[{"day":"01","file":[{"content_type":"application/zip","relation":"main_file","access_level":"open_access","success":1,"file_id":"14593","checksum":"0108616e2a59e51879ea51299a29b091","file_size":49297,"date_updated":"2023-11-22T14:58:44Z","creator":"fschur","file_name":"3Dprint-files_download_v2.zip","date_created":"2023-11-22T14:58:44Z"},{"file_name":"readme.txt","date_created":"2023-12-01T10:39:59Z","creator":"cchlebak","file_size":641,"date_updated":"2023-12-01T10:39:59Z","success":1,"checksum":"4c66ddedee4d01c1c4a7978208350cfc","file_id":"14637","relation":"main_file","access_level":"open_access","content_type":"text/plain"}],"has_accepted_license":"1","year":"2020","doi":"10.15479/AT:ISTA:14592","date_published":"2020-12-01T00:00:00Z","related_material":{"record":[{"relation":"research_data","status":"public","id":"8586"}]},"date_created":"2023-11-22T15:00:57Z","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","contributor":[{"last_name":"Fäßler","orcid":"0000-0001-7149-769X","contributor_type":"researcher","id":"404F5528-F248-11E8-B48F-1D18A9856A87","first_name":"Florian"},{"contributor_type":"researcher","id":"45FD126C-F248-11E8-B48F-1D18A9856A87","first_name":"Bettina","last_name":"Zens"},{"last_name":"Hauschild","first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM","contributor_type":"researcher","last_name":"Schur","orcid":"0000-0003-4790-8078"}],"oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"month":"12","publisher":"Institute of Science and Technology Austria","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"citation":{"ista":"Schur FK. 2020. STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy, Institute of Science and Technology Austria, 10.15479/AT:ISTA:14592.","chicago":"Schur, Florian KM. “STL-Files for 3D-Printed Grid Holders Described in Fäßler F, Zens B, et Al.; 3D Printed Cell Culture Grid Holders for Improved Cellular Specimen Preparation in Cryo-Electron Microscopy.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:14592.","ieee":"F. K. Schur, “STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy.” Institute of Science and Technology Austria, 2020.","short":"F.K. Schur, (2020).","ama":"Schur FK. STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. 2020. doi:10.15479/AT:ISTA:14592","apa":"Schur, F. K. (2020). STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14592","mla":"Schur, Florian KM. STL-Files for 3D-Printed Grid Holders Described in Fäßler F, Zens B, et Al.; 3D Printed Cell Culture Grid Holders for Improved Cellular Specimen Preparation in Cryo-Electron Microscopy. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:14592."},"date_updated":"2024-02-21T12:44:48Z","title":"STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy","file_date_updated":"2023-12-01T10:39:59Z","department":[{"_id":"FlSc"}],"author":[{"orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM"}],"article_processing_charge":"No","_id":"14592","status":"public","project":[{"grant_number":"P33367","name":"Structure and isoform diversity of the Arp2/3 complex","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A"}],"type":"research_data","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"}},{"ddc":["004"],"date_updated":"2024-02-22T13:16:06Z","file_date_updated":"2020-10-08T08:16:48Z","department":[{"_id":"DaAl"}],"_id":"7213","status":"public","conference":{"start_date":"2019-12-10","end_date":"2019-12-12","location":"Lisbon, Portugal","name":"COMPLEX: International Conference on Complex Networks and their Applications"},"type":"conference","language":[{"iso":"eng"}],"file":[{"date_updated":"2020-10-08T08:16:48Z","file_size":310598,"creator":"bchatter","date_created":"2020-10-08T08:16:48Z","file_name":"main.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"8951f094c8c7dae9ff8db885199bc296","file_id":"8625","success":1}],"publication_status":"published","publication_identifier":{"issn":["1860949X"],"eissn":["18609503"],"isbn":["9783030366865"]},"ec_funded":1,"volume":881,"oa_version":"Submitted Version","abstract":[{"text":"Persistent homology is a powerful tool in Topological Data Analysis (TDA) to capture the topological properties of data succinctly at different spatial resolutions. For graphical data, the shape, and structure of the neighborhood of individual data items (nodes) are an essential means of characterizing their properties. We propose the use of persistent homology methods to capture structural and topological properties of graphs and use it to address the problem of link prediction. We achieve encouraging results on nine different real-world datasets that attest to the potential of persistent homology-based methods for network analysis.","lang":"eng"}],"intvolume":" 881","month":"01","alternative_title":["SCI"],"scopus_import":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Bhatia S, Chatterjee B, Nathani D, Kaul M. 2020. A persistent homology perspective to the link prediction problem. Complex Networks and their applications VIII. COMPLEX: International Conference on Complex Networks and their Applications, SCI, vol. 881, 27–39.","chicago":"Bhatia, Sumit, Bapi Chatterjee, Deepak Nathani, and Manohar Kaul. “A Persistent Homology Perspective to the Link Prediction Problem.” In Complex Networks and Their Applications VIII, 881:27–39. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-36687-2_3.","short":"S. Bhatia, B. Chatterjee, D. Nathani, M. Kaul, in:, Complex Networks and Their Applications VIII, Springer Nature, 2020, pp. 27–39.","ieee":"S. Bhatia, B. Chatterjee, D. Nathani, and M. Kaul, “A persistent homology perspective to the link prediction problem,” in Complex Networks and their applications VIII, Lisbon, Portugal, 2020, vol. 881, pp. 27–39.","apa":"Bhatia, S., Chatterjee, B., Nathani, D., & Kaul, M. (2020). A persistent homology perspective to the link prediction problem. In Complex Networks and their applications VIII (Vol. 881, pp. 27–39). Lisbon, Portugal: Springer Nature. https://doi.org/10.1007/978-3-030-36687-2_3","ama":"Bhatia S, Chatterjee B, Nathani D, Kaul M. A persistent homology perspective to the link prediction problem. In: Complex Networks and Their Applications VIII. Vol 881. Springer Nature; 2020:27-39. doi:10.1007/978-3-030-36687-2_3","mla":"Bhatia, Sumit, et al. “A Persistent Homology Perspective to the Link Prediction Problem.” Complex Networks and Their Applications VIII, vol. 881, Springer Nature, 2020, pp. 27–39, doi:10.1007/978-3-030-36687-2_3."},"title":"A persistent homology perspective to the link prediction problem","article_processing_charge":"No","external_id":{"isi":["000843927300003"]},"author":[{"full_name":"Bhatia, Sumit","last_name":"Bhatia","first_name":"Sumit"},{"id":"3C41A08A-F248-11E8-B48F-1D18A9856A87","first_name":"Bapi","full_name":"Chatterjee, Bapi","orcid":"0000-0002-2742-4028","last_name":"Chatterjee"},{"first_name":"Deepak","full_name":"Nathani, Deepak","last_name":"Nathani"},{"full_name":"Kaul, Manohar","last_name":"Kaul","first_name":"Manohar"}],"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"publication":"Complex Networks and their applications VIII","day":"01","year":"2020","has_accepted_license":"1","isi":1,"date_created":"2019-12-29T23:00:45Z","date_published":"2020-01-01T00:00:00Z","doi":"10.1007/978-3-030-36687-2_3","page":"27-39","oa":1,"publisher":"Springer Nature","quality_controlled":"1"},{"department":[{"_id":"ElKo"}],"date_updated":"2024-02-22T13:10:45Z","status":"public","conference":{"location":"Virtual, United States","end_date":"2020-11-13","start_date":"2020-11-09","name":"CCS: Computer and Communications Security"},"type":"conference","_id":"10556","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"isbn":["978-1-4503-7089-9"]},"month":"10","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2019/1015"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"lang":"eng","text":"In this paper, we present the first Asynchronous Distributed Key Generation (ADKG) algorithm which is also the first distributed key generation algorithm that can generate cryptographic keys with a dual (f,2f+1)-threshold (where f is the number of faulty parties). As a result, using our ADKG we remove the trusted setup assumption that the most scalable consensus algorithms make. In order to create a DKG with a dual (f,2f+1)- threshold we first answer in the affirmative the open question posed by Cachin et al. [7] on how to create an Asynchronous Verifiable Secret Sharing (AVSS) protocol with a reconstruction threshold of f+1Proceedings of the 2020 ACM SIGSAC Conference on Computer and Communications Security, 1751–1767. Association for Computing Machinery, 2020. https://doi.org/10.1145/3372297.3423364.","ama":"Kokoris Kogias E, Malkhi D, Spiegelman A. Asynchronous distributed key generation for computationally-secure randomness, consensus, and threshold signatures. In: Proceedings of the 2020 ACM SIGSAC Conference on Computer and Communications Security. Association for Computing Machinery; 2020:1751–1767. doi:10.1145/3372297.3423364","apa":"Kokoris Kogias, E., Malkhi, D., & Spiegelman, A. (2020). Asynchronous distributed key generation for computationally-secure randomness, consensus, and threshold signatures. In Proceedings of the 2020 ACM SIGSAC Conference on Computer and Communications Security (pp. 1751–1767). Virtual, United States: Association for Computing Machinery. https://doi.org/10.1145/3372297.3423364","ieee":"E. Kokoris Kogias, D. Malkhi, and A. Spiegelman, “Asynchronous distributed key generation for computationally-secure randomness, consensus, and threshold signatures,” in Proceedings of the 2020 ACM SIGSAC Conference on Computer and Communications Security, Virtual, United States, 2020, pp. 1751–1767.","short":"E. Kokoris Kogias, D. Malkhi, A. Spiegelman, in:, Proceedings of the 2020 ACM SIGSAC Conference on Computer and Communications Security, Association for Computing Machinery, 2020, pp. 1751–1767.","mla":"Kokoris Kogias, Eleftherios, et al. “Asynchronous Distributed Key Generation for Computationally-Secure Randomness, Consensus, and Threshold Signatures.” Proceedings of the 2020 ACM SIGSAC Conference on Computer and Communications Security, Association for Computing Machinery, 2020, pp. 1751–1767, doi:10.1145/3372297.3423364."},"date_created":"2021-12-16T13:23:27Z","date_published":"2020-10-30T00:00:00Z","doi":"10.1145/3372297.3423364","page":"1751–1767","publication":"Proceedings of the 2020 ACM SIGSAC Conference on Computer and Communications Security","day":"30","year":"2020","isi":1,"oa":1,"publisher":"Association for Computing Machinery","quality_controlled":"1","acknowledgement":"We would like to thank Ittai Abraham for the discussions and guidance during the initial conception of the project, especially for HAVSS. Furthermore, we would like to thank the anonymous reviewers for pointing out the relevance of this work to MPC protocols."},{"_id":"9202","status":"public","conference":{"start_date":"2020-12-01","end_date":"2020-12-04","location":"Houston, TX, USA ","name":"RTTS: Real-Time Systems Symposium"},"type":"conference","ddc":["000"],"date_updated":"2024-02-22T13:25:19Z","file_date_updated":"2021-02-26T16:38:14Z","department":[{"_id":"ToHe"}],"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"We propose a novel hybridization method for stability analysis that over-approximates nonlinear dynamical systems by switched systems with linear inclusion dynamics. We observe that existing hybridization techniques for safety analysis that over-approximate nonlinear dynamical systems by switched affine inclusion dynamics and provide fixed approximation error, do not suffice for stability analysis. Hence, we propose a hybridization method that provides a state-dependent error which converges to zero as the state tends to the equilibrium point. The crux of our hybridization computation is an elegant recursive algorithm that uses partial derivatives of a given function to obtain upper and lower bound matrices for the over-approximating linear inclusion. We illustrate our method on some examples to demonstrate the application of the theory for stability analysis. In particular, our method is able to establish stability of a nonlinear system which does not admit a polynomial Lyapunov function."}],"month":"12","language":[{"iso":"eng"}],"file":[{"checksum":"8f97f229316c3b3a6f0cf99297aa0941","file_id":"9203","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"main.pdf","date_created":"2021-02-26T16:38:14Z","file_size":1125794,"date_updated":"2021-02-26T16:38:14Z","creator":"mgarcias"}],"publication_status":"published","publication_identifier":{"eissn":["2576-3172"],"eisbn":["9781728183244"]},"project":[{"grant_number":"Z211","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Garcia Soto, Miriam, and Pavithra Prabhakar. “Hybridization for Stability Verification of Nonlinear Switched Systems.” 2020 IEEE Real-Time Systems Symposium, IEEE, 2020, pp. 244–56, doi:10.1109/RTSS49844.2020.00031.","short":"M. Garcia Soto, P. Prabhakar, in:, 2020 IEEE Real-Time Systems Symposium, IEEE, 2020, pp. 244–256.","ieee":"M. Garcia Soto and P. Prabhakar, “Hybridization for stability verification of nonlinear switched systems,” in 2020 IEEE Real-Time Systems Symposium, Houston, TX, USA , 2020, pp. 244–256.","apa":"Garcia Soto, M., & Prabhakar, P. (2020). Hybridization for stability verification of nonlinear switched systems. In 2020 IEEE Real-Time Systems Symposium (pp. 244–256). Houston, TX, USA : IEEE. https://doi.org/10.1109/RTSS49844.2020.00031","ama":"Garcia Soto M, Prabhakar P. Hybridization for stability verification of nonlinear switched systems. In: 2020 IEEE Real-Time Systems Symposium. IEEE; 2020:244-256. doi:10.1109/RTSS49844.2020.00031","chicago":"Garcia Soto, Miriam, and Pavithra Prabhakar. “Hybridization for Stability Verification of Nonlinear Switched Systems.” In 2020 IEEE Real-Time Systems Symposium, 244–56. IEEE, 2020. https://doi.org/10.1109/RTSS49844.2020.00031.","ista":"Garcia Soto M, Prabhakar P. 2020. Hybridization for stability verification of nonlinear switched systems. 2020 IEEE Real-Time Systems Symposium. RTTS: Real-Time Systems Symposium, 244–256."},"title":"Hybridization for stability verification of nonlinear switched systems","article_processing_charge":"No","external_id":{"isi":["000680435100021"]},"author":[{"full_name":"Garcia Soto, Miriam","orcid":"0000-0003-2936-5719","last_name":"Garcia Soto","id":"4B3207F6-F248-11E8-B48F-1D18A9856A87","first_name":"Miriam"},{"last_name":"Prabhakar","full_name":"Prabhakar, Pavithra","first_name":"Pavithra"}],"acknowledgement":"Miriam Garc´ıa Soto was partially supported by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award). Pavithra Prabhakar was partially supported by NSF CAREER Award No. 1552668, NSF Award No. 2008957 and ONR YIP Award No. N000141712577.","oa":1,"publisher":"IEEE","quality_controlled":"1","publication":"2020 IEEE Real-Time Systems Symposium","day":"01","year":"2020","isi":1,"has_accepted_license":"1","date_created":"2021-02-26T16:38:24Z","doi":"10.1109/RTSS49844.2020.00031","date_published":"2020-12-01T00:00:00Z","page":"244-256"},{"year":"2020","isi":1,"publication":"Communications in Mathematical Physics","day":"01","page":"1311-1395","date_created":"2019-09-24T17:30:59Z","doi":"10.1007/s00220-019-03555-9","date_published":"2020-06-01T00:00:00Z","acknowledgement":"We would like to thank P. T. Nam and R. Seiringer for several useful discussions and\r\nfor suggesting us to use the localization techniques from [9]. C. Boccato has received funding from the\r\nEuropean Research Council (ERC) under the programme Horizon 2020 (Grant Agreement 694227). B. Schlein gratefully acknowledges support from the NCCR SwissMAP and from the Swiss National Foundation of Science (Grant No. 200020_1726230) through the SNF Grant “Dynamical and energetic properties of Bose–Einstein condensates”.","oa":1,"publisher":"Springer","quality_controlled":"1","citation":{"short":"C. Boccato, C. Brennecke, S. Cenatiempo, B. Schlein, Communications in Mathematical Physics 376 (2020) 1311–1395.","ieee":"C. Boccato, C. Brennecke, S. Cenatiempo, and B. Schlein, “Optimal rate for Bose-Einstein condensation in the Gross-Pitaevskii regime,” Communications in Mathematical Physics, vol. 376. Springer, pp. 1311–1395, 2020.","apa":"Boccato, C., Brennecke, C., Cenatiempo, S., & Schlein, B. (2020). Optimal rate for Bose-Einstein condensation in the Gross-Pitaevskii regime. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-019-03555-9","ama":"Boccato C, Brennecke C, Cenatiempo S, Schlein B. Optimal rate for Bose-Einstein condensation in the Gross-Pitaevskii regime. Communications in Mathematical Physics. 2020;376:1311-1395. doi:10.1007/s00220-019-03555-9","mla":"Boccato, Chiara, et al. “Optimal Rate for Bose-Einstein Condensation in the Gross-Pitaevskii Regime.” Communications in Mathematical Physics, vol. 376, Springer, 2020, pp. 1311–95, doi:10.1007/s00220-019-03555-9.","ista":"Boccato C, Brennecke C, Cenatiempo S, Schlein B. 2020. Optimal rate for Bose-Einstein condensation in the Gross-Pitaevskii regime. Communications in Mathematical Physics. 376, 1311–1395.","chicago":"Boccato, Chiara, Christian Brennecke, Serena Cenatiempo, and Benjamin Schlein. “Optimal Rate for Bose-Einstein Condensation in the Gross-Pitaevskii Regime.” Communications in Mathematical Physics. Springer, 2020. https://doi.org/10.1007/s00220-019-03555-9."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","external_id":{"isi":["000536053300012"],"arxiv":["1812.03086"]},"article_processing_charge":"No","author":[{"first_name":"Chiara","id":"342E7E22-F248-11E8-B48F-1D18A9856A87","full_name":"Boccato, Chiara","last_name":"Boccato"},{"first_name":"Christian","full_name":"Brennecke, Christian","last_name":"Brennecke"},{"first_name":"Serena","full_name":"Cenatiempo, Serena","last_name":"Cenatiempo"},{"first_name":"Benjamin","full_name":"Schlein, Benjamin","last_name":"Schlein"}],"title":"Optimal rate for Bose-Einstein condensation in the Gross-Pitaevskii regime","project":[{"call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems","grant_number":"694227"}],"publication_status":"published","publication_identifier":{"eissn":["1432-0916"],"issn":["0010-3616"]},"language":[{"iso":"eng"}],"ec_funded":1,"volume":376,"abstract":[{"text":"We consider systems of bosons trapped in a box, in the Gross–Pitaevskii regime. We show that low-energy states exhibit complete Bose–Einstein condensation with an optimal bound on the number of orthogonal excitations. This extends recent results obtained in Boccato et al. (Commun Math Phys 359(3):975–1026, 2018), removing the assumption of small interaction potential.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1812.03086","open_access":"1"}],"scopus_import":"1","intvolume":" 376","month":"06","date_updated":"2024-02-22T13:33:02Z","department":[{"_id":"RoSe"}],"_id":"6906","type":"journal_article","article_type":"original","status":"public"},{"page":"319-341","date_created":"2020-01-30T09:24:06Z","doi":"10.1016/bs.ctdb.2019.07.001","date_published":"2020-01-01T00:00:00Z","year":"2020","isi":1,"publication":"Gastrulation: From Embryonic Pattern to Form","day":"01","publisher":"Elsevier","quality_controlled":"1","article_processing_charge":"No","external_id":{"isi":["000611830600012"]},"author":[{"full_name":"Bruce, Ashley E.E.","last_name":"Bruce","first_name":"Ashley E.E."},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg"}],"editor":[{"full_name":"Solnica-Krezel, Lilianna ","last_name":"Solnica-Krezel","first_name":"Lilianna "}],"title":"Mechanisms of zebrafish epiboly: A current view","citation":{"chicago":"Bruce, Ashley E.E., and Carl-Philipp J Heisenberg. “Mechanisms of Zebrafish Epiboly: A Current View.” In Gastrulation: From Embryonic Pattern to Form, edited by Lilianna Solnica-Krezel, 136:319–41. Current Topics in Developmental Biology. Elsevier, 2020. https://doi.org/10.1016/bs.ctdb.2019.07.001.","ista":"Bruce AEE, Heisenberg C-PJ. 2020.Mechanisms of zebrafish epiboly: A current view. In: Gastrulation: From Embryonic Pattern to Form. vol. 136, 319–341.","mla":"Bruce, Ashley E. E., and Carl-Philipp J. Heisenberg. “Mechanisms of Zebrafish Epiboly: A Current View.” Gastrulation: From Embryonic Pattern to Form, edited by Lilianna Solnica-Krezel, vol. 136, Elsevier, 2020, pp. 319–41, doi:10.1016/bs.ctdb.2019.07.001.","apa":"Bruce, A. E. E., & Heisenberg, C.-P. J. (2020). Mechanisms of zebrafish epiboly: A current view. In L. Solnica-Krezel (Ed.), Gastrulation: From Embryonic Pattern to Form (Vol. 136, pp. 319–341). Elsevier. https://doi.org/10.1016/bs.ctdb.2019.07.001","ama":"Bruce AEE, Heisenberg C-PJ. Mechanisms of zebrafish epiboly: A current view. In: Solnica-Krezel L, ed. Gastrulation: From Embryonic Pattern to Form. Vol 136. Current Topics in Developmental Biology. Elsevier; 2020:319-341. doi:10.1016/bs.ctdb.2019.07.001","short":"A.E.E. Bruce, C.-P.J. Heisenberg, in:, L. Solnica-Krezel (Ed.), Gastrulation: From Embryonic Pattern to Form, Elsevier, 2020, pp. 319–341.","ieee":"A. E. E. Bruce and C.-P. J. Heisenberg, “Mechanisms of zebrafish epiboly: A current view,” in Gastrulation: From Embryonic Pattern to Form, vol. 136, L. Solnica-Krezel, Ed. Elsevier, 2020, pp. 319–341."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","volume":136,"publication_status":"published","publication_identifier":{"isbn":["9780128127988"],"issn":["0070-2153"]},"language":[{"iso":"eng"}],"scopus_import":"1","intvolume":" 136","month":"01","abstract":[{"text":"Epiboly is a conserved gastrulation movement describing the thinning and spreading of a sheet or multi-layer of cells. The zebrafish embryo has emerged as a vital model system to address the cellular and molecular mechanisms that drive epiboly. In the zebrafish embryo, the blastoderm, consisting of a simple squamous epithelium (the enveloping layer) and an underlying mass of deep cells, as well as a yolk nuclear syncytium (the yolk syncytial layer) undergo epiboly to internalize the yolk cell during gastrulation. The major events during zebrafish epiboly are: expansion of the enveloping layer and the internal yolk syncytial layer, reduction and removal of the yolk membrane ahead of the advancing blastoderm margin and deep cell rearrangements between the enveloping layer and yolk syncytial layer to thin the blastoderm. Here, work addressing the cellular and molecular mechanisms as well as the sources of the mechanical forces that underlie these events is reviewed. The contribution of recent findings to the current model of epiboly as well as open questions and future prospects are also discussed.","lang":"eng"}],"oa_version":"None","department":[{"_id":"CaHe"}],"date_updated":"2024-02-22T13:23:09Z","type":"book_chapter","status":"public","series_title":"Current Topics in Developmental Biology","_id":"7410"},{"department":[{"_id":"ChLa"}],"file_date_updated":"2020-07-14T12:47:45Z","date_updated":"2024-02-22T14:57:30Z","ddc":["004"],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"6944","related_material":{"record":[{"status":"public","id":"6482","relation":"earlier_version"}],"link":[{"relation":"erratum","url":"https://doi.org/10.1007/s11263-019-01262-5"}]},"issue":"4","volume":128,"ec_funded":1,"license":"https://creativecommons.org/licenses/by/4.0/","publication_identifier":{"eissn":["1573-1405"],"issn":["0920-5691"]},"publication_status":"published","file":[{"file_size":1715072,"date_updated":"2020-07-14T12:47:45Z","creator":"dernst","file_name":"2019_IJCV_Sun.pdf","date_created":"2019-11-26T10:30:02Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"7110","checksum":"155e63edf664dcacb3bdc1c2223e606f"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"04","intvolume":" 128","abstract":[{"text":"We study the problem of automatically detecting if a given multi-class classifier operates outside of its specifications (out-of-specs), i.e. on input data from a different distribution than what it was trained for. This is an important problem to solve on the road towards creating reliable computer vision systems for real-world applications, because the quality of a classifier’s predictions cannot be guaranteed if it operates out-of-specs. Previously proposed methods for out-of-specs detection make decisions on the level of single inputs. This, however, is insufficient to achieve low false positive rate and high false negative rates at the same time. In this work, we describe a new procedure named KS(conf), based on statistical reasoning. Its main component is a classical Kolmogorov–Smirnov test that is applied to the set of predicted confidence values for batches of samples. Working with batches instead of single samples allows increasing the true positive rate without negatively affecting the false positive rate, thereby overcoming a crucial limitation of single sample tests. We show by extensive experiments using a variety of convolutional network architectures and datasets that KS(conf) reliably detects out-of-specs situations even under conditions where other tests fail. It furthermore has a number of properties that make it an excellent candidate for practical deployment: it is easy to implement, adds almost no overhead to the system, works with any classifier that outputs confidence scores, and requires no a priori knowledge about how the data distribution could change.","lang":"eng"}],"oa_version":"Published Version","author":[{"first_name":"Rémy","last_name":"Sun","full_name":"Sun, Rémy"},{"orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","last_name":"Lampert","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["000494406800001"]},"article_processing_charge":"Yes (via OA deal)","title":"KS(conf): A light-weight test if a multiclass classifier operates outside of its specifications","citation":{"mla":"Sun, Rémy, and Christoph Lampert. “KS(Conf): A Light-Weight Test If a Multiclass Classifier Operates Outside of Its Specifications.” International Journal of Computer Vision, vol. 128, no. 4, Springer Nature, 2020, pp. 970–95, doi:10.1007/s11263-019-01232-x.","apa":"Sun, R., & Lampert, C. (2020). KS(conf): A light-weight test if a multiclass classifier operates outside of its specifications. International Journal of Computer Vision. Springer Nature. https://doi.org/10.1007/s11263-019-01232-x","ama":"Sun R, Lampert C. KS(conf): A light-weight test if a multiclass classifier operates outside of its specifications. International Journal of Computer Vision. 2020;128(4):970-995. doi:10.1007/s11263-019-01232-x","ieee":"R. Sun and C. Lampert, “KS(conf): A light-weight test if a multiclass classifier operates outside of its specifications,” International Journal of Computer Vision, vol. 128, no. 4. Springer Nature, pp. 970–995, 2020.","short":"R. Sun, C. Lampert, International Journal of Computer Vision 128 (2020) 970–995.","chicago":"Sun, Rémy, and Christoph Lampert. “KS(Conf): A Light-Weight Test If a Multiclass Classifier Operates Outside of Its Specifications.” International Journal of Computer Vision. Springer Nature, 2020. https://doi.org/10.1007/s11263-019-01232-x.","ista":"Sun R, Lampert C. 2020. KS(conf): A light-weight test if a multiclass classifier operates outside of its specifications. International Journal of Computer Vision. 128(4), 970–995."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","project":[{"name":"Lifelong Learning of Visual Scene Understanding","grant_number":"308036","_id":"2532554C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"page":"970-995","date_published":"2020-04-01T00:00:00Z","doi":"10.1007/s11263-019-01232-x","date_created":"2019-10-14T09:14:28Z","has_accepted_license":"1","isi":1,"year":"2020","day":"01","publication":"International Journal of Computer Vision","quality_controlled":"1","publisher":"Springer Nature","oa":1},{"article_processing_charge":"No","external_id":{"arxiv":["1902.04744"]},"author":[{"last_name":"Wang","full_name":"Wang, Peixin","first_name":"Peixin"},{"first_name":"Hongfei","last_name":"Fu","full_name":"Fu, Hongfei"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"last_name":"Deng","full_name":"Deng, Yuxin","first_name":"Yuxin"},{"first_name":"Ming","full_name":"Xu, Ming","last_name":"Xu"}],"title":"Proving expected sensitivity of probabilistic programs with randomized variable-dependent termination time","citation":{"chicago":"Wang, Peixin, Hongfei Fu, Krishnendu Chatterjee, Yuxin Deng, and Ming Xu. “Proving Expected Sensitivity of Probabilistic Programs with Randomized Variable-Dependent Termination Time.” In Proceedings of the ACM on Programming Languages, Vol. 4. ACM, 2020. https://doi.org/10.1145/3371093.","ista":"Wang P, Fu H, Chatterjee K, Deng Y, Xu M. 2020. Proving expected sensitivity of probabilistic programs with randomized variable-dependent termination time. Proceedings of the ACM on Programming Languages. vol. 4, 25.","mla":"Wang, Peixin, et al. “Proving Expected Sensitivity of Probabilistic Programs with Randomized Variable-Dependent Termination Time.” Proceedings of the ACM on Programming Languages, vol. 4, no. POPL, 25, ACM, 2020, doi:10.1145/3371093.","ama":"Wang P, Fu H, Chatterjee K, Deng Y, Xu M. Proving expected sensitivity of probabilistic programs with randomized variable-dependent termination time. In: Proceedings of the ACM on Programming Languages. Vol 4. ACM; 2020. doi:10.1145/3371093","apa":"Wang, P., Fu, H., Chatterjee, K., Deng, Y., & Xu, M. (2020). Proving expected sensitivity of probabilistic programs with randomized variable-dependent termination time. In Proceedings of the ACM on Programming Languages (Vol. 4). ACM. https://doi.org/10.1145/3371093","ieee":"P. Wang, H. Fu, K. Chatterjee, Y. Deng, and M. Xu, “Proving expected sensitivity of probabilistic programs with randomized variable-dependent termination time,” in Proceedings of the ACM on Programming Languages, 2020, vol. 4, no. POPL.","short":"P. Wang, H. Fu, K. Chatterjee, Y. Deng, M. Xu, in:, Proceedings of the ACM on Programming Languages, ACM, 2020."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","project":[{"name":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"article_number":"25","date_created":"2020-08-30T22:01:12Z","doi":"10.1145/3371093","date_published":"2020-01-01T00:00:00Z","year":"2020","has_accepted_license":"1","publication":"Proceedings of the ACM on Programming Languages","day":"01","oa":1,"publisher":"ACM","quality_controlled":"1","acknowledgement":"We thank anonymous reviewers for helpful comments, especially for pointing to us a scenario of piecewise-linear approximation (Remark5). The research was partially supported by the National Natural Science Foundation of China (NSFC) under Grant No. 61802254, 61672229, 61832015,61772336,11871221 and Austrian Science Fund (FWF) NFN under Grant No. S11407-N23 (RiSE/SHiNE). We thank Prof. Yuxi Fu, director of the BASICS Lab at Shanghai Jiao Tong University, for his support.","file_date_updated":"2020-09-01T11:12:58Z","department":[{"_id":"KrCh"}],"date_updated":"2024-02-22T15:16:45Z","ddc":["004"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"conference","status":"public","_id":"8324","related_material":{"link":[{"relation":"software","url":"https://doi.org/10.5281/zenodo.3533633"}]},"issue":"POPL","volume":4,"publication_status":"published","publication_identifier":{"eissn":["2475-1421"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2020-09-01T11:12:58Z","file_name":"2019_ACM_POPL_Wang.pdf","creator":"cziletti","date_updated":"2020-09-01T11:12:58Z","file_size":564151,"file_id":"8328","checksum":"c6193d109ff4ecb17e7a6513d8eb34c0","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"scopus_import":"1","intvolume":" 4","month":"01","abstract":[{"lang":"eng","text":"The notion of program sensitivity (aka Lipschitz continuity) specifies that changes in the program input result in proportional changes to the program output. For probabilistic programs the notion is naturally extended to expected sensitivity. A previous approach develops a relational program logic framework for proving expected sensitivity of probabilistic while loops, where the number of iterations is fixed and bounded. In this work, we consider probabilistic while loops where the number of iterations is not fixed, but randomized and depends on the initial input values. We present a sound approach for proving expected sensitivity of such programs. Our sound approach is martingale-based and can be automated through existing martingale-synthesis algorithms. Furthermore, our approach is compositional for sequential composition of while loops under a mild side condition. We demonstrate the effectiveness of our approach on several classical examples from Gambler's Ruin, stochastic hybrid systems and stochastic gradient descent. We also present experimental results showing that our automated approach can handle various probabilistic programs in the literature."}],"oa_version":"Published Version"},{"issue":"1-4","volume":94,"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1421-9743"],"issn":["0006-8977"]},"publication_status":"published","month":"01","intvolume":" 94","scopus_import":"1","pmid":1,"oa_version":"None","abstract":[{"text":"Nocturnal animals that rely on their visual system for foraging, mating, and navigation usually exhibit specific traits associated with living in scotopic conditions. Most nocturnal birds have several visual specializations, such as enlarged eyes and an increased orbital convergence. However, the actual role of binocular vision in nocturnal foraging is still debated. Nightjars (Aves: Caprimulgidae) are predators that actively pursue and capture flying insects in crepuscular and nocturnal environments, mainly using a conspicuous “sit-and-wait” tactic on which pursuit begins with an insect flying over the bird that sits on the ground. In this study, we describe the visual system of the band-winged nightjar (Systellura longirostris), with emphasis on anatomical features previously described as relevant for nocturnal birds. Orbit convergence, determined by 3D scanning of the skull, was 73.28°. The visual field, determined by ophthalmoscopic reflex, exhibits an area of maximum binocular overlap of 42°, and it is dorsally oriented. The eyes showed a nocturnal-like normalized corneal aperture/axial length index. Retinal ganglion cells (RGCs) were relatively scant, and distributed in an unusual oblique-band pattern, with higher concentrations in the ventrotemporal quadrant. Together, these results indicate that the band-winged nightjar exhibits a retinal specialization associated with the binocular area of their dorsal visual field, a relevant area for pursuit triggering and prey attacks. The RGC distribution observed is unusual among birds, but similar to that of some visually dependent insectivorous bats, suggesting that those features might be convergent in relation to feeding strategies.","lang":"eng"}],"department":[{"_id":"MaJö"}],"date_updated":"2024-02-22T15:18:34Z","status":"public","article_type":"original","type":"journal_article","_id":"7160","doi":"10.1159/000504162","date_published":"2020-01-01T00:00:00Z","date_created":"2019-12-09T09:04:13Z","page":"27-36","day":"01","publication":"Brain, Behavior and Evolution","isi":1,"year":"2020","publisher":"Karger Publishers","quality_controlled":"1","title":"Anatomical specializations related to foraging in the visual system of a nocturnal insectivorous bird, the band-winged nightjar (Aves: Caprimulgiformes)","author":[{"first_name":"Juan Esteban","full_name":"Salazar, Juan Esteban","last_name":"Salazar"},{"first_name":"Daniel","full_name":"Severin, Daniel","last_name":"Severin"},{"last_name":"Vega Zuniga","full_name":"Vega Zuniga, Tomas A","first_name":"Tomas A","id":"2E7C4E78-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Pedro","full_name":"Fernández-Aburto, Pedro","last_name":"Fernández-Aburto"},{"last_name":"Deichler","full_name":"Deichler, Alfonso","first_name":"Alfonso"},{"first_name":"Michel","last_name":"Sallaberry A.","full_name":"Sallaberry A., Michel"},{"last_name":"Mpodozis","full_name":"Mpodozis, Jorge","first_name":"Jorge"}],"external_id":{"isi":["000522856600004"],"pmid":["31751995"]},"article_processing_charge":"No","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Salazar, Juan Esteban, et al. “Anatomical Specializations Related to Foraging in the Visual System of a Nocturnal Insectivorous Bird, the Band-Winged Nightjar (Aves: Caprimulgiformes).” Brain, Behavior and Evolution, vol. 94, no. 1–4, Karger Publishers, 2020, pp. 27–36, doi:10.1159/000504162.","ama":"Salazar JE, Severin D, Vega Zuniga TA, et al. Anatomical specializations related to foraging in the visual system of a nocturnal insectivorous bird, the band-winged nightjar (Aves: Caprimulgiformes). Brain, Behavior and Evolution. 2020;94(1-4):27-36. doi:10.1159/000504162","apa":"Salazar, J. E., Severin, D., Vega Zuniga, T. A., Fernández-Aburto, P., Deichler, A., Sallaberry A., M., & Mpodozis, J. (2020). Anatomical specializations related to foraging in the visual system of a nocturnal insectivorous bird, the band-winged nightjar (Aves: Caprimulgiformes). Brain, Behavior and Evolution. Karger Publishers. https://doi.org/10.1159/000504162","ieee":"J. E. Salazar et al., “Anatomical specializations related to foraging in the visual system of a nocturnal insectivorous bird, the band-winged nightjar (Aves: Caprimulgiformes),” Brain, Behavior and Evolution, vol. 94, no. 1–4. Karger Publishers, pp. 27–36, 2020.","short":"J.E. Salazar, D. Severin, T.A. Vega Zuniga, P. Fernández-Aburto, A. Deichler, M. Sallaberry A., J. Mpodozis, Brain, Behavior and Evolution 94 (2020) 27–36.","chicago":"Salazar, Juan Esteban, Daniel Severin, Tomas A Vega Zuniga, Pedro Fernández-Aburto, Alfonso Deichler, Michel Sallaberry A., and Jorge Mpodozis. “Anatomical Specializations Related to Foraging in the Visual System of a Nocturnal Insectivorous Bird, the Band-Winged Nightjar (Aves: Caprimulgiformes).” Brain, Behavior and Evolution. Karger Publishers, 2020. https://doi.org/10.1159/000504162.","ista":"Salazar JE, Severin D, Vega Zuniga TA, Fernández-Aburto P, Deichler A, Sallaberry A. M, Mpodozis J. 2020. Anatomical specializations related to foraging in the visual system of a nocturnal insectivorous bird, the band-winged nightjar (Aves: Caprimulgiformes). Brain, Behavior and Evolution. 94(1–4), 27–36."}},{"year":"2020","isi":1,"publication":"Annals of Probability","day":"01","page":"963-1001","date_created":"2019-03-28T09:20:08Z","date_published":"2020-03-01T00:00:00Z","doi":"10.1214/19-AOP1379","oa":1,"publisher":"Institute of Mathematical Statistics","quality_controlled":"1","citation":{"ista":"Alt J, Erdös L, Krüger TH, Schröder DJ. 2020. Correlated random matrices: Band rigidity and edge universality. Annals of Probability. 48(2), 963–1001.","chicago":"Alt, Johannes, László Erdös, Torben H Krüger, and Dominik J Schröder. “Correlated Random Matrices: Band Rigidity and Edge Universality.” Annals of Probability. Institute of Mathematical Statistics, 2020. https://doi.org/10.1214/19-AOP1379.","ama":"Alt J, Erdös L, Krüger TH, Schröder DJ. Correlated random matrices: Band rigidity and edge universality. Annals of Probability. 2020;48(2):963-1001. doi:10.1214/19-AOP1379","apa":"Alt, J., Erdös, L., Krüger, T. H., & Schröder, D. J. (2020). Correlated random matrices: Band rigidity and edge universality. Annals of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/19-AOP1379","ieee":"J. Alt, L. Erdös, T. H. Krüger, and D. J. Schröder, “Correlated random matrices: Band rigidity and edge universality,” Annals of Probability, vol. 48, no. 2. Institute of Mathematical Statistics, pp. 963–1001, 2020.","short":"J. Alt, L. Erdös, T.H. Krüger, D.J. Schröder, Annals of Probability 48 (2020) 963–1001.","mla":"Alt, Johannes, et al. “Correlated Random Matrices: Band Rigidity and Edge Universality.” Annals of Probability, vol. 48, no. 2, Institute of Mathematical Statistics, 2020, pp. 963–1001, doi:10.1214/19-AOP1379."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["1804.07744"],"isi":["000528269100013"]},"article_processing_charge":"No","author":[{"id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes","last_name":"Alt","full_name":"Alt, Johannes"},{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","orcid":"0000-0001-5366-9603","full_name":"Erdös, László","last_name":"Erdös"},{"first_name":"Torben H","id":"3020C786-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4821-3297","full_name":"Krüger, Torben H","last_name":"Krüger"},{"full_name":"Schröder, Dominik J","orcid":"0000-0002-2904-1856","last_name":"Schröder","id":"408ED176-F248-11E8-B48F-1D18A9856A87","first_name":"Dominik J"}],"title":"Correlated random matrices: Band rigidity and edge universality","project":[{"name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"publication_status":"published","publication_identifier":{"issn":["0091-1798"]},"language":[{"iso":"eng"}],"ec_funded":1,"related_material":{"record":[{"status":"public","id":"149","relation":"dissertation_contains"},{"id":"6179","status":"public","relation":"dissertation_contains"}]},"issue":"2","volume":48,"abstract":[{"text":"We prove edge universality for a general class of correlated real symmetric or complex Hermitian Wigner matrices with arbitrary expectation. Our theorem also applies to internal edges of the self-consistent density of states. In particular, we establish a strong form of band rigidity which excludes mismatches between location and label of eigenvalues close to internal edges in these general models.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.07744"}],"scopus_import":"1","intvolume":" 48","month":"03","date_updated":"2024-02-22T14:34:33Z","department":[{"_id":"LaEr"}],"_id":"6184","type":"journal_article","article_type":"original","status":"public"},{"intvolume":" 13","month":"05","abstract":[{"lang":"eng","text":"Protein abundance and localization at the plasma membrane (PM) shapes plant development and mediates adaptation to changing environmental conditions. It is regulated by ubiquitination, a post-translational modification crucial for the proper sorting of endocytosed PM proteins to the vacuole for subsequent degradation. To understand the significance and the variety of roles played by this reversible modification, the function of ubiquitin receptors, which translate the ubiquitin signature into a cellular response, needs to be elucidated. In this study, we show that TOL (TOM1-like) proteins function in plants as multivalent ubiquitin receptors, governing ubiquitinated cargo delivery to the vacuole via the conserved Endosomal Sorting Complex Required for Transport (ESCRT) pathway. TOL2 and TOL6 interact with components of the ESCRT machinery and bind to K63-linked ubiquitin via two tandemly arranged conserved ubiquitin-binding domains. Mutation of these domains results not only in a loss of ubiquitin binding but also altered localization, abolishing TOL6 ubiquitin receptor activity. Function and localization of TOL6 is itself regulated by ubiquitination, whereby TOL6 ubiquitination potentially modulates degradation of PM-localized cargoes, assisting in the fine-tuning of the delicate interplay between protein recycling and downregulation. Taken together, our findings demonstrate the function and regulation of a ubiquitin receptor that mediates vacuolar degradation of PM proteins in higher plants."}],"oa_version":"Published Version","pmid":1,"issue":"5","volume":13,"publication_status":"published","publication_identifier":{"issn":["1674-2052"]},"language":[{"iso":"eng"}],"file":[{"date_updated":"2024-02-28T12:39:56Z","file_size":3089212,"creator":"dernst","date_created":"2024-02-28T12:39:56Z","file_name":"2020_MolecularPlant_MoulinierAnzola.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"c538a5008f7827f62d17d40a3bfabe65","file_id":"15038","success":1}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","keyword":["Plant Science","Molecular Biology"],"status":"public","_id":"15037","file_date_updated":"2024-02-28T12:39:56Z","department":[{"_id":"EvBe"}],"date_updated":"2024-02-28T12:41:52Z","ddc":["580"],"oa":1,"publisher":"Elsevier","quality_controlled":"1","page":"717-731","date_created":"2024-02-28T08:55:56Z","doi":"10.1016/j.molp.2020.02.012","date_published":"2020-05-04T00:00:00Z","year":"2020","has_accepted_license":"1","publication":"Molecular Plant","day":"04","external_id":{"pmid":["32087370"]},"article_processing_charge":"No","author":[{"first_name":"Jeanette","full_name":"Moulinier-Anzola, Jeanette","last_name":"Moulinier-Anzola"},{"full_name":"Schwihla, Maximilian","last_name":"Schwihla","first_name":"Maximilian"},{"last_name":"De-Araújo","full_name":"De-Araújo, Lucinda","first_name":"Lucinda"},{"last_name":"Artner","full_name":"Artner, Christina","id":"45DF286A-F248-11E8-B48F-1D18A9856A87","first_name":"Christina"},{"first_name":"Lisa","last_name":"Jörg","full_name":"Jörg, Lisa"},{"last_name":"Konstantinova","full_name":"Konstantinova, Nataliia","first_name":"Nataliia"},{"full_name":"Luschnig, Christian","last_name":"Luschnig","first_name":"Christian"},{"first_name":"Barbara","last_name":"Korbei","full_name":"Korbei, Barbara"}],"title":"TOLs function as ubiquitin receptors in the early steps of the ESCRT pathway in higher plants","citation":{"chicago":"Moulinier-Anzola, Jeanette, Maximilian Schwihla, Lucinda De-Araújo, Christina Artner, Lisa Jörg, Nataliia Konstantinova, Christian Luschnig, and Barbara Korbei. “TOLs Function as Ubiquitin Receptors in the Early Steps of the ESCRT Pathway in Higher Plants.” Molecular Plant. Elsevier, 2020. https://doi.org/10.1016/j.molp.2020.02.012.","ista":"Moulinier-Anzola J, Schwihla M, De-Araújo L, Artner C, Jörg L, Konstantinova N, Luschnig C, Korbei B. 2020. TOLs function as ubiquitin receptors in the early steps of the ESCRT pathway in higher plants. Molecular Plant. 13(5), 717–731.","mla":"Moulinier-Anzola, Jeanette, et al. “TOLs Function as Ubiquitin Receptors in the Early Steps of the ESCRT Pathway in Higher Plants.” Molecular Plant, vol. 13, no. 5, Elsevier, 2020, pp. 717–31, doi:10.1016/j.molp.2020.02.012.","ama":"Moulinier-Anzola J, Schwihla M, De-Araújo L, et al. TOLs function as ubiquitin receptors in the early steps of the ESCRT pathway in higher plants. Molecular Plant. 2020;13(5):717-731. doi:10.1016/j.molp.2020.02.012","apa":"Moulinier-Anzola, J., Schwihla, M., De-Araújo, L., Artner, C., Jörg, L., Konstantinova, N., … Korbei, B. (2020). TOLs function as ubiquitin receptors in the early steps of the ESCRT pathway in higher plants. Molecular Plant. Elsevier. https://doi.org/10.1016/j.molp.2020.02.012","ieee":"J. Moulinier-Anzola et al., “TOLs function as ubiquitin receptors in the early steps of the ESCRT pathway in higher plants,” Molecular Plant, vol. 13, no. 5. Elsevier, pp. 717–731, 2020.","short":"J. Moulinier-Anzola, M. Schwihla, L. De-Araújo, C. Artner, L. Jörg, N. Konstantinova, C. Luschnig, B. Korbei, Molecular Plant 13 (2020) 717–731."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"article_type":"original","type":"journal_article","status":"public","keyword":["Molecular Biology","Structural Biology"],"_id":"15036","department":[{"_id":"MaLo"}],"date_updated":"2024-02-28T12:37:54Z","main_file_link":[{"url":"https://doi.org/10.1016/j.jmb.2020.09.001","open_access":"1"}],"month":"10","intvolume":" 432","abstract":[{"lang":"eng","text":"The assembly of a septin filament requires that homologous monomers must distinguish between one another in establishing appropriate interfaces with their neighbors. To understand this phenomenon at the molecular level, we present the first four crystal structures of heterodimeric septin complexes. We describe in detail the two distinct types of G-interface present within the octameric particles, which must polymerize to form filaments. These are formed between SEPT2 and SEPT6 and between SEPT7 and SEPT3, and their description permits an understanding of the structural basis for the selectivity necessary for correct filament assembly. By replacing SEPT6 by SEPT8 or SEPT11, it is possible to rationalize Kinoshita's postulate, which predicts the exchangeability of septins from within a subgroup. Switches I and II, which in classical small GTPases provide a mechanism for nucleotide-dependent conformational change, have been repurposed in septins to play a fundamental role in molecular recognition. Specifically, it is switch I which holds the key to discriminating between the two different G-interfaces. Moreover, residues which are characteristic for a given subgroup play subtle, but pivotal, roles in guaranteeing that the correct interfaces are formed."}],"pmid":1,"oa_version":"Published Version","volume":432,"issue":"21","publication_identifier":{"issn":["0022-2836"]},"publication_status":"published","language":[{"iso":"eng"}],"author":[{"first_name":"Higor Vinícius Dias","last_name":"Rosa","full_name":"Rosa, Higor Vinícius Dias"},{"first_name":"Diego Antonio","full_name":"Leonardo, Diego Antonio","last_name":"Leonardo"},{"id":"D96FFDA0-A884-11E9-9968-DC26E6697425","first_name":"Gabriel","full_name":"Brognara, Gabriel","last_name":"Brognara"},{"last_name":"Brandão-Neto","full_name":"Brandão-Neto, José","first_name":"José"},{"last_name":"D'Muniz Pereira","full_name":"D'Muniz Pereira, Humberto","first_name":"Humberto"},{"first_name":"Ana Paula Ulian","full_name":"Araújo, Ana Paula Ulian","last_name":"Araújo"},{"first_name":"Richard Charles","last_name":"Garratt","full_name":"Garratt, Richard Charles"}],"article_processing_charge":"No","external_id":{"pmid":["32910969"]},"title":"Molecular recognition at septin interfaces: The switches hold the key","citation":{"chicago":"Rosa, Higor Vinícius Dias, Diego Antonio Leonardo, Gabriel Brognara, José Brandão-Neto, Humberto D’Muniz Pereira, Ana Paula Ulian Araújo, and Richard Charles Garratt. “Molecular Recognition at Septin Interfaces: The Switches Hold the Key.” Journal of Molecular Biology. Elsevier, 2020. https://doi.org/10.1016/j.jmb.2020.09.001.","ista":"Rosa HVD, Leonardo DA, Brognara G, Brandão-Neto J, D’Muniz Pereira H, Araújo APU, Garratt RC. 2020. Molecular recognition at septin interfaces: The switches hold the key. Journal of Molecular Biology. 432(21), 5784–5801.","mla":"Rosa, Higor Vinícius Dias, et al. “Molecular Recognition at Septin Interfaces: The Switches Hold the Key.” Journal of Molecular Biology, vol. 432, no. 21, Elsevier, 2020, pp. 5784–801, doi:10.1016/j.jmb.2020.09.001.","short":"H.V.D. Rosa, D.A. Leonardo, G. Brognara, J. Brandão-Neto, H. D’Muniz Pereira, A.P.U. Araújo, R.C. Garratt, Journal of Molecular Biology 432 (2020) 5784–5801.","ieee":"H. V. D. Rosa et al., “Molecular recognition at septin interfaces: The switches hold the key,” Journal of Molecular Biology, vol. 432, no. 21. Elsevier, pp. 5784–5801, 2020.","apa":"Rosa, H. V. D., Leonardo, D. A., Brognara, G., Brandão-Neto, J., D’Muniz Pereira, H., Araújo, A. P. U., & Garratt, R. C. (2020). Molecular recognition at septin interfaces: The switches hold the key. Journal of Molecular Biology. Elsevier. https://doi.org/10.1016/j.jmb.2020.09.001","ama":"Rosa HVD, Leonardo DA, Brognara G, et al. Molecular recognition at septin interfaces: The switches hold the key. Journal of Molecular Biology. 2020;432(21):5784-5801. doi:10.1016/j.jmb.2020.09.001"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Elsevier","quality_controlled":"1","oa":1,"page":"5784-5801","doi":"10.1016/j.jmb.2020.09.001","date_published":"2020-10-02T00:00:00Z","date_created":"2024-02-28T08:50:34Z","year":"2020","day":"02","publication":"Journal of Molecular Biology"},{"month":"07","intvolume":" 39","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1145/3386569.3392405"}],"oa_version":"Submitted Version","acknowledged_ssus":[{"_id":"ScienComp"}],"abstract":[{"lang":"eng","text":"Previous research on animations of soap bubbles, films, and foams largely focuses on the motion and geometric shape of the bubble surface. These works neglect the evolution of the bubble’s thickness, which is normally responsible for visual phenomena like surface vortices, Newton’s interference patterns, capillary waves, and deformation-dependent rupturing of films in a foam. In this paper, we model these natural phenomena by introducing the film thickness as a reduced degree of freedom in the Navier-Stokes equations and deriving their equations of motion. We discretize the equations on a nonmanifold triangle mesh surface and couple it to an existing bubble solver. In doing so, we also introduce an incompressible fluid solver for 2.5D films and a novel advection algorithm for convecting fields across non-manifold surface junctions. Our simulations enhance state-of-the-art bubble solvers with additional effects caused by convection, rippling, draining, and evaporation of the thin film."}],"volume":39,"issue":"4","ec_funded":1,"file":[{"success":1,"file_id":"8795","checksum":"813831ca91319d794d9748c276b24578","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2020_soapfilm_submitted.pdf","date_created":"2020-11-23T09:03:19Z","file_size":14935529,"date_updated":"2020-11-23T09:03:19Z","creator":"dernst"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["07300301"],"eissn":["15577368"]},"publication_status":"published","status":"public","type":"journal_article","article_type":"original","_id":"8384","file_date_updated":"2020-11-23T09:03:19Z","department":[{"_id":"ChWo"}],"ddc":["000"],"date_updated":"2024-02-28T12:57:31Z","quality_controlled":"1","publisher":"Association for Computing Machinery","oa":1,"acknowledgement":"We wish to thank the anonymous reviewers and the members of the Visual Computing Group at IST Austria for their valuable feedback, especially Camille Schreck for her help in rendering. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing. We would like to thank the authors of [Belcour and Barla 2017] for providing their implementation, the authors of [Atkins and Elliott 2010] and [Seychelles et al. 2008] for allowing us to use their results, and Rok Grah for helpful discussions. Finally, we thank Ryoichi Ando for many discussions from the beginning of the project that resulted in important contents of the paper including our formulation, numerical scheme, and initial implementation. This project has received funding from the\r\nEuropean Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 638176.","doi":"10.1145/3386569.3392405","date_published":"2020-07-08T00:00:00Z","date_created":"2020-09-13T22:01:18Z","day":"08","publication":"ACM Transactions on Graphics","has_accepted_license":"1","isi":1,"year":"2020","project":[{"_id":"2533E772-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"638176","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales"}],"article_number":"31","title":"A model for soap film dynamics with evolving thickness","author":[{"full_name":"Ishida, Sadashige","last_name":"Ishida","first_name":"Sadashige","id":"6F7C4B96-A8E9-11E9-A7CA-09ECE5697425"},{"last_name":"Synak","full_name":"Synak, Peter","first_name":"Peter","id":"331776E2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Narita","full_name":"Narita, Fumiya","first_name":"Fumiya"},{"first_name":"Toshiya","full_name":"Hachisuka, Toshiya","last_name":"Hachisuka"},{"full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","last_name":"Wojtan","first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"isi":["000583700300004"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Ishida S, Synak P, Narita F, Hachisuka T, Wojtan C. A model for soap film dynamics with evolving thickness. ACM Transactions on Graphics. 2020;39(4). doi:10.1145/3386569.3392405","apa":"Ishida, S., Synak, P., Narita, F., Hachisuka, T., & Wojtan, C. (2020). A model for soap film dynamics with evolving thickness. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3386569.3392405","ieee":"S. Ishida, P. Synak, F. Narita, T. Hachisuka, and C. Wojtan, “A model for soap film dynamics with evolving thickness,” ACM Transactions on Graphics, vol. 39, no. 4. Association for Computing Machinery, 2020.","short":"S. Ishida, P. Synak, F. Narita, T. Hachisuka, C. Wojtan, ACM Transactions on Graphics 39 (2020).","mla":"Ishida, Sadashige, et al. “A Model for Soap Film Dynamics with Evolving Thickness.” ACM Transactions on Graphics, vol. 39, no. 4, 31, Association for Computing Machinery, 2020, doi:10.1145/3386569.3392405.","ista":"Ishida S, Synak P, Narita F, Hachisuka T, Wojtan C. 2020. A model for soap film dynamics with evolving thickness. ACM Transactions on Graphics. 39(4), 31.","chicago":"Ishida, Sadashige, Peter Synak, Fumiya Narita, Toshiya Hachisuka, and Chris Wojtan. “A Model for Soap Film Dynamics with Evolving Thickness.” ACM Transactions on Graphics. Association for Computing Machinery, 2020. https://doi.org/10.1145/3386569.3392405."}},{"day":"01","publication":"Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020)","isi":1,"year":"2020","date_published":"2020-07-01T00:00:00Z","doi":"10.1145/3350755.3400282","date_created":"2020-05-06T08:53:34Z","page":"175-185","quality_controlled":"1","publisher":"Association for Computing Machinery","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Czumaj, Artur, Peter Davies, and Merav Parter. “Graph Sparsification for Derandomizing Massively Parallel Computation with Low Space.” In Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020), 175–85. Association for Computing Machinery, 2020. https://doi.org/10.1145/3350755.3400282.","ista":"Czumaj A, Davies P, Parter M. 2020. Graph sparsification for derandomizing massively parallel computation with low space. Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020). SPAA: Symposium on Parallelism in Algorithms and Architectures, 175–185.","mla":"Czumaj, Artur, et al. “Graph Sparsification for Derandomizing Massively Parallel Computation with Low Space.” Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020), no. 7, Association for Computing Machinery, 2020, pp. 175–85, doi:10.1145/3350755.3400282.","apa":"Czumaj, A., Davies, P., & Parter, M. (2020). Graph sparsification for derandomizing massively parallel computation with low space. In Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020) (pp. 175–185). Virtual Event, United States: Association for Computing Machinery. https://doi.org/10.1145/3350755.3400282","ama":"Czumaj A, Davies P, Parter M. Graph sparsification for derandomizing massively parallel computation with low space. In: Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020). Association for Computing Machinery; 2020:175-185. doi:10.1145/3350755.3400282","short":"A. Czumaj, P. Davies, M. Parter, in:, Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020), Association for Computing Machinery, 2020, pp. 175–185.","ieee":"A. Czumaj, P. Davies, and M. Parter, “Graph sparsification for derandomizing massively parallel computation with low space,” in Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020), Virtual Event, United States, 2020, no. 7, pp. 175–185."},"title":"Graph sparsification for derandomizing massively parallel computation with low space","author":[{"full_name":"Czumaj, Artur","orcid":"0000-0002-5646-9524","last_name":"Czumaj","first_name":"Artur"},{"full_name":"Davies, Peter","orcid":"0000-0002-5646-9524","last_name":"Davies","id":"11396234-BB50-11E9-B24C-90FCE5697425","first_name":"Peter"},{"last_name":"Parter","full_name":"Parter, Merav","first_name":"Merav"}],"external_id":{"isi":["000744436200015"],"arxiv":["1912.05390"]},"article_processing_charge":"No","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"publication_status":"published","related_material":{"record":[{"relation":"later_version","id":"9541","status":"public"}]},"issue":"7","ec_funded":1,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"The Massively Parallel Computation (MPC) model is an emerging model which distills core aspects of distributed and parallel computation. It has been developed as a tool to solve (typically graph) problems in systems where the input is distributed over many machines with limited space.\r\n\t\r\nRecent work has focused on the regime in which machines have sublinear (in $n$, the number of nodes in the input graph) space, with randomized algorithms presented for fundamental graph problems of Maximal Matching and Maximal Independent Set. However, there have been no prior corresponding deterministic algorithms.\r\n\t\r\n\tA major challenge underlying the sublinear space setting is that the local space of each machine might be too small to store all the edges incident to a single node. This poses a considerable obstacle compared to the classical models in which each node is assumed to know and have easy access to its incident edges. To overcome this barrier we introduce a new graph sparsification technique that deterministically computes a low-degree subgraph with additional desired properties. The degree of the nodes in this subgraph is small in the sense that the edges of each node can be now stored on a single machine. This low-degree subgraph also has the property that solving the problem on this subgraph provides \\emph{significant} global progress, i.e., progress towards solving the problem for the original input graph.\r\n\t\r\nUsing this framework to derandomize the well-known randomized algorithm of Luby [SICOMP'86], we obtain $O(\\log \\Delta+\\log\\log n)$-round deterministic MPC algorithms for solving the fundamental problems of Maximal Matching and Maximal Independent Set with $O(n^{\\epsilon})$ space on each machine for any constant $\\epsilon > 0$. Based on the recent work of Ghaffari et al. [FOCS'18], this additive $O(\\log\\log n)$ factor is conditionally essential. These algorithms can also be shown to run in $O(\\log \\Delta)$ rounds in the closely related model of CONGESTED CLIQUE, improving upon the state-of-the-art bound of $O(\\log^2 \\Delta)$ rounds by Censor-Hillel et al. [DISC'17]."}],"month":"07","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1912.05390"}],"date_updated":"2024-02-28T12:53:09Z","department":[{"_id":"DaAl"}],"_id":"7802","status":"public","type":"conference","conference":{"location":"Virtual Event, United States","end_date":"2020-07-17","start_date":"2020-07-15","name":"SPAA: Symposium on Parallelism in Algorithms and Architectures"}},{"status":"public","conference":{"name":"PPOPP: Principles and Practice of Parallel Programming","location":"San Diego, CA, United States","end_date":"2020-02-26","start_date":"2020-02-22"},"type":"conference","_id":"7636","department":[{"_id":"DaAl"}],"date_updated":"2024-02-28T12:55:14Z","month":"02","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1145/3332466.3374542"}],"scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Balanced search trees typically use key comparisons to guide their operations, and achieve logarithmic running time. By relying on numerical properties of the keys, interpolation search achieves lower search complexity and better performance. Although interpolation-based data structures were investigated in the past, their non-blocking concurrent variants have received very little attention so far.\r\nIn this paper, we propose the first non-blocking implementation of the classic interpolation search tree (IST) data structure. For arbitrary key distributions, the data structure ensures worst-case O(log n + p) amortized time for search, insertion and deletion traversals. When the input key distributions are smooth, lookups run in expected O(log log n + p) time, and insertion and deletion run in expected amortized O(log log n + p) time, where p is a bound on the number of threads. To improve the scalability of concurrent insertion and deletion, we propose a novel parallel rebuilding technique, which should be of independent interest.\r\nWe evaluate whether the theoretical improvements translate to practice by implementing the concurrent interpolation search tree, and benchmarking it on uniform and nonuniform key distributions, for dataset sizes in the millions to billions of keys. Relative to the state-of-the-art concurrent data structures, the concurrent interpolation search tree achieves performance improvements of up to 15% under high update rates, and of up to 50% under moderate update rates. Further, ISTs exhibit up to 2X less cache-misses, and consume 1.2 -- 2.6X less memory compared to the next best alternative on typical dataset sizes. We find that the results are surprisingly robust to distributional skew, which suggests that our data structure can be a promising alternative to classic concurrent search structures."}],"ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"isbn":["9781450368186"]},"project":[{"_id":"268A44D6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"805223","name":"Elastic Coordination for Scalable Machine Learning"}],"title":"Non-blocking interpolation search trees with doubly-logarithmic running time","external_id":{"isi":["000564476500020"]},"article_processing_charge":"No","author":[{"full_name":"Brown, Trevor A","last_name":"Brown","id":"3569F0A0-F248-11E8-B48F-1D18A9856A87","first_name":"Trevor A"},{"first_name":"Aleksandar","full_name":"Prokopec, Aleksandar","last_name":"Prokopec"},{"first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Brown, Trevor A, Aleksandar Prokopec, and Dan-Adrian Alistarh. “Non-Blocking Interpolation Search Trees with Doubly-Logarithmic Running Time.” In Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, 276–91. Association for Computing Machinery, 2020. https://doi.org/10.1145/3332466.3374542.","ista":"Brown TA, Prokopec A, Alistarh D-A. 2020. Non-blocking interpolation search trees with doubly-logarithmic running time. Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. PPOPP: Principles and Practice of Parallel Programming, 276–291.","mla":"Brown, Trevor A., et al. “Non-Blocking Interpolation Search Trees with Doubly-Logarithmic Running Time.” Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2020, pp. 276–91, doi:10.1145/3332466.3374542.","ama":"Brown TA, Prokopec A, Alistarh D-A. Non-blocking interpolation search trees with doubly-logarithmic running time. In: Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. Association for Computing Machinery; 2020:276-291. doi:10.1145/3332466.3374542","apa":"Brown, T. A., Prokopec, A., & Alistarh, D.-A. (2020). Non-blocking interpolation search trees with doubly-logarithmic running time. In Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (pp. 276–291). San Diego, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3332466.3374542","short":"T.A. Brown, A. Prokopec, D.-A. Alistarh, in:, Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2020, pp. 276–291.","ieee":"T. A. Brown, A. Prokopec, and D.-A. Alistarh, “Non-blocking interpolation search trees with doubly-logarithmic running time,” in Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, San Diego, CA, United States, 2020, pp. 276–291."},"oa":1,"quality_controlled":"1","publisher":"Association for Computing Machinery","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union Horizon 2020 research and innovation program, grant agreement No 805223, ERC Starting Grant ScaleML. We acknowledge the support of the Natural Sciences and\r\nEngineering Research Council of Canada (NSERC). ","date_created":"2020-04-05T22:00:49Z","date_published":"2020-02-19T00:00:00Z","doi":"10.1145/3332466.3374542","page":"276-291","publication":"Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming","day":"19","year":"2020","isi":1},{"title":"Memory tagging: Minimalist synchronization for scalable concurrent data structures","department":[{"_id":"DaAl"}],"external_id":{"isi":["000744436200004"]},"article_processing_charge":"No","author":[{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"id":"3569F0A0-F248-11E8-B48F-1D18A9856A87","first_name":"Trevor A","last_name":"Brown","full_name":"Brown, Trevor A"},{"first_name":"Nandini","full_name":"Singhal, Nandini","last_name":"Singhal"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-02-28T12:56:32Z","citation":{"chicago":"Alistarh, Dan-Adrian, Trevor A Brown, and Nandini Singhal. “Memory Tagging: Minimalist Synchronization for Scalable Concurrent Data Structures.” In Annual ACM Symposium on Parallelism in Algorithms and Architectures, 37–49. Association for Computing Machinery, 2020. https://doi.org/10.1145/3350755.3400213.","ista":"Alistarh D-A, Brown TA, Singhal N. 2020. Memory tagging: Minimalist synchronization for scalable concurrent data structures. Annual ACM Symposium on Parallelism in Algorithms and Architectures. SPAA: Symposium on Parallelism in Algorithms and Architectures, 37–49.","mla":"Alistarh, Dan-Adrian, et al. “Memory Tagging: Minimalist Synchronization for Scalable Concurrent Data Structures.” Annual ACM Symposium on Parallelism in Algorithms and Architectures, no. 7, Association for Computing Machinery, 2020, pp. 37–49, doi:10.1145/3350755.3400213.","apa":"Alistarh, D.-A., Brown, T. A., & Singhal, N. (2020). Memory tagging: Minimalist synchronization for scalable concurrent data structures. In Annual ACM Symposium on Parallelism in Algorithms and Architectures (pp. 37–49). Virtual Event, United States: Association for Computing Machinery. https://doi.org/10.1145/3350755.3400213","ama":"Alistarh D-A, Brown TA, Singhal N. Memory tagging: Minimalist synchronization for scalable concurrent data structures. In: Annual ACM Symposium on Parallelism in Algorithms and Architectures. Association for Computing Machinery; 2020:37-49. doi:10.1145/3350755.3400213","short":"D.-A. Alistarh, T.A. Brown, N. Singhal, in:, Annual ACM Symposium on Parallelism in Algorithms and Architectures, Association for Computing Machinery, 2020, pp. 37–49.","ieee":"D.-A. Alistarh, T. A. Brown, and N. Singhal, “Memory tagging: Minimalist synchronization for scalable concurrent data structures,” in Annual ACM Symposium on Parallelism in Algorithms and Architectures, Virtual Event, United States, 2020, no. 7, pp. 37–49."},"status":"public","conference":{"end_date":"2020-07-17","location":"Virtual Event, United States","start_date":"2020-07-15","name":"SPAA: Symposium on Parallelism in Algorithms and Architectures"},"type":"conference","_id":"8191","date_created":"2020-08-02T22:00:58Z","doi":"10.1145/3350755.3400213","issue":"7","date_published":"2020-07-06T00:00:00Z","page":"37-49","publication":"Annual ACM Symposium on Parallelism in Algorithms and Architectures","language":[{"iso":"eng"}],"day":"06","year":"2020","publication_status":"published","publication_identifier":{"isbn":["9781450369350"]},"isi":1,"month":"07","scopus_import":"1","publisher":"Association for Computing Machinery","quality_controlled":"1","oa_version":"None","abstract":[{"lang":"eng","text":"There has been a significant amount of research on hardware and software support for efficient concurrent data structures; yet, the question of how to build correct, simple, and scalable data structures has not yet been definitively settled. In this paper, we revisit this question from a minimalist perspective, and ask: what is the smallest amount of synchronization required for correct and efficient concurrent search data structures, and how could this minimal synchronization support be provided in hardware?\r\n\r\nTo address these questions, we introduce memory tagging, a simple hardware mechanism which enables the programmer to \"tag\" a dynamic set of memory locations, at cache-line granularity, and later validate whether the memory has been concurrently modified, with the possibility of updating one of the underlying locations atomically if validation succeeds. We provide several examples showing that this mechanism can enable fast and arguably simple concurrent data structure designs, such as lists, binary search trees, balanced search trees, range queries, and Software Transactional Memory (STM) implementations. We provide an implementation of memory tags in the Graphite multi-core simulator, showing that the mechanism can be implemented entirely at the level of L1 cache, and that it can enable non-trivial speedups versus existing implementations of the above data structures."}]},{"oa_version":"None","abstract":[{"lang":"eng","text":"Concurrent programming can be notoriously complex and error-prone. Programming bugs can arise from a variety of sources, such as operation re-reordering, or incomplete understanding of the memory model. A variety of formal and model checking methods have been developed to address this fundamental difficulty. While technically interesting, existing academic methods are still hard to apply to the large codebases typical of industrial deployments, which limits their practical impact."}],"month":"02","scopus_import":"1","publisher":"Association for Computing Machinery","quality_controlled":"1","language":[{"iso":"eng"}],"publication":"Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, PPOPP","day":"19","publication_status":"published","year":"2020","publication_identifier":{"isbn":["9781450368186"]},"date_created":"2020-04-05T22:00:48Z","doi":"10.1145/3332466.3374503","date_published":"2020-02-19T00:00:00Z","page":"423-424","_id":"7635","status":"public","conference":{"name":"PPOPP: Principles and Practice of Parallel Programming","start_date":"2020-02-22","location":"San Diego, CA, United States","end_date":"2020-02-26"},"type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Koval, Nikita, Mariia Sokolova, Alexander Fedorov, Dan-Adrian Alistarh, and Dmitry Tsitelov. “Testing Concurrency on the JVM with Lincheck.” In Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, PPOPP, 423–24. Association for Computing Machinery, 2020. https://doi.org/10.1145/3332466.3374503.","ista":"Koval N, Sokolova M, Fedorov A, Alistarh D-A, Tsitelov D. 2020. Testing concurrency on the JVM with Lincheck. Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, PPOPP. PPOPP: Principles and Practice of Parallel Programming, 423–424.","mla":"Koval, Nikita, et al. “Testing Concurrency on the JVM with Lincheck.” Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, PPOPP, Association for Computing Machinery, 2020, pp. 423–24, doi:10.1145/3332466.3374503.","apa":"Koval, N., Sokolova, M., Fedorov, A., Alistarh, D.-A., & Tsitelov, D. (2020). Testing concurrency on the JVM with Lincheck. In Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, PPOPP (pp. 423–424). San Diego, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3332466.3374503","ama":"Koval N, Sokolova M, Fedorov A, Alistarh D-A, Tsitelov D. Testing concurrency on the JVM with Lincheck. In: Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, PPOPP. Association for Computing Machinery; 2020:423-424. doi:10.1145/3332466.3374503","short":"N. Koval, M. Sokolova, A. Fedorov, D.-A. Alistarh, D. Tsitelov, in:, Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, PPOPP, Association for Computing Machinery, 2020, pp. 423–424.","ieee":"N. Koval, M. Sokolova, A. Fedorov, D.-A. Alistarh, and D. Tsitelov, “Testing concurrency on the JVM with Lincheck,” in Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, PPOPP, San Diego, CA, United States, 2020, pp. 423–424."},"date_updated":"2024-02-28T12:53:46Z","title":"Testing concurrency on the JVM with Lincheck","department":[{"_id":"DaAl"}],"article_processing_charge":"No","author":[{"first_name":"Nikita","id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87","full_name":"Koval, Nikita","last_name":"Koval"},{"first_name":"Mariia","id":"26217AE4-77FF-11EA-8101-AD24D49E41F4","last_name":"Sokolova","full_name":"Sokolova, Mariia"},{"full_name":"Fedorov, Alexander","last_name":"Fedorov","first_name":"Alexander"},{"last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Dmitry","full_name":"Tsitelov, Dmitry","last_name":"Tsitelov"}]},{"page":"54-56","date_created":"2020-09-13T22:01:18Z","date_published":"2020-07-31T00:00:00Z","doi":"10.1145/3382734.3405743","year":"2020","publication_status":"published","publication_identifier":{"isbn":["9781450375825"]},"publication":"Proceedings of the 39th Symposium on Principles of Distributed Computing","language":[{"iso":"eng"}],"day":"31","publisher":"Association for Computing Machinery","scopus_import":"1","quality_controlled":"1","month":"07","abstract":[{"text":"We introduce extension-based proofs, a class of impossibility proofs that includes valency arguments. They are modelled as an interaction between a prover and a protocol. Using proofs based on combinatorial topology, it has been shown that it is impossible to deterministically solve k-set agreement among n > k ≥ 2 processes in a wait-free manner. However, it was unknown whether proofs based on simpler techniques were possible. We explain why this impossibility result cannot be obtained by an extension-based proof and, hence, extension-based proofs are limited in power.","lang":"eng"}],"oa_version":"None","article_processing_charge":"No","author":[{"first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X"},{"first_name":"James","full_name":"Aspnes, James","last_name":"Aspnes"},{"last_name":"Ellen","full_name":"Ellen, Faith","first_name":"Faith"},{"first_name":"Rati","last_name":"Gelashvili","full_name":"Gelashvili, Rati"},{"first_name":"Leqi","full_name":"Zhu, Leqi","last_name":"Zhu"}],"title":"Brief Announcement: Why Extension-Based Proofs Fail","department":[{"_id":"DaAl"}],"date_updated":"2024-02-28T12:54:19Z","citation":{"ista":"Alistarh D-A, Aspnes J, Ellen F, Gelashvili R, Zhu L. 2020. Brief Announcement: Why Extension-Based Proofs Fail. Proceedings of the 39th Symposium on Principles of Distributed Computing. PODC: Principles of Distributed Computing, 54–56.","chicago":"Alistarh, Dan-Adrian, James Aspnes, Faith Ellen, Rati Gelashvili, and Leqi Zhu. “Brief Announcement: Why Extension-Based Proofs Fail.” In Proceedings of the 39th Symposium on Principles of Distributed Computing, 54–56. Association for Computing Machinery, 2020. https://doi.org/10.1145/3382734.3405743.","ama":"Alistarh D-A, Aspnes J, Ellen F, Gelashvili R, Zhu L. Brief Announcement: Why Extension-Based Proofs Fail. In: Proceedings of the 39th Symposium on Principles of Distributed Computing. Association for Computing Machinery; 2020:54-56. doi:10.1145/3382734.3405743","apa":"Alistarh, D.-A., Aspnes, J., Ellen, F., Gelashvili, R., & Zhu, L. (2020). Brief Announcement: Why Extension-Based Proofs Fail. In Proceedings of the 39th Symposium on Principles of Distributed Computing (pp. 54–56). Virtual, Italy: Association for Computing Machinery. https://doi.org/10.1145/3382734.3405743","ieee":"D.-A. Alistarh, J. Aspnes, F. Ellen, R. Gelashvili, and L. Zhu, “Brief Announcement: Why Extension-Based Proofs Fail,” in Proceedings of the 39th Symposium on Principles of Distributed Computing, Virtual, Italy, 2020, pp. 54–56.","short":"D.-A. Alistarh, J. Aspnes, F. Ellen, R. Gelashvili, L. Zhu, in:, Proceedings of the 39th Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2020, pp. 54–56.","mla":"Alistarh, Dan-Adrian, et al. “Brief Announcement: Why Extension-Based Proofs Fail.” Proceedings of the 39th Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2020, pp. 54–56, doi:10.1145/3382734.3405743."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","conference":{"name":"PODC: Principles of Distributed Computing","end_date":"2020-08-07","location":"Virtual, Italy","start_date":"2020-08-03"},"type":"conference","status":"public","_id":"8383"},{"quality_controlled":"1","publisher":"Association for Computing Machinery","oa":1,"acknowledgement":"We wish to thank the anonymous reviewers and the members of the Visual Computing Group at IST Austria for their valuable feedback. We also thank the creators of the Berkeley Garment Library [de Joya et al. 2012] for providing garment meshes, [Krishnamurthy and Levoy 1996] and [Turk and Levoy 1994] for the armadillo and bunny meshes, the creators of libWetCloth [Fei et al. 2018] for their implementation of discrete elastic rod forces, and Tomáš Skřivan for\r\ninspiring discussions and help with Mathematica code generation. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 638176. Rahul Narain is supported by a Pankaj Gupta Young Faculty Fellowship and a gift from Adobe Inc.","doi":"10.1145/3386569.3392412","date_published":"2020-07-08T00:00:00Z","date_created":"2020-09-13T22:01:18Z","day":"08","publication":"ACM Transactions on Graphics","has_accepted_license":"1","isi":1,"year":"2020","project":[{"call_identifier":"H2020","_id":"2533E772-B435-11E9-9278-68D0E5697425","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","grant_number":"638176"}],"article_number":"48","title":"Homogenized yarn-level cloth","author":[{"full_name":"Sperl, Georg","last_name":"Sperl","first_name":"Georg","id":"4DD40360-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Narain","full_name":"Narain, Rahul","first_name":"Rahul"},{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J","orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J","last_name":"Wojtan"}],"external_id":{"isi":["000583700300021"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Sperl, Georg, et al. “Homogenized Yarn-Level Cloth.” ACM Transactions on Graphics, vol. 39, no. 4, 48, Association for Computing Machinery, 2020, doi:10.1145/3386569.3392412.","short":"G. Sperl, R. Narain, C. Wojtan, ACM Transactions on Graphics 39 (2020).","ieee":"G. Sperl, R. Narain, and C. Wojtan, “Homogenized yarn-level cloth,” ACM Transactions on Graphics, vol. 39, no. 4. Association for Computing Machinery, 2020.","apa":"Sperl, G., Narain, R., & Wojtan, C. (2020). Homogenized yarn-level cloth. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3386569.3392412","ama":"Sperl G, Narain R, Wojtan C. Homogenized yarn-level cloth. ACM Transactions on Graphics. 2020;39(4). doi:10.1145/3386569.3392412","chicago":"Sperl, Georg, Rahul Narain, and Chris Wojtan. “Homogenized Yarn-Level Cloth.” ACM Transactions on Graphics. Association for Computing Machinery, 2020. https://doi.org/10.1145/3386569.3392412.","ista":"Sperl G, Narain R, Wojtan C. 2020. Homogenized yarn-level cloth. ACM Transactions on Graphics. 39(4), 48."},"month":"07","intvolume":" 39","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1145/3386569.3392412","open_access":"1"}],"oa_version":"Submitted Version","acknowledged_ssus":[{"_id":"ScienComp"}],"abstract":[{"lang":"eng","text":"We present a method for animating yarn-level cloth effects using a thin-shell solver. We accomplish this through numerical homogenization: we first use a large number of yarn-level simulations to build a model of the potential energy density of the cloth, and then use this energy density function to compute forces in a thin shell simulator. We model several yarn-based materials, including both woven and knitted fabrics. Our model faithfully reproduces expected effects like the stiffness of woven fabrics, and the highly deformable nature and anisotropy of knitted fabrics. Our approach does not require any real-world experiments nor measurements; because the method is based entirely on simulations, it can generate entirely new material models quickly, without the need for testing apparatuses or human intervention. We provide data-driven models of several woven and knitted fabrics, which can be used for efficient simulation with an off-the-shelf cloth solver."}],"volume":39,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"12358"}]},"issue":"4","ec_funded":1,"file":[{"date_updated":"2020-11-23T09:01:22Z","file_size":38922662,"creator":"dernst","date_created":"2020-11-23T09:01:22Z","file_name":"2020_hylc_submitted.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"cf4c1d361c3196c4bd424520a5588205","file_id":"8794","success":1}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["07300301"],"eissn":["15577368"]},"publication_status":"published","status":"public","article_type":"original","type":"journal_article","_id":"8385","department":[{"_id":"ChWo"}],"file_date_updated":"2020-11-23T09:01:22Z","ddc":["000"],"date_updated":"2024-02-28T12:57:47Z"},{"project":[{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"article_number":"204905","title":"Shear-induced ordering in systems with competing interactions: A machine learning study","external_id":{"arxiv":["2002.07294"],"isi":["000537900300001"]},"article_processing_charge":"No","author":[{"first_name":"J.","last_name":"Pȩkalski","full_name":"Pȩkalski, J."},{"orcid":"0000-0002-1106-4419","full_name":"Rzadkowski, Wojciech","last_name":"Rzadkowski","id":"48C55298-F248-11E8-B48F-1D18A9856A87","first_name":"Wojciech"},{"full_name":"Panagiotopoulos, A. Z.","last_name":"Panagiotopoulos","first_name":"A. Z."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Pȩkalski J, Rzadkowski W, Panagiotopoulos AZ. 2020. Shear-induced ordering in systems with competing interactions: A machine learning study. The Journal of chemical physics. 152(20), 204905.","chicago":"Pȩkalski, J., Wojciech Rzadkowski, and A. Z. Panagiotopoulos. “Shear-Induced Ordering in Systems with Competing Interactions: A Machine Learning Study.” The Journal of Chemical Physics. AIP Publishing, 2020. https://doi.org/10.1063/5.0005194.","ama":"Pȩkalski J, Rzadkowski W, Panagiotopoulos AZ. Shear-induced ordering in systems with competing interactions: A machine learning study. The Journal of chemical physics. 2020;152(20). doi:10.1063/5.0005194","apa":"Pȩkalski, J., Rzadkowski, W., & Panagiotopoulos, A. Z. (2020). Shear-induced ordering in systems with competing interactions: A machine learning study. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/5.0005194","ieee":"J. Pȩkalski, W. Rzadkowski, and A. Z. Panagiotopoulos, “Shear-induced ordering in systems with competing interactions: A machine learning study,” The Journal of chemical physics, vol. 152, no. 20. AIP Publishing, 2020.","short":"J. Pȩkalski, W. Rzadkowski, A.Z. Panagiotopoulos, The Journal of Chemical Physics 152 (2020).","mla":"Pȩkalski, J., et al. “Shear-Induced Ordering in Systems with Competing Interactions: A Machine Learning Study.” The Journal of Chemical Physics, vol. 152, no. 20, 204905, AIP Publishing, 2020, doi:10.1063/5.0005194."},"oa":1,"quality_controlled":"1","publisher":"AIP Publishing","date_created":"2020-06-14T22:00:49Z","date_published":"2020-05-29T00:00:00Z","doi":"10.1063/5.0005194","publication":"The Journal of chemical physics","day":"29","year":"2020","isi":1,"status":"public","type":"journal_article","article_type":"original","_id":"7956","department":[{"_id":"MiLe"}],"date_updated":"2024-02-28T13:00:28Z","intvolume":" 152","month":"05","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1063/5.0005194"}],"scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"When short-range attractions are combined with long-range repulsions in colloidal particle systems, complex microphases can emerge. Here, we study a system of isotropic particles, which can form lamellar structures or a disordered fluid phase when temperature is varied. We show that, at equilibrium, the lamellar structure crystallizes, while out of equilibrium, the system forms a variety of structures at different shear rates and temperatures above melting. The shear-induced ordering is analyzed by means of principal component analysis and artificial neural networks, which are applied to data of reduced dimensionality. Our results reveal the possibility of inducing ordering by shear, potentially providing a feasible route to the fabrication of ordered lamellar structures from isotropic particles.","lang":"eng"}],"ec_funded":1,"issue":"20","related_material":{"record":[{"relation":"dissertation_contains","id":"10759","status":"public"}]},"volume":152,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["10897690"]}},{"oa_version":"Preprint","abstract":[{"text":"We present the first deterministic wait-free long-lived snapshot algorithm, using only read and write operations, that guarantees polylogarithmic amortized step complexity in all executions. This is the first non-blocking snapshot algorithm, using reads and writes only, that has sub-linear amortized step complexity in executions of arbitrary length. The key to our construction is a novel implementation of a 2-component max array object which may be of independent interest.","lang":"eng"}],"month":"07","quality_controlled":"1","publisher":"Association for Computing Machinery","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://hal.archives-ouvertes.fr/hal-02860087/document"}],"oa":1,"day":"31","language":[{"iso":"eng"}],"publication":"Proceedings of the 39th Symposium on Principles of Distributed Computing","publication_identifier":{"isbn":["9781450375825"]},"year":"2020","publication_status":"published","date_published":"2020-07-31T00:00:00Z","doi":"10.1145/3382734.3406005","date_created":"2020-09-13T22:01:17Z","page":"31-40","_id":"8382","status":"public","type":"conference","conference":{"name":"PODC: Principles of Distributed Computing","start_date":"2020-08-03","end_date":"2020-08-07","location":"Virtual, Italy"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-02-28T12:54:30Z","citation":{"ista":"Baig MA, Hendler D, Milani A, Travers C. 2020. Long-lived snapshots with polylogarithmic amortized step complexity. Proceedings of the 39th Symposium on Principles of Distributed Computing. PODC: Principles of Distributed Computing, 31–40.","chicago":"Baig, Mirza Ahad, Danny Hendler, Alessia Milani, and Corentin Travers. “Long-Lived Snapshots with Polylogarithmic Amortized Step Complexity.” In Proceedings of the 39th Symposium on Principles of Distributed Computing, 31–40. Association for Computing Machinery, 2020. https://doi.org/10.1145/3382734.3406005.","ieee":"M. A. Baig, D. Hendler, A. Milani, and C. Travers, “Long-lived snapshots with polylogarithmic amortized step complexity,” in Proceedings of the 39th Symposium on Principles of Distributed Computing, Virtual, Italy, 2020, pp. 31–40.","short":"M.A. Baig, D. Hendler, A. Milani, C. Travers, in:, Proceedings of the 39th Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2020, pp. 31–40.","apa":"Baig, M. A., Hendler, D., Milani, A., & Travers, C. (2020). Long-lived snapshots with polylogarithmic amortized step complexity. In Proceedings of the 39th Symposium on Principles of Distributed Computing (pp. 31–40). Virtual, Italy: Association for Computing Machinery. https://doi.org/10.1145/3382734.3406005","ama":"Baig MA, Hendler D, Milani A, Travers C. Long-lived snapshots with polylogarithmic amortized step complexity. In: Proceedings of the 39th Symposium on Principles of Distributed Computing. Association for Computing Machinery; 2020:31-40. doi:10.1145/3382734.3406005","mla":"Baig, Mirza Ahad, et al. “Long-Lived Snapshots with Polylogarithmic Amortized Step Complexity.” Proceedings of the 39th Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2020, pp. 31–40, doi:10.1145/3382734.3406005."},"title":"Long-lived snapshots with polylogarithmic amortized step complexity","author":[{"last_name":"Baig","full_name":"Baig, Mirza Ahad","first_name":"Mirza Ahad","id":"3EDE6DE4-AA5A-11E9-986D-341CE6697425"},{"first_name":"Danny","last_name":"Hendler","full_name":"Hendler, Danny"},{"full_name":"Milani, Alessia","last_name":"Milani","first_name":"Alessia"},{"first_name":"Corentin","last_name":"Travers","full_name":"Travers, Corentin"}],"article_processing_charge":"No"},{"volume":101,"issue":"2","publication_status":"published","publication_identifier":{"eissn":["24699969"],"issn":["24699950"]},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1907.02077"}],"scopus_import":"1","intvolume":" 101","month":"01","abstract":[{"lang":"eng","text":"In the superconducting regime of FeTe(1−x)Sex, there exist two types of vortices which are distinguished by the presence or absence of zero-energy states in their core. To understand their origin, we examine the interplay of Zeeman coupling and superconducting pairings in three-dimensional metals with band inversion. Weak Zeeman fields are found to suppress intraorbital spin-singlet pairing, known to localize the states at the ends of the vortices on the surface. On the other hand, an orbital-triplet pairing is shown to be stable against Zeeman interactions, but leads to delocalized zero-energy Majorana modes which extend through the vortex. In contrast, the finite-energy vortex modes remain localized at the vortex ends even when the pairing is of orbital-triplet form. Phenomenologically, this manifests as an observed disappearance of zero-bias peaks within the cores of topological vortices upon an increase of the applied magnetic field. The presence of magnetic impurities in FeTe(1−x)Sex, which are attracted to the vortices, would lead to such Zeeman-induced delocalization of Majorana modes in a fraction of vortices that capture a large enough number of magnetic impurities. Our results provide an explanation for the dichotomy between topological and nontopological vortices recently observed in FeTe(1−x)Sex."}],"oa_version":"Preprint","department":[{"_id":"MiLe"}],"date_updated":"2024-02-28T13:11:13Z","article_type":"original","type":"journal_article","status":"public","_id":"7428","date_created":"2020-02-02T23:01:01Z","date_published":"2020-01-13T00:00:00Z","doi":"10.1103/PhysRevB.101.020504","year":"2020","isi":1,"publication":"Physical Review B","day":"13","oa":1,"publisher":"American Physical Society","quality_controlled":"1","external_id":{"isi":["000506843500001"],"arxiv":["1907.02077"]},"article_processing_charge":"No","author":[{"last_name":"Ghazaryan","full_name":"Ghazaryan, Areg","orcid":"0000-0001-9666-3543","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","first_name":"Areg"},{"first_name":"P. L.S.","last_name":"Lopes","full_name":"Lopes, P. L.S."},{"first_name":"Pavan","full_name":"Hosur, Pavan","last_name":"Hosur"},{"first_name":"Matthew J.","last_name":"Gilbert","full_name":"Gilbert, Matthew J."},{"first_name":"Pouyan","full_name":"Ghaemi, Pouyan","last_name":"Ghaemi"}],"title":"Effect of Zeeman coupling on the Majorana vortex modes in iron-based topological superconductors","citation":{"ista":"Ghazaryan A, Lopes PLS, Hosur P, Gilbert MJ, Ghaemi P. 2020. Effect of Zeeman coupling on the Majorana vortex modes in iron-based topological superconductors. Physical Review B. 101(2), 020504.","chicago":"Ghazaryan, Areg, P. L.S. Lopes, Pavan Hosur, Matthew J. Gilbert, and Pouyan Ghaemi. “Effect of Zeeman Coupling on the Majorana Vortex Modes in Iron-Based Topological Superconductors.” Physical Review B. American Physical Society, 2020. https://doi.org/10.1103/PhysRevB.101.020504.","ama":"Ghazaryan A, Lopes PLS, Hosur P, Gilbert MJ, Ghaemi P. Effect of Zeeman coupling on the Majorana vortex modes in iron-based topological superconductors. Physical Review B. 2020;101(2). doi:10.1103/PhysRevB.101.020504","apa":"Ghazaryan, A., Lopes, P. L. S., Hosur, P., Gilbert, M. J., & Ghaemi, P. (2020). Effect of Zeeman coupling on the Majorana vortex modes in iron-based topological superconductors. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.101.020504","ieee":"A. Ghazaryan, P. L. S. Lopes, P. Hosur, M. J. Gilbert, and P. Ghaemi, “Effect of Zeeman coupling on the Majorana vortex modes in iron-based topological superconductors,” Physical Review B, vol. 101, no. 2. American Physical Society, 2020.","short":"A. Ghazaryan, P.L.S. Lopes, P. Hosur, M.J. Gilbert, P. Ghaemi, Physical Review B 101 (2020).","mla":"Ghazaryan, Areg, et al. “Effect of Zeeman Coupling on the Majorana Vortex Modes in Iron-Based Topological Superconductors.” Physical Review B, vol. 101, no. 2, 020504, American Physical Society, 2020, doi:10.1103/PhysRevB.101.020504."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"020504"},{"article_number":"012224","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Wu, Yunfan, et al. “Retrieval of Cavity-Generated Atomic Spin Squeezing after Free-Space Release.” Physical Review A, vol. 102, no. 1, 012224, American Physical Society, 2020, doi:10.1103/PhysRevA.102.012224.","ama":"Wu Y, Krishnakumar R, Martínez-Rincón J, Malia BK, Hosten O, Kasevich MA. Retrieval of cavity-generated atomic spin squeezing after free-space release. Physical Review A. 2020;102(1). doi:10.1103/PhysRevA.102.012224","apa":"Wu, Y., Krishnakumar, R., Martínez-Rincón, J., Malia, B. K., Hosten, O., & Kasevich, M. A. (2020). Retrieval of cavity-generated atomic spin squeezing after free-space release. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.102.012224","short":"Y. Wu, R. Krishnakumar, J. Martínez-Rincón, B.K. Malia, O. Hosten, M.A. Kasevich, Physical Review A 102 (2020).","ieee":"Y. Wu, R. Krishnakumar, J. Martínez-Rincón, B. K. Malia, O. Hosten, and M. A. Kasevich, “Retrieval of cavity-generated atomic spin squeezing after free-space release,” Physical Review A, vol. 102, no. 1. American Physical Society, 2020.","chicago":"Wu, Yunfan, Rajiv Krishnakumar, Julián Martínez-Rincón, Benjamin K. Malia, Onur Hosten, and Mark A. Kasevich. “Retrieval of Cavity-Generated Atomic Spin Squeezing after Free-Space Release.” Physical Review A. American Physical Society, 2020. https://doi.org/10.1103/PhysRevA.102.012224.","ista":"Wu Y, Krishnakumar R, Martínez-Rincón J, Malia BK, Hosten O, Kasevich MA. 2020. Retrieval of cavity-generated atomic spin squeezing after free-space release. Physical Review A. 102(1), 012224."},"title":"Retrieval of cavity-generated atomic spin squeezing after free-space release","article_processing_charge":"No","external_id":{"arxiv":["1912.08334"],"isi":["000555104200011"]},"author":[{"first_name":"Yunfan","full_name":"Wu, Yunfan","last_name":"Wu"},{"last_name":"Krishnakumar","full_name":"Krishnakumar, Rajiv","first_name":"Rajiv"},{"first_name":"Julián","full_name":"Martínez-Rincón, Julián","last_name":"Martínez-Rincón"},{"full_name":"Malia, Benjamin K.","last_name":"Malia","first_name":"Benjamin K."},{"id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","first_name":"Onur","orcid":"0000-0002-2031-204X","full_name":"Hosten, Onur","last_name":"Hosten"},{"first_name":"Mark A.","full_name":"Kasevich, Mark A.","last_name":"Kasevich"}],"acknowledgement":"We thank N. Engelsen for comments on the manuscript. This work was supported by the Office of Naval Research, Vannevar Bush Faculty Fellowship, Department of Energy, and Defense Threat Reduction Agency. R.K. was partly supported by the AQT/INQNET program at Caltech.","oa":1,"quality_controlled":"1","publisher":"American Physical Society","publication":"Physical Review A","day":"30","year":"2020","isi":1,"date_created":"2020-08-30T22:01:10Z","date_published":"2020-07-30T00:00:00Z","doi":"10.1103/PhysRevA.102.012224","_id":"8319","status":"public","article_type":"original","type":"journal_article","date_updated":"2024-02-28T13:11:28Z","department":[{"_id":"OnHo"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We demonstrate that releasing atoms into free space from an optical lattice does not deteriorate cavity-generated spin squeezing for metrological purposes. In this work, an ensemble of 500000 spin-squeezed atoms in a high-finesse optical cavity with near-uniform atom-cavity coupling is prepared, released into free space, recaptured in the cavity, and probed. Up to ∼10 dB of metrologically relevant squeezing is retrieved for 700μs free-fall times, and decaying levels of squeezing are realized for up to 3 ms free-fall times. The degradation of squeezing results from loss of atom-cavity coupling homogeneity between the initial squeezed state generation and final collective state readout. A theoretical model is developed to quantify this degradation and this model is experimentally validated."}],"intvolume":" 102","month":"07","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1912.08334"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["24699934"],"issn":["24699926"]},"volume":102,"issue":"1"},{"department":[{"_id":"ChWo"},{"_id":"BeBi"}],"date_updated":"2024-02-28T13:58:11Z","article_type":"original","type":"journal_article","conference":{"name":"SCA: Symposium on Computer Animation","start_date":"2020-10-06","location":"Online Symposium","end_date":"2020-10-09"},"status":"public","_id":"8766","volume":39,"issue":"8","ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","month":"12","intvolume":" 39","abstract":[{"lang":"eng","text":"The “procedural” approach to animating ocean waves is the dominant algorithm for animating larger bodies of water in\r\ninteractive applications as well as in off-line productions — it provides high visual quality with a low computational demand. In this paper, we widen the applicability of procedural water wave animation with an extension that guarantees the satisfaction of boundary conditions imposed by terrain while still approximating physical wave behavior. In combination with a particle system that models wave breaking, foam, and spray, this allows us to naturally model waves interacting with beaches and rocks. Our system is able to animate waves at large scales at interactive frame rates on a commodity PC."}],"oa_version":"None","author":[{"full_name":"Jeschke, Stefan","last_name":"Jeschke","first_name":"Stefan","id":"44D6411A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Christian","id":"400429CC-F248-11E8-B48F-1D18A9856A87","full_name":"Hafner, Christian","last_name":"Hafner"},{"last_name":"Chentanez","full_name":"Chentanez, Nuttapong","first_name":"Nuttapong"},{"last_name":"Macklin","full_name":"Macklin, Miles","first_name":"Miles"},{"full_name":"Müller-Fischer, Matthias","last_name":"Müller-Fischer","first_name":"Matthias"},{"first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J"}],"article_processing_charge":"No","external_id":{"isi":["000591780400005"]},"title":"Making procedural water waves boundary-aware","citation":{"short":"S. Jeschke, C. Hafner, N. Chentanez, M. Macklin, M. Müller-Fischer, C. Wojtan, Computer Graphics Forum 39 (2020) 47–54.","ieee":"S. Jeschke, C. Hafner, N. Chentanez, M. Macklin, M. Müller-Fischer, and C. Wojtan, “Making procedural water waves boundary-aware,” Computer Graphics forum, vol. 39, no. 8. Wiley, pp. 47–54, 2020.","apa":"Jeschke, S., Hafner, C., Chentanez, N., Macklin, M., Müller-Fischer, M., & Wojtan, C. (2020). Making procedural water waves boundary-aware. Computer Graphics Forum. Online Symposium: Wiley. https://doi.org/10.1111/cgf.14100","ama":"Jeschke S, Hafner C, Chentanez N, Macklin M, Müller-Fischer M, Wojtan C. Making procedural water waves boundary-aware. Computer Graphics forum. 2020;39(8):47-54. doi:10.1111/cgf.14100","mla":"Jeschke, Stefan, et al. “Making Procedural Water Waves Boundary-Aware.” Computer Graphics Forum, vol. 39, no. 8, Wiley, 2020, pp. 47–54, doi:10.1111/cgf.14100.","ista":"Jeschke S, Hafner C, Chentanez N, Macklin M, Müller-Fischer M, Wojtan C. 2020. Making procedural water waves boundary-aware. Computer Graphics forum. 39(8), 47–54.","chicago":"Jeschke, Stefan, Christian Hafner, Nuttapong Chentanez, Miles Macklin, Matthias Müller-Fischer, and Chris Wojtan. “Making Procedural Water Waves Boundary-Aware.” Computer Graphics Forum. Wiley, 2020. https://doi.org/10.1111/cgf.14100."},"user_id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"2533E772-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","grant_number":"638176"},{"call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling"}],"page":"47-54","doi":"10.1111/cgf.14100","date_published":"2020-12-01T00:00:00Z","date_created":"2020-11-17T10:47:48Z","isi":1,"year":"2020","day":"01","publication":"Computer Graphics forum","publisher":"Wiley","quality_controlled":"1"},{"title":"Reinforcement learning of risk-constrained policies in Markov decision processes","article_processing_charge":"No","external_id":{"arxiv":["2002.12086"]},"author":[{"full_name":"Brázdil, Tomáš","last_name":"Brázdil","first_name":"Tomáš"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"last_name":"Novotný","full_name":"Novotný, Petr","first_name":"Petr"},{"last_name":"Vahala","full_name":"Vahala, Jiří","first_name":"Jiří"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Brázdil T, Chatterjee K, Novotný P, Vahala J. 2020. Reinforcement learning of risk-constrained policies in Markov decision processes. Proceedings of the 34th AAAI Conference on Artificial Intelligence. 34(06), 9794–9801.","chicago":"Brázdil, Tomáš, Krishnendu Chatterjee, Petr Novotný, and Jiří Vahala. “Reinforcement Learning of Risk-Constrained Policies in Markov Decision Processes.” Proceedings of the 34th AAAI Conference on Artificial Intelligence. Association for the Advancement of Artificial Intelligence, 2020. https://doi.org/10.1609/aaai.v34i06.6531.","apa":"Brázdil, T., Chatterjee, K., Novotný, P., & Vahala, J. (2020). Reinforcement learning of risk-constrained policies in Markov decision processes. Proceedings of the 34th AAAI Conference on Artificial Intelligence. New York, NY, United States: Association for the Advancement of Artificial Intelligence. https://doi.org/10.1609/aaai.v34i06.6531","ama":"Brázdil T, Chatterjee K, Novotný P, Vahala J. Reinforcement learning of risk-constrained policies in Markov decision processes. Proceedings of the 34th AAAI Conference on Artificial Intelligence. 2020;34(06):9794-9801. doi:10.1609/aaai.v34i06.6531","ieee":"T. Brázdil, K. Chatterjee, P. Novotný, and J. Vahala, “Reinforcement learning of risk-constrained policies in Markov decision processes,” Proceedings of the 34th AAAI Conference on Artificial Intelligence, vol. 34, no. 06. Association for the Advancement of Artificial Intelligence, pp. 9794–9801, 2020.","short":"T. Brázdil, K. Chatterjee, P. Novotný, J. Vahala, Proceedings of the 34th AAAI Conference on Artificial Intelligence 34 (2020) 9794–9801.","mla":"Brázdil, Tomáš, et al. “Reinforcement Learning of Risk-Constrained Policies in Markov Decision Processes.” Proceedings of the 34th AAAI Conference on Artificial Intelligence, vol. 34, no. 06, Association for the Advancement of Artificial Intelligence, 2020, pp. 9794–801, doi:10.1609/aaai.v34i06.6531."},"project":[{"name":"Game Theory","grant_number":"S11407","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425"}],"date_created":"2024-03-04T08:07:22Z","date_published":"2020-04-03T00:00:00Z","doi":"10.1609/aaai.v34i06.6531","page":"9794-9801","publication":"Proceedings of the 34th AAAI Conference on Artificial Intelligence","day":"03","year":"2020","oa":1,"publisher":"Association for the Advancement of Artificial Intelligence","quality_controlled":"1","acknowledgement":"Krishnendu Chatterjee is supported by the Austrian Science Fund (FWF) NFN Grant No. S11407-N23 (RiSE/SHiNE), and COST Action GAMENET. Tomas Brazdil is supported by the Grant Agency of Masaryk University grant no. MUNI/G/0739/2017 and by the Czech Science Foundation grant No. 18-11193S. Petr Novotny and Jirı Vahala are supported by the Czech Science Foundation grant No. GJ19-15134Y.","department":[{"_id":"KrCh"}],"date_updated":"2024-03-04T08:30:16Z","keyword":["General Medicine"],"status":"public","conference":{"location":"New York, NY, United States","end_date":"2020-02-12","start_date":"2020-02-07","name":"AAAI: Conference on Artificial Intelligence"},"type":"journal_article","article_type":"original","_id":"15055","issue":"06","volume":34,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["2374-3468"]},"intvolume":" 34","month":"04","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2002.12086"}],"oa_version":"Preprint","abstract":[{"text":"Markov decision processes (MDPs) are the defacto framework for sequential decision making in the presence of stochastic uncertainty. A classical optimization criterion for MDPs is to maximize the expected discounted-sum payoff, which ignores low probability catastrophic events with highly negative impact on the system. On the other hand, risk-averse policies require the probability of undesirable events to be below a given threshold, but they do not account for optimization of the expected payoff. We consider MDPs with discounted-sum payoff with failure states which represent catastrophic outcomes. The objective of risk-constrained planning is to maximize the expected discounted-sum payoff among risk-averse policies that ensure the probability to encounter a failure state is below a desired threshold. Our main contribution is an efficient risk-constrained planning algorithm that combines UCT-like search with a predictor learned through interaction with the MDP (in the style of AlphaZero) and with a risk-constrained action selection via linear programming. We demonstrate the effectiveness of our approach with experiments on classical MDPs from the literature, including benchmarks with an order of 106 states.","lang":"eng"}]},{"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. ","quality_controlled":"1","publisher":"American Association for the Advancement of Science","oa":1,"has_accepted_license":"1","year":"2020","day":"01","publication":"Science Advances","date_published":"2020-07-01T00:00:00Z","doi":"10.1126/sciadv.aaw7824","date_created":"2024-03-04T09:41:57Z","article_number":"aaw7824","citation":{"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.","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.","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.","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).","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"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Sangsoon","full_name":"Park, Sangsoon","last_name":"Park"},{"id":"C407B586-6052-11E9-B3AE-7006E6697425","first_name":"Murat","last_name":"Artan","orcid":"0000-0001-8945-6992","full_name":"Artan, Murat"},{"last_name":"Han","full_name":"Han, Seung Hyun","first_name":"Seung Hyun"},{"last_name":"Park","full_name":"Park, Hae-Eun H.","first_name":"Hae-Eun H."},{"last_name":"Jung","full_name":"Jung, Yoonji","first_name":"Yoonji"},{"full_name":"Hwang, Ara B.","last_name":"Hwang","first_name":"Ara B."},{"last_name":"Shin","full_name":"Shin, Won Sik","first_name":"Won Sik"},{"first_name":"Kyong-Tai","last_name":"Kim","full_name":"Kim, Kyong-Tai"},{"last_name":"Lee","full_name":"Lee, Seung-Jae V.","first_name":"Seung-Jae V."}],"article_processing_charge":"No","title":"VRK-1 extends life span by activation of AMPK via phosphorylation","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."}],"oa_version":"Published Version","month":"07","intvolume":" 6","publication_identifier":{"eissn":["2375-2548"]},"publication_status":"published","file":[{"date_created":"2024-03-04T09:46:41Z","file_name":"2020_ScienceAdvances_Park.pdf","creator":"dernst","date_updated":"2024-03-04T09:46:41Z","file_size":1864415,"file_id":"15058","checksum":"a37157cd0de709dce5fe03f4a31cd0b6","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"volume":6,"issue":"27","license":"https://creativecommons.org/licenses/by-nc/4.0/","_id":"15057","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"status":"public","date_updated":"2024-03-04T09:52:09Z","ddc":["570"],"department":[{"_id":"MaDe"}],"file_date_updated":"2024-03-04T09:46:41Z"},{"year":"2020","day":"08","publication":"Proceedings of the National Academy of Sciences","page":"22101-22112","doi":"10.1073/pnas.1917269117","date_published":"2020-09-08T00:00:00Z","date_created":"2024-03-04T10:03:52Z","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. ","quality_controlled":"1","publisher":"Proceedings of the National Academy of Sciences","oa":1,"citation":{"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.","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","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","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.","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.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Pinotsis","full_name":"Pinotsis, Nikos","first_name":"Nikos"},{"full_name":"Zielinska, Karolina","last_name":"Zielinska","first_name":"Karolina"},{"last_name":"Babuta","full_name":"Babuta, Mrigya","first_name":"Mrigya"},{"last_name":"Arolas","full_name":"Arolas, Joan L.","first_name":"Joan L."},{"full_name":"Kostan, Julius","last_name":"Kostan","first_name":"Julius"},{"full_name":"Khan, Muhammad Bashir","last_name":"Khan","first_name":"Muhammad Bashir"},{"full_name":"Schreiner, Claudia","last_name":"Schreiner","first_name":"Claudia"},{"id":"41F1F098-F248-11E8-B48F-1D18A9856A87","first_name":"Anita P","full_name":"Testa Salmazo, Anita P","last_name":"Testa Salmazo"},{"full_name":"Ciccarelli, Luciano","last_name":"Ciccarelli","first_name":"Luciano"},{"first_name":"Martin","last_name":"Puchinger","full_name":"Puchinger, Martin"},{"first_name":"Eirini A.","full_name":"Gkougkoulia, Eirini A.","last_name":"Gkougkoulia"},{"full_name":"Ribeiro, Euripedes de Almeida","last_name":"Ribeiro","first_name":"Euripedes de Almeida"},{"full_name":"Marlovits, Thomas C.","last_name":"Marlovits","first_name":"Thomas C."},{"last_name":"Bhattacharya","full_name":"Bhattacharya, Alok","first_name":"Alok"},{"full_name":"Djinovic-Carugo, Kristina","last_name":"Djinovic-Carugo","first_name":"Kristina"}],"article_processing_charge":"No","external_id":{"pmid":["32848067"]},"title":"Calcium modulates the domain flexibility and function of an α-actinin similar to the ancestral α-actinin","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":117,"issue":"36","abstract":[{"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.","lang":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"}],"oa_version":"Published Version","pmid":1,"main_file_link":[{"url":"https://doi.org/10.1073/pnas.191726911","open_access":"1"}],"month":"09","intvolume":" 117","date_updated":"2024-03-04T10:14:44Z","department":[{"_id":"CaBe"}],"_id":"15061","article_type":"original","type":"journal_article","status":"public"},{"page":"455-480","date_created":"2024-03-04T10:47:49Z","doi":"10.1007/s41468-020-00058-8","date_published":"2020-12-01T00:00:00Z","year":"2020","has_accepted_license":"1","publication":"Journal of Applied and Computational Topology","day":"01","oa":1,"publisher":"Springer Nature","quality_controlled":"1","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)","author":[{"first_name":"U.","last_name":"Bauer","full_name":"Bauer, U."},{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner"},{"full_name":"Jablonski, Grzegorz","orcid":"0000-0002-3536-9866","last_name":"Jablonski","first_name":"Grzegorz","id":"4483EF78-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Mrozek","full_name":"Mrozek, M.","first_name":"M."}],"title":"Čech-Delaunay gradient flow and homology inference for self-maps","citation":{"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.","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.","short":"U. Bauer, H. Edelsbrunner, G. Jablonski, M. Mrozek, Journal of Applied and Computational Topology 4 (2020) 455–480.","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","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","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"4","volume":4,"publication_status":"published","publication_identifier":{"eissn":["2367-1734"],"issn":["2367-1726"]},"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"15065","checksum":"eed1168b6e66cd55272c19bb7fca8a1c","success":1,"creator":"dernst","date_updated":"2024-03-04T10:52:42Z","file_size":851190,"date_created":"2024-03-04T10:52:42Z","file_name":"2020_JourApplCompTopology_Bauer.pdf"}],"scopus_import":"1","intvolume":" 4","month":"12","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."}],"oa_version":"Published Version","file_date_updated":"2024-03-04T10:52:42Z","department":[{"_id":"HeEd"}],"date_updated":"2024-03-04T10:54:04Z","ddc":["500"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","_id":"15064"},{"department":[{"_id":"LaEr"}],"date_updated":"2024-03-04T10:33:15Z","status":"public","keyword":["General Medicine"],"type":"journal_article","article_type":"original","_id":"15063","volume":1,"issue":"1","ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2690-1005","2690-0998"]},"publication_status":"published","month":"11","intvolume":" 1","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1908.01653"}],"oa_version":"Preprint","abstract":[{"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).","lang":"eng"}],"title":"Optimal lower bound on the least singular value of the shifted Ginibre ensemble","author":[{"id":"42198EFA-F248-11E8-B48F-1D18A9856A87","first_name":"Giorgio","last_name":"Cipolloni","full_name":"Cipolloni, Giorgio","orcid":"0000-0002-4901-7992"},{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","full_name":"Erdös, László","orcid":"0000-0001-5366-9603","last_name":"Erdös"},{"id":"408ED176-F248-11E8-B48F-1D18A9856A87","first_name":"Dominik J","last_name":"Schröder","full_name":"Schröder, Dominik J","orcid":"0000-0002-2904-1856"}],"article_processing_charge":"No","external_id":{"arxiv":["1908.01653"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Probability and Mathematical Physics 1 (2020) 101–146.","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","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","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.","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.","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."},"project":[{"name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"},{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"doi":"10.2140/pmp.2020.1.101","date_published":"2020-11-16T00:00:00Z","date_created":"2024-03-04T10:27:57Z","page":"101-146","day":"16","publication":"Probability and Mathematical Physics","year":"2020","publisher":"Mathematical Sciences Publishers","quality_controlled":"1","oa":1,"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"},{"publisher":"IEEE","quality_controlled":"1","month":"07","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."}],"oa_version":"None","acknowledgement":"This work has been financially supported by Comunidad de Madrid S2018/NMT-4333 ARTINLARA-CM projects, and “FUNDACIÓN SENER” REFTA projects.","date_published":"2020-07-08T00:00:00Z","doi":"10.23919/eucap48036.2020.9135962","date_created":"2024-03-04T09:57:48Z","publication_identifier":{"eisbn":["9788831299008"]},"publication_status":"published","year":"2020","day":"08","publication":"14th European Conference on Antennas and Propagation","language":[{"iso":"eng"}],"type":"conference","conference":{"name":"EuCAP: European Conference on Antennas and Propagation","start_date":"2020-03-15","end_date":"2020-03-20","location":"Copenhagen, Denmark"},"status":"public","_id":"15059","author":[{"first_name":"Michal","full_name":"Wasiak, Michal","last_name":"Wasiak"},{"first_name":"Gabriel Santamaria","last_name":"Botello","full_name":"Botello, Gabriel Santamaria"},{"last_name":"Abdalmalak","full_name":"Abdalmalak, Kerlos Atia","first_name":"Kerlos Atia"},{"full_name":"Sedlmeir, Florian","last_name":"Sedlmeir","first_name":"Florian"},{"id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","first_name":"Alfredo R","orcid":"0000-0001-6249-5860","full_name":"Rueda Sanchez, Alfredo R","last_name":"Rueda Sanchez"},{"first_name":"Daniel","full_name":"Segovia-Vargas, Daniel","last_name":"Segovia-Vargas"},{"full_name":"Schwefel, Harald G. L.","last_name":"Schwefel","first_name":"Harald G. L."},{"first_name":"Luis Enrique Garcia","last_name":"Munoz","full_name":"Munoz, Luis Enrique Garcia"}],"article_processing_charge":"No","title":"Compact millimeter and submillimeter-wave photonic radiometer for cubesats","department":[{"_id":"JoFi"}],"citation":{"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.","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","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.","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.","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.","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."},"date_updated":"2024-03-04T10:02:49Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"type":"conference","conference":{"start_date":"2020-10-12","end_date":"2020-10-16","location":"Virtual","name":"DISC: Symposium on Distributed Computing"},"tmp":{"short":"CC BY (3.0)","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)"},"status":"public","_id":"15074","file_date_updated":"2024-03-05T07:08:27Z","department":[{"_id":"DaAl"}],"date_updated":"2024-03-05T07:13:13Z","ddc":["000"],"scopus_import":"1","alternative_title":["LIPIcs"],"month":"10","intvolume":" 179","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","volume":179,"related_material":{"record":[{"status":"public","id":"9678","relation":"later_version"}]},"license":"https://creativecommons.org/licenses/by/3.0/","publication_status":"published","file":[{"date_created":"2024-03-05T07:08:27Z","file_name":"2020_LIPIcs_Brandt.pdf","date_updated":"2024-03-05T07:08:27Z","file_size":303529,"creator":"dernst","file_id":"15075","checksum":"23e2d9321aef53092dc1e24a8ab82d72","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"article_number":"40","author":[{"first_name":"Sebastian","full_name":"Brandt, Sebastian","last_name":"Brandt"},{"first_name":"Barbara","full_name":"Keller, Barbara","last_name":"Keller"},{"orcid":"0000-0002-6432-6646","full_name":"Rybicki, Joel","last_name":"Rybicki","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","first_name":"Joel"},{"full_name":"Suomela, Jukka","last_name":"Suomela","first_name":"Jukka"},{"first_name":"Jara","full_name":"Uitto, Jara","last_name":"Uitto"}],"external_id":{"arxiv":["2005.07761"]},"article_processing_charge":"No","title":"Brief announcement: Efficient load-balancing through distributed token dropping","citation":{"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.","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.","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","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.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","oa":1,"doi":"10.4230/LIPIcs.DISC.2020.40","date_published":"2020-10-07T00:00:00Z","date_created":"2024-03-05T07:09:12Z","has_accepted_license":"1","year":"2020","day":"07","publication":"34th International Symposium on Distributed Computing"},{"file_date_updated":"2024-03-05T07:25:15Z","department":[{"_id":"DaAl"}],"date_updated":"2024-03-05T07:35:53Z","ddc":["000"],"conference":{"name":"ICALP: International Colloquium on Automata, Languages, and Programming","location":"Saarbrücken, Germany, Virtual","end_date":"2020-07-11","start_date":"2020-07-08"},"tmp":{"short":"CC BY (3.0)","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)"},"type":"conference","status":"public","_id":"15077","ec_funded":1,"related_material":{"record":[{"id":"8286","status":"public","relation":"later_version"}]},"volume":168,"publication_status":"published","language":[{"iso":"eng"}],"file":[{"date_updated":"2024-03-05T07:25:15Z","file_size":782987,"creator":"dernst","date_created":"2024-03-05T07:25:15Z","file_name":"2020_LIPIcs_Alistarh.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"15078","checksum":"e5eb16199f4ccfd77a321977eb3f026f","success":1}],"alternative_title":["LIPIcs"],"scopus_import":"1","intvolume":" 168","month":"06","abstract":[{"lang":"eng","text":"We consider the following dynamic load-balancing process: given an underlying graph G with n nodes, in each step t≥ 0, one unit of load is created, and placed at a randomly chosen graph node. In the same step, the chosen node picks a random neighbor, and the two nodes balance their loads by averaging them. We are interested in the expected gap between the minimum and maximum loads at nodes as the process progresses, and its dependence on n and on the graph structure. Variants of the above graphical balanced allocation process have been studied previously by Peres, Talwar, and Wieder [Peres et al., 2015], and by Sauerwald and Sun [Sauerwald and Sun, 2015]. These authors left as open the question of characterizing the gap in the case of cycle graphs in the dynamic case, where weights are created during the algorithm’s execution. For this case, the only known upper bound is of 𝒪(n log n), following from a majorization argument due to [Peres et al., 2015], which analyzes a related graphical allocation process. In this paper, we provide an upper bound of 𝒪 (√n log n) on the expected gap of the above process for cycles of length n. We introduce a new potential analysis technique, which enables us to bound the difference in load between k-hop neighbors on the cycle, for any k ≤ n/2. We complement this with a \"gap covering\" argument, which bounds the maximum value of the gap by bounding its value across all possible subsets of a certain structure, and recursively bounding the gaps within each subset. We provide analytical and experimental evidence that our upper bound on the gap is tight up to a logarithmic factor."}],"oa_version":"Published Version","article_processing_charge":"No","external_id":{"arxiv":["2003.09297"]},"author":[{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh"},{"id":"3279A00C-F248-11E8-B48F-1D18A9856A87","first_name":"Giorgi","full_name":"Nadiradze, Giorgi","orcid":"0000-0001-5634-0731","last_name":"Nadiradze"},{"full_name":"Sabour, Amirmojtaba","last_name":"Sabour","id":"bcc145fd-e77f-11ea-ae8b-80d661dbff67","first_name":"Amirmojtaba"}],"title":"Dynamic averaging load balancing on cycles","citation":{"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.","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.","short":"D.-A. Alistarh, G. Nadiradze, A. Sabour, in:, 47th International Colloquium on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020.","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","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","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"call_identifier":"H2020","_id":"268A44D6-B435-11E9-9278-68D0E5697425","name":"Elastic Coordination for Scalable Machine Learning","grant_number":"805223"}],"article_number":"7","date_created":"2024-03-05T07:25:37Z","date_published":"2020-06-29T00:00:00Z","doi":"10.4230/LIPIcs.ICALP.2020.7","year":"2020","has_accepted_license":"1","publication":"47th International Colloquium on Automata, Languages, and Programming","day":"29","oa":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","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"},{"oa_version":"Published Version","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.","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."}],"month":"04","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://www1.pub.informatik.uni-wuerzburg.de/eurocg2020/data/uploads/papers/eurocg20_paper_56.pdf"}],"oa":1,"day":"01","language":[{"iso":"eng"}],"publication":"36th European Workshop on Computational Geometry","publication_status":"published","year":"2020","date_published":"2020-04-01T00:00:00Z","date_created":"2024-03-05T08:57:17Z","article_number":"56","_id":"15082","status":"public","type":"conference","conference":{"start_date":"2020-03-16","end_date":"2020-03-18","location":"Würzburg, Germany, Virtual","name":"EuroCG: European Workshop on Computational Geometry"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Aichholzer, Oswin, et al. “Disjoint Tree-Compatible Plane Perfect Matchings.” 36th European Workshop on Computational Geometry, 56, 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.","short":"O. Aichholzer, J. Obmann, P. Patak, D. Perz, J. Tkadlec, in:, 36th European Workshop on Computational Geometry, 2020.","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.","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."},"date_updated":"2024-03-05T09:00:07Z","title":"Disjoint tree-compatible plane perfect matchings","department":[{"_id":"KrCh"},{"_id":"UlWa"}],"author":[{"full_name":"Aichholzer, Oswin","last_name":"Aichholzer","first_name":"Oswin"},{"last_name":"Obmann","full_name":"Obmann, Julia","first_name":"Julia"},{"full_name":"Patak, Pavel","last_name":"Patak","first_name":"Pavel","id":"B593B804-1035-11EA-B4F1-947645A5BB83"},{"first_name":"Daniel","last_name":"Perz","full_name":"Perz, Daniel"},{"id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","first_name":"Josef","full_name":"Tkadlec, Josef","orcid":"0000-0002-1097-9684","last_name":"Tkadlec"}],"article_processing_charge":"No"},{"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1932-6157"],"eissn":["1941-7330"]},"publication_status":"published","issue":"6","volume":48,"oa_version":"Preprint","abstract":[{"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.","lang":"eng"}],"month":"12","intvolume":" 48","main_file_link":[{"url":"https://arxiv.org/abs/1901.01375","open_access":"1"}],"date_updated":"2024-03-06T08:28:50Z","department":[{"_id":"MaMo"}],"_id":"6748","status":"public","article_type":"original","type":"journal_article","day":"11","publication":"Annals of Statistics","isi":1,"year":"2020","date_published":"2020-12-11T00:00:00Z","doi":"10.1214/20-AOS1945","date_created":"2019-07-31T09:39:42Z","page":"3619-3642","quality_controlled":"1","publisher":"Institute of Mathematical Statistics","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","short":"A. Javanmard, M. Mondelli, A. Montanari, Annals of Statistics 48 (2020) 3619–3642.","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","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."},"title":"Analysis of a two-layer neural network via displacement convexity","author":[{"full_name":"Javanmard, Adel","last_name":"Javanmard","first_name":"Adel"},{"full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020","last_name":"Mondelli","first_name":"Marco","id":"27EB676C-8706-11E9-9510-7717E6697425"},{"first_name":"Andrea","full_name":"Montanari, Andrea","last_name":"Montanari"}],"article_processing_charge":"No","external_id":{"isi":["000598369200021"],"arxiv":["1901.01375"]}},{"oa_version":"None","abstract":[{"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.","lang":"eng"}],"intvolume":" 16","month":"06","publisher":"European Mathematical Society","quality_controlled":"1","publication":"Oberwolfach Reports","language":[{"iso":"eng"}],"day":"04","year":"2020","publication_status":"published","publication_identifier":{"issn":["1660-8933"]},"date_created":"2024-03-04T11:36:31Z","issue":"2","doi":"10.4171/owr/2019/23","date_published":"2020-06-04T00:00:00Z","volume":16,"page":"1357-1417","_id":"15070","keyword":["Organic Chemistry","Biochemistry"],"status":"public","article_type":"original","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-03-11T09:20:34Z","citation":{"ista":"Anderson L, Hausel T, Mazzeo R, Schaposnik L. 2020. Geometry and physics of Higgs bundles. Oberwolfach Reports. 16(2), 1357–1417.","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.","short":"L. Anderson, T. Hausel, R. Mazzeo, L. Schaposnik, Oberwolfach Reports 16 (2020) 1357–1417.","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","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","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."},"department":[{"_id":"TaHa"}],"title":"Geometry and physics of Higgs bundles","article_processing_charge":"No","author":[{"first_name":"Lara","last_name":"Anderson","full_name":"Anderson, Lara"},{"last_name":"Hausel","full_name":"Hausel, Tamás","first_name":"Tamás","id":"4A0666D8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Mazzeo","full_name":"Mazzeo, Rafe","first_name":"Rafe"},{"first_name":"Laura","last_name":"Schaposnik","full_name":"Schaposnik, Laura"}]},{"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.","quality_controlled":"1","publisher":"The Royal Society","oa":1,"day":"01","publication":"Royal Society Open Science","has_accepted_license":"1","isi":1,"year":"2020","doi":"10.1098/rsos.200599","date_published":"2020-06-01T00:00:00Z","date_created":"2020-11-08T23:01:25Z","article_number":"200599","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","short":"A.K. Klose, V. Karle, R. Winkelmann, J.F. Donges, Royal Society Open Science 7 (2020).","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","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."},"title":"Emergence of cascading dynamics in interacting tipping elements of ecology and climate: Cascading dynamics in tipping elements","author":[{"first_name":"Ann Kristin","last_name":"Klose","full_name":"Klose, Ann Kristin"},{"id":"D7C012AE-D7ED-11E9-95E8-1EC5E5697425","first_name":"Volker","orcid":"0000-0002-6963-0129","full_name":"Karle, Volker","last_name":"Karle"},{"full_name":"Winkelmann, Ricarda","last_name":"Winkelmann","first_name":"Ricarda"},{"last_name":"Donges","full_name":"Donges, Jonathan F.","first_name":"Jonathan F."}],"external_id":{"arxiv":["1910.12042"],"isi":["000545625200001"]},"article_processing_charge":"No","oa_version":"Published Version","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."}],"month":"06","intvolume":" 7","scopus_import":"1","file":[{"success":1,"checksum":"5505c445de373bfd836eb4d3b48b1f37","file_id":"8748","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2020_RoyalSocOpenScience_Klose.pdf","date_created":"2020-11-09T09:07:11Z","creator":"dernst","file_size":1611485,"date_updated":"2020-11-09T09:07:11Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["20545703"]},"publication_status":"published","issue":"6","volume":7,"_id":"8741","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["530","550"],"date_updated":"2024-03-12T12:31:30Z","department":[{"_id":"MiLe"}],"file_date_updated":"2020-11-09T09:07:11Z"},{"issue":"1","volume":73,"publication_identifier":{"issn":["1022-2588"]},"publication_status":"published","file":[{"date_updated":"2024-03-12T10:12:33Z","file_size":579291,"creator":"dernst","date_created":"2020-06-17T10:50:13Z","file_name":"2020_VOEB_Ernst.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"fee784f15a489deb7def6ccf8c5bf8c3","file_id":"7970"}],"language":[{"iso":"ger"}],"scopus_import":"1","month":"04","intvolume":" 73","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."}],"oa_version":"Published Version","file_date_updated":"2024-03-12T10:12:33Z","department":[{"_id":"E-Lib"}],"date_updated":"2024-03-12T10:12:33Z","ddc":["020"],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"7687","page":"46-59","date_published":"2020-04-28T00:00:00Z","doi":"10.31263/voebm.v73i1.3491","date_created":"2020-04-28T08:37:38Z","popular_science":"1","has_accepted_license":"1","year":"2020","day":"28","publication":"Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare","publisher":"Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare","oa":1,"author":[{"id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","first_name":"Doris","orcid":"0000-0002-2354-0195","full_name":"Ernst, Doris","last_name":"Ernst"},{"last_name":"Novotny","full_name":"Novotny, Gertraud","first_name":"Gertraud"},{"full_name":"Schönher, Eva Maria","last_name":"Schönher","first_name":"Eva Maria"}],"article_processing_charge":"No","title":"(Core Trust) Seal your repository!","citation":{"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.","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.","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.","ista":"Ernst D, Novotny G, Schönher EM. 2020. (Core Trust) Seal your repository! Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. 73(1), 46–59."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"day":"19","publication":"Oberwolfach Reports","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1660-8933"]},"year":"2020","publication_status":"published","doi":"10.4171/owr/2019/56","date_published":"2020-11-19T00:00:00Z","volume":16,"issue":"4","date_created":"2024-03-05T07:54:44Z","page":"3459-3527","oa_version":"None","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."}],"month":"11","intvolume":" 16","quality_controlled":"1","publisher":"European Mathematical Society","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Erdös L, Götze F, Guionnet A. 2020. Random matrices. Oberwolfach Reports. 16(4), 3459–3527.","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.","short":"L. Erdös, F. Götze, A. Guionnet, Oberwolfach Reports 16 (2020) 3459–3527.","apa":"Erdös, L., Götze, F., & Guionnet, A. (2020). Random matrices. Oberwolfach Reports. European Mathematical Society. https://doi.org/10.4171/owr/2019/56","ama":"Erdös L, Götze F, Guionnet A. Random matrices. Oberwolfach Reports. 2020;16(4):3459-3527. doi:10.4171/owr/2019/56","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."},"date_updated":"2024-03-12T12:25:18Z","department":[{"_id":"LaEr"}],"title":"Random matrices","author":[{"last_name":"Erdös","orcid":"0000-0001-5366-9603","full_name":"Erdös, László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László"},{"first_name":"Friedrich","full_name":"Götze, Friedrich","last_name":"Götze"},{"first_name":"Alice","full_name":"Guionnet, Alice","last_name":"Guionnet"}],"article_processing_charge":"No","_id":"15079","status":"public","type":"journal_article","article_type":"original"},{"day":"10","language":[{"iso":"eng"}],"publication":"Oberwolfach Reports","publication_identifier":{"issn":["1660-8933"]},"publication_status":"published","year":"2020","volume":16,"doi":"10.4171/owr/2019/41","issue":"3","date_published":"2020-09-10T00:00:00Z","date_created":"2024-03-04T11:46:12Z","page":"2541-2603","oa_version":"None","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."}],"month":"09","intvolume":" 16","publisher":"European Mathematical Society","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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","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","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.","short":"C. Hainzl, B. Schlein, R. Seiringer, S. Warzel, Oberwolfach Reports 16 (2020) 2541–2603.","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.","ista":"Hainzl C, Schlein B, Seiringer R, Warzel S. 2020. Many-body quantum systems. Oberwolfach Reports. 16(3), 2541–2603."},"date_updated":"2024-03-12T12:02:00Z","department":[{"_id":"RoSe"}],"title":"Many-body quantum systems","author":[{"first_name":"Christian","full_name":"Hainzl, Christian","last_name":"Hainzl"},{"first_name":"Benjamin","full_name":"Schlein, Benjamin","last_name":"Schlein"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","last_name":"Seiringer"},{"full_name":"Warzel, Simone","last_name":"Warzel","first_name":"Simone"}],"article_processing_charge":"No","_id":"15072","status":"public","article_type":"original","type":"journal_article"},{"oa":1,"publisher":"MDPI","quality_controlled":"1","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. ","date_created":"2024-03-04T11:41:31Z","date_published":"2020-11-02T00:00:00Z","doi":"10.3390/ecm2020-07116","publication":"Proceedings of 1st International Electronic Conference on Microbiology","day":"02","year":"2020","has_accepted_license":"1","title":"Characterization of methanosarcina mazei JL01 isolated from holocene arctic permafrost and study of the archaeon cooperation with bacterium Sphaerochaeta associata GLS2T","article_processing_charge":"Yes","author":[{"full_name":"Oshurkova, Viktoriia","last_name":"Oshurkova","first_name":"Viktoriia"},{"full_name":"Troshina, Olga","last_name":"Troshina","first_name":"Olga"},{"full_name":"Trubitsyn, Vladimir","last_name":"Trubitsyn","first_name":"Vladimir"},{"full_name":"Ryzhmanova, Yana","last_name":"Ryzhmanova","first_name":"Yana"},{"orcid":"0000-0003-1006-6639","full_name":"Bochkareva, Olga","last_name":"Bochkareva","id":"C4558D3C-6102-11E9-A62E-F418E6697425","first_name":"Olga"},{"full_name":"Shcherbakova, Viktoria","last_name":"Shcherbakova","first_name":"Viktoria"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","short":"V. Oshurkova, O. Troshina, V. Trubitsyn, Y. Ryzhmanova, O. Bochkareva, V. Shcherbakova, in:, Proceedings of 1st International Electronic Conference on Microbiology, MDPI, 2020.","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.","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","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","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."},"month":"11","oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"language":[{"iso":"eng"}],"file":[{"creator":"dernst","file_size":595543,"date_updated":"2024-03-20T08:05:46Z","file_name":"2020_ECM_Oshurkova.pdf","date_created":"2024-03-20T08:05:46Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"d1914af7811a21a4b2744eb51b5834e3","file_id":"15127"}],"publication_status":"published","status":"public","conference":{"end_date":"2020-11-30","location":"Virtual","start_date":"2020-11-02","name":"ECM: Electronic Conference on Microbiology"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"conference","_id":"15071","department":[{"_id":"FyKo"}],"file_date_updated":"2024-03-20T08:05:46Z","ddc":["570"],"date_updated":"2024-03-20T08:06:22Z"},{"extern":"1","date_updated":"2024-03-25T12:25:02Z","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"status":"public","article_type":"original","type":"journal_article","_id":"15153","volume":9,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["2050-084X"]},"intvolume":" 9","month":"02","main_file_link":[{"open_access":"1","url":"https://doi.org/10.7554/eLife.55275"}],"scopus_import":"1","oa_version":"Published Version","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."}],"title":"Dynamics at the serine loop underlie differential affinity of cryptochromes for CLOCK:BMAL1 to control circadian timing","article_processing_charge":"No","author":[{"last_name":"Fribourgh","full_name":"Fribourgh, Jennifer L","first_name":"Jennifer L"},{"last_name":"Srivastava","full_name":"Srivastava, Ashutosh","first_name":"Ashutosh"},{"full_name":"Sandate, Colby R","last_name":"Sandate","first_name":"Colby R"},{"last_name":"Michael","full_name":"Michael, Alicia Kathleen","first_name":"Alicia Kathleen","id":"6437c950-2a03-11ee-914d-d6476dd7b75c"},{"first_name":"Peter L","last_name":"Hsu","full_name":"Hsu, Peter L"},{"first_name":"Christin","last_name":"Rakers","full_name":"Rakers, Christin"},{"first_name":"Leslee T","full_name":"Nguyen, Leslee T","last_name":"Nguyen"},{"full_name":"Torgrimson, Megan R","last_name":"Torgrimson","first_name":"Megan R"},{"last_name":"Parico","full_name":"Parico, Gian Carlo G","first_name":"Gian Carlo G"},{"full_name":"Tripathi, Sarvind","last_name":"Tripathi","first_name":"Sarvind"},{"first_name":"Ning","last_name":"Zheng","full_name":"Zheng, Ning"},{"last_name":"Lander","full_name":"Lander, Gabriel C","first_name":"Gabriel C"},{"first_name":"Tsuyoshi","last_name":"Hirota","full_name":"Hirota, Tsuyoshi"},{"full_name":"Tama, Florence","last_name":"Tama","first_name":"Florence"},{"first_name":"Carrie L","full_name":"Partch, Carrie L","last_name":"Partch"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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","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).","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.","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.","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."},"article_number":"55275","date_created":"2024-03-21T07:55:12Z","date_published":"2020-02-26T00:00:00Z","doi":"10.7554/elife.55275","publication":"eLife","day":"26","year":"2020","oa":1,"quality_controlled":"1","publisher":"eLife Sciences Publications"},{"publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"publication_status":"published","year":"2020","day":"23","publication":"Science","language":[{"iso":"eng"}],"page":"1460-1465","date_published":"2020-04-23T00:00:00Z","volume":368,"issue":"6498","doi":"10.1126/science.abb0074","date_created":"2024-03-21T07:54:44Z","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."}],"oa_version":"None","quality_controlled":"1","scopus_import":"1","publisher":"American Association for the Advancement of Science ","month":"04","intvolume":" 368","date_updated":"2024-03-25T12:29:34Z","citation":{"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.","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.","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.","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."},"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Alicia Kathleen","id":"6437c950-2a03-11ee-914d-d6476dd7b75c","last_name":"Michael","full_name":"Michael, Alicia Kathleen","orcid":"0000-0002-6080-839X"},{"first_name":"Ralph S.","full_name":"Grand, Ralph S.","last_name":"Grand"},{"last_name":"Isbel","full_name":"Isbel, Luke","first_name":"Luke"},{"last_name":"Cavadini","full_name":"Cavadini, Simone","first_name":"Simone"},{"first_name":"Zuzanna","last_name":"Kozicka","full_name":"Kozicka, Zuzanna"},{"first_name":"Georg","full_name":"Kempf, Georg","last_name":"Kempf"},{"first_name":"Richard D.","last_name":"Bunker","full_name":"Bunker, Richard D."},{"full_name":"Schenk, Andreas D.","last_name":"Schenk","first_name":"Andreas D."},{"first_name":"Alexandra","full_name":"Graff-Meyer, Alexandra","last_name":"Graff-Meyer"},{"last_name":"Pathare","full_name":"Pathare, Ganesh R.","first_name":"Ganesh R."},{"first_name":"Joscha","full_name":"Weiss, Joscha","last_name":"Weiss"},{"first_name":"Syota","full_name":"Matsumoto, Syota","last_name":"Matsumoto"},{"first_name":"Lukas","last_name":"Burger","full_name":"Burger, Lukas"},{"first_name":"Dirk","last_name":"Schübeler","full_name":"Schübeler, Dirk"},{"full_name":"Thomä, Nicolas H.","last_name":"Thomä","first_name":"Nicolas H."}],"article_processing_charge":"No","title":"Mechanisms of OCT4-SOX2 motif readout on nucleosomes","_id":"15152","article_type":"original","type":"journal_article","status":"public"},{"status":"public","keyword":["Cav2.3","medial habenula (MHb)","interpeduncular nucleus (IPN)"],"type":"dissertation","_id":"7525","file_date_updated":"2021-03-01T23:30:04Z","department":[{"_id":"RySh"}],"ddc":["570"],"supervisor":[{"last_name":"Shigemoto","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-07T13:20:03Z","month":"02","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"EM-Fac"}],"abstract":[{"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","lang":"eng"}],"file":[{"date_created":"2020-02-28T08:37:53Z","title":"Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway","file_name":"Pradeep Bhandari Thesis.pdf","creator":"pbhandari","date_updated":"2021-03-01T23:30:04Z","file_size":9646346,"file_id":"7538","checksum":"4589234fdb12b4ad72273b311723a7b4","embargo":"2021-02-28","access_level":"open_access","relation":"main_file","content_type":"application/pdf"},{"date_updated":"2021-03-01T23:30:04Z","file_size":35252164,"creator":"pbhandari","date_created":"2020-02-28T08:47:14Z","title":"Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway","file_name":"Pradeep Bhandari Thesis.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","access_level":"closed","relation":"source_file","checksum":"aa79490553ca0a5c9b6fbcd152e93928","file_id":"7539"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","title":"Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway","author":[{"orcid":"0000-0003-0863-4481","full_name":"Bhandari, Pradeep","last_name":"Bhandari","first_name":"Pradeep","id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","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","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.","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.","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.","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.","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."},"publisher":"Institute of Science and Technology Austria","oa":1,"date_published":"2020-02-28T00:00:00Z","doi":"10.15479/AT:ISTA:7525","date_created":"2020-02-26T10:56:37Z","page":"79","day":"28","has_accepted_license":"1","year":"2020"},{"oa":1,"quality_controlled":"1","publisher":"Elsevier","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.","date_created":"2020-09-29T13:24:06Z","date_published":"2020-12-01T00:00:00Z","doi":"10.1016/j.jsb.2020.107633","year":"2020","has_accepted_license":"1","isi":1,"publication":"Journal of Structural Biology","day":"01","project":[{"grant_number":"P33367","name":"Structure and isoform diversity of the Arp2/3 complex","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A"},{"name":"NÖ-Fonds Preis für die Jungforscherin des Jahres am IST Austria","_id":"059B463C-7A3F-11EA-A408-12923DDC885E"}],"article_number":"107633","article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000600997800008"]},"author":[{"id":"404F5528-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","last_name":"Fäßler","full_name":"Fäßler, Florian","orcid":"0000-0001-7149-769X"},{"first_name":"Bettina","id":"45FD126C-F248-11E8-B48F-1D18A9856A87","last_name":"Zens","full_name":"Zens, Bettina","orcid":"0000-0002-9561-1239"},{"full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","last_name":"Hauschild","first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM","last_name":"Schur","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM"}],"title":"3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy","citation":{"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).","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.","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","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","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","intvolume":" 212","month":"12","abstract":[{"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.","lang":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"oa_version":"Published Version","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"14592"},{"id":"12491","status":"public","relation":"dissertation_contains"}]},"issue":"3","volume":212,"publication_status":"published","publication_identifier":{"issn":["1047-8477"]},"language":[{"iso":"eng"}],"file":[{"date_updated":"2020-12-10T14:01:10Z","file_size":7076870,"creator":"dernst","date_created":"2020-12-10T14:01:10Z","file_name":"2020_JourStrucBiology_Faessler.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"c48cbf594e84fc2f91966ffaafc0918c","file_id":"8937","success":1}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","keyword":["electron microscopy","cryo-EM","EM sample preparation","3D printing","cell culture"],"status":"public","_id":"8586","department":[{"_id":"FlSc"}],"file_date_updated":"2020-12-10T14:01:10Z","date_updated":"2024-03-27T23:30:05Z","ddc":["570"]},{"has_accepted_license":"1","year":"2020","day":"14","page":"271","doi":"10.15479/AT:ISTA:8657","date_published":"2020-10-14T00:00:00Z","date_created":"2020-10-13T16:46:14Z","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.","publisher":"Institute of Science and Technology Austria","oa":1,"citation":{"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.","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","ama":"Kavcic B. Perturbations of protein synthesis: from antibiotics to genetics and physiology. 2020. doi: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.","short":"B. Kavcic, Perturbations of Protein Synthesis: From Antibiotics to Genetics and Physiology, Institute of Science and Technology Austria, 2020.","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.","ista":"Kavcic B. 2020. Perturbations of protein synthesis: from antibiotics to genetics and physiology. Institute of Science and Technology Austria."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Bor","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","last_name":"Kavcic","full_name":"Kavcic, Bor","orcid":"0000-0001-6041-254X"}],"article_processing_charge":"No","title":"Perturbations of protein synthesis: from antibiotics to genetics and physiology","publication_identifier":{"isbn":["978-3-99078-011-4"],"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","embargo":"2021-10-06","file_id":"8663","checksum":"d708ecd62b6fcc3bc1feb483b8dbe9eb","file_size":52636162,"date_updated":"2021-10-07T22:30:03Z","creator":"bkavcic","file_name":"kavcicB_thesis202009.pdf","date_created":"2020-10-15T06:41:20Z"},{"creator":"bkavcic","file_size":321681247,"date_updated":"2021-10-07T22:30:03Z","file_name":"2020b.zip","date_created":"2020-10-15T06:41:53Z","relation":"source_file","access_level":"closed","embargo_to":"open_access","content_type":"application/zip","file_id":"8664","checksum":"bb35f2352a04db19164da609f00501f3"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"7673"},{"relation":"part_of_dissertation","status":"public","id":"8250"}]},"abstract":[{"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.","lang":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"M-Shop"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"10","supervisor":[{"first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper"},{"orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Mark Tobias","last_name":"Bollenbach","first_name":"Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-07T13:20:48Z","ddc":["571","530","570"],"file_date_updated":"2021-10-07T22:30:03Z","department":[{"_id":"GaTk"}],"_id":"8657","type":"dissertation","status":"public"},{"external_id":{"isi":["000520854700008"],"pmid":["31928842"]},"article_processing_charge":"No","author":[{"orcid":"0000-0003-0005-401X","full_name":"Borges Merjane, Carolina","last_name":"Borges Merjane","first_name":"Carolina","id":"4305C450-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kim, Olena","last_name":"Kim","id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87","first_name":"Olena"},{"first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804"}],"title":"Functional electron microscopy (“Flash and Freeze”) of identified cortical synapses in acute brain slices","citation":{"ieee":"C. Borges Merjane, O. Kim, and P. M. Jonas, “Functional electron microscopy (‘Flash and Freeze’) of identified cortical synapses in acute brain slices,” Neuron, vol. 105. Elsevier, pp. 992–1006, 2020.","short":"C. Borges Merjane, O. Kim, P.M. Jonas, Neuron 105 (2020) 992–1006.","ama":"Borges Merjane C, Kim O, Jonas PM. Functional electron microscopy (“Flash and Freeze”) of identified cortical synapses in acute brain slices. Neuron. 2020;105:992-1006. doi:10.1016/j.neuron.2019.12.022","apa":"Borges Merjane, C., Kim, O., & Jonas, P. M. (2020). Functional electron microscopy (“Flash and Freeze”) of identified cortical synapses in acute brain slices. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2019.12.022","mla":"Borges Merjane, Carolina, et al. “Functional Electron Microscopy (‘Flash and Freeze’) of Identified Cortical Synapses in Acute Brain Slices.” Neuron, vol. 105, Elsevier, 2020, pp. 992–1006, doi:10.1016/j.neuron.2019.12.022.","ista":"Borges Merjane C, Kim O, Jonas PM. 2020. Functional electron microscopy (“Flash and Freeze”) of identified cortical synapses in acute brain slices. Neuron. 105, 992–1006.","chicago":"Borges Merjane, Carolina, Olena Kim, and Peter M Jonas. “Functional Electron Microscopy (‘Flash and Freeze’) of Identified Cortical Synapses in Acute Brain Slices.” Neuron. Elsevier, 2020. https://doi.org/10.1016/j.neuron.2019.12.022."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glumatergic synapse"},{"_id":"25BAF7B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"708497","name":"Presynaptic calcium channels distribution and impact on coupling at the hippocampal mossy fiber synapse"},{"call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425","grant_number":"Z00312","name":"The Wittgenstein Prize"},{"_id":"25C3DBB6-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"W01205","name":"Zellkommunikation in Gesundheit und Krankheit"}],"page":"992-1006","date_created":"2020-02-10T15:59:45Z","date_published":"2020-03-18T00:00:00Z","doi":"10.1016/j.neuron.2019.12.022","year":"2020","has_accepted_license":"1","isi":1,"publication":"Neuron","day":"18","oa":1,"quality_controlled":"1","publisher":"Elsevier","acknowledgement":"This project has received funding from the European Research Council (ERC) and European Commission (EC), under the European Union’s Horizon 2020 research and innovation programme (ERC grant agreement No. 692692 and Marie Sklodowska-Curie 708497) and from Fonds zur Förderung der Wissenschaftlichen Forschung (Z 312-B27 Wittgenstein award and DK W1205-B09). We thank Johann Danzl and Ryuichi Shigemoto for critically reading the manuscript; Walter Kaufmann, Daniel Gutl, and Vanessa Zheden for extensive EM training, advice, and experimental assistance; Benjamin Suter for substantial help with light stimulation, ImageJ plugins for analysis, and manuscript editing; Florian Marr and Christina Altmutter for technical support; Eleftheria Kralli-Beller for manuscript editing; Julia König and Paul Wurzinger (Leica Microsystems) for helpful technical discussions; and Taija Makinen for providing the Prox1-CreERT2 mouse line.","file_date_updated":"2020-11-20T08:58:53Z","department":[{"_id":"PeJo"}],"date_updated":"2024-03-27T23:30:07Z","ddc":["570"],"tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"type":"journal_article","article_type":"original","status":"public","_id":"7473","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","ec_funded":1,"volume":105,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"11196"}],"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/flash-and-freeze-reveals-dynamics-of-nerve-connections/","relation":"press_release"}]},"publication_status":"published","publication_identifier":{"issn":["0896-6273"]},"language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"3582664addf26859e86ac5bec3e01416","file_id":"8778","creator":"dernst","file_size":9712957,"date_updated":"2020-11-20T08:58:53Z","file_name":"2020_Neuron_BorgesMerjane.pdf","date_created":"2020-11-20T08:58:53Z"}],"scopus_import":"1","intvolume":" 105","month":"03","abstract":[{"lang":"eng","text":"How structural and functional properties of synapses relate to each other is a fundamental question in neuroscience. Electrophysiology has elucidated mechanisms of synaptic transmission, and electron microscopy (EM) has provided insight into morphological properties of synapses. Here we describe an enhanced method for functional EM (“flash and freeze”), combining optogenetic stimulation with high-pressure freezing. We demonstrate that the improved method can be applied to intact networks in acute brain slices and organotypic slice cultures from mice. As a proof of concept, we probed vesicle pool changes during synaptic transmission at the hippocampal mossy fiber-CA3 pyramidal neuron synapse. Our findings show overlap of the docked vesicle pool and the functionally defined readily releasable pool and provide evidence of fast endocytosis at this synapse. Functional EM with acute slices and slice cultures has the potential to reveal the structural and functional mechanisms of transmission in intact, genetically perturbed, and disease-affected synapses."}],"pmid":1,"oa_version":"Published Version"},{"ddc":["570"],"date_updated":"2024-03-27T23:30:08Z","department":[{"_id":"GaTk"}],"file_date_updated":"2020-08-17T07:36:57Z","_id":"8250","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"date_created":"2020-08-17T07:36:57Z","file_name":"2020_NatureComm_Kavcic.pdf","creator":"dernst","date_updated":"2020-08-17T07:36:57Z","file_size":1965672,"checksum":"986bebb308850a55850028d3d2b5b664","file_id":"8275","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2041-1723"]},"publication_status":"published","volume":11,"related_material":{"record":[{"status":"public","id":"8657","relation":"dissertation_contains"}]},"oa_version":"Published Version","abstract":[{"text":"Antibiotics that interfere with translation, when combined, interact in diverse and difficult-to-predict ways. Here, we explain these interactions by “translation bottlenecks”: points in the translation cycle where antibiotics block ribosomal progression. To elucidate the underlying mechanisms of drug interactions between translation inhibitors, we generate translation bottlenecks genetically using inducible 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 causes these interactions. We further show that growth laws, combined with drug uptake and binding kinetics, enable the direct prediction of a large fraction of observed interactions, yet fail to predict suppression. However, varying two translation bottlenecks simultaneously supports that dense traffic of ribosomes and competition for translation factors account for the previously unexplained suppression. These results highlight the importance of “continuous epistasis” in bacterial physiology.","lang":"eng"}],"month":"08","intvolume":" 11","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Kavcic B, Tkačik G, Bollenbach MT. 2020. Mechanisms of drug interactions between translation-inhibiting antibiotics. Nature Communications. 11, 4013.","chicago":"Kavcic, Bor, Gašper Tkačik, and Mark Tobias Bollenbach. “Mechanisms of Drug Interactions between Translation-Inhibiting Antibiotics.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-17734-z.","ama":"Kavcic B, Tkačik G, Bollenbach MT. Mechanisms of drug interactions between translation-inhibiting antibiotics. Nature Communications. 2020;11. doi:10.1038/s41467-020-17734-z","apa":"Kavcic, B., Tkačik, G., & Bollenbach, M. T. (2020). Mechanisms of drug interactions between translation-inhibiting antibiotics. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-17734-z","ieee":"B. Kavcic, G. Tkačik, and M. T. Bollenbach, “Mechanisms of drug interactions between translation-inhibiting antibiotics,” Nature Communications, vol. 11. Springer Nature, 2020.","short":"B. Kavcic, G. Tkačik, M.T. Bollenbach, Nature Communications 11 (2020).","mla":"Kavcic, Bor, et al. “Mechanisms of Drug Interactions between Translation-Inhibiting Antibiotics.” Nature Communications, vol. 11, 4013, Springer Nature, 2020, doi:10.1038/s41467-020-17734-z."},"title":"Mechanisms of drug interactions between translation-inhibiting antibiotics","author":[{"last_name":"Kavcic","full_name":"Kavcic, Bor","orcid":"0000-0001-6041-254X","first_name":"Bor","id":"350F91D2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Tkačik","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Tobias","last_name":"Bollenbach"}],"external_id":{"isi":["000562769300008"]},"article_processing_charge":"No","article_number":"4013","project":[{"_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Revealing the mechanisms underlying drug interactions","grant_number":"P27201-B22"},{"grant_number":"P28844-B27","name":"Biophysics of information processing in gene regulation","_id":"254E9036-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"day":"11","publication":"Nature Communications","has_accepted_license":"1","isi":1,"year":"2020","doi":"10.1038/s41467-020-17734-z","date_published":"2020-08-11T00:00:00Z","date_created":"2020-08-12T09:13:50Z","acknowledgement":"We thank M. Hennessey-Wesen, I. Tomanek, K. Jain, A. Staron, K. Tomasek, M. Scott,\r\nK.C. Huang, and Z. Gitai for reading the manuscript and constructive comments. B.K. is\r\nindebted to C. Guet for additional guidance and generous support, which rendered this\r\nwork possible. B.K. thanks all members of Guet group for many helpful discussions and\r\nsharing of resources. B.K. additionally acknowledges the tremendous support from A.\r\nAngermayr and K. Mitosch with experimental work. We further thank E. Brown for\r\nhelpful comments regarding lamotrigine, and A. Buskirk for valuable suggestions\r\nregarding the ribosome footprint size. This work was supported in part by Austrian\r\nScience Fund (FWF) standalone grants P 27201-B22 (to T.B.) and P 28844 (to G.T.),\r\nHFSP program Grant RGP0042/2013 (to T.B.), German Research Foundation (DFG)\r\nstandalone grant BO 3502/2-1 (to T.B.), and German Research Foundation (DFG)\r\nCollaborative Research Centre (SFB) 1310 (to T.B.). Open access funding provided by\r\nProjekt DEAL.","quality_controlled":"1","publisher":"Springer Nature","oa":1},{"date_updated":"2024-03-27T23:30:08Z","citation":{"ista":"Kavcic B, Tkačik G, Bollenbach MT. 2020. A minimal biophysical model of combined antibiotic action. bioRxiv, 10.1101/2020.04.18.047886.","chicago":"Kavcic, Bor, Gašper Tkačik, and Mark Tobias Bollenbach. “A Minimal Biophysical Model of Combined Antibiotic Action.” BioRxiv. Cold Spring Harbor Laboratory, 2020. https://doi.org/10.1101/2020.04.18.047886.","apa":"Kavcic, B., Tkačik, G., & Bollenbach, M. T. (2020). A minimal biophysical model of combined antibiotic action. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2020.04.18.047886","ama":"Kavcic B, Tkačik G, Bollenbach MT. A minimal biophysical model of combined antibiotic action. bioRxiv. 2020. doi:10.1101/2020.04.18.047886","ieee":"B. Kavcic, G. Tkačik, and M. T. Bollenbach, “A minimal biophysical model of combined antibiotic action,” bioRxiv. Cold Spring Harbor Laboratory, 2020.","short":"B. Kavcic, G. Tkačik, M.T. Bollenbach, BioRxiv (2020).","mla":"Kavcic, Bor, et al. “A Minimal Biophysical Model of Combined Antibiotic Action.” BioRxiv, Cold Spring Harbor Laboratory, 2020, doi:10.1101/2020.04.18.047886."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"first_name":"Bor","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","last_name":"Kavcic","full_name":"Kavcic, Bor","orcid":"0000-0001-6041-254X"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","last_name":"Tkačik","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455"},{"full_name":"Bollenbach, Tobias","orcid":"0000-0003-4398-476X","last_name":"Bollenbach","first_name":"Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"}],"title":"A minimal biophysical model of combined antibiotic action","department":[{"_id":"GaTk"}],"_id":"7673","type":"preprint","status":"public","project":[{"name":"Revealing the mechanisms underlying drug interactions","grant_number":"P27201-B22","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425","name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27"}],"year":"2020","publication_status":"published","publication":"bioRxiv","language":[{"iso":"eng"}],"day":"18","date_created":"2020-04-22T08:27:56Z","date_published":"2020-04-18T00:00:00Z","related_material":{"record":[{"relation":"later_version","status":"public","id":"8997"},{"relation":"dissertation_contains","id":"8657","status":"public"}]},"doi":"10.1101/2020.04.18.047886","abstract":[{"lang":"eng","text":"Combining drugs can improve the efficacy of treatments. However, predicting the effect of drug combinations is still challenging. The combined potency of drugs determines the drug interaction, which is classified as synergistic, additive, antagonistic, or suppressive. While probabilistic, non-mechanistic models exist, there is currently no biophysical model that can predict antibiotic interactions. Here, we present a physiologically relevant model of the combined action of antibiotics that inhibit protein synthesis by targeting the ribosome. This model captures the kinetics of antibiotic binding and transport, and uses bacterial growth laws to predict growth in the presence of antibiotic combinations. We find that this biophysical model can produce all drug interaction types except suppression. We show analytically that antibiotics which cannot bind to the ribosome simultaneously generally act as substitutes for one another, leading to additive drug interactions. Previously proposed null expectations for higher-order drug interactions follow as a limiting case of our model. We further extend the model to include the effects of direct physical or allosteric interactions between individual drugs on the ribosome. Notably, such direct interactions profoundly change the combined drug effect, depending on the kinetic parameters of the drugs used. The model makes additional predictions for the effects of resistance genes on drug interactions and for interactions between ribosome-targeting antibiotics and antibiotics with other targets. These findings enhance our understanding of the interplay between drug action and cell physiology and are a key step toward a general framework for predicting drug interactions."}],"oa_version":"Preprint","main_file_link":[{"url":"https://doi.org/10.1101/2020.04.18.047886 ","open_access":"1"}],"oa":1,"publisher":"Cold Spring Harbor Laboratory","month":"04"},{"date_updated":"2024-03-27T23:30:11Z","ddc":["580"],"file_date_updated":"2020-07-14T12:48:07Z","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"_id":"8002","article_type":"original","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"status":"public","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"publication_status":"published","file":[{"date_created":"2020-06-23T11:30:53Z","file_name":"2020_PNAS_Hoermayer.pdf","date_updated":"2020-07-14T12:48:07Z","file_size":2407102,"creator":"dernst","file_id":"8009","checksum":"908b09437680181de9990915f2113aca","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"volume":117,"related_material":{"record":[{"id":"9992","status":"public","relation":"dissertation_contains"}],"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/how-wounded-plants-coordinate-their-healing/","description":"News on IST Homepage"}]},"issue":"26","ec_funded":1,"abstract":[{"lang":"eng","text":"Wound healing in plant tissues, consisting of rigid cell wall-encapsulated cells, represents a considerable challenge and occurs through largely unknown mechanisms distinct from those in animals. Owing to their inability to migrate, plant cells rely on targeted cell division and expansion to regenerate wounds. Strict coordination of these wound-induced responses is essential to ensure efficient, spatially restricted wound healing. Single-cell tracking by live imaging allowed us to gain mechanistic insight into the wound perception and coordination of wound responses after laser-based wounding in Arabidopsis root. We revealed a crucial contribution of the collapse of damaged cells in wound perception and detected an auxin increase specific to cells immediately adjacent to the wound. This localized auxin increase balances wound-induced cell expansion and restorative division rates in a dose-dependent manner, leading to tumorous overproliferation when the canonical TIR1 auxin signaling is disrupted. Auxin and wound-induced turgor pressure changes together also spatially define the activation of key components of regeneration, such as the transcription regulator ERF115. Our observations suggest that the wound signaling involves the sensing of collapse of damaged cells and a local auxin signaling activation to coordinate the downstream transcriptional responses in the immediate wound vicinity."}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"pmid":1,"oa_version":"None","scopus_import":"1","month":"06","intvolume":" 117","citation":{"chicago":"Hörmayer, Lukas, Juan C Montesinos López, Petra Marhavá, Eva Benková, Saiko Yoshida, and Jiří Friml. “Wounding-Induced Changes in Cellular Pressure and Localized Auxin Signalling Spatially Coordinate Restorative Divisions in Roots.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.2003346117.","ista":"Hörmayer L, Montesinos López JC, Marhavá P, Benková E, Yoshida S, Friml J. 2020. Wounding-induced changes in cellular pressure and localized auxin signalling spatially coordinate restorative divisions in roots. Proceedings of the National Academy of Sciences. 117(26), 202003346.","mla":"Hörmayer, Lukas, et al. “Wounding-Induced Changes in Cellular Pressure and Localized Auxin Signalling Spatially Coordinate Restorative Divisions in Roots.” Proceedings of the National Academy of Sciences, vol. 117, no. 26, 202003346, Proceedings of the National Academy of Sciences, 2020, doi:10.1073/pnas.2003346117.","apa":"Hörmayer, L., Montesinos López, J. C., Marhavá, P., Benková, E., Yoshida, S., & Friml, J. (2020). Wounding-induced changes in cellular pressure and localized auxin signalling spatially coordinate restorative divisions in roots. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2003346117","ama":"Hörmayer L, Montesinos López JC, Marhavá P, Benková E, Yoshida S, Friml J. Wounding-induced changes in cellular pressure and localized auxin signalling spatially coordinate restorative divisions in roots. Proceedings of the National Academy of Sciences. 2020;117(26). doi:10.1073/pnas.2003346117","ieee":"L. Hörmayer, J. C. Montesinos López, P. Marhavá, E. Benková, S. Yoshida, and J. Friml, “Wounding-induced changes in cellular pressure and localized auxin signalling spatially coordinate restorative divisions in roots,” Proceedings of the National Academy of Sciences, vol. 117, no. 26. Proceedings of the National Academy of Sciences, 2020.","short":"L. Hörmayer, J.C. Montesinos López, P. Marhavá, E. Benková, S. Yoshida, J. Friml, Proceedings of the National Academy of Sciences 117 (2020)."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"orcid":"0000-0001-8295-2926","full_name":"Hörmayer, Lukas","last_name":"Hörmayer","first_name":"Lukas","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Juan C","id":"310A8E3E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9179-6099","full_name":"Montesinos López, Juan C","last_name":"Montesinos López"},{"full_name":"Marhavá, Petra","last_name":"Marhavá","id":"44E59624-F248-11E8-B48F-1D18A9856A87","first_name":"Petra"},{"full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva"},{"full_name":"Yoshida, Saiko","last_name":"Yoshida","id":"2E46069C-F248-11E8-B48F-1D18A9856A87","first_name":"Saiko"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"isi":["000565729700033"],"pmid":["32541049"]},"title":"Wounding-induced changes in cellular pressure and localized auxin signalling spatially coordinate restorative divisions in roots","article_number":"202003346","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"call_identifier":"FWF","_id":"262EF96E-B435-11E9-9278-68D0E5697425","name":"RNA-directed DNA methylation in plant development","grant_number":"P29988"}],"isi":1,"has_accepted_license":"1","year":"2020","day":"30","publication":"Proceedings of the National Academy of Sciences","date_published":"2020-06-30T00:00:00Z","doi":"10.1073/pnas.2003346117","date_created":"2020-06-22T13:33:52Z","publisher":"Proceedings of the National Academy of Sciences","quality_controlled":"1","oa":1},{"date_created":"2020-04-24T16:00:51Z","doi":"10.15479/AT:ISTA:7680","date_published":"2020-04-24T00:00:00Z","page":"98","day":"24","year":"2020","has_accepted_license":"1","oa":1,"publisher":"Institute of Science and Technology Austria","title":"Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals","article_processing_charge":"No","author":[{"full_name":"Kainrath, Stephanie","last_name":"Kainrath","id":"32CFBA64-F248-11E8-B48F-1D18A9856A87","first_name":"Stephanie"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Kainrath, Stephanie. “Synthetic Tools for Optogenetic and Chemogenetic Inhibition of Cellular Signals.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7680.","ista":"Kainrath S. 2020. Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals. Institute of Science and Technology Austria.","mla":"Kainrath, Stephanie. Synthetic Tools for Optogenetic and Chemogenetic Inhibition of Cellular Signals. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7680.","apa":"Kainrath, S. (2020). Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7680","ama":"Kainrath S. Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals. 2020. doi:10.15479/AT:ISTA:7680","ieee":"S. Kainrath, “Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals,” Institute of Science and Technology Austria, 2020.","short":"S. Kainrath, Synthetic Tools for Optogenetic and Chemogenetic Inhibition of Cellular Signals, Institute of Science and Technology Austria, 2020."},"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"1028"}]},"language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","embargo":"2021-10-30","checksum":"fb9a4468eb27be92690728e35c823796","file_id":"7692","creator":"stgingl","file_size":3268017,"date_updated":"2021-10-31T23:30:05Z","file_name":"Thesis_without-signatures_PDFA.pdf","date_created":"2020-04-28T11:19:21Z"},{"file_id":"7693","checksum":"f6c80ca97104a631a328cb79a2c53493","embargo_to":"open_access","content_type":"application/octet-stream","relation":"source_file","access_level":"closed","file_name":"Thesis_without signatures.docx","date_created":"2020-04-28T11:19:24Z","file_size":5167703,"date_updated":"2021-10-31T23:30:05Z","creator":"stgingl"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"eissn":["2663-337X"]},"month":"04","alternative_title":["ISTA Thesis"],"oa_version":"None","abstract":[{"lang":"eng","text":"Proteins and their complex dynamic interactions regulate cellular mechanisms from sensing and transducing extracellular signals, to mediating genetic responses, and sustaining or changing cell morphology. To manipulate these protein-protein interactions (PPIs) that govern the behavior and fate of cells, synthetically constructed, genetically encoded tools provide the means to precisely target proteins of interest (POIs), and control their subcellular localization and activity in vitro and in vivo. Ideal synthetic tools react to an orthogonal cue, i.e. a trigger that does not activate any other endogenous process, thereby allowing manipulation of the POI alone.\r\nIn optogenetics, naturally occurring photosensory domain from plants, algae and bacteria are re-purposed and genetically fused to POIs. Illumination with light of a specific wavelength triggers a conformational change that can mediate PPIs, such as dimerization or oligomerization. By using light as a trigger, these tools can be activated with high spatial and temporal precision, on subcellular and millisecond scales. Chemogenetic tools consist of protein domains that recognize and bind small molecules. By genetic fusion to POIs, these domains can mediate PPIs upon addition of their specific ligands, which are often synthetically designed to provide highly specific interactions and exhibit good bioavailability.\r\nMost optogenetic tools to mediate PPIs are based on well-studied photoreceptors responding to red, blue or near-UV light, leaving a striking gap in the green band of the visible light spectrum. Among both optogenetic and chemogenetic tools, there is an abundance of methods to induce PPIs, but tools to disrupt them require UV illumination, rely on covalent linkage and subsequent enzymatic cleavage or initially result in protein clustering of unknown stoichiometry.\r\nThis work describes how the recently structurally and photochemically characterized green-light responsive cobalamin-binding domains (CBDs) from bacterial transcription factors were re-purposed to function as a green-light responsive optogenetic tool. In contrast to previously engineered optogenetic tools, CBDs do not induce PPI, but rather confer a PPI already upon expression, which can be rapidly disrupted by illumination. This was employed to mimic inhibition of constitutive activity of a growth factor receptor, and successfully implement for cell signalling in mammalian cells and in vivo to rescue development in zebrafish. This work further describes the development and application of a chemically induced de-dimerizer (CDD) based on a recently identified and structurally described bacterial oxyreductase. CDD forms a dimer upon expression in absence of its cofactor, the flavin derivative F420. Safety and of domain expression and ligand exposure are demonstrated in vitro and in vivo in zebrafish. The system is further applied to inhibit cell signalling output from a chimeric receptor upon F420 treatment.\r\nCBDs and CDD expand the repertoire of synthetic tools by providing novel mechanisms of mediating PPIs, and by recognizing previously not utilized cues. In the future, they can readily be combined with existing synthetic tools to functionally manipulate PPIs in vitro and in vivo."}],"file_date_updated":"2021-10-31T23:30:05Z","department":[{"_id":"CaGu"}],"ddc":["570"],"date_updated":"2023-09-22T09:20:10Z","supervisor":[{"id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","first_name":"Harald L","last_name":"Janovjak","full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315"}],"status":"public","type":"dissertation","_id":"7680"}]