--- _id: '15057' abstract: - lang: eng text: Vaccinia virus–related kinase (VRK) is an evolutionarily conserved nuclear protein kinase. VRK-1, the single Caenorhabditis elegans VRK ortholog, functions in cell division and germline proliferation. However, the role of VRK-1 in postmitotic cells and adult life span remains unknown. Here, we show that VRK-1 increases organismal longevity by activating the cellular energy sensor, AMP-activated protein kinase (AMPK), via direct phosphorylation. We found that overexpression of vrk-1 in the soma of adult C. elegans increased life span and, conversely, inhibition of vrk-1 decreased life span. In addition, vrk-1 was required for longevity conferred by mutations that inhibit C. elegans mitochondrial respiration, which requires AMPK. VRK-1 directly phosphorylated and up-regulated AMPK in both C. elegans and cultured human cells. Thus, our data show that the somatic nuclear kinase, VRK-1, promotes longevity through AMPK activation, and this function appears to be conserved between C. elegans and humans. acknowledgement: 'This research was supported by grants NRF-2019R1A3B2067745 and NRF-2017R1A5A1015366 funded by the Korean Government (MSIT) through the National Research Foundation (NRF) of Korea to S.-J.V.L. and by grant Basic Science Research Program (No. 2019R1A2C2009440) funded by the Korean Government (MSIT) through the NRF of Korea to K.-T.K. ' article_number: aaw7824 article_processing_charge: No article_type: original author: - first_name: Sangsoon full_name: Park, Sangsoon last_name: Park - first_name: Murat full_name: Artan, Murat id: C407B586-6052-11E9-B3AE-7006E6697425 last_name: Artan orcid: 0000-0001-8945-6992 - first_name: Seung Hyun full_name: Han, Seung Hyun last_name: Han - first_name: Hae-Eun H. full_name: Park, Hae-Eun H. last_name: Park - first_name: Yoonji full_name: Jung, Yoonji last_name: Jung - first_name: Ara B. full_name: Hwang, Ara B. last_name: Hwang - first_name: Won Sik full_name: Shin, Won Sik last_name: Shin - first_name: Kyong-Tai full_name: Kim, Kyong-Tai last_name: Kim - first_name: Seung-Jae V. full_name: Lee, Seung-Jae V. last_name: Lee citation: ama: Park S, Artan M, Han SH, et al. VRK-1 extends life span by activation of AMPK via phosphorylation. Science Advances. 2020;6(27). doi:10.1126/sciadv.aaw7824 apa: Park, S., Artan, M., Han, S. H., Park, H.-E. H., Jung, Y., Hwang, A. B., … Lee, S.-J. V. (2020). VRK-1 extends life span by activation of AMPK via phosphorylation. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.aaw7824 chicago: Park, Sangsoon, Murat Artan, Seung Hyun Han, Hae-Eun H. Park, Yoonji Jung, Ara B. Hwang, Won Sik Shin, Kyong-Tai Kim, and Seung-Jae V. Lee. “VRK-1 Extends Life Span by Activation of AMPK via Phosphorylation.” Science Advances. American Association for the Advancement of Science, 2020. https://doi.org/10.1126/sciadv.aaw7824. ieee: S. Park et al., “VRK-1 extends life span by activation of AMPK via phosphorylation,” Science Advances, vol. 6, no. 27. American Association for the Advancement of Science, 2020. ista: Park S, Artan M, Han SH, Park H-EH, Jung Y, Hwang AB, Shin WS, Kim K-T, Lee S-JV. 2020. VRK-1 extends life span by activation of AMPK via phosphorylation. Science Advances. 6(27), aaw7824. mla: Park, Sangsoon, et al. “VRK-1 Extends Life Span by Activation of AMPK via Phosphorylation.” Science Advances, vol. 6, no. 27, aaw7824, American Association for the Advancement of Science, 2020, doi:10.1126/sciadv.aaw7824. short: S. Park, M. Artan, S.H. Han, H.-E.H. Park, Y. Jung, A.B. Hwang, W.S. Shin, K.-T. Kim, S.-J.V. Lee, Science Advances 6 (2020). date_created: 2024-03-04T09:41:57Z date_published: 2020-07-01T00:00:00Z date_updated: 2024-03-04T09:52:09Z day: '01' ddc: - '570' department: - _id: MaDe doi: 10.1126/sciadv.aaw7824 file: - access_level: open_access checksum: a37157cd0de709dce5fe03f4a31cd0b6 content_type: application/pdf creator: dernst date_created: 2024-03-04T09:46:41Z date_updated: 2024-03-04T09:46:41Z file_id: '15058' file_name: 2020_ScienceAdvances_Park.pdf file_size: 1864415 relation: main_file success: 1 file_date_updated: 2024-03-04T09:46:41Z has_accepted_license: '1' intvolume: ' 6' issue: '27' language: - iso: eng license: https://creativecommons.org/licenses/by-nc/4.0/ month: '07' oa: 1 oa_version: Published Version publication: Science Advances publication_identifier: eissn: - 2375-2548 publication_status: published publisher: American Association for the Advancement of Science quality_controlled: '1' status: public title: VRK-1 extends life span by activation of AMPK via phosphorylation tmp: image: /images/cc_by_nc.png 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) short: CC BY-NC (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 6 year: '2020' ... --- _id: '15061' abstract: - lang: eng text: The actin cytoskeleton, a dynamic network of actin filaments and associated F-actin–binding proteins, is fundamentally important in eukaryotes. α-Actinins are major F-actin bundlers that are inhibited by Ca2+ in nonmuscle cells. Here we report the mechanism of Ca2+-mediated regulation of Entamoeba histolytica α-actinin-2 (EhActn2) with features expected for the common ancestor of Entamoeba and higher eukaryotic α-actinins. Crystal structures of Ca2+-free and Ca2+-bound EhActn2 reveal a calmodulin-like domain (CaMD) uniquely inserted within the rod domain. Integrative studies reveal an exceptionally high affinity of the EhActn2 CaMD for Ca2+, binding of which can only be regulated in the presence of physiological concentrations of Mg2+. Ca2+ binding triggers an increase in protein multidomain rigidity, reducing conformational flexibility of F-actin–binding domains via interdomain cross-talk and consequently inhibiting F-actin bundling. In vivo studies uncover that EhActn2 plays an important role in phagocytic cup formation and might constitute a new drug target for amoebic dysentery. acknowledged_ssus: - _id: LifeSc acknowledgement: "We thank the staff of the macromolecular crystallography (MX) and SAXS beamlines at the European Synchrotron Radiation facility, Diamond, and Swiss Light Source for excellent support, and the Life Sciences Facility of the Institute of Science and Technology Austria for usage of the rheometer. We thank Life Sciences editors for editing assistance. EM data were\r\nrecorded at the EM Facility of the Vienna BioCenter Core Facilities (Austria). Confocal microscopy was carried out at the Advanced Instrument Research Facility, Jawaharlal Nehru University. K.D.-C.’s research was supported by the Initial Training Network MUZIC (ITN-MUZIC) (N°238423), Austrian Science Fund (FWF) Projects I525, I1593, P22276, P19060, and W1221, Laura Bassi Centre of Optimized Structural Studies (N°253275), a Wellcome Trust Collaborative Award (201543/Z/16/Z), COST Action BM1405, Vienna Science and Technology Fund (WWTF) Chemical Biology Project LS17-008, and Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology. K.Z., J.L.A., C.S., E.A.G., and A.S. were supported by the University of Vienna, J.K. by a Wellcome Trust Collaborative Award and by the Centre of Optimized Structural Studies, M.P. by FWF Project I1593, E.d.A.R. ITN-MUZIC, and FWF Projects I525 and I1593, and T.C.M. and L.C. by FWF Project I 2408-B22. E.A.G. acknowledges the PhD program Structure and Interaction of Biological Macromolecules. M.B. acknowledges the University Grant Commission, India, for a senior research fellowship. A.B. acknowledges a JC Bose Fellowship from the Science Engineering Research Council. " article_processing_charge: No article_type: original author: - first_name: Nikos full_name: Pinotsis, Nikos last_name: Pinotsis - first_name: Karolina full_name: Zielinska, Karolina last_name: Zielinska - first_name: Mrigya full_name: Babuta, Mrigya last_name: Babuta - first_name: Joan L. full_name: Arolas, Joan L. last_name: Arolas - first_name: Julius full_name: Kostan, Julius last_name: Kostan - first_name: Muhammad Bashir full_name: Khan, Muhammad Bashir last_name: Khan - first_name: Claudia full_name: Schreiner, Claudia last_name: Schreiner - first_name: Anita P full_name: Testa Salmazo, Anita P id: 41F1F098-F248-11E8-B48F-1D18A9856A87 last_name: Testa Salmazo - first_name: Luciano full_name: Ciccarelli, Luciano last_name: Ciccarelli - first_name: Martin full_name: Puchinger, Martin last_name: Puchinger - first_name: Eirini A. full_name: Gkougkoulia, Eirini A. last_name: Gkougkoulia - first_name: Euripedes de Almeida full_name: Ribeiro, Euripedes de Almeida last_name: Ribeiro - first_name: Thomas C. full_name: Marlovits, Thomas C. last_name: Marlovits - first_name: Alok full_name: Bhattacharya, Alok last_name: Bhattacharya - first_name: Kristina full_name: Djinovic-Carugo, Kristina last_name: Djinovic-Carugo citation: ama: Pinotsis N, Zielinska K, Babuta M, et al. Calcium modulates the domain flexibility and function of an α-actinin similar to the ancestral α-actinin. Proceedings of the National Academy of Sciences. 2020;117(36):22101-22112. doi:10.1073/pnas.1917269117 apa: Pinotsis, N., Zielinska, K., Babuta, M., Arolas, J. L., Kostan, J., Khan, M. B., … Djinovic-Carugo, K. (2020). Calcium modulates the domain flexibility and function of an α-actinin similar to the ancestral α-actinin. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1917269117 chicago: Pinotsis, Nikos, Karolina Zielinska, Mrigya Babuta, Joan L. Arolas, Julius Kostan, Muhammad Bashir Khan, Claudia Schreiner, et al. “Calcium Modulates the Domain Flexibility and Function of an α-Actinin Similar to the Ancestral α-Actinin.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.1917269117. ieee: N. Pinotsis et al., “Calcium modulates the domain flexibility and function of an α-actinin similar to the ancestral α-actinin,” Proceedings of the National Academy of Sciences, vol. 117, no. 36. Proceedings of the National Academy of Sciences, pp. 22101–22112, 2020. ista: Pinotsis N, Zielinska K, Babuta M, Arolas JL, Kostan J, Khan MB, Schreiner C, Testa Salmazo AP, Ciccarelli L, Puchinger M, Gkougkoulia EA, Ribeiro E de A, Marlovits TC, Bhattacharya A, Djinovic-Carugo K. 2020. Calcium modulates the domain flexibility and function of an α-actinin similar to the ancestral α-actinin. Proceedings of the National Academy of Sciences. 117(36), 22101–22112. mla: Pinotsis, Nikos, et al. “Calcium Modulates the Domain Flexibility and Function of an α-Actinin Similar to the Ancestral α-Actinin.” Proceedings of the National Academy of Sciences, vol. 117, no. 36, Proceedings of the National Academy of Sciences, 2020, pp. 22101–12, doi:10.1073/pnas.1917269117. short: N. Pinotsis, K. Zielinska, M. Babuta, J.L. Arolas, J. Kostan, M.B. Khan, C. Schreiner, A.P. Testa Salmazo, L. Ciccarelli, M. Puchinger, E.A. Gkougkoulia, E. de A. Ribeiro, T.C. Marlovits, A. Bhattacharya, K. Djinovic-Carugo, Proceedings of the National Academy of Sciences 117 (2020) 22101–22112. date_created: 2024-03-04T10:03:52Z date_published: 2020-09-08T00:00:00Z date_updated: 2024-03-04T10:14:44Z day: '08' department: - _id: CaBe doi: 10.1073/pnas.1917269117 external_id: pmid: - '32848067' intvolume: ' 117' issue: '36' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1073/pnas.191726911 month: '09' oa: 1 oa_version: Published Version page: 22101-22112 pmid: 1 publication: Proceedings of the National Academy of Sciences publication_identifier: eissn: - 1091-6490 issn: - 0027-8424 publication_status: published publisher: Proceedings of the National Academy of Sciences quality_controlled: '1' status: public title: Calcium modulates the domain flexibility and function of an α-actinin similar to the ancestral α-actinin type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 117 year: '2020' ... --- _id: '15064' abstract: - lang: eng text: We call a continuous self-map that reveals itself through a discrete set of point-value pairs a sampled dynamical system. Capturing the available information with chain maps on Delaunay complexes, we use persistent homology to quantify the evidence of recurrent behavior. We establish a sampling theorem to recover the eigenspaces of the endomorphism on homology induced by the self-map. Using a combinatorial gradient flow arising from the discrete Morse theory for Čech and Delaunay complexes, we construct a chain map to transform the problem from the natural but expensive Čech complexes to the computationally efficient Delaunay triangulations. The fast chain map algorithm has applications beyond dynamical systems. acknowledgement: This research has been supported by the DFG Collaborative Research Center SFB/TRR 109 “Discretization in Geometry and Dynamics”, by Polish MNiSzW Grant No. 2621/7.PR/12/2013/2, by the Polish National Science Center under Maestro Grant No. 2014/14/A/ST1/00453 and Grant No. DEC-2013/09/N/ST6/02995. Open Access funding provided by Projekt DEAL. article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: U. full_name: Bauer, U. last_name: Bauer - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Grzegorz full_name: Jablonski, Grzegorz id: 4483EF78-F248-11E8-B48F-1D18A9856A87 last_name: Jablonski orcid: 0000-0002-3536-9866 - first_name: M. full_name: Mrozek, M. last_name: Mrozek citation: ama: Bauer U, Edelsbrunner H, Jablonski G, Mrozek M. Čech-Delaunay gradient flow and homology inference for self-maps. Journal of Applied and Computational Topology. 2020;4(4):455-480. doi:10.1007/s41468-020-00058-8 apa: Bauer, U., Edelsbrunner, H., Jablonski, G., & Mrozek, M. (2020). Čech-Delaunay gradient flow and homology inference for self-maps. Journal of Applied and Computational Topology. Springer Nature. https://doi.org/10.1007/s41468-020-00058-8 chicago: Bauer, U., Herbert Edelsbrunner, Grzegorz Jablonski, and M. Mrozek. “Čech-Delaunay Gradient Flow and Homology Inference for Self-Maps.” Journal of Applied and Computational Topology. Springer Nature, 2020. https://doi.org/10.1007/s41468-020-00058-8. ieee: U. Bauer, H. Edelsbrunner, G. Jablonski, and M. Mrozek, “Čech-Delaunay gradient flow and homology inference for self-maps,” Journal of Applied and Computational Topology, vol. 4, no. 4. Springer Nature, pp. 455–480, 2020. ista: Bauer U, Edelsbrunner H, Jablonski G, Mrozek M. 2020. Čech-Delaunay gradient flow and homology inference for self-maps. Journal of Applied and Computational Topology. 4(4), 455–480. mla: Bauer, U., et al. “Čech-Delaunay Gradient Flow and Homology Inference for Self-Maps.” Journal of Applied and Computational Topology, vol. 4, no. 4, Springer Nature, 2020, pp. 455–80, doi:10.1007/s41468-020-00058-8. short: U. Bauer, H. Edelsbrunner, G. Jablonski, M. Mrozek, Journal of Applied and Computational Topology 4 (2020) 455–480. date_created: 2024-03-04T10:47:49Z date_published: 2020-12-01T00:00:00Z date_updated: 2024-03-04T10:54:04Z day: '01' ddc: - '500' department: - _id: HeEd doi: 10.1007/s41468-020-00058-8 file: - access_level: open_access checksum: eed1168b6e66cd55272c19bb7fca8a1c content_type: application/pdf creator: dernst date_created: 2024-03-04T10:52:42Z date_updated: 2024-03-04T10:52:42Z file_id: '15065' file_name: 2020_JourApplCompTopology_Bauer.pdf file_size: 851190 relation: main_file success: 1 file_date_updated: 2024-03-04T10:52:42Z has_accepted_license: '1' intvolume: ' 4' issue: '4' language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '12' oa: 1 oa_version: Published Version page: 455-480 publication: Journal of Applied and Computational Topology publication_identifier: eissn: - 2367-1734 issn: - 2367-1726 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Čech-Delaunay gradient flow and homology inference for self-maps tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 4 year: '2020' ... --- _id: '15063' abstract: - lang: eng text: We consider the least singular value of a large random matrix with real or complex i.i.d. Gaussian entries shifted by a constant z∈C. We prove an optimal lower tail estimate on this singular value in the critical regime where z is around the spectral edge, thus improving the classical bound of Sankar, Spielman and Teng (SIAM J. Matrix Anal. Appl. 28:2 (2006), 446–476) for the particular shift-perturbation in the edge regime. Lacking Brézin–Hikami formulas in the real case, we rely on the superbosonization formula (Comm. Math. Phys. 283:2 (2008), 343–395). acknowledgement: Partially supported by ERC Advanced Grant No. 338804. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreement No. 66538 article_processing_charge: No article_type: original author: - first_name: Giorgio full_name: Cipolloni, Giorgio id: 42198EFA-F248-11E8-B48F-1D18A9856A87 last_name: Cipolloni orcid: 0000-0002-4901-7992 - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Dominik J full_name: Schröder, Dominik J id: 408ED176-F248-11E8-B48F-1D18A9856A87 last_name: Schröder orcid: 0000-0002-2904-1856 citation: ama: Cipolloni G, Erdös L, Schröder DJ. Optimal lower bound on the least singular value of the shifted Ginibre ensemble. Probability and Mathematical Physics. 2020;1(1):101-146. doi:10.2140/pmp.2020.1.101 apa: Cipolloni, G., Erdös, L., & Schröder, D. J. (2020). Optimal lower bound on the least singular value of the shifted Ginibre ensemble. Probability and Mathematical Physics. Mathematical Sciences Publishers. https://doi.org/10.2140/pmp.2020.1.101 chicago: Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Optimal Lower Bound on the Least Singular Value of the Shifted Ginibre Ensemble.” Probability and Mathematical Physics. Mathematical Sciences Publishers, 2020. https://doi.org/10.2140/pmp.2020.1.101. ieee: G. Cipolloni, L. Erdös, and D. J. Schröder, “Optimal lower bound on the least singular value of the shifted Ginibre ensemble,” Probability and Mathematical Physics, vol. 1, no. 1. Mathematical Sciences Publishers, pp. 101–146, 2020. ista: Cipolloni G, Erdös L, Schröder DJ. 2020. Optimal lower bound on the least singular value of the shifted Ginibre ensemble. Probability and Mathematical Physics. 1(1), 101–146. mla: Cipolloni, Giorgio, et al. “Optimal Lower Bound on the Least Singular Value of the Shifted Ginibre Ensemble.” Probability and Mathematical Physics, vol. 1, no. 1, Mathematical Sciences Publishers, 2020, pp. 101–46, doi:10.2140/pmp.2020.1.101. short: G. Cipolloni, L. Erdös, D.J. Schröder, Probability and Mathematical Physics 1 (2020) 101–146. date_created: 2024-03-04T10:27:57Z date_published: 2020-11-16T00:00:00Z date_updated: 2024-03-04T10:33:15Z day: '16' department: - _id: LaEr doi: 10.2140/pmp.2020.1.101 ec_funded: 1 external_id: arxiv: - '1908.01653' intvolume: ' 1' issue: '1' keyword: - General Medicine language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.1908.01653 month: '11' oa: 1 oa_version: Preprint page: 101-146 project: - _id: 258DCDE6-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '338804' name: Random matrices, universality and disordered quantum systems - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication: Probability and Mathematical Physics publication_identifier: issn: - 2690-1005 - 2690-0998 publication_status: published publisher: Mathematical Sciences Publishers quality_controlled: '1' scopus_import: '1' status: public title: Optimal lower bound on the least singular value of the shifted Ginibre ensemble type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 1 year: '2020' ... --- _id: '15059' abstract: - lang: eng text: "In this paper we present a room temperature radiometer that can eliminate the need of using cryostats in satellite payload reducing its weight and improving reliability. The proposed radiometer is based on an electro-optic upconverter that boosts up microwave photons energy by upconverting them into an optical domain what makes them immune to thermal noise even if operating at room temperature. The converter uses a high-quality factor whispering gallery\r\nmode (WGM) resonator providing naturally narrow bandwidth and therefore might be useful for applications like microwave hyperspectral sensing. The upconversion process is explained by\r\nproviding essential information about photon conversion efficiency and sensitivity. To prove the concept, we describe an experiment which shows state-of-the-art photon conversion efficiency n=10-5 per mW of pump power at the frequency of 80 GHz." acknowledgement: This work has been financially supported by Comunidad de Madrid S2018/NMT-4333 ARTINLARA-CM projects, and “FUNDACIÓN SENER” REFTA projects. article_processing_charge: No author: - first_name: Michal full_name: Wasiak, Michal last_name: Wasiak - first_name: Gabriel Santamaria full_name: Botello, Gabriel Santamaria last_name: Botello - first_name: Kerlos Atia full_name: Abdalmalak, Kerlos Atia last_name: Abdalmalak - first_name: Florian full_name: Sedlmeir, Florian last_name: Sedlmeir - first_name: Alfredo R full_name: Rueda Sanchez, Alfredo R id: 3B82B0F8-F248-11E8-B48F-1D18A9856A87 last_name: Rueda Sanchez orcid: 0000-0001-6249-5860 - first_name: Daniel full_name: Segovia-Vargas, Daniel last_name: Segovia-Vargas - first_name: Harald G. L. full_name: Schwefel, Harald G. L. last_name: Schwefel - first_name: Luis Enrique Garcia full_name: Munoz, Luis Enrique Garcia last_name: Munoz citation: ama: 'Wasiak M, Botello GS, Abdalmalak KA, et al. Compact millimeter and submillimeter-wave photonic radiometer for cubesats. In: 14th European Conference on Antennas and Propagation. IEEE; 2020. doi:10.23919/eucap48036.2020.9135962' apa: 'Wasiak, M., Botello, G. S., Abdalmalak, K. A., Sedlmeir, F., Rueda Sanchez, A. R., Segovia-Vargas, D., … Munoz, L. E. G. (2020). Compact millimeter and submillimeter-wave photonic radiometer for cubesats. In 14th European Conference on Antennas and Propagation. Copenhagen, Denmark: IEEE. https://doi.org/10.23919/eucap48036.2020.9135962' chicago: Wasiak, Michal, Gabriel Santamaria Botello, Kerlos Atia Abdalmalak, Florian Sedlmeir, Alfredo R Rueda Sanchez, Daniel Segovia-Vargas, Harald G. L. Schwefel, and Luis Enrique Garcia Munoz. “Compact Millimeter and Submillimeter-Wave Photonic Radiometer for Cubesats.” In 14th European Conference on Antennas and Propagation. IEEE, 2020. https://doi.org/10.23919/eucap48036.2020.9135962. ieee: M. Wasiak et al., “Compact millimeter and submillimeter-wave photonic radiometer for cubesats,” in 14th European Conference on Antennas and Propagation, Copenhagen, Denmark, 2020. ista: 'Wasiak M, Botello GS, Abdalmalak KA, Sedlmeir F, Rueda Sanchez AR, Segovia-Vargas D, Schwefel HGL, Munoz LEG. 2020. Compact millimeter and submillimeter-wave photonic radiometer for cubesats. 14th European Conference on Antennas and Propagation. EuCAP: European Conference on Antennas and Propagation.' mla: Wasiak, Michal, et al. “Compact Millimeter and Submillimeter-Wave Photonic Radiometer for Cubesats.” 14th European Conference on Antennas and Propagation, IEEE, 2020, doi:10.23919/eucap48036.2020.9135962. short: M. Wasiak, G.S. Botello, K.A. Abdalmalak, F. Sedlmeir, A.R. Rueda Sanchez, D. Segovia-Vargas, H.G.L. Schwefel, L.E.G. Munoz, in:, 14th European Conference on Antennas and Propagation, IEEE, 2020. conference: end_date: 2020-03-20 location: Copenhagen, Denmark name: 'EuCAP: European Conference on Antennas and Propagation' start_date: 2020-03-15 date_created: 2024-03-04T09:57:48Z date_published: 2020-07-08T00:00:00Z date_updated: 2024-03-04T10:02:49Z day: '08' department: - _id: JoFi doi: 10.23919/eucap48036.2020.9135962 language: - iso: eng month: '07' oa_version: None publication: 14th European Conference on Antennas and Propagation publication_identifier: eisbn: - '9788831299008' publication_status: published publisher: IEEE quality_controlled: '1' status: public title: Compact millimeter and submillimeter-wave photonic radiometer for cubesats type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2020' ... --- _id: '15074' abstract: - lang: eng text: We introduce a new graph problem, the token dropping game, and we show how to solve it efficiently in a distributed setting. We use the token dropping game as a tool to design an efficient distributed algorithm for the stable orientation problem, which is a special case of the more general locally optimal semi-matching problem. The prior work by Czygrinow et al. (DISC 2012) finds a locally optimal semi-matching in O(Δ⁵) rounds in graphs of maximum degree Δ, which directly implies an algorithm with the same runtime for stable orientations. We improve the runtime to O(Δ⁴) for stable orientations and prove a lower bound of Ω(Δ) rounds. alternative_title: - LIPIcs article_number: '40' article_processing_charge: No author: - first_name: Sebastian full_name: Brandt, Sebastian last_name: Brandt - first_name: Barbara full_name: Keller, Barbara last_name: Keller - first_name: Joel full_name: Rybicki, Joel id: 334EFD2E-F248-11E8-B48F-1D18A9856A87 last_name: Rybicki orcid: 0000-0002-6432-6646 - first_name: Jukka full_name: Suomela, Jukka last_name: Suomela - first_name: Jara full_name: Uitto, Jara last_name: Uitto citation: ama: 'Brandt S, Keller B, Rybicki J, Suomela J, Uitto J. Brief announcement: Efficient load-balancing through distributed token dropping. In: 34th International Symposium on Distributed Computing. Vol 179. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2020. doi:10.4230/LIPIcs.DISC.2020.40' apa: 'Brandt, S., Keller, B., Rybicki, J., Suomela, J., & Uitto, J. (2020). Brief announcement: Efficient load-balancing through distributed token dropping. In 34th International Symposium on Distributed Computing (Vol. 179). Virtual: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.DISC.2020.40' chicago: 'Brandt, Sebastian, Barbara Keller, Joel Rybicki, Jukka Suomela, and Jara Uitto. “Brief Announcement: Efficient Load-Balancing through Distributed Token Dropping.” In 34th International Symposium on Distributed Computing, Vol. 179. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. https://doi.org/10.4230/LIPIcs.DISC.2020.40.' ieee: 'S. Brandt, B. Keller, J. Rybicki, J. Suomela, and J. Uitto, “Brief announcement: Efficient load-balancing through distributed token dropping,” in 34th International Symposium on Distributed Computing, Virtual, 2020, vol. 179.' ista: 'Brandt S, Keller B, Rybicki J, Suomela J, Uitto J. 2020. Brief announcement: Efficient load-balancing through distributed token dropping. 34th International Symposium on Distributed Computing. DISC: Symposium on Distributed Computing, LIPIcs, vol. 179, 40.' mla: 'Brandt, Sebastian, et al. “Brief Announcement: Efficient Load-Balancing through Distributed Token Dropping.” 34th International Symposium on Distributed Computing, vol. 179, 40, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020, doi:10.4230/LIPIcs.DISC.2020.40.' short: S. Brandt, B. Keller, J. Rybicki, J. Suomela, J. Uitto, in:, 34th International Symposium on Distributed Computing, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. conference: end_date: 2020-10-16 location: Virtual name: 'DISC: Symposium on Distributed Computing' start_date: 2020-10-12 date_created: 2024-03-05T07:09:12Z date_published: 2020-10-07T00:00:00Z date_updated: 2024-03-05T07:13:13Z day: '07' ddc: - '000' department: - _id: DaAl doi: 10.4230/LIPIcs.DISC.2020.40 external_id: arxiv: - '2005.07761' file: - access_level: open_access checksum: 23e2d9321aef53092dc1e24a8ab82d72 content_type: application/pdf creator: dernst date_created: 2024-03-05T07:08:27Z date_updated: 2024-03-05T07:08:27Z file_id: '15075' file_name: 2020_LIPIcs_Brandt.pdf file_size: 303529 relation: main_file success: 1 file_date_updated: 2024-03-05T07:08:27Z has_accepted_license: '1' intvolume: ' 179' language: - iso: eng license: https://creativecommons.org/licenses/by/3.0/ month: '10' oa: 1 oa_version: Published Version publication: 34th International Symposium on Distributed Computing publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' related_material: record: - id: '9678' relation: later_version status: public scopus_import: '1' status: public title: 'Brief announcement: Efficient load-balancing through distributed token dropping' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode name: Creative Commons Attribution 3.0 Unported (CC BY 3.0) short: CC BY (3.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 179 year: '2020' ... --- _id: '15077' abstract: - lang: eng text: "We consider the following dynamic load-balancing process: given an underlying graph G with n nodes, in each step t≥ 0, one unit of load is created, and placed at a randomly chosen graph node. In the same step, the chosen node picks a random neighbor, and the two nodes balance their loads by averaging them. We are interested in the expected gap between the minimum and maximum loads at nodes as the process progresses, and its dependence on n and on the graph structure. Variants of the above graphical balanced allocation process have been studied previously by Peres, Talwar, and Wieder [Peres et al., 2015], and by Sauerwald and Sun [Sauerwald and Sun, 2015]. These authors left as open the question of characterizing the gap in the case of cycle graphs in the dynamic case, where weights are created during the algorithm’s execution. For this case, the only known upper bound is of \U0001D4AA(n log n), following from a majorization argument due to [Peres et al., 2015], which analyzes a related graphical allocation process. In this paper, we provide an upper bound of \U0001D4AA (√n log n) on the expected gap of the above process for cycles of length n. We introduce a new potential analysis technique, which enables us to bound the difference in load between k-hop neighbors on the cycle, for any k ≤ n/2. We complement this with a \"gap covering\" argument, which bounds the maximum value of the gap by bounding its value across all possible subsets of a certain structure, and recursively bounding the gaps within each subset. We provide analytical and experimental evidence that our upper bound on the gap is tight up to a logarithmic factor." acknowledgement: "The authors sincerely thank Thomas Sauerwald and George Giakkoupis for insightful discussions, and Mohsen Ghaffari, Yuval Peres, and Udi Wieder for feedback on earlier\r\nversions of this draft. We also thank the ICALP anonymous reviewers for their very useful comments.\r\nFunding: European Research Council funding award PR1042ERC01" alternative_title: - LIPIcs article_number: '7' article_processing_charge: No author: - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: Giorgi full_name: Nadiradze, Giorgi id: 3279A00C-F248-11E8-B48F-1D18A9856A87 last_name: Nadiradze orcid: 0000-0001-5634-0731 - first_name: Amirmojtaba full_name: Sabour, Amirmojtaba id: bcc145fd-e77f-11ea-ae8b-80d661dbff67 last_name: Sabour citation: ama: 'Alistarh D-A, Nadiradze G, Sabour A. Dynamic averaging load balancing on cycles. In: 47th International Colloquium on Automata, Languages, and Programming. Vol 168. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2020. doi:10.4230/LIPIcs.ICALP.2020.7' apa: 'Alistarh, D.-A., Nadiradze, G., & Sabour, A. (2020). Dynamic averaging load balancing on cycles. In 47th International Colloquium on Automata, Languages, and Programming (Vol. 168). Saarbrücken, Germany, Virtual: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2020.7' chicago: Alistarh, Dan-Adrian, Giorgi Nadiradze, and Amirmojtaba Sabour. “Dynamic Averaging Load Balancing on Cycles.” In 47th International Colloquium on Automata, Languages, and Programming, Vol. 168. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. https://doi.org/10.4230/LIPIcs.ICALP.2020.7. ieee: D.-A. Alistarh, G. Nadiradze, and A. Sabour, “Dynamic averaging load balancing on cycles,” in 47th International Colloquium on Automata, Languages, and Programming, Saarbrücken, Germany, Virtual, 2020, vol. 168. ista: 'Alistarh D-A, Nadiradze G, Sabour A. 2020. Dynamic averaging load balancing on cycles. 47th International Colloquium on Automata, Languages, and Programming. ICALP: International Colloquium on Automata, Languages, and Programming, LIPIcs, vol. 168, 7.' mla: Alistarh, Dan-Adrian, et al. “Dynamic Averaging Load Balancing on Cycles.” 47th International Colloquium on Automata, Languages, and Programming, vol. 168, 7, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020, doi:10.4230/LIPIcs.ICALP.2020.7. short: D.-A. Alistarh, G. Nadiradze, A. Sabour, in:, 47th International Colloquium on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. conference: end_date: 2020-07-11 location: Saarbrücken, Germany, Virtual name: 'ICALP: International Colloquium on Automata, Languages, and Programming' start_date: 2020-07-08 date_created: 2024-03-05T07:25:37Z date_published: 2020-06-29T00:00:00Z date_updated: 2024-03-05T07:35:53Z day: '29' ddc: - '000' department: - _id: DaAl doi: 10.4230/LIPIcs.ICALP.2020.7 ec_funded: 1 external_id: arxiv: - '2003.09297' file: - access_level: open_access checksum: e5eb16199f4ccfd77a321977eb3f026f content_type: application/pdf creator: dernst date_created: 2024-03-05T07:25:15Z date_updated: 2024-03-05T07:25:15Z file_id: '15078' file_name: 2020_LIPIcs_Alistarh.pdf file_size: 782987 relation: main_file success: 1 file_date_updated: 2024-03-05T07:25:15Z has_accepted_license: '1' intvolume: ' 168' language: - iso: eng month: '06' oa: 1 oa_version: Published Version project: - _id: 268A44D6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '805223' name: Elastic Coordination for Scalable Machine Learning publication: 47th International Colloquium on Automata, Languages, and Programming publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' related_material: record: - id: '8286' relation: later_version status: public scopus_import: '1' status: public title: Dynamic averaging load balancing on cycles tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode name: Creative Commons Attribution 3.0 Unported (CC BY 3.0) short: CC BY (3.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 168 year: '2020' ... --- _id: '15082' abstract: - lang: eng text: "Two plane drawings of geometric graphs on the same set of points are called disjoint compatible if their union is plane and they do not have an edge in common. For a given set S of 2n points two plane drawings of perfect matchings M1 and M2 (which do not need to be disjoint nor compatible) are disjoint tree-compatible if there exists a plane drawing of a spanning tree T on S which is disjoint compatible to both M1 and M2.\r\nWe show that the graph of all disjoint tree-compatible perfect geometric matchings on 2n points in convex position is connected if and only if 2n ≥ 10. Moreover, in that case the diameter\r\nof this graph is either 4 or 5, independent of n." acknowledgement: Research on this work was initiated at the 6th Austrian-Japanese-Mexican-Spanish Workshop on Discrete Geometry and continued during the 16th European Geometric Graph-Week, both held near Strobl, Austria. We are grateful to the participants for the inspiring atmosphere. We especially thank Alexander Pilz for bringing this class of problems to our attention and Birgit Vogtenhuber for inspiring discussions. D.P. is partially supported by the FWF grant I 3340-N35 (Collaborative DACH project Arrangements and Drawings). The research stay of P.P. at IST Austria is funded by the project CZ.02.2.69/0.0/0.0/17_050/0008466 Improvement of internationalization in the field of research and development at Charles University, through the support of quality projects MSCA-IF. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 734922. article_number: '56' article_processing_charge: No author: - first_name: Oswin full_name: Aichholzer, Oswin last_name: Aichholzer - first_name: Julia full_name: Obmann, Julia last_name: Obmann - first_name: Pavel full_name: Patak, Pavel id: B593B804-1035-11EA-B4F1-947645A5BB83 last_name: Patak - first_name: Daniel full_name: Perz, Daniel last_name: Perz - first_name: Josef full_name: Tkadlec, Josef id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87 last_name: Tkadlec orcid: 0000-0002-1097-9684 citation: ama: 'Aichholzer O, Obmann J, Patak P, Perz D, Tkadlec J. Disjoint tree-compatible plane perfect matchings. In: 36th European Workshop on Computational Geometry. ; 2020.' apa: Aichholzer, O., Obmann, J., Patak, P., Perz, D., & Tkadlec, J. (2020). Disjoint tree-compatible plane perfect matchings. In 36th European Workshop on Computational Geometry. Würzburg, Germany, Virtual. chicago: Aichholzer, Oswin, Julia Obmann, Pavel Patak, Daniel Perz, and Josef Tkadlec. “Disjoint Tree-Compatible Plane Perfect Matchings.” In 36th European Workshop on Computational Geometry, 2020. ieee: O. Aichholzer, J. Obmann, P. Patak, D. Perz, and J. Tkadlec, “Disjoint tree-compatible plane perfect matchings,” in 36th European Workshop on Computational Geometry, Würzburg, Germany, Virtual, 2020. ista: 'Aichholzer O, Obmann J, Patak P, Perz D, Tkadlec J. 2020. Disjoint tree-compatible plane perfect matchings. 36th European Workshop on Computational Geometry. EuroCG: European Workshop on Computational Geometry, 56.' mla: Aichholzer, Oswin, et al. “Disjoint Tree-Compatible Plane Perfect Matchings.” 36th European Workshop on Computational Geometry, 56, 2020. short: O. Aichholzer, J. Obmann, P. Patak, D. Perz, J. Tkadlec, in:, 36th European Workshop on Computational Geometry, 2020. conference: end_date: 2020-03-18 location: Würzburg, Germany, Virtual name: 'EuroCG: European Workshop on Computational Geometry' start_date: 2020-03-16 date_created: 2024-03-05T08:57:17Z date_published: 2020-04-01T00:00:00Z date_updated: 2024-03-05T09:00:07Z day: '01' department: - _id: KrCh - _id: UlWa language: - iso: eng main_file_link: - open_access: '1' url: https://www1.pub.informatik.uni-wuerzburg.de/eurocg2020/data/uploads/papers/eurocg20_paper_56.pdf month: '04' oa: 1 oa_version: Published Version publication: 36th European Workshop on Computational Geometry publication_status: published quality_controlled: '1' status: public title: Disjoint tree-compatible plane perfect matchings type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2020' ... --- _id: '6748' abstract: - lang: eng text: "Fitting a function by using linear combinations of a large number N of `simple' components is one of the most fruitful ideas in statistical learning. This idea lies at the core of a variety of methods, from two-layer neural networks to kernel regression, to boosting. In general, the resulting risk minimization problem is non-convex and is solved by gradient descent or its variants. Unfortunately, little is known about global convergence properties of these approaches.\r\nHere we consider the problem of learning a concave function f on a compact convex domain Ω⊆ℝd, using linear combinations of `bump-like' components (neurons). The parameters to be fitted are the centers of N bumps, and the resulting empirical risk minimization problem is highly non-convex. We prove that, in the limit in which the number of neurons diverges, the evolution of gradient descent converges to a Wasserstein gradient flow in the space of probability distributions over Ω. Further, when the bump width δ tends to 0, this gradient flow has a limit which is a viscous porous medium equation. Remarkably, the cost function optimized by this gradient flow exhibits a special property known as displacement convexity, which implies exponential convergence rates for N→∞, δ→0. Surprisingly, this asymptotic theory appears to capture well the behavior for moderate values of δ,N. Explaining this phenomenon, and understanding the dependence on δ,N in a quantitative manner remains an outstanding challenge." article_processing_charge: No article_type: original author: - first_name: Adel full_name: Javanmard, Adel last_name: Javanmard - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 - first_name: Andrea full_name: Montanari, Andrea last_name: Montanari citation: ama: Javanmard A, Mondelli M, Montanari A. Analysis of a two-layer neural network via displacement convexity. Annals of Statistics. 2020;48(6):3619-3642. doi:10.1214/20-AOS1945 apa: Javanmard, A., Mondelli, M., & Montanari, A. (2020). Analysis of a two-layer neural network via displacement convexity. Annals of Statistics. Institute of Mathematical Statistics. https://doi.org/10.1214/20-AOS1945 chicago: Javanmard, Adel, Marco Mondelli, and Andrea Montanari. “Analysis of a Two-Layer Neural Network via Displacement Convexity.” Annals of Statistics. Institute of Mathematical Statistics, 2020. https://doi.org/10.1214/20-AOS1945. ieee: A. Javanmard, M. Mondelli, and A. Montanari, “Analysis of a two-layer neural network via displacement convexity,” Annals of Statistics, vol. 48, no. 6. Institute of Mathematical Statistics, pp. 3619–3642, 2020. ista: Javanmard A, Mondelli M, Montanari A. 2020. Analysis of a two-layer neural network via displacement convexity. Annals of Statistics. 48(6), 3619–3642. mla: Javanmard, Adel, et al. “Analysis of a Two-Layer Neural Network via Displacement Convexity.” Annals of Statistics, vol. 48, no. 6, Institute of Mathematical Statistics, 2020, pp. 3619–42, doi:10.1214/20-AOS1945. short: A. Javanmard, M. Mondelli, A. Montanari, Annals of Statistics 48 (2020) 3619–3642. date_created: 2019-07-31T09:39:42Z date_published: 2020-12-11T00:00:00Z date_updated: 2024-03-06T08:28:50Z day: '11' department: - _id: MaMo doi: 10.1214/20-AOS1945 external_id: arxiv: - '1901.01375' isi: - '000598369200021' intvolume: ' 48' isi: 1 issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1901.01375 month: '12' oa: 1 oa_version: Preprint page: 3619-3642 publication: Annals of Statistics publication_identifier: eissn: - 1941-7330 issn: - 1932-6157 publication_status: published publisher: Institute of Mathematical Statistics quality_controlled: '1' status: public title: Analysis of a two-layer neural network via displacement convexity type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 48 year: '2020' ... --- _id: '15070' abstract: - lang: eng text: This workshop focused on interactions between the various perspectives on the moduli space of Higgs bundles over a Riemann surface. This subject draws on algebraic geometry, geometric topology, geometric analysis and mathematical physics, and the goal was to promote interactions between these various branches of the subject. The main current directions of research were well represented by the participants, and the talks included many from both senior and junior participants. article_processing_charge: No article_type: original author: - first_name: Lara full_name: Anderson, Lara last_name: Anderson - first_name: Tamás full_name: Hausel, Tamás id: 4A0666D8-F248-11E8-B48F-1D18A9856A87 last_name: Hausel - first_name: Rafe full_name: Mazzeo, Rafe last_name: Mazzeo - first_name: Laura full_name: Schaposnik, Laura last_name: Schaposnik citation: ama: Anderson L, Hausel T, Mazzeo R, Schaposnik L. Geometry and physics of Higgs bundles. Oberwolfach Reports. 2020;16(2):1357-1417. doi:10.4171/owr/2019/23 apa: Anderson, L., Hausel, T., Mazzeo, R., & Schaposnik, L. (2020). Geometry and physics of Higgs bundles. Oberwolfach Reports. European Mathematical Society. https://doi.org/10.4171/owr/2019/23 chicago: Anderson, Lara, Tamás Hausel, Rafe Mazzeo, and Laura Schaposnik. “Geometry and Physics of Higgs Bundles.” Oberwolfach Reports. European Mathematical Society, 2020. https://doi.org/10.4171/owr/2019/23. ieee: L. Anderson, T. Hausel, R. Mazzeo, and L. Schaposnik, “Geometry and physics of Higgs bundles,” Oberwolfach Reports, vol. 16, no. 2. European Mathematical Society, pp. 1357–1417, 2020. ista: Anderson L, Hausel T, Mazzeo R, Schaposnik L. 2020. Geometry and physics of Higgs bundles. Oberwolfach Reports. 16(2), 1357–1417. mla: Anderson, Lara, et al. “Geometry and Physics of Higgs Bundles.” Oberwolfach Reports, vol. 16, no. 2, European Mathematical Society, 2020, pp. 1357–417, doi:10.4171/owr/2019/23. short: L. Anderson, T. Hausel, R. Mazzeo, L. Schaposnik, Oberwolfach Reports 16 (2020) 1357–1417. date_created: 2024-03-04T11:36:31Z date_published: 2020-06-04T00:00:00Z date_updated: 2024-03-11T09:20:34Z day: '04' department: - _id: TaHa doi: 10.4171/owr/2019/23 intvolume: ' 16' issue: '2' keyword: - Organic Chemistry - Biochemistry language: - iso: eng month: '06' oa_version: None page: 1357-1417 publication: Oberwolfach Reports publication_identifier: issn: - 1660-8933 publication_status: published publisher: European Mathematical Society quality_controlled: '1' status: public title: Geometry and physics of Higgs bundles type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 16 year: '2020' ... --- _id: '8741' abstract: - lang: eng text: "In ecology, climate and other fields, (sub)systems have been identified that can transition into a qualitatively different state when a critical threshold or tipping point in a driving process is crossed. An understanding of those tipping elements is of great interest given the increasing influence of humans on the biophysical Earth system. Complex interactions exist between tipping elements, e.g. physical mechanisms connect subsystems of the climate system. Based on earlier work on such coupled nonlinear systems, we systematically assessed the qualitative long-term behaviour of interacting tipping elements. We developed an understanding of the consequences of interactions\r\non the tipping behaviour allowing for tipping cascades to emerge under certain conditions. The (narrative) application of\r\nthese qualitative results to real-world examples of interacting tipping elements indicates that tipping cascades with profound consequences may occur: the interacting Greenland ice sheet and thermohaline ocean circulation might tip before the tipping points of the isolated subsystems are crossed. The eutrophication of the first lake in a lake chain might propagate through the following lakes without a crossing of their individual critical nutrient input levels. The possibility of emerging cascading tipping dynamics calls for the development of a unified theory of interacting tipping elements and the quantitative analysis of interacting real-world tipping elements." acknowledgement: "V.K. thanks the German National Academic Foundation (Studienstiftung des deutschen Volkes) for financial\r\nsupport. J.F.D. is grateful for financial support by the Stordalen Foundation via the Planetary Boundary Research\r\nNetwork (PB.net), the Earth League’s EarthDoc program and the European Research Council Advanced Grant\r\nproject ERA (Earth Resilience in the Anthropocene). We are thankful for support by the Leibniz Association\r\n(project DominoES).\r\nAcknowledgements. This work has been performed in the context of the copan collaboration and the FutureLab on Earth\r\nResilience in the Anthropocene at the Potsdam Institute for Climate Impact Research. Furthermore, we acknowledge\r\ndiscussions with and helpful comments by N. Wunderling, J. Heitzig and M. Wiedermann." article_number: '200599' article_processing_charge: No article_type: original author: - first_name: Ann Kristin full_name: Klose, Ann Kristin last_name: Klose - first_name: Volker full_name: Karle, Volker id: D7C012AE-D7ED-11E9-95E8-1EC5E5697425 last_name: Karle orcid: 0000-0002-6963-0129 - first_name: Ricarda full_name: Winkelmann, Ricarda last_name: Winkelmann - first_name: Jonathan F. full_name: Donges, Jonathan F. last_name: Donges citation: ama: 'Klose AK, Karle V, Winkelmann R, Donges JF. Emergence of cascading dynamics in interacting tipping elements of ecology and climate: Cascading dynamics in tipping elements. Royal Society Open Science. 2020;7(6). doi:10.1098/rsos.200599' apa: 'Klose, A. K., Karle, V., Winkelmann, R., & Donges, J. F. (2020). Emergence of cascading dynamics in interacting tipping elements of ecology and climate: Cascading dynamics in tipping elements. Royal Society Open Science. The Royal Society. https://doi.org/10.1098/rsos.200599' chicago: 'Klose, Ann Kristin, Volker Karle, Ricarda Winkelmann, and Jonathan F. Donges. “Emergence of Cascading Dynamics in Interacting Tipping Elements of Ecology and Climate: Cascading Dynamics in Tipping Elements.” Royal Society Open Science. The Royal Society, 2020. https://doi.org/10.1098/rsos.200599.' ieee: 'A. K. Klose, V. Karle, R. Winkelmann, and J. F. Donges, “Emergence of cascading dynamics in interacting tipping elements of ecology and climate: Cascading dynamics in tipping elements,” Royal Society Open Science, vol. 7, no. 6. The Royal Society, 2020.' ista: 'Klose AK, Karle V, Winkelmann R, Donges JF. 2020. Emergence of cascading dynamics in interacting tipping elements of ecology and climate: Cascading dynamics in tipping elements. Royal Society Open Science. 7(6), 200599.' mla: 'Klose, Ann Kristin, et al. “Emergence of Cascading Dynamics in Interacting Tipping Elements of Ecology and Climate: Cascading Dynamics in Tipping Elements.” Royal Society Open Science, vol. 7, no. 6, 200599, The Royal Society, 2020, doi:10.1098/rsos.200599.' short: A.K. Klose, V. Karle, R. Winkelmann, J.F. Donges, Royal Society Open Science 7 (2020). date_created: 2020-11-08T23:01:25Z date_published: 2020-06-01T00:00:00Z date_updated: 2024-03-12T12:31:30Z day: '01' ddc: - '530' - '550' department: - _id: MiLe doi: 10.1098/rsos.200599 external_id: arxiv: - '1910.12042' isi: - '000545625200001' file: - access_level: open_access checksum: 5505c445de373bfd836eb4d3b48b1f37 content_type: application/pdf creator: dernst date_created: 2020-11-09T09:07:11Z date_updated: 2020-11-09T09:07:11Z file_id: '8748' file_name: 2020_RoyalSocOpenScience_Klose.pdf file_size: 1611485 relation: main_file success: 1 file_date_updated: 2020-11-09T09:07:11Z has_accepted_license: '1' intvolume: ' 7' isi: 1 issue: '6' language: - iso: eng month: '06' oa: 1 oa_version: Published Version publication: Royal Society Open Science publication_identifier: eissn: - '20545703' publication_status: published publisher: The Royal Society quality_controlled: '1' scopus_import: '1' status: public title: 'Emergence of cascading dynamics in interacting tipping elements of ecology and climate: Cascading dynamics in tipping elements' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 7 year: '2020' ... --- _id: '7687' abstract: - lang: eng text: A working group, which was established within the Network of Repository Managers (RepManNet), has dealt with common certifications for repositories. In addition, current requirements of the research funding agencies FWF and EU were also taken into account. The Core Trust Seal was examined in more detail. For this purpose, a questionnaire was sent to those organizations that are already certified with CTS in Austria. The answers were summarized and evaluated anonymously. It is recommended to go for a repository certification. Moreover, the development of a DINI certificate in Austria is strongly suggested. - lang: ger text: ' Eine Arbeitsgruppe, die im Rahmen des Netzwerks für RepositorienmanagerInnen (RepManNet) entstanden ist, hat sich mit gängigen Zertifizierungen für Repositorien beschäftigt. Weiters wurden aktuelle Vorgaben der Forschungsförderer FWF und EU herangezogen. Das Core Trust Seal wurde genauer betrachtet. Hierfür wurden jenen Organisationen, die in Österreich bereits mit CTS zertifiziert sind, ein Fragebogen übermittelt. Die Antworten wurden anonymisiert zusammengefasst und ausgewertet. Plädiert wird für eine Zertifizierung von Repositorien und die Entwicklung einer DINI-Zertifizierung in Österreich.' article_processing_charge: No article_type: original author: - first_name: Doris full_name: Ernst, Doris id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 last_name: Ernst orcid: 0000-0002-2354-0195 - first_name: Gertraud full_name: Novotny, Gertraud last_name: Novotny - first_name: Eva Maria full_name: Schönher, Eva Maria last_name: Schönher citation: ama: Ernst D, Novotny G, Schönher EM. (Core Trust) Seal your repository! Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. 2020;73(1):46-59. doi:10.31263/voebm.v73i1.3491 apa: Ernst, D., Novotny, G., & Schönher, E. M. (2020). (Core Trust) Seal your repository! Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare. https://doi.org/10.31263/voebm.v73i1.3491 chicago: Ernst, Doris, Gertraud Novotny, and Eva Maria Schönher. “(Core Trust) Seal your repository!” Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare, 2020. https://doi.org/10.31263/voebm.v73i1.3491. ieee: D. Ernst, G. Novotny, and E. M. Schönher, “(Core Trust) Seal your repository!,” Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, vol. 73, no. 1. Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare, pp. 46–59, 2020. ista: Ernst D, Novotny G, Schönher EM. 2020. (Core Trust) Seal your repository! Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. 73(1), 46–59. mla: Ernst, Doris, et al. “(Core Trust) Seal your repository!” Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, vol. 73, no. 1, Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare, 2020, pp. 46–59, doi:10.31263/voebm.v73i1.3491. short: D. Ernst, G. Novotny, E.M. Schönher, Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare 73 (2020) 46–59. date_created: 2020-04-28T08:37:38Z date_published: 2020-04-28T00:00:00Z date_updated: 2024-03-12T10:12:33Z day: '28' ddc: - '020' department: - _id: E-Lib doi: 10.31263/voebm.v73i1.3491 file: - access_level: open_access checksum: fee784f15a489deb7def6ccf8c5bf8c3 content_type: application/pdf creator: dernst date_created: 2020-06-17T10:50:13Z date_updated: 2024-03-12T10:12:33Z file_id: '7970' file_name: 2020_VOEB_Ernst.pdf file_size: 579291 relation: main_file file_date_updated: 2024-03-12T10:12:33Z has_accepted_license: '1' intvolume: ' 73' issue: '1' language: - iso: ger month: '04' oa: 1 oa_version: Published Version page: 46-59 popular_science: '1' publication: Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare publication_identifier: issn: - 1022-2588 publication_status: published publisher: Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare scopus_import: '1' status: public title: (Core Trust) Seal your repository! tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 73 year: '2020' ... --- _id: '15079' abstract: - lang: eng text: "Large complex systems tend to develop universal patterns that often represent their essential characteristics. For example, the cumulative effects of independent or weakly dependent random variables often yield the Gaussian universality class via the central limit theorem. For non-commutative random variables, e.g. matrices, the Gaussian behavior is often replaced by another universality class, commonly called random matrix statistics. Nearby eigenvalues are strongly correlated, and, remarkably, their correlation structure is universal, depending only on the symmetry type of the matrix. Even more surprisingly, this feature is not restricted to matrices; in fact Eugene Wigner, the pioneer of the field, discovered in the 1950s that distributions of the gaps between energy levels of complicated quantum systems universally follow the same random matrix statistics. This claim has never been rigorously proved for any realistic physical system but experimental data and extensive numerics leave no doubt as to its correctness. Since then random matrices have proved to be extremely useful phenomenological models in a wide range of applications beyond quantum physics that include number theory, statistics, neuroscience, population dynamics, wireless communication and mathematical finance. The ubiquity of random matrices in natural sciences is still a mystery, but recent years have witnessed a breakthrough in the mathematical description of the statistical structure of their spectrum. Random matrices and closely related areas such as log-gases have become an extremely active research area in probability theory.\r\nThis workshop brought together outstanding researchers from a variety of mathematical backgrounds whose areas of research are linked to random matrices. While there are strong links between their motivations, the techniques used by these researchers span a large swath of mathematics, ranging from purely algebraic techniques to stochastic analysis, classical probability theory, operator algebra, supersymmetry, orthogonal polynomials, etc." article_processing_charge: No article_type: original author: - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Friedrich full_name: Götze, Friedrich last_name: Götze - first_name: Alice full_name: Guionnet, Alice last_name: Guionnet citation: ama: Erdös L, Götze F, Guionnet A. Random matrices. Oberwolfach Reports. 2020;16(4):3459-3527. doi:10.4171/owr/2019/56 apa: Erdös, L., Götze, F., & Guionnet, A. (2020). Random matrices. Oberwolfach Reports. European Mathematical Society. https://doi.org/10.4171/owr/2019/56 chicago: Erdös, László, Friedrich Götze, and Alice Guionnet. “Random Matrices.” Oberwolfach Reports. European Mathematical Society, 2020. https://doi.org/10.4171/owr/2019/56. ieee: L. Erdös, F. Götze, and A. Guionnet, “Random matrices,” Oberwolfach Reports, vol. 16, no. 4. European Mathematical Society, pp. 3459–3527, 2020. ista: Erdös L, Götze F, Guionnet A. 2020. Random matrices. Oberwolfach Reports. 16(4), 3459–3527. mla: Erdös, László, et al. “Random Matrices.” Oberwolfach Reports, vol. 16, no. 4, European Mathematical Society, 2020, pp. 3459–527, doi:10.4171/owr/2019/56. short: L. Erdös, F. Götze, A. Guionnet, Oberwolfach Reports 16 (2020) 3459–3527. date_created: 2024-03-05T07:54:44Z date_published: 2020-11-19T00:00:00Z date_updated: 2024-03-12T12:25:18Z day: '19' department: - _id: LaEr doi: 10.4171/owr/2019/56 intvolume: ' 16' issue: '4' language: - iso: eng month: '11' oa_version: None page: 3459-3527 publication: Oberwolfach Reports publication_identifier: issn: - 1660-8933 publication_status: published publisher: European Mathematical Society quality_controlled: '1' status: public title: Random matrices type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 16 year: '2020' ... --- _id: '15072' abstract: - lang: eng text: The interaction among fundamental particles in nature leads to many interesting effects in quantum statistical mechanics; examples include superconductivity for charged systems and superfluidity in cold gases. It is a huge challenge for mathematical physics to understand the collective behavior of systems containing a large number of particles, emerging from known microscopic interactions. In this workshop we brought together researchers working on different aspects of many-body quantum mechanics to discuss recent developments, exchange ideas and propose new challenges and research directions. article_processing_charge: No article_type: original author: - first_name: Christian full_name: Hainzl, Christian last_name: Hainzl - first_name: Benjamin full_name: Schlein, Benjamin last_name: Schlein - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 - first_name: Simone full_name: Warzel, Simone last_name: Warzel citation: ama: Hainzl C, Schlein B, Seiringer R, Warzel S. Many-body quantum systems. Oberwolfach Reports. 2020;16(3):2541-2603. doi:10.4171/owr/2019/41 apa: Hainzl, C., Schlein, B., Seiringer, R., & Warzel, S. (2020). Many-body quantum systems. Oberwolfach Reports. European Mathematical Society. https://doi.org/10.4171/owr/2019/41 chicago: Hainzl, Christian, Benjamin Schlein, Robert Seiringer, and Simone Warzel. “Many-Body Quantum Systems.” Oberwolfach Reports. European Mathematical Society, 2020. https://doi.org/10.4171/owr/2019/41. ieee: C. Hainzl, B. Schlein, R. Seiringer, and S. Warzel, “Many-body quantum systems,” Oberwolfach Reports, vol. 16, no. 3. European Mathematical Society, pp. 2541–2603, 2020. ista: Hainzl C, Schlein B, Seiringer R, Warzel S. 2020. Many-body quantum systems. Oberwolfach Reports. 16(3), 2541–2603. mla: Hainzl, Christian, et al. “Many-Body Quantum Systems.” Oberwolfach Reports, vol. 16, no. 3, European Mathematical Society, 2020, pp. 2541–603, doi:10.4171/owr/2019/41. short: C. Hainzl, B. Schlein, R. Seiringer, S. Warzel, Oberwolfach Reports 16 (2020) 2541–2603. date_created: 2024-03-04T11:46:12Z date_published: 2020-09-10T00:00:00Z date_updated: 2024-03-12T12:02:00Z day: '10' department: - _id: RoSe doi: 10.4171/owr/2019/41 intvolume: ' 16' issue: '3' language: - iso: eng month: '09' oa_version: None page: 2541-2603 publication: Oberwolfach Reports publication_identifier: issn: - 1660-8933 publication_status: published publisher: European Mathematical Society quality_controlled: '1' status: public title: Many-body quantum systems type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 16 year: '2020' ... --- _id: '15071' abstract: - lang: eng text: "A mesophilic methanogenic culture, designated JL01, was isolated from Holocene permafrost in the Russian Arctic [1]. After long-term extensive cultivation at 15°C it turned out to be a tied binary culture of archaeal (JL01) and bacterial (Sphaerochaeta associata GLS2) strains.\r\nStrain JL01 was a strict anaerobe and grew on methanol, acetate and methylamines as energy and carbon sources. Cells were irregular coccoid, non-motile, non-spore-forming, and Gram-stainpositive. Optimum conditions for growth were 24-28 oC, pH 6.8–7.3 and 0.075-0.1 M NaCl.\r\nPhylogenetic tree reconstructions based on 16S rRNA and concatenated alignment of broadly\r\nconserved protein-coding genes revealed its close relation to Methanosarcina mazei S-6\r\nT (similarity 99.5%). The comparison of whole genomic sequences (ANI) of the isolate and the type strain of M.mazei was 98.5%, which is higher than the values recommended for new species. Thus strain JL01 (=VKM B-2370=JCM 31898) represents the first M. mazei isolated from permanently subzero Arcticsediments. The long-term co-cultivation of JL01 with S. associata GLS2T showed the methane production without any additional carbon and energy sources. Genome analysis of S. associata GLS2T revealed putative genes involved in methanochondroithin catabolism." acknowledgement: "The work was supported by of Russian Foundation of Basic Research: grant № 19-04-00831 for Viktoria Shcherbakova and Olga Troshina, grant № 18-34-00334 for Viktoriia Oshurkova and Vladimir Trubitsyn. \r\nWe thank Dr Natalia Suzina (IBPM RAS, Federal Research Center Pushchino Center for\r\nBiological Research RAS) for the help with the microscopic studies, respectively; Dr. Margarita Meyer (Division of Genetics, Department of Medicine, BWH and HMS, USA) and Dr Fedor Kondrashov (IST, Austria) for their help in obtaining the genomic sequence of strain JL01. " article_processing_charge: Yes author: - first_name: Viktoriia full_name: Oshurkova, Viktoriia last_name: Oshurkova - first_name: Olga full_name: Troshina, Olga last_name: Troshina - first_name: Vladimir full_name: Trubitsyn, Vladimir last_name: Trubitsyn - first_name: Yana full_name: Ryzhmanova, Yana last_name: Ryzhmanova - first_name: Olga full_name: Bochkareva, Olga id: C4558D3C-6102-11E9-A62E-F418E6697425 last_name: Bochkareva orcid: 0000-0003-1006-6639 - first_name: Viktoria full_name: Shcherbakova, Viktoria last_name: Shcherbakova citation: ama: 'Oshurkova V, Troshina O, Trubitsyn V, Ryzhmanova Y, Bochkareva O, Shcherbakova V. Characterization of methanosarcina mazei JL01 isolated from holocene arctic permafrost and study of the archaeon cooperation with bacterium Sphaerochaeta associata GLS2T. In: Proceedings of 1st International Electronic Conference on Microbiology. MDPI; 2020. doi:10.3390/ecm2020-07116' apa: 'Oshurkova, V., Troshina, O., Trubitsyn, V., Ryzhmanova, Y., Bochkareva, O., & Shcherbakova, V. (2020). Characterization of methanosarcina mazei JL01 isolated from holocene arctic permafrost and study of the archaeon cooperation with bacterium Sphaerochaeta associata GLS2T. In Proceedings of 1st International Electronic Conference on Microbiology. Virtual: MDPI. https://doi.org/10.3390/ecm2020-07116' chicago: Oshurkova, Viktoriia, Olga Troshina, Vladimir Trubitsyn, Yana Ryzhmanova, Olga Bochkareva, and Viktoria Shcherbakova. “Characterization of Methanosarcina Mazei JL01 Isolated from Holocene Arctic Permafrost and Study of the Archaeon Cooperation with Bacterium Sphaerochaeta Associata GLS2T.” In Proceedings of 1st International Electronic Conference on Microbiology. MDPI, 2020. https://doi.org/10.3390/ecm2020-07116. ieee: V. Oshurkova, O. Troshina, V. Trubitsyn, Y. Ryzhmanova, O. Bochkareva, and V. Shcherbakova, “Characterization of methanosarcina mazei JL01 isolated from holocene arctic permafrost and study of the archaeon cooperation with bacterium Sphaerochaeta associata GLS2T,” in Proceedings of 1st International Electronic Conference on Microbiology, Virtual, 2020. ista: 'Oshurkova V, Troshina O, Trubitsyn V, Ryzhmanova Y, Bochkareva O, Shcherbakova V. 2020. Characterization of methanosarcina mazei JL01 isolated from holocene arctic permafrost and study of the archaeon cooperation with bacterium Sphaerochaeta associata GLS2T. Proceedings of 1st International Electronic Conference on Microbiology. ECM: Electronic Conference on Microbiology.' mla: Oshurkova, Viktoriia, et al. “Characterization of Methanosarcina Mazei JL01 Isolated from Holocene Arctic Permafrost and Study of the Archaeon Cooperation with Bacterium Sphaerochaeta Associata GLS2T.” Proceedings of 1st International Electronic Conference on Microbiology, MDPI, 2020, doi:10.3390/ecm2020-07116. short: V. Oshurkova, O. Troshina, V. Trubitsyn, Y. Ryzhmanova, O. Bochkareva, V. Shcherbakova, in:, Proceedings of 1st International Electronic Conference on Microbiology, MDPI, 2020. conference: end_date: 2020-11-30 location: Virtual name: 'ECM: Electronic Conference on Microbiology' start_date: 2020-11-02 date_created: 2024-03-04T11:41:31Z date_published: 2020-11-02T00:00:00Z date_updated: 2024-03-20T08:06:22Z day: '02' ddc: - '570' department: - _id: FyKo doi: 10.3390/ecm2020-07116 file: - access_level: open_access checksum: d1914af7811a21a4b2744eb51b5834e3 content_type: application/pdf creator: dernst date_created: 2024-03-20T08:05:46Z date_updated: 2024-03-20T08:05:46Z file_id: '15127' file_name: 2020_ECM_Oshurkova.pdf file_size: 595543 relation: main_file success: 1 file_date_updated: 2024-03-20T08:05:46Z has_accepted_license: '1' language: - iso: eng month: '11' oa: 1 oa_version: Published Version publication: Proceedings of 1st International Electronic Conference on Microbiology publication_status: published publisher: MDPI quality_controlled: '1' status: public title: Characterization of methanosarcina mazei JL01 isolated from holocene arctic permafrost and study of the archaeon cooperation with bacterium Sphaerochaeta associata GLS2T tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2020' ... --- _id: '15153' abstract: - lang: eng text: Mammalian circadian rhythms are generated by a transcription-based feedback loop in which CLOCK:BMAL1 drives transcription of its repressors (PER1/2, CRY1/2), which ultimately interact with CLOCK:BMAL1 to close the feedback loop with ~24 hr periodicity. Here we pinpoint a key difference between CRY1 and CRY2 that underlies their differential strengths as transcriptional repressors. Both cryptochromes bind the BMAL1 transactivation domain similarly to sequester it from coactivators and repress CLOCK:BMAL1 activity. However, we find that CRY1 is recruited with much higher affinity to the PAS domain core of CLOCK:BMAL1, allowing it to serve as a stronger repressor that lengthens circadian period. We discovered a dynamic serine-rich loop adjacent to the secondary pocket in the photolyase homology region (PHR) domain that regulates differential binding of cryptochromes to the PAS domain core of CLOCK:BMAL1. Notably, binding of the co-repressor PER2 remodels the serine loop of CRY2, making it more CRY1-like and enhancing its affinity for CLOCK:BMAL1. article_number: '55275' article_processing_charge: No article_type: original author: - first_name: Jennifer L full_name: Fribourgh, Jennifer L last_name: Fribourgh - first_name: Ashutosh full_name: Srivastava, Ashutosh last_name: Srivastava - first_name: Colby R full_name: Sandate, Colby R last_name: Sandate - first_name: Alicia Kathleen full_name: Michael, Alicia Kathleen id: 6437c950-2a03-11ee-914d-d6476dd7b75c last_name: Michael - first_name: Peter L full_name: Hsu, Peter L last_name: Hsu - first_name: Christin full_name: Rakers, Christin last_name: Rakers - first_name: Leslee T full_name: Nguyen, Leslee T last_name: Nguyen - first_name: Megan R full_name: Torgrimson, Megan R last_name: Torgrimson - first_name: Gian Carlo G full_name: Parico, Gian Carlo G last_name: Parico - first_name: Sarvind full_name: Tripathi, Sarvind last_name: Tripathi - first_name: Ning full_name: Zheng, Ning last_name: Zheng - first_name: Gabriel C full_name: Lander, Gabriel C last_name: Lander - first_name: Tsuyoshi full_name: Hirota, Tsuyoshi last_name: Hirota - first_name: Florence full_name: Tama, Florence last_name: Tama - first_name: Carrie L full_name: Partch, Carrie L last_name: Partch citation: ama: Fribourgh JL, Srivastava A, Sandate CR, et al. Dynamics at the serine loop underlie differential affinity of cryptochromes for CLOCK:BMAL1 to control circadian timing. eLife. 2020;9. doi:10.7554/elife.55275 apa: Fribourgh, J. L., Srivastava, A., Sandate, C. R., Michael, A. K., Hsu, P. L., Rakers, C., … Partch, C. L. (2020). Dynamics at the serine loop underlie differential affinity of cryptochromes for CLOCK:BMAL1 to control circadian timing. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.55275 chicago: Fribourgh, Jennifer L, Ashutosh Srivastava, Colby R Sandate, Alicia K. Michael, Peter L Hsu, Christin Rakers, Leslee T Nguyen, et al. “Dynamics at the Serine Loop Underlie Differential Affinity of Cryptochromes for CLOCK:BMAL1 to Control Circadian Timing.” ELife. eLife Sciences Publications, 2020. https://doi.org/10.7554/elife.55275. ieee: J. L. Fribourgh et al., “Dynamics at the serine loop underlie differential affinity of cryptochromes for CLOCK:BMAL1 to control circadian timing,” eLife, vol. 9. eLife Sciences Publications, 2020. ista: Fribourgh JL, Srivastava A, Sandate CR, Michael AK, Hsu PL, Rakers C, Nguyen LT, Torgrimson MR, Parico GCG, Tripathi S, Zheng N, Lander GC, Hirota T, Tama F, Partch CL. 2020. Dynamics at the serine loop underlie differential affinity of cryptochromes for CLOCK:BMAL1 to control circadian timing. eLife. 9, 55275. mla: Fribourgh, Jennifer L., et al. “Dynamics at the Serine Loop Underlie Differential Affinity of Cryptochromes for CLOCK:BMAL1 to Control Circadian Timing.” ELife, vol. 9, 55275, eLife Sciences Publications, 2020, doi:10.7554/elife.55275. short: J.L. Fribourgh, A. Srivastava, C.R. Sandate, A.K. Michael, P.L. Hsu, C. Rakers, L.T. Nguyen, M.R. Torgrimson, G.C.G. Parico, S. Tripathi, N. Zheng, G.C. Lander, T. Hirota, F. Tama, C.L. Partch, ELife 9 (2020). date_created: 2024-03-21T07:55:12Z date_published: 2020-02-26T00:00:00Z date_updated: 2024-03-25T12:25:02Z day: '26' doi: 10.7554/elife.55275 extern: '1' intvolume: ' 9' keyword: - General Immunology and Microbiology - General Biochemistry - Genetics and Molecular Biology - General Medicine - General Neuroscience language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.7554/eLife.55275 month: '02' oa: 1 oa_version: Published Version publication: eLife publication_identifier: issn: - 2050-084X publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' scopus_import: '1' status: public title: Dynamics at the serine loop underlie differential affinity of cryptochromes for CLOCK:BMAL1 to control circadian timing type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2020' ... --- _id: '15152' abstract: - lang: eng text: Transcription factors (TFs) regulate gene expression through chromatin where nucleosomes restrict DNA access. To study how TFs bind nucleosome-occupied motifs, we focused on the reprogramming factors OCT4 and SOX2 in mouse embryonic stem cells. We determined TF engagement throughout a nucleosome at base-pair resolution in vitro, enabling structure determination by cryo–electron microscopy at two preferred positions. Depending on motif location, OCT4 and SOX2 differentially distort nucleosomal DNA. At one position, OCT4-SOX2 removes DNA from histone H2A and histone H3; however, at an inverted motif, the TFs only induce local DNA distortions. OCT4 uses one of its two DNA-binding domains to engage DNA in both structures, reading out a partial motif. These findings explain site-specific nucleosome engagement by the pluripotency factors OCT4 and SOX2, and they reveal how TFs distort nucleosomes to access chromatinized motifs. article_processing_charge: No article_type: original author: - first_name: Alicia Kathleen full_name: Michael, Alicia Kathleen id: 6437c950-2a03-11ee-914d-d6476dd7b75c last_name: Michael orcid: 0000-0002-6080-839X - first_name: Ralph S. full_name: Grand, Ralph S. last_name: Grand - first_name: Luke full_name: Isbel, Luke last_name: Isbel - first_name: Simone full_name: Cavadini, Simone last_name: Cavadini - first_name: Zuzanna full_name: Kozicka, Zuzanna last_name: Kozicka - first_name: Georg full_name: Kempf, Georg last_name: Kempf - first_name: Richard D. full_name: Bunker, Richard D. last_name: Bunker - first_name: Andreas D. full_name: Schenk, Andreas D. last_name: Schenk - first_name: Alexandra full_name: Graff-Meyer, Alexandra last_name: Graff-Meyer - first_name: Ganesh R. full_name: Pathare, Ganesh R. last_name: Pathare - first_name: Joscha full_name: Weiss, Joscha last_name: Weiss - first_name: Syota full_name: Matsumoto, Syota last_name: Matsumoto - first_name: Lukas full_name: Burger, Lukas last_name: Burger - first_name: Dirk full_name: Schübeler, Dirk last_name: Schübeler - first_name: Nicolas H. full_name: Thomä, Nicolas H. last_name: Thomä citation: ama: Michael AK, Grand RS, Isbel L, et al. Mechanisms of OCT4-SOX2 motif readout on nucleosomes. Science. 2020;368(6498):1460-1465. doi:10.1126/science.abb0074 apa: Michael, A. K., Grand, R. S., Isbel, L., Cavadini, S., Kozicka, Z., Kempf, G., … Thomä, N. H. (2020). Mechanisms of OCT4-SOX2 motif readout on nucleosomes. Science. American Association for the Advancement of Science . https://doi.org/10.1126/science.abb0074 chicago: Michael, Alicia K., Ralph S. Grand, Luke Isbel, Simone Cavadini, Zuzanna Kozicka, Georg Kempf, Richard D. Bunker, et al. “Mechanisms of OCT4-SOX2 Motif Readout on Nucleosomes.” Science. American Association for the Advancement of Science , 2020. https://doi.org/10.1126/science.abb0074. ieee: A. K. Michael et al., “Mechanisms of OCT4-SOX2 motif readout on nucleosomes,” Science, vol. 368, no. 6498. American Association for the Advancement of Science , pp. 1460–1465, 2020. ista: Michael AK, Grand RS, Isbel L, Cavadini S, Kozicka Z, Kempf G, Bunker RD, Schenk AD, Graff-Meyer A, Pathare GR, Weiss J, Matsumoto S, Burger L, Schübeler D, Thomä NH. 2020. Mechanisms of OCT4-SOX2 motif readout on nucleosomes. Science. 368(6498), 1460–1465. mla: Michael, Alicia K., et al. “Mechanisms of OCT4-SOX2 Motif Readout on Nucleosomes.” Science, vol. 368, no. 6498, American Association for the Advancement of Science , 2020, pp. 1460–65, doi:10.1126/science.abb0074. short: A.K. Michael, R.S. Grand, L. Isbel, S. Cavadini, Z. Kozicka, G. Kempf, R.D. Bunker, A.D. Schenk, A. Graff-Meyer, G.R. Pathare, J. Weiss, S. Matsumoto, L. Burger, D. Schübeler, N.H. Thomä, Science 368 (2020) 1460–1465. date_created: 2024-03-21T07:54:44Z date_published: 2020-04-23T00:00:00Z date_updated: 2024-03-25T12:29:34Z day: '23' doi: 10.1126/science.abb0074 extern: '1' intvolume: ' 368' issue: '6498' language: - iso: eng month: '04' oa_version: None page: 1460-1465 publication: Science publication_identifier: eissn: - 1095-9203 issn: - 0036-8075 publication_status: published publisher: 'American Association for the Advancement of Science ' quality_controlled: '1' scopus_import: '1' status: public title: Mechanisms of OCT4-SOX2 motif readout on nucleosomes type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 368 year: '2020' ... --- _id: '7525' abstract: - lang: eng text: "The medial habenula (MHb) is an evolutionary conserved epithalamic structure important for the modulation of emotional memory. It is involved in regulation of anxiety, compulsive behavior, addiction (nicotinic and opioid), sexual and feeding behavior. MHb receives inputs from septal regions and projects exclusively to the interpeduncular nucleus (IPN). Distinct sub-regions of the septum project to different subnuclei of MHb: the bed nucleus of anterior commissure projects to dorsal MHb and the triangular septum projects to ventral MHb. Furthermore, the dorsal and ventral MHb project to the lateral and rostral/central IPN, respectively. Importantly, these projections have unique features of prominent co-release of different neurotransmitters and requirement of a peculiar type of calcium channel for release. In general, synaptic neurotransmission requires an activity-dependent influx of Ca2+ into the presynaptic terminal through voltage-gated calcium channels. The calcium channel family most commonly involved in neurotransmitter release comprises three members, P/Q-, N- and R-type with Cav2.1, Cav2.2 and Cav2.3 subunits, respectively. In contrast to most CNS synapses that mainly express Cav2.1 and/or Cav2.2, MHb terminals in the IPN exclusively express Cav2.3. In other parts of the brain, such as the hippocampus, Cav2.3 is mostly located to postsynaptic elements. This unusual presynaptic location of Cav2.3 in the MHb-IPN pathway implies unique mechanisms of glutamate release in this pathway. One potential example of such uniqueness is the facilitation of release by GABAB receptor (GBR) activation. Presynaptic GBRs usually inhibit the release of neurotransmitters by inhibiting presynaptic calcium channels. MHb shows the highest expression levels of GBR in the brain. GBRs comprise two subunits, GABAB1 (GB1) and GABAB2 (GB2), and are associated with auxiliary subunits, called potassium channel tetramerization domain containing proteins (KCTD) 8, 12, 12b and 16. Among these four subunits, KCTD12b is exclusively expressed in ventral MHb, and KCTD8 shows the strongest expression in the whole MHb among other brain regions, indicating that KCTD8 and KCTD12b may be involved in the unique mechanisms of neurotransmitter release mediated by Cav2.3 and regulated by GBRs in this pathway. \r\nIn the present study, we first verified that neurotransmission in both dorsal and ventral MHb-IPN pathways is mainly mediated by Cav2.3 using a selective blocker of R-type channels, SNX-482. We next found that baclofen, a GBR agonist, has facilitatory effects on release from ventral MHb terminal in rostral IPN, whereas it has inhibitory effects on release from dorsal MHb terminals in lateral IPN, indicating that KCTD12b expressed exclusively in ventral MHb may have a role in the facilitatory effects of GBR activation. In a heterologous expression system using HEK cells, we found that KCTD8 and KCTD12b but not KCTD12 directly bind with Cav2.3. Pre-embedding immunogold electron microscopy data show that Cav2.3 and KCTD12b are distributed most densely in presynaptic active zone in IPN with KCTD12b being present only in rostral/central but not lateral IPN, whereas GABAB, KCTD8 and KCTD12 are distributed most densely in perisynaptic sites with KCTD12 present more frequently in postsynaptic elements and only in rostral/central IPN. In freeze-fracture replica labelling, Cav2.3, KCTD8 and KCTD12b are co-localized with each other in the same active zone indicating that they may form complexes regulating vesicle release in rostral IPN. \r\nOn electrophysiological studies of wild type (WT) mice, we found that paired-pulse ratio in rostral IPN of KCTD12b knock-out (KO) mice is lower than those of WT and KCTD8 KO mice. Consistent with this finding, in mean variance analysis, release probability in rostral IPN of KCTD12b KO mice is higher than that of WT and KCTD8 KO mice. Although paired-pulse ratios are not different between WT and KCTD8 KO mice, the mean variance analysis revealed significantly lower release probability in rostral IPN of KCTD8 KO than WT mice. These results demonstrate bidirectional regulation of Cav2.3-mediated release by KCTD8 and KCTD12b without GBR activation in rostral IPN. Finally, we examined the baclofen effects in rostral IPN of KCTD8 and KCTD12b KO mice, and found the facilitation of release remained in both KO mice, indicating that the peculiar effects of the GBR activation in this pathway do not depend on the selective expression of these KCTD subunits in ventral MHb. However, we found that presynaptic potentiation of evoked EPSC amplitude by baclofen falls to baseline after washout faster in KCTD12b KO mice than WT, KCTD8 KO and KCTD8/12b double KO mice. This result indicates that KCTD12b is involved in sustained potentiation of vesicle release by GBR activation, whereas KCTD8 is involved in its termination in the absence of KCTD12b. Consistent with these functional findings, replica labelling revealed an increase in density of KCTD8, but not Cav2.3 or GBR at active zone in rostral IPN of KCTD12b KO mice compared with that of WT mice, suggesting that increased association of KCTD8 with Cav2.3 facilitates the release probability and termination of the GBR effect in the absence of KCTD12b.\r\nIn summary, our study provided new insights into the physiological roles of presynaptic Cav2.3, GBRs and their auxiliary subunits KCTDs at an evolutionary conserved neuronal circuit. Future studies will be required to identify the exact molecular mechanism underlying the GBR-mediated presynaptic potentiation on ventral MHb terminals. It remains to be determined whether the prominent presence of presynaptic KCTDs at active zone could exert similar neuromodulatory functions in different pathways of the brain.\r\n" acknowledged_ssus: - _id: EM-Fac alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Pradeep full_name: Bhandari, Pradeep id: 45EDD1BC-F248-11E8-B48F-1D18A9856A87 last_name: Bhandari orcid: 0000-0003-0863-4481 citation: ama: Bhandari P. Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway. 2020. doi:10.15479/AT:ISTA:7525 apa: Bhandari, P. (2020). Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7525 chicago: Bhandari, Pradeep. “Localization and Functional Role of Cav2.3 in the Medial Habenula to Interpeduncular Nucleus Pathway.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7525. ieee: P. Bhandari, “Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway,” Institute of Science and Technology Austria, 2020. ista: Bhandari P. 2020. Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway. Institute of Science and Technology Austria. mla: Bhandari, Pradeep. Localization and Functional Role of Cav2.3 in the Medial Habenula to Interpeduncular Nucleus Pathway. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7525. short: P. Bhandari, Localization and Functional Role of Cav2.3 in the Medial Habenula to Interpeduncular Nucleus Pathway, Institute of Science and Technology Austria, 2020. date_created: 2020-02-26T10:56:37Z date_published: 2020-02-28T00:00:00Z date_updated: 2023-09-07T13:20:03Z day: '28' ddc: - '570' degree_awarded: PhD department: - _id: RySh doi: 10.15479/AT:ISTA:7525 file: - access_level: open_access checksum: 4589234fdb12b4ad72273b311723a7b4 content_type: application/pdf creator: pbhandari date_created: 2020-02-28T08:37:53Z date_updated: 2021-03-01T23:30:04Z embargo: 2021-02-28 file_id: '7538' file_name: Pradeep Bhandari Thesis.pdf file_size: 9646346 relation: main_file title: Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway - access_level: closed checksum: aa79490553ca0a5c9b6fbcd152e93928 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: pbhandari date_created: 2020-02-28T08:47:14Z date_updated: 2021-03-01T23:30:04Z embargo_to: open_access file_id: '7539' file_name: Pradeep Bhandari Thesis.docx file_size: 35252164 relation: source_file title: Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway file_date_updated: 2021-03-01T23:30:04Z has_accepted_license: '1' keyword: - Cav2.3 - medial habenula (MHb) - interpeduncular nucleus (IPN) language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: '79' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 title: Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2020' ... --- _id: '8586' abstract: - lang: eng text: Cryo-electron microscopy (cryo-EM) of cellular specimens provides insights into biological processes and structures within a native context. However, a major challenge still lies in the efficient and reproducible preparation of adherent cells for subsequent cryo-EM analysis. This is due to the sensitivity of many cellular specimens to the varying seeding and culturing conditions required for EM experiments, the often limited amount of cellular material and also the fragility of EM grids and their substrate. Here, we present low-cost and reusable 3D printed grid holders, designed to improve specimen preparation when culturing challenging cellular samples directly on grids. The described grid holders increase cell culture reproducibility and throughput, and reduce the resources required for cell culturing. We show that grid holders can be integrated into various cryo-EM workflows, including micro-patterning approaches to control cell seeding on grids, and for generating samples for cryo-focused ion beam milling and cryo-electron tomography experiments. Their adaptable design allows for the generation of specialized grid holders customized to a large variety of applications. acknowledged_ssus: - _id: ScienComp - _id: LifeSc - _id: Bio - _id: EM-Fac acknowledgement: This work was supported by the Austrian Science Fund (FWF, P33367) to FKMS. BZ acknowledges support by the Niederösterreich Fond. This research was also supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the BioImaging Facility (BIF) and the Electron Microscopy Facility (EMF). We thank Georgi Dimchev (IST Austria) and Sonja Jacob (Vienna Biocenter Core Facilities) for testing our grid holders in different experimental setups and Daniel Gütl and the Kondrashov group (IST Austria) for granting us repeated access to their 3D printers. We also thank Jonna Alanko and the Sixt lab (IST Austria) for providing us HeLa cells, primary BL6 mouse tail fibroblasts, NIH 3T3 fibroblasts and human telomerase immortalised foreskin fibroblasts for our experiments. We are thankful to Ori Avinoam and William Wan for helpful comments on the manuscript and also thank Dorotea Fracchiolla (Art&Science) for illustrating the graphical abstract. article_number: '107633' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Florian full_name: Fäßler, Florian id: 404F5528-F248-11E8-B48F-1D18A9856A87 last_name: Fäßler orcid: 0000-0001-7149-769X - first_name: Bettina full_name: Zens, Bettina id: 45FD126C-F248-11E8-B48F-1D18A9856A87 last_name: Zens orcid: 0000-0002-9561-1239 - first_name: Robert full_name: Hauschild, Robert id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87 last_name: Hauschild orcid: 0000-0001-9843-3522 - first_name: Florian KM full_name: Schur, Florian KM id: 48AD8942-F248-11E8-B48F-1D18A9856A87 last_name: Schur orcid: 0000-0003-4790-8078 citation: ama: Fäßler F, Zens B, Hauschild R, Schur FK. 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. Journal of Structural Biology. 2020;212(3). doi:10.1016/j.jsb.2020.107633 apa: Fäßler, F., Zens, B., Hauschild, R., & Schur, F. K. (2020). 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. Journal of Structural Biology. Elsevier. https://doi.org/10.1016/j.jsb.2020.107633 chicago: Fäßler, Florian, Bettina Zens, Robert Hauschild, and Florian KM Schur. “3D Printed Cell Culture Grid Holders for Improved Cellular Specimen Preparation in Cryo-Electron Microscopy.” Journal of Structural Biology. Elsevier, 2020. https://doi.org/10.1016/j.jsb.2020.107633. ieee: F. Fäßler, B. Zens, R. Hauschild, and F. K. Schur, “3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy,” Journal of Structural Biology, vol. 212, no. 3. Elsevier, 2020. ista: Fäßler F, Zens B, Hauschild R, Schur FK. 2020. 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. Journal of Structural Biology. 212(3), 107633. mla: Fäßler, Florian, et al. “3D Printed Cell Culture Grid Holders for Improved Cellular Specimen Preparation in Cryo-Electron Microscopy.” Journal of Structural Biology, vol. 212, no. 3, 107633, Elsevier, 2020, doi:10.1016/j.jsb.2020.107633. short: F. Fäßler, B. Zens, R. Hauschild, F.K. Schur, Journal of Structural Biology 212 (2020). date_created: 2020-09-29T13:24:06Z date_published: 2020-12-01T00:00:00Z date_updated: 2024-03-27T23:30:05Z day: '01' ddc: - '570' department: - _id: FlSc doi: 10.1016/j.jsb.2020.107633 external_id: isi: - '000600997800008' file: - access_level: open_access checksum: c48cbf594e84fc2f91966ffaafc0918c content_type: application/pdf creator: dernst date_created: 2020-12-10T14:01:10Z date_updated: 2020-12-10T14:01:10Z file_id: '8937' file_name: 2020_JourStrucBiology_Faessler.pdf file_size: 7076870 relation: main_file success: 1 file_date_updated: 2020-12-10T14:01:10Z has_accepted_license: '1' intvolume: ' 212' isi: 1 issue: '3' keyword: - electron microscopy - cryo-EM - EM sample preparation - 3D printing - cell culture language: - iso: eng month: '12' oa: 1 oa_version: Published Version project: - _id: 9B954C5C-BA93-11EA-9121-9846C619BF3A grant_number: P33367 name: Structure and isoform diversity of the Arp2/3 complex - _id: 059B463C-7A3F-11EA-A408-12923DDC885E name: NÖ-Fonds Preis für die Jungforscherin des Jahres am IST Austria publication: Journal of Structural Biology publication_identifier: issn: - 1047-8477 publication_status: published publisher: Elsevier quality_controlled: '1' related_material: record: - id: '14592' relation: used_in_publication status: public - id: '12491' relation: dissertation_contains status: public scopus_import: '1' status: public title: 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 212 year: '2020' ... --- _id: '8657' abstract: - lang: eng text: "Synthesis of proteins – translation – is a fundamental process of life. Quantitative studies anchor translation into the context of bacterial physiology and reveal several mathematical relationships, called “growth laws,” which capture physiological feedbacks between protein synthesis and cell growth. Growth laws describe the dependency of the ribosome abundance as a function of growth rate, which can change depending on the growth conditions. Perturbations of translation reveal that bacteria employ a compensatory strategy in which the reduced translation capability results in increased expression of the translation machinery.\r\nPerturbations of translation are achieved in various ways; clinically interesting is the application of translation-targeting antibiotics – translation inhibitors. The antibiotic effects on bacterial physiology are often poorly understood. Bacterial responses to two or more simultaneously applied antibiotics are even more puzzling. The combined antibiotic effect determines the type of drug interaction, which ranges from synergy (the effect is stronger than expected) to antagonism (the effect is weaker) and suppression (one of the drugs loses its potency).\r\nIn the first part of this work, we systematically measure the pairwise interaction network for translation inhibitors that interfere with different steps in translation. We find that the interactions are surprisingly diverse and tend to be more antagonistic. To explore the underlying mechanisms, we begin with a minimal biophysical model of combined antibiotic action. We base this model on the kinetics of antibiotic uptake and binding together with the physiological response described by the growth laws. The biophysical model explains some drug interactions, but not all; it specifically fails to predict suppression.\r\nIn the second part of this work, we hypothesize that elusive suppressive drug interactions result from the interplay between ribosomes halted in different stages of translation. To elucidate this putative mechanism of drug interactions between translation inhibitors, we generate translation bottlenecks genetically using in- ducible control of translation factors that regulate well-defined translation cycle steps. These perturbations accurately mimic antibiotic action and drug interactions, supporting that the interplay of different translation bottlenecks partially causes these interactions.\r\nWe extend this approach by varying two translation bottlenecks simultaneously. This approach reveals the suppression of translocation inhibition by inhibited translation. We rationalize this effect by modeling dense traffic of ribosomes that move on transcripts in a translation factor-mediated manner. This model predicts a dissolution of traffic jams caused by inhibited translocation when the density of ribosome traffic is reduced by lowered initiation. We base this model on the growth laws and quantitative relationships between different translation and growth parameters.\r\nIn the final part of this work, we describe a set of tools aimed at quantification of physiological and translation parameters. We further develop a simple model that directly connects the abundance of a translation factor with the growth rate, which allows us to extract physiological parameters describing initiation. We demonstrate the development of tools for measuring translation rate.\r\nThis thesis showcases how a combination of high-throughput growth rate mea- surements, genetics, and modeling can reveal mechanisms of drug interactions. Furthermore, by a gradual transition from combinations of antibiotics to precise genetic interventions, we demonstrated the equivalency between genetic and chemi- cal perturbations of translation. These findings tile the path for quantitative studies of antibiotic combinations and illustrate future approaches towards the quantitative description of translation." acknowledged_ssus: - _id: LifeSc - _id: M-Shop acknowledgement: I thank Life Science Facilities for their continuous support with providing top-notch laboratory materials, keeping the devices humming, and coordinating the repairs and building of custom-designed laboratory equipment with the MIBA Machine shop. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Bor full_name: Kavcic, Bor id: 350F91D2-F248-11E8-B48F-1D18A9856A87 last_name: Kavcic orcid: 0000-0001-6041-254X citation: ama: 'Kavcic B. Perturbations of protein synthesis: from antibiotics to genetics and physiology. 2020. doi:10.15479/AT:ISTA:8657' apa: 'Kavcic, B. (2020). Perturbations of protein synthesis: from antibiotics to genetics and physiology. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8657' chicago: 'Kavcic, Bor. “Perturbations of Protein Synthesis: From Antibiotics to Genetics and Physiology.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8657.' ieee: 'B. Kavcic, “Perturbations of protein synthesis: from antibiotics to genetics and physiology,” Institute of Science and Technology Austria, 2020.' ista: 'Kavcic B. 2020. Perturbations of protein synthesis: from antibiotics to genetics and physiology. Institute of Science and Technology Austria.' mla: 'Kavcic, Bor. Perturbations of Protein Synthesis: From Antibiotics to Genetics and Physiology. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8657.' short: 'B. Kavcic, Perturbations of Protein Synthesis: From Antibiotics to Genetics and Physiology, Institute of Science and Technology Austria, 2020.' date_created: 2020-10-13T16:46:14Z date_published: 2020-10-14T00:00:00Z date_updated: 2023-09-07T13:20:48Z day: '14' ddc: - '571' - '530' - '570' degree_awarded: PhD department: - _id: GaTk doi: 10.15479/AT:ISTA:8657 file: - access_level: open_access checksum: d708ecd62b6fcc3bc1feb483b8dbe9eb content_type: application/pdf creator: bkavcic date_created: 2020-10-15T06:41:20Z date_updated: 2021-10-07T22:30:03Z embargo: 2021-10-06 file_id: '8663' file_name: kavcicB_thesis202009.pdf file_size: 52636162 relation: main_file - access_level: closed checksum: bb35f2352a04db19164da609f00501f3 content_type: application/zip creator: bkavcic date_created: 2020-10-15T06:41:53Z date_updated: 2021-10-07T22:30:03Z embargo_to: open_access file_id: '8664' file_name: 2020b.zip file_size: 321681247 relation: source_file file_date_updated: 2021-10-07T22:30:03Z has_accepted_license: '1' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: '271' publication_identifier: isbn: - 978-3-99078-011-4 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '7673' relation: part_of_dissertation status: public - id: '8250' relation: part_of_dissertation status: public status: public supervisor: - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 - first_name: Mark Tobias full_name: Bollenbach, Mark Tobias id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87 last_name: Bollenbach orcid: 0000-0003-4398-476X title: 'Perturbations of protein synthesis: from antibiotics to genetics and physiology' type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2020' ...