Wigner matrices. Forum of Mathematics, Sigma. Cambridge University Press. https://doi.org/10.1017/fms.2021.38","ista":"Bao Z, Erdös L, Schnelli K. 2021. Equipartition principle for Wigner matrices. Forum of Mathematics, Sigma. 9, e44.","chicago":"Bao, Zhigang, László Erdös, and Kevin Schnelli. “Equipartition Principle for Wigner Matrices.” Forum of Mathematics, Sigma. Cambridge University Press, 2021. https://doi.org/10.1017/fms.2021.38."},"year":"2021","date_updated":"2023-08-08T14:03:40Z","arxiv":1,"abstract":[{"lang":"eng","text":"We prove that the energy of any eigenvector of a sum of several independent large Wigner matrices is equally distributed among these matrices with very high precision. This shows a particularly strong microcanonical form of the equipartition principle for quantum systems whose components are modelled by Wigner matrices. "}],"_id":"9550","article_number":"e44","oa":1,"publication_identifier":{"eissn":["20505094"]},"status":"public","ec_funded":1,"month":"05","date_created":"2021-06-13T22:01:33Z","publication":"Forum of Mathematics, Sigma","has_accepted_license":"1","language":[{"iso":"eng"}],"department":[{"_id":"LaEr"}],"type":"journal_article","article_type":"original","article_processing_charge":"No","external_id":{"isi":["000654960800001"],"arxiv":["2008.07061"]},"quality_controlled":"1","volume":9,"day":"27","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledgement":"The first author is supported in part by Hong Kong RGC Grant GRF 16301519 and NSFC 11871425. The second author is supported in part by ERC Advanced Grant RANMAT 338804. The third author is supported in part by Swedish Research Council Grant VR-2017-05195 and the Knut and Alice Wallenberg Foundation","file":[{"file_size":483458,"success":1,"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"9555","creator":"cziletti","checksum":"47c986578de132200d41e6d391905519","date_created":"2021-06-15T14:40:45Z","date_updated":"2021-06-15T14:40:45Z","file_name":"2021_ForumMath_Bao.pdf"}],"project":[{"call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804"}],"isi":1,"author":[{"id":"442E6A6C-F248-11E8-B48F-1D18A9856A87","last_name":"Bao","first_name":"Zhigang","orcid":"0000-0003-3036-1475","full_name":"Bao, Zhigang"},{"first_name":"László","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","full_name":"Erdös, László"},{"full_name":"Schnelli, Kevin","last_name":"Schnelli","id":"434AD0AE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0954-3231","first_name":"Kevin"}],"title":"Equipartition principle for Wigner matrices","publisher":"Cambridge University Press","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"doi":"10.1103/PhysRevLett.126.244502","publication_status":"published","oa_version":"Preprint","date_published":"2021-06-18T00:00:00Z","main_file_link":[{"url":"https://arxiv.org/abs/2007.02584","open_access":"1"}],"citation":{"apa":"Yalniz, G., Hof, B., & Budanur, N. B. (2021). Coarse graining the state space of a turbulent flow using periodic orbits. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.126.244502","ista":"Yalniz G, Hof B, Budanur NB. 2021. Coarse graining the state space of a turbulent flow using periodic orbits. Physical Review Letters. 126(24), 244502.","mla":"Yalniz, Gökhan, et al. “Coarse Graining the State Space of a Turbulent Flow Using Periodic Orbits.” Physical Review Letters, vol. 126, no. 24, 244502, American Physical Society, 2021, doi:10.1103/PhysRevLett.126.244502.","chicago":"Yalniz, Gökhan, Björn Hof, and Nazmi B Budanur. “Coarse Graining the State Space of a Turbulent Flow Using Periodic Orbits.” Physical Review Letters. American Physical Society, 2021. https://doi.org/10.1103/PhysRevLett.126.244502.","ama":"Yalniz G, Hof B, Budanur NB. Coarse graining the state space of a turbulent flow using periodic orbits. Physical Review Letters. 2021;126(24). doi:10.1103/PhysRevLett.126.244502","ieee":"G. Yalniz, B. Hof, and N. B. Budanur, “Coarse graining the state space of a turbulent flow using periodic orbits,” Physical Review Letters, vol. 126, no. 24. American Physical Society, 2021.","short":"G. Yalniz, B. Hof, N.B. Budanur, Physical Review Letters 126 (2021)."},"intvolume":" 126","arxiv":1,"issue":"24","abstract":[{"text":"We show that turbulent dynamics that arise in simulations of the three-dimensional Navier--Stokes equations in a triply-periodic domain under sinusoidal forcing can be described as transient visits to the neighborhoods of unstable time-periodic solutions. Based on this description, we reduce the original system with more than 10^5 degrees of freedom to a 17-node Markov chain where each node corresponds to the neighborhood of a periodic orbit. The model accurately reproduces long-term averages of the system's observables as weighted sums over the periodic orbits.\r\n","lang":"eng"}],"date_updated":"2023-08-08T14:08:36Z","year":"2021","acknowledged_ssus":[{"_id":"ScienComp"}],"article_number":"244502","_id":"9558","status":"public","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"oa":1,"month":"06","publication":"Physical Review Letters","date_created":"2021-06-16T15:45:36Z","type":"journal_article","department":[{"_id":"GradSch"},{"_id":"BjHo"}],"language":[{"iso":"eng"}],"article_processing_charge":"No","article_type":"letter_note","volume":126,"quality_controlled":"1","external_id":{"arxiv":["2007.02584"],"isi":["000663310100008"]},"related_material":{"link":[{"url":"https://ist.ac.at/en/news/turbulent-flow-simplified/","relation":"press_release","description":"News on IST Homepage"}]},"acknowledgement":"We thank the referees for improving this Letter with their comments. We acknowledge stimulating discussions with\r\nH. Edelsbrunner. This work was supported by Grant No. 662960 from the Simons Foundation (B. H.). The numerical calculations were performed at TUBITAK ULAKBIM High Performance and Grid Computing Center (TRUBA resources) and IST Austria High Performance Computing cluster.","day":"18","author":[{"id":"66E74FA2-D8BF-11E9-8249-8DE2E5697425","last_name":"Yalniz","first_name":"Gökhan","orcid":"0000-0002-8490-9312","full_name":"Yalniz, Gökhan"},{"last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn"},{"full_name":"Budanur, Nazmi B","last_name":"Budanur","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0423-5010","first_name":"Nazmi B"}],"isi":1,"project":[{"grant_number":"662960","_id":"238598C6-32DE-11EA-91FC-C7463DDC885E","name":"Revisiting the Turbulence Problem Using Statistical Mechanics: Experimental Studies on Transitional and Turbulent Flows"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"American Physical Society","title":"Coarse graining the state space of a turbulent flow using periodic orbits"}]