[{"language":[{"iso":"eng"}],"oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ama":"Forkert DL. Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7629\">10.15479/AT:ISTA:7629</a>","ieee":"D. L. Forkert, “Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains,” Institute of Science and Technology Austria, 2020.","short":"D.L. Forkert, Gradient Flows in Spaces of Probability Measures for Finite-Volume Schemes, Metric Graphs and Non-Reversible Markov Chains, Institute of Science and Technology Austria, 2020.","ista":"Forkert DL. 2020. Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains. Institute of Science and Technology Austria.","chicago":"Forkert, Dominik L. “Gradient Flows in Spaces of Probability Measures for Finite-Volume Schemes, Metric Graphs and Non-Reversible Markov Chains.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:7629\">https://doi.org/10.15479/AT:ISTA:7629</a>.","apa":"Forkert, D. L. (2020). <i>Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:7629\">https://doi.org/10.15479/AT:ISTA:7629</a>","mla":"Forkert, Dominik L. <i>Gradient Flows in Spaces of Probability Measures for Finite-Volume Schemes, Metric Graphs and Non-Reversible Markov Chains</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7629\">10.15479/AT:ISTA:7629</a>."},"month":"03","supervisor":[{"orcid":"0000-0002-0845-1338","first_name":"Jan","last_name":"Maas","full_name":"Maas, Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87"}],"file":[{"file_id":"7657","date_created":"2020-04-14T10:47:59Z","file_size":3297129,"creator":"dernst","date_updated":"2020-07-14T12:48:01Z","relation":"main_file","checksum":"c814a1a6195269ca6fe48b0dca45ae8a","file_name":"Thesis_Forkert_PDFA.pdf","content_type":"application/pdf","access_level":"open_access"},{"checksum":"ceafb53f923d1b5bdf14b2b0f22e4a81","relation":"source_file","access_level":"closed","content_type":"application/x-zip-compressed","file_name":"Thesis_Forkert_source.zip","file_id":"7658","date_updated":"2020-07-14T12:48:01Z","creator":"dernst","date_created":"2020-04-14T10:47:59Z","file_size":1063908}],"department":[{"_id":"JaMa"}],"abstract":[{"text":"This thesis is based on three main topics: In the first part, we study convergence of discrete gradient flow structures associated with regular finite-volume discretisations of Fokker-Planck equations. We show evolutionary I convergence of the discrete gradient flows to the L2-Wasserstein gradient flow corresponding to the solution of a Fokker-Planck\r\nequation in arbitrary dimension d >= 1. Along the argument, we prove Mosco- and I-convergence results for discrete energy functionals, which are of independent interest for convergence of equivalent gradient flow structures in Hilbert spaces.\r\nThe second part investigates L2-Wasserstein flows on metric graph. The starting point is a Benamou-Brenier formula for the L2-Wasserstein distance, which is proved via a regularisation scheme for solutions of the continuity equation, adapted to the peculiar geometric structure of metric graphs. Based on those results, we show that the L2-Wasserstein space over a metric graph admits a gradient flow which may be identified as a solution of a Fokker-Planck equation.\r\nIn the third part, we focus again on the discrete gradient flows, already encountered in the first part. We propose a variational structure which extends the gradient flow structure to Markov chains violating the detailed-balance conditions. Using this structure, we characterise contraction estimates for the discrete heat flow in terms of convexity of\r\ncorresponding path-dependent energy functionals. In addition, we use this approach to derive several functional inequalities for said functionals.","lang":"eng"}],"has_accepted_license":"1","publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","file_date_updated":"2020-07-14T12:48:01Z","oa_version":"Published Version","title":"Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains","author":[{"full_name":"Forkert, Dominik L","id":"35C79D68-F248-11E8-B48F-1D18A9856A87","last_name":"Forkert","first_name":"Dominik L"}],"day":"31","date_created":"2020-04-02T06:40:23Z","project":[{"name":"Optimal Transport and Stochastic Dynamics","grant_number":"716117","call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425"}],"status":"public","degree_awarded":"PhD","date_published":"2020-03-31T00:00:00Z","ec_funded":1,"year":"2020","ddc":["510"],"page":"154","publisher":"Institute of Science and Technology Austria","doi":"10.15479/AT:ISTA:7629","article_processing_charge":"No","alternative_title":["ISTA Thesis"],"type":"dissertation","date_updated":"2023-09-07T13:03:12Z","_id":"7629"},{"file_date_updated":"2020-07-14T12:48:01Z","publication_status":"published","publication_identifier":{"eissn":["20452322"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":"        10","abstract":[{"text":"The posterior parietal cortex (PPC) and frontal motor areas comprise a cortical network supporting goal-directed behaviour, with functions including sensorimotor transformations and decision making. In primates, this network links performed and observed actions via mirror neurons, which fire both when individuals perform an action and when they observe the same action performed by a conspecific. Mirror neurons are believed to be important for social learning, but it is not known whether mirror-like neurons occur in similar networks in other social species, such as rodents, or if they can be measured in such models using paradigms where observers passively view a demonstrator. Therefore, we imaged Ca2+ responses in PPC and secondary motor cortex (M2) while mice performed and observed pellet-reaching and wheel-running tasks, and found that cell populations in both areas robustly encoded several naturalistic behaviours. However, neural responses to the same set of observed actions were absent, although we verified that observer mice were attentive to performers and that PPC neurons responded reliably to visual cues. Statistical modelling also indicated that executed actions outperformed observed actions in predicting neural responses. These results raise the possibility that sensorimotor action recognition in rodents could take place outside of the parieto-frontal circuit, and underscore that detecting socially-driven neural coding depends critically on the species and behavioural paradigm used.","lang":"eng"}],"has_accepted_license":"1","date_created":"2020-04-05T22:00:47Z","article_type":"original","volume":10,"title":"Action representation in the mouse parieto-frontal network","oa_version":"Published Version","scopus_import":"1","day":"27","author":[{"last_name":"Tombaz","full_name":"Tombaz, Tuce","first_name":"Tuce"},{"first_name":"Benjamin A.","full_name":"Dunn, Benjamin A.","last_name":"Dunn"},{"first_name":"Karoline","full_name":"Hovde, Karoline","last_name":"Hovde"},{"full_name":"Cubero, Ryan J","id":"850B2E12-9CD4-11E9-837F-E719E6697425","last_name":"Cubero","first_name":"Ryan J","orcid":"0000-0003-0002-1867"},{"last_name":"Mimica","full_name":"Mimica, Bartul","first_name":"Bartul"},{"full_name":"Mamidanna, Pranav","last_name":"Mamidanna","first_name":"Pranav"},{"first_name":"Yasser","last_name":"Roudi","full_name":"Roudi, Yasser"},{"first_name":"Jonathan R.","full_name":"Whitlock, Jonathan R.","last_name":"Whitlock"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ama":"Tombaz T, Dunn BA, Hovde K, et al. Action representation in the mouse parieto-frontal network. <i>Scientific reports</i>. 2020;10(1). doi:<a href=\"https://doi.org/10.1038/s41598-020-62089-6\">10.1038/s41598-020-62089-6</a>","ieee":"T. Tombaz <i>et al.</i>, “Action representation in the mouse parieto-frontal network,” <i>Scientific reports</i>, vol. 10, no. 1. Springer Nature, 2020.","short":"T. Tombaz, B.A. Dunn, K. Hovde, R.J. Cubero, B. Mimica, P. Mamidanna, Y. Roudi, J.R. Whitlock, Scientific Reports 10 (2020).","ista":"Tombaz T, Dunn BA, Hovde K, Cubero RJ, Mimica B, Mamidanna P, Roudi Y, Whitlock JR. 2020. Action representation in the mouse parieto-frontal network. Scientific reports. 10(1), 5559.","chicago":"Tombaz, Tuce, Benjamin A. Dunn, Karoline Hovde, Ryan J Cubero, Bartul Mimica, Pranav Mamidanna, Yasser Roudi, and Jonathan R. Whitlock. “Action Representation in the Mouse Parieto-Frontal Network.” <i>Scientific Reports</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41598-020-62089-6\">https://doi.org/10.1038/s41598-020-62089-6</a>.","apa":"Tombaz, T., Dunn, B. A., Hovde, K., Cubero, R. J., Mimica, B., Mamidanna, P., … Whitlock, J. R. (2020). Action representation in the mouse parieto-frontal network. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41598-020-62089-6\">https://doi.org/10.1038/s41598-020-62089-6</a>","mla":"Tombaz, Tuce, et al. “Action Representation in the Mouse Parieto-Frontal Network.” <i>Scientific Reports</i>, vol. 10, no. 1, 5559, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41598-020-62089-6\">10.1038/s41598-020-62089-6</a>."},"issue":"1","language":[{"iso":"eng"}],"oa":1,"article_number":"5559","file":[{"file_id":"7644","date_created":"2020-04-06T10:44:23Z","file_size":2621249,"creator":"dernst","date_updated":"2020-07-14T12:48:01Z","relation":"main_file","checksum":"e6cfaaaf7986532132934400038b824a","file_name":"2020_ScientificReports_Tombaz.pdf","access_level":"open_access","content_type":"application/pdf"}],"department":[{"_id":"SaSi"}],"month":"03","quality_controlled":"1","ddc":["570"],"type":"journal_article","_id":"7632","date_updated":"2023-08-18T10:25:13Z","publisher":"Springer Nature","article_processing_charge":"No","doi":"10.1038/s41598-020-62089-6","date_published":"2020-03-27T00:00:00Z","publication":"Scientific reports","status":"public","external_id":{"isi":["000560406800007"]},"year":"2020","isi":1},{"status":"public","publication":"ACS Nano","date_published":"2020-03-24T00:00:00Z","acknowledgement":"This work is partly supported by Grants-in-Aid for Scientific Research by Young Scientist A (KAKENHI Wakate-A) No. JP17H04802, Grants-in-Aid for Scientific Research No. JP19H05602 from the Japan Society for the Promotion of Science, and RIKEN Incentive Research Grant (Shoreikadai) 2016. M.V.K. and M.I. acknowledge financial support from the European Union (EU) via FP7 ERC Starting Grant 2012 (Project NANOSOLID, GA No. 306733) and ETH Zurich via ETH career seed grant (SEED-18 16-2). Support from Cambridge Display Technology, Ltd., and Sumitomo Chemical Company is also acknowledged. We thank Mrs. T. Kikitsu and Dr. D. Hashizume (RIKEN-CEMS) for access to the transmission electron microscope facility.","pmid":1,"external_id":{"isi":["000526301400057"],"pmid":["32073817"]},"year":"2020","isi":1,"page":"3242-3250","quality_controlled":"1","publisher":"American Chemical Society","doi":"10.1021/acsnano.9b08687","article_processing_charge":"No","type":"journal_article","date_updated":"2023-08-18T10:25:40Z","_id":"7634","language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"3","citation":{"short":"R. Miranti, D. Shin, R.D. Septianto, M. Ibáñez, M.V. Kovalenko, N. Matsushita, Y. Iwasa, S.Z. Bisri, ACS Nano 14 (2020) 3242–3250.","ieee":"R. Miranti <i>et al.</i>, “Exclusive electron transport in Core@Shell PbTe@PbS colloidal semiconductor nanocrystal assemblies,” <i>ACS Nano</i>, vol. 14, no. 3. American Chemical Society, pp. 3242–3250, 2020.","ama":"Miranti R, Shin D, Septianto RD, et al. Exclusive electron transport in Core@Shell PbTe@PbS colloidal semiconductor nanocrystal assemblies. <i>ACS Nano</i>. 2020;14(3):3242-3250. doi:<a href=\"https://doi.org/10.1021/acsnano.9b08687\">10.1021/acsnano.9b08687</a>","mla":"Miranti, Retno, et al. “Exclusive Electron Transport in Core@Shell PbTe@PbS Colloidal Semiconductor Nanocrystal Assemblies.” <i>ACS Nano</i>, vol. 14, no. 3, American Chemical Society, 2020, pp. 3242–50, doi:<a href=\"https://doi.org/10.1021/acsnano.9b08687\">10.1021/acsnano.9b08687</a>.","apa":"Miranti, R., Shin, D., Septianto, R. D., Ibáñez, M., Kovalenko, M. V., Matsushita, N., … Bisri, S. Z. (2020). Exclusive electron transport in Core@Shell PbTe@PbS colloidal semiconductor nanocrystal assemblies. <i>ACS Nano</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acsnano.9b08687\">https://doi.org/10.1021/acsnano.9b08687</a>","chicago":"Miranti, Retno, Daiki Shin, Ricky Dwi Septianto, Maria Ibáñez, Maksym V. Kovalenko, Nobuhiro Matsushita, Yoshihiro Iwasa, and Satria Zulkarnaen Bisri. “Exclusive Electron Transport in Core@Shell PbTe@PbS Colloidal Semiconductor Nanocrystal Assemblies.” <i>ACS Nano</i>. American Chemical Society, 2020. <a href=\"https://doi.org/10.1021/acsnano.9b08687\">https://doi.org/10.1021/acsnano.9b08687</a>.","ista":"Miranti R, Shin D, Septianto RD, Ibáñez M, Kovalenko MV, Matsushita N, Iwasa Y, Bisri SZ. 2020. Exclusive electron transport in Core@Shell PbTe@PbS colloidal semiconductor nanocrystal assemblies. ACS Nano. 14(3), 3242–3250."},"month":"03","department":[{"_id":"MaIb"}],"intvolume":"        14","abstract":[{"lang":"eng","text":"Assemblies of colloidal semiconductor nanocrystals (NCs) in the form of thin solid films leverage the size-dependent quantum confinement properties and the wet chemical methods vital for the development of the emerging solution-processable electronics, photonics, and optoelectronics technologies. The ability to control the charge carrier transport in the colloidal NC assemblies is fundamental for altering their electronic and optical properties for the desired applications. Here we demonstrate a strategy to render the solids of narrow-bandgap NC assemblies exclusively electron-transporting by creating a type-II heterojunction via shelling. Electronic transport of molecularly cross-linked PbTe@PbS core@shell NC assemblies is measured using both a conventional solid gate transistor and an electric-double-layer transistor, as well as compared with those of core-only PbTe NCs. In contrast to the ambipolar characteristics demonstrated by many narrow-bandgap NCs, the core@shell NCs exhibit exclusive n-type transport, i.e., drastically suppressed contribution of holes to the overall transport. The PbS shell that forms a type-II heterojunction assists the selective carrier transport by heavy doping of electrons into the PbTe-core conduction level and simultaneously strongly localizes the holes within the NC core valence level. This strongly enhanced n-type transport makes these core@shell NCs suitable for applications where ambipolar characteristics should be actively suppressed, in particular, for thermoelectric and electron-transporting layers in photovoltaic devices."}],"publication_identifier":{"eissn":["1936-086X"]},"publication_status":"published","title":"Exclusive electron transport in Core@Shell PbTe@PbS colloidal semiconductor nanocrystal assemblies","oa_version":"None","author":[{"last_name":"Miranti","full_name":"Miranti, Retno","first_name":"Retno"},{"first_name":"Daiki","last_name":"Shin","full_name":"Shin, Daiki"},{"first_name":"Ricky Dwi","full_name":"Septianto, Ricky Dwi","last_name":"Septianto"},{"orcid":"0000-0001-5013-2843","first_name":"Maria","full_name":"Ibáñez, Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","last_name":"Ibáñez"},{"first_name":"Maksym V.","full_name":"Kovalenko, Maksym V.","last_name":"Kovalenko"},{"full_name":"Matsushita, Nobuhiro","last_name":"Matsushita","first_name":"Nobuhiro"},{"first_name":"Yoshihiro","full_name":"Iwasa, Yoshihiro","last_name":"Iwasa"},{"full_name":"Bisri, Satria Zulkarnaen","last_name":"Bisri","first_name":"Satria Zulkarnaen"}],"day":"24","scopus_import":"1","article_type":"original","date_created":"2020-04-05T22:00:48Z","volume":14},{"department":[{"_id":"DaAl"}],"month":"02","year":"2020","date_published":"2020-02-19T00:00:00Z","conference":{"location":"San Diego, CA, United States","name":"PPOPP: Principles and Practice of Parallel Programming","start_date":"2020-02-22","end_date":"2020-02-26"},"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 <i>Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, PPOPP</i>, 423–24. Association for Computing Machinery, 2020. <a href=\"https://doi.org/10.1145/3332466.3374503\">https://doi.org/10.1145/3332466.3374503</a>.","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.","apa":"Koval, N., Sokolova, M., Fedorov, A., Alistarh, D.-A., &#38; Tsitelov, D. (2020). Testing concurrency on the JVM with Lincheck. In <i>Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, PPOPP</i> (pp. 423–424). San Diego, CA, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3332466.3374503\">https://doi.org/10.1145/3332466.3374503</a>","mla":"Koval, Nikita, et al. “Testing Concurrency on the JVM with Lincheck.” <i>Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, PPOPP</i>, Association for Computing Machinery, 2020, pp. 423–24, doi:<a href=\"https://doi.org/10.1145/3332466.3374503\">10.1145/3332466.3374503</a>.","ama":"Koval N, Sokolova M, Fedorov A, Alistarh D-A, Tsitelov D. Testing concurrency on the JVM with Lincheck. In: <i>Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, PPOPP</i>. Association for Computing Machinery; 2020:423-424. doi:<a href=\"https://doi.org/10.1145/3332466.3374503\">10.1145/3332466.3374503</a>","ieee":"N. Koval, M. Sokolova, A. Fedorov, D.-A. Alistarh, and D. Tsitelov, “Testing concurrency on the JVM with Lincheck,” in <i>Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, PPOPP</i>, San Diego, CA, United States, 2020, pp. 423–424.","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."},"publication":"Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, PPOPP","status":"public","language":[{"iso":"eng"}],"type":"conference","date_created":"2020-04-05T22:00:48Z","date_updated":"2024-02-28T12:53:46Z","_id":"7635","publisher":"Association for Computing Machinery","title":"Testing concurrency on the JVM with Lincheck","oa_version":"None","doi":"10.1145/3332466.3374503","author":[{"first_name":"Nikita","id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87","full_name":"Koval, Nikita","last_name":"Koval"},{"first_name":"Mariia","last_name":"Sokolova","full_name":"Sokolova, Mariia","id":"26217AE4-77FF-11EA-8101-AD24D49E41F4"},{"full_name":"Fedorov, Alexander","last_name":"Fedorov","first_name":"Alexander"},{"first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Tsitelov","full_name":"Tsitelov, Dmitry","first_name":"Dmitry"}],"article_processing_charge":"No","day":"19","scopus_import":"1","quality_controlled":"1","publication_status":"published","publication_identifier":{"isbn":["9781450368186"]},"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."}],"page":"423-424"},{"page":"276-291","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1145/3332466.3374542"}],"quality_controlled":"1","doi":"10.1145/3332466.3374542","article_processing_charge":"No","publisher":"Association for Computing Machinery","date_updated":"2024-02-28T12:55:14Z","_id":"7636","type":"conference","project":[{"_id":"268A44D6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"805223","name":"Elastic Coordination for Scalable Machine Learning"}],"publication":"Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming","status":"public","ec_funded":1,"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). ","conference":{"start_date":"2020-02-22","end_date":"2020-02-26","name":"PPOPP: Principles and Practice of Parallel Programming","location":"San Diego, CA, United States"},"date_published":"2020-02-19T00:00:00Z","year":"2020","isi":1,"external_id":{"isi":["000564476500020"]},"abstract":[{"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.","lang":"eng"}],"publication_identifier":{"isbn":["9781450368186"]},"publication_status":"published","author":[{"id":"3569F0A0-F248-11E8-B48F-1D18A9856A87","full_name":"Brown, Trevor A","last_name":"Brown","first_name":"Trevor A"},{"full_name":"Prokopec, Aleksandar","last_name":"Prokopec","first_name":"Aleksandar"},{"first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh"}],"day":"19","scopus_import":"1","oa_version":"Published Version","title":"Non-blocking interpolation search trees with doubly-logarithmic running time","date_created":"2020-04-05T22:00:49Z","oa":1,"language":[{"iso":"eng"}],"citation":{"apa":"Brown, T. A., Prokopec, A., &#38; Alistarh, D.-A. (2020). Non-blocking interpolation search trees with doubly-logarithmic running time. In <i>Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i> (pp. 276–291). San Diego, CA, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3332466.3374542\">https://doi.org/10.1145/3332466.3374542</a>","mla":"Brown, Trevor A., et al. “Non-Blocking Interpolation Search Trees with Doubly-Logarithmic Running Time.” <i>Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i>, Association for Computing Machinery, 2020, pp. 276–91, doi:<a href=\"https://doi.org/10.1145/3332466.3374542\">10.1145/3332466.3374542</a>.","chicago":"Brown, Trevor A, Aleksandar Prokopec, and Dan-Adrian Alistarh. “Non-Blocking Interpolation Search Trees with Doubly-Logarithmic Running Time.” In <i>Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i>, 276–91. Association for Computing Machinery, 2020. <a href=\"https://doi.org/10.1145/3332466.3374542\">https://doi.org/10.1145/3332466.3374542</a>.","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.","ieee":"T. A. Brown, A. Prokopec, and D.-A. Alistarh, “Non-blocking interpolation search trees with doubly-logarithmic running time,” in <i>Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i>, San Diego, CA, United States, 2020, pp. 276–291.","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.","ama":"Brown TA, Prokopec A, Alistarh D-A. Non-blocking interpolation search trees with doubly-logarithmic running time. In: <i>Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i>. Association for Computing Machinery; 2020:276-291. doi:<a href=\"https://doi.org/10.1145/3332466.3374542\">10.1145/3332466.3374542</a>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"02","department":[{"_id":"DaAl"}]},{"article_processing_charge":"No","doi":"10.1088/1361-6544/ab5174","publisher":"IOP Publishing","_id":"7637","date_updated":"2023-08-18T10:26:07Z","type":"journal_article","page":"864-891","main_file_link":[{"url":"https://arxiv.org/abs/1811.06448","open_access":"1"}],"quality_controlled":"1","isi":1,"year":"2020","external_id":{"isi":["000508175400001"],"arxiv":["1811.06448"]},"publication":"Nonlinearity","status":"public","date_published":"2020-01-10T00:00:00Z","scopus_import":"1","day":"10","author":[{"orcid":"0000-0002-6269-5149","first_name":"Federico","last_name":"Cornalba","full_name":"Cornalba, Federico","id":"2CEB641C-A400-11E9-A717-D712E6697425"},{"first_name":"Tony","full_name":"Shardlow, Tony","last_name":"Shardlow"},{"first_name":"Johannes","last_name":"Zimmer","full_name":"Zimmer, Johannes"}],"title":"From weakly interacting particles to a regularised Dean-Kawasaki model","oa_version":"Preprint","volume":33,"date_created":"2020-04-05T22:00:49Z","article_type":"original","abstract":[{"lang":"eng","text":"The evolution of finitely many particles obeying Langevin dynamics is described by Dean–Kawasaki equations, a class of stochastic equations featuring a non-Lipschitz multiplicative noise in divergence form. We derive a regularised Dean–Kawasaki model based on second order Langevin dynamics by analysing a system of particles interacting via a pairwise potential. Key tools of our analysis are the propagation of chaos and Simon's compactness criterion. The model we obtain is a small-noise stochastic perturbation of the undamped McKean–Vlasov equation. We also provide a high-probability result for existence and uniqueness for our model."}],"intvolume":"        33","publication_status":"published","publication_identifier":{"eissn":["13616544"],"issn":["09517715"]},"arxiv":1,"month":"01","department":[{"_id":"JuFi"}],"oa":1,"language":[{"iso":"eng"}],"citation":{"ista":"Cornalba F, Shardlow T, Zimmer J. 2020. From weakly interacting particles to a regularised Dean-Kawasaki model. Nonlinearity. 33(2), 864–891.","chicago":"Cornalba, Federico, Tony Shardlow, and Johannes Zimmer. “From Weakly Interacting Particles to a Regularised Dean-Kawasaki Model.” <i>Nonlinearity</i>. IOP Publishing, 2020. <a href=\"https://doi.org/10.1088/1361-6544/ab5174\">https://doi.org/10.1088/1361-6544/ab5174</a>.","mla":"Cornalba, Federico, et al. “From Weakly Interacting Particles to a Regularised Dean-Kawasaki Model.” <i>Nonlinearity</i>, vol. 33, no. 2, IOP Publishing, 2020, pp. 864–91, doi:<a href=\"https://doi.org/10.1088/1361-6544/ab5174\">10.1088/1361-6544/ab5174</a>.","apa":"Cornalba, F., Shardlow, T., &#38; Zimmer, J. (2020). From weakly interacting particles to a regularised Dean-Kawasaki model. <i>Nonlinearity</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1361-6544/ab5174\">https://doi.org/10.1088/1361-6544/ab5174</a>","ama":"Cornalba F, Shardlow T, Zimmer J. From weakly interacting particles to a regularised Dean-Kawasaki model. <i>Nonlinearity</i>. 2020;33(2):864-891. doi:<a href=\"https://doi.org/10.1088/1361-6544/ab5174\">10.1088/1361-6544/ab5174</a>","short":"F. Cornalba, T. Shardlow, J. Zimmer, Nonlinearity 33 (2020) 864–891.","ieee":"F. Cornalba, T. Shardlow, and J. Zimmer, “From weakly interacting particles to a regularised Dean-Kawasaki model,” <i>Nonlinearity</i>, vol. 33, no. 2. IOP Publishing, pp. 864–891, 2020."},"issue":"2","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"department":[{"_id":"MaSe"}],"article_number":"013106","file":[{"file_id":"7648","date_created":"2020-04-06T13:15:49Z","file_size":3159026,"date_updated":"2020-07-14T12:48:01Z","creator":"dernst","relation":"main_file","checksum":"4030e683c15d30b7b4794ec7dc1b6537","file_name":"2020_JournStatisticalMech_DeNicola.pdf","access_level":"open_access","content_type":"application/pdf"}],"month":"01","arxiv":1,"issue":"1","citation":{"ama":"De Nicola S, Doyon B, Bhaseen MJ. Non-equilibrium quantum spin dynamics from classical stochastic processes. <i>Journal of Statistical Mechanics: Theory and Experiment</i>. 2020;2020(1). doi:<a href=\"https://doi.org/10.1088/1742-5468/ab6093\">10.1088/1742-5468/ab6093</a>","short":"S. De Nicola, B. Doyon, M.J. Bhaseen, Journal of Statistical Mechanics: Theory and Experiment 2020 (2020).","ieee":"S. De Nicola, B. Doyon, and M. J. Bhaseen, “Non-equilibrium quantum spin dynamics from classical stochastic processes,” <i>Journal of Statistical Mechanics: Theory and Experiment</i>, vol. 2020, no. 1. IOP Publishing, 2020.","ista":"De Nicola S, Doyon B, Bhaseen MJ. 2020. Non-equilibrium quantum spin dynamics from classical stochastic processes. Journal of Statistical Mechanics: Theory and Experiment. 2020(1), 013106.","chicago":"De Nicola, Stefano, B. Doyon, and M. J. Bhaseen. “Non-Equilibrium Quantum Spin Dynamics from Classical Stochastic Processes.” <i>Journal of Statistical Mechanics: Theory and Experiment</i>. IOP Publishing, 2020. <a href=\"https://doi.org/10.1088/1742-5468/ab6093\">https://doi.org/10.1088/1742-5468/ab6093</a>.","mla":"De Nicola, Stefano, et al. “Non-Equilibrium Quantum Spin Dynamics from Classical Stochastic Processes.” <i>Journal of Statistical Mechanics: Theory and Experiment</i>, vol. 2020, no. 1, 013106, IOP Publishing, 2020, doi:<a href=\"https://doi.org/10.1088/1742-5468/ab6093\">10.1088/1742-5468/ab6093</a>.","apa":"De Nicola, S., Doyon, B., &#38; Bhaseen, M. J. (2020). Non-equilibrium quantum spin dynamics from classical stochastic processes. <i>Journal of Statistical Mechanics: Theory and Experiment</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1742-5468/ab6093\">https://doi.org/10.1088/1742-5468/ab6093</a>"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"language":[{"iso":"eng"}],"volume":2020,"article_type":"original","date_created":"2020-04-05T22:00:50Z","author":[{"orcid":"0000-0002-4842-6671","first_name":"Stefano","id":"42832B76-F248-11E8-B48F-1D18A9856A87","full_name":"De Nicola, Stefano","last_name":"De Nicola"},{"first_name":"B.","last_name":"Doyon","full_name":"Doyon, B."},{"first_name":"M. J.","full_name":"Bhaseen, M. J.","last_name":"Bhaseen"}],"day":"22","scopus_import":"1","title":"Non-equilibrium quantum spin dynamics from classical stochastic processes","oa_version":"Published Version","publication_identifier":{"eissn":["17425468"]},"publication_status":"published","file_date_updated":"2020-07-14T12:48:01Z","has_accepted_license":"1","intvolume":"      2020","abstract":[{"text":"Following on from our recent work, we investigate a stochastic approach to non-equilibrium quantum spin systems. We show how the method can be applied to a variety of physical observables and for different initial conditions. We provide exact formulae of broad applicability for the time-dependence of expectation values and correlation functions following a quantum quench in terms of averages over classical stochastic processes. We further explore the behavior of the classical stochastic variables in the presence of dynamical quantum phase transitions, including results for their distributions and correlation functions. We provide details on the numerical solution of the associated stochastic differential equations, and examine the growth of fluctuations in the classical description. We discuss the strengths and limitations of the current implementation of the stochastic approach and the potential for further development.","lang":"eng"}],"year":"2020","isi":1,"external_id":{"arxiv":["1909.13142"],"isi":["000520187500001"]},"ec_funded":1,"date_published":"2020-01-22T00:00:00Z","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"publication":"Journal of Statistical Mechanics: Theory and Experiment","status":"public","date_updated":"2023-08-18T10:27:15Z","_id":"7638","type":"journal_article","doi":"10.1088/1742-5468/ab6093","article_processing_charge":"No","publisher":"IOP Publishing","quality_controlled":"1","ddc":["530"]},{"acknowledgement":"This work was supported by the European Research Council under the European Union’s Horizon 2020 research and innovation Programme (ERC grant agreement number 742985), and the Austrian Science Fund (FWF, grant number I 3630-B25) to JF. HH is supported by the China Scholarship Council (CSC scholarship). ","date_published":"2020-05-08T00:00:00Z","pmid":1,"ec_funded":1,"project":[{"grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425"}],"publication":"Plant Physiology","status":"public","external_id":{"pmid":["32107280"],"isi":["000536641800018"]},"related_material":{"record":[{"id":"8589","relation":"dissertation_contains","status":"public"}]},"isi":1,"year":"2020","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.1104/pp.20.00212","open_access":"1"}],"page":"37-40","type":"journal_article","date_updated":"2023-09-07T13:13:04Z","_id":"7643","publisher":"American Society of Plant Biologists","doi":"10.1104/pp.20.00212","article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"5","citation":{"ieee":"H. Han, H. Rakusova, I. Verstraeten, Y. Zhang, and J. Friml, “SCF TIR1/AFB auxin signaling for bending termination during shoot gravitropism,” <i>Plant Physiology</i>, vol. 183, no. 5. American Society of Plant Biologists, pp. 37–40, 2020.","short":"H. Han, H. Rakusova, I. Verstraeten, Y. Zhang, J. Friml, Plant Physiology 183 (2020) 37–40.","ama":"Han H, Rakusova H, Verstraeten I, Zhang Y, Friml J. SCF TIR1/AFB auxin signaling for bending termination during shoot gravitropism. <i>Plant Physiology</i>. 2020;183(5):37-40. doi:<a href=\"https://doi.org/10.1104/pp.20.00212\">10.1104/pp.20.00212</a>","apa":"Han, H., Rakusova, H., Verstraeten, I., Zhang, Y., &#38; Friml, J. (2020). SCF TIR1/AFB auxin signaling for bending termination during shoot gravitropism. <i>Plant Physiology</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1104/pp.20.00212\">https://doi.org/10.1104/pp.20.00212</a>","mla":"Han, Huibin, et al. “SCF TIR1/AFB Auxin Signaling for Bending Termination during Shoot Gravitropism.” <i>Plant Physiology</i>, vol. 183, no. 5, American Society of Plant Biologists, 2020, pp. 37–40, doi:<a href=\"https://doi.org/10.1104/pp.20.00212\">10.1104/pp.20.00212</a>.","ista":"Han H, Rakusova H, Verstraeten I, Zhang Y, Friml J. 2020. SCF TIR1/AFB auxin signaling for bending termination during shoot gravitropism. Plant Physiology. 183(5), 37–40.","chicago":"Han, Huibin, Hana Rakusova, Inge Verstraeten, Yuzhou Zhang, and Jiří Friml. “SCF TIR1/AFB Auxin Signaling for Bending Termination during Shoot Gravitropism.” <i>Plant Physiology</i>. American Society of Plant Biologists, 2020. <a href=\"https://doi.org/10.1104/pp.20.00212\">https://doi.org/10.1104/pp.20.00212</a>."},"language":[{"iso":"eng"}],"oa":1,"department":[{"_id":"JiFr"}],"month":"05","publication_identifier":{"issn":["0032-0889"],"eissn":["1532-2548"]},"publication_status":"published","intvolume":"       183","article_type":"letter_note","date_created":"2020-04-06T10:06:40Z","volume":183,"oa_version":"Published Version","title":"SCF TIR1/AFB auxin signaling for bending termination during shoot gravitropism","author":[{"first_name":"Huibin","full_name":"Han, Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87","last_name":"Han"},{"first_name":"Hana","id":"4CAAA450-78D2-11EA-8E57-B40A396E08BA","full_name":"Rakusova, Hana","last_name":"Rakusova"},{"orcid":"0000-0001-7241-2328","first_name":"Inge","last_name":"Verstraeten","full_name":"Verstraeten, Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Zhang","full_name":"Zhang, Yuzhou","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","first_name":"Yuzhou","orcid":"0000-0003-2627-6956"},{"orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"scopus_import":"1","day":"08"},{"issue":"14","citation":{"ama":"Lee E, Vila Nova Santana B, Samuels E, et al. Rare earth elements induce cytoskeleton-dependent and PI4P-associated rearrangement of SYT1/SYT5 ER-PM contact site complexes in Arabidopsis. <i>Journal of Experimental Botany</i>. 2020;71(14):3986–3998. doi:<a href=\"https://doi.org/10.1093/jxb/eraa138\">10.1093/jxb/eraa138</a>","short":"E. Lee, B. Vila Nova Santana, E. Samuels, F. Benitez-Fuente, E. Corsi, M. Botella, J. Perez-Sancho, S. Vanneste, J. Friml, A. Macho, A. Alves Azevedo, A. Rosado, Journal of Experimental Botany 71 (2020) 3986–3998.","ieee":"E. Lee <i>et al.</i>, “Rare earth elements induce cytoskeleton-dependent and PI4P-associated rearrangement of SYT1/SYT5 ER-PM contact site complexes in Arabidopsis,” <i>Journal of Experimental Botany</i>, vol. 71, no. 14. Oxford University Press, pp. 3986–3998, 2020.","chicago":"Lee, E, B Vila Nova Santana, E Samuels, F Benitez-Fuente, E Corsi, MA Botella, J Perez-Sancho, et al. “Rare Earth Elements Induce Cytoskeleton-Dependent and PI4P-Associated Rearrangement of SYT1/SYT5 ER-PM Contact Site Complexes in Arabidopsis.” <i>Journal of Experimental Botany</i>. Oxford University Press, 2020. <a href=\"https://doi.org/10.1093/jxb/eraa138\">https://doi.org/10.1093/jxb/eraa138</a>.","ista":"Lee E, Vila Nova Santana B, Samuels E, Benitez-Fuente F, Corsi E, Botella M, Perez-Sancho J, Vanneste S, Friml J, Macho A, Alves Azevedo A, Rosado A. 2020. Rare earth elements induce cytoskeleton-dependent and PI4P-associated rearrangement of SYT1/SYT5 ER-PM contact site complexes in Arabidopsis. Journal of Experimental Botany. 71(14), 3986–3998.","mla":"Lee, E., et al. “Rare Earth Elements Induce Cytoskeleton-Dependent and PI4P-Associated Rearrangement of SYT1/SYT5 ER-PM Contact Site Complexes in Arabidopsis.” <i>Journal of Experimental Botany</i>, vol. 71, no. 14, Oxford University Press, 2020, pp. 3986–3998, doi:<a href=\"https://doi.org/10.1093/jxb/eraa138\">10.1093/jxb/eraa138</a>.","apa":"Lee, E., Vila Nova Santana, B., Samuels, E., Benitez-Fuente, F., Corsi, E., Botella, M., … Rosado, A. (2020). Rare earth elements induce cytoskeleton-dependent and PI4P-associated rearrangement of SYT1/SYT5 ER-PM contact site complexes in Arabidopsis. <i>Journal of Experimental Botany</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/jxb/eraa138\">https://doi.org/10.1093/jxb/eraa138</a>"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"language":[{"iso":"eng"}],"department":[{"_id":"JiFr"}],"file":[{"file_id":"8613","file_size":1916031,"date_created":"2020-10-06T07:41:35Z","date_updated":"2020-10-06T07:41:35Z","creator":"dernst","relation":"main_file","checksum":"b06aaaa93dc41896da805fe4b75cf3a1","file_name":"2020_JourExperimBotany_Lee.pdf","success":1,"content_type":"application/pdf","access_level":"open_access"}],"month":"07","publication_status":"published","publication_identifier":{"issn":["0022-0957"],"eissn":["1460-2431"]},"file_date_updated":"2020-10-06T07:41:35Z","has_accepted_license":"1","intvolume":"        71","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"lang":"eng","text":"In plant cells, environmental stressors promote changes in connectivity between the cortical ER and the PM. Although this process is tightly regulated in space and time, the molecular signals and structural components mediating these changes in inter-organelle communication are only starting to be characterized. In this report, we confirm the presence of a putative tethering complex containing the synaptotagmins 1 and 5 (SYT1 and SYT5) and the Ca2+ and lipid binding protein 1 (CLB1/SYT7). This complex is enriched at ER-PM contact sites (EPCS), have slow responses to changes in extracellular Ca2+, and display severe cytoskeleton-dependent rearrangements in response to the trivalent lanthanum (La3+) and gadolinium (Gd3+) rare earth elements (REEs). Although REEs are generally used as non-selective cation channel blockers at the PM, here we show that the slow internalization of REEs into the cytosol underlies the activation of the Ca2+/Calmodulin intracellular signaling, the accumulation of phosphatidylinositol-4-phosphate (PI4P) at the PM, and the cytoskeleton-dependent rearrangement of the SYT1/SYT5 EPCS complexes. We propose that the observed EPCS rearrangements act as a slow adaptive response to sustained stress conditions, and that this process involves the accumulation of stress-specific phosphoinositides species at the PM."}],"volume":71,"article_type":"original","date_created":"2020-04-06T10:57:08Z","author":[{"last_name":"Lee","full_name":"Lee, E","first_name":"E"},{"first_name":"B","full_name":"Vila Nova Santana, B","last_name":"Vila Nova Santana"},{"full_name":"Samuels, E","last_name":"Samuels","first_name":"E"},{"first_name":"F","last_name":"Benitez-Fuente","full_name":"Benitez-Fuente, F"},{"last_name":"Corsi","full_name":"Corsi, E","first_name":"E"},{"first_name":"MA","full_name":"Botella, MA","last_name":"Botella"},{"first_name":"J","last_name":"Perez-Sancho","full_name":"Perez-Sancho, J"},{"first_name":"S","full_name":"Vanneste, S","last_name":"Vanneste"},{"last_name":"Friml","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596"},{"first_name":"A","full_name":"Macho, A","last_name":"Macho"},{"last_name":"Alves Azevedo","full_name":"Alves Azevedo, A","first_name":"A"},{"first_name":"A","full_name":"Rosado, A","last_name":"Rosado"}],"day":"06","title":"Rare earth elements induce cytoskeleton-dependent and PI4P-associated rearrangement of SYT1/SYT5 ER-PM contact site complexes in Arabidopsis","oa_version":"Published Version","pmid":1,"date_published":"2020-07-06T00:00:00Z","status":"public","publication":"Journal of Experimental Botany","isi":1,"year":"2020","external_id":{"isi":["000553125400007"],"pmid":["32179893"]},"quality_controlled":"1","page":"3986–3998","ddc":["580"],"date_updated":"2023-08-18T10:27:52Z","_id":"7646","type":"journal_article","doi":"10.1093/jxb/eraa138","article_processing_charge":"No","publisher":"Oxford University Press"},{"file_date_updated":"2020-11-20T13:17:42Z","publication_status":"published","publication_identifier":{"issn":["0003-9527"],"eissn":["1432-0673"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":"       236","abstract":[{"lang":"eng","text":"We consider a dilute, homogeneous Bose gas at positive temperature. The system is investigated in the Gross–Pitaevskii limit, where the scattering length a is so small that the interaction energy is of the same order of magnitude as the spectral gap of the Laplacian, and for temperatures that are comparable to the critical temperature of the ideal gas. We show that the difference between the specific free energy of the interacting system and the one of the ideal gas is to leading order given by 4πa(2ϱ2−ϱ20). Here ϱ denotes the density of the system and ϱ0 is the expected condensate density of the ideal gas. Additionally, we show that the one-particle density matrix of any approximate minimizer of the Gibbs free energy functional is to leading order given by the one of the ideal gas. This in particular proves Bose–Einstein condensation with critical temperature given by the one of the ideal gas to leading order. One key ingredient of our proof is a novel use of the Gibbs variational principle that goes hand in hand with the c-number substitution."}],"has_accepted_license":"1","date_created":"2020-04-08T15:18:03Z","article_type":"original","volume":236,"title":"Gross-Pitaevskii limit of a homogeneous Bose gas at positive temperature","oa_version":"Published Version","day":"09","scopus_import":"1","author":[{"orcid":"0000-0003-3146-6746","first_name":"Andreas","id":"4DA65CD0-F248-11E8-B48F-1D18A9856A87","full_name":"Deuchert, Andreas","last_name":"Deuchert"},{"last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","first_name":"Robert"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Deuchert, Andreas, and Robert Seiringer. “Gross-Pitaevskii Limit of a Homogeneous Bose Gas at Positive Temperature.” <i>Archive for Rational Mechanics and Analysis</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/s00205-020-01489-4\">https://doi.org/10.1007/s00205-020-01489-4</a>.","ista":"Deuchert A, Seiringer R. 2020. Gross-Pitaevskii limit of a homogeneous Bose gas at positive temperature. Archive for Rational Mechanics and Analysis. 236(6), 1217–1271.","mla":"Deuchert, Andreas, and Robert Seiringer. “Gross-Pitaevskii Limit of a Homogeneous Bose Gas at Positive Temperature.” <i>Archive for Rational Mechanics and Analysis</i>, vol. 236, no. 6, Springer Nature, 2020, pp. 1217–71, doi:<a href=\"https://doi.org/10.1007/s00205-020-01489-4\">10.1007/s00205-020-01489-4</a>.","apa":"Deuchert, A., &#38; Seiringer, R. (2020). Gross-Pitaevskii limit of a homogeneous Bose gas at positive temperature. <i>Archive for Rational Mechanics and Analysis</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00205-020-01489-4\">https://doi.org/10.1007/s00205-020-01489-4</a>","ama":"Deuchert A, Seiringer R. Gross-Pitaevskii limit of a homogeneous Bose gas at positive temperature. <i>Archive for Rational Mechanics and Analysis</i>. 2020;236(6):1217-1271. doi:<a href=\"https://doi.org/10.1007/s00205-020-01489-4\">10.1007/s00205-020-01489-4</a>","short":"A. Deuchert, R. Seiringer, Archive for Rational Mechanics and Analysis 236 (2020) 1217–1271.","ieee":"A. Deuchert and R. Seiringer, “Gross-Pitaevskii limit of a homogeneous Bose gas at positive temperature,” <i>Archive for Rational Mechanics and Analysis</i>, vol. 236, no. 6. Springer Nature, pp. 1217–1271, 2020."},"issue":"6","language":[{"iso":"eng"}],"oa":1,"file":[{"checksum":"b645fb64bfe95bbc05b3eea374109a9c","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_name":"2020_ArchRatMechanicsAnalysis_Deuchert.pdf","success":1,"file_id":"8785","date_updated":"2020-11-20T13:17:42Z","creator":"dernst","date_created":"2020-11-20T13:17:42Z","file_size":704633}],"department":[{"_id":"RoSe"}],"month":"03","arxiv":1,"quality_controlled":"1","ddc":["510"],"page":"1217-1271","type":"journal_article","_id":"7650","date_updated":"2023-09-05T14:18:49Z","publisher":"Springer Nature","article_processing_charge":"Yes (via OA deal)","doi":"10.1007/s00205-020-01489-4","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). It is a pleasure to thank Jakob Yngvason for helpful discussions. Financial support by the European Research Council (ERC) under the European Union’sHorizon 2020 research and innovation programme (Grant Agreement No. 694227) is gratefully acknowledged. A. D. acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreement No. 836146.","date_published":"2020-03-09T00:00:00Z","ec_funded":1,"status":"public","publication":"Archive for Rational Mechanics and Analysis","project":[{"grant_number":"694227","name":"Analysis of quantum many-body systems","call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"external_id":{"arxiv":["1901.11363"],"isi":["000519415000001"]},"isi":1,"year":"2020"},{"department":[{"_id":"NiBa"}],"file":[{"relation":"main_file","checksum":"4eb102304402f5c56432516b84df86d6","file_name":"2020_JournRoyalSociety_Larsson.pdf","access_level":"open_access","content_type":"application/pdf","file_id":"7660","date_created":"2020-04-14T12:31:16Z","file_size":1556190,"date_updated":"2020-07-14T12:48:01Z","creator":"dernst"}],"article_number":"20190721","month":"02","issue":"163","citation":{"ieee":"J. Larsson, A. M. Westram, S. Bengmark, T. Lundh, and R. K. Butlin, “A developmentally descriptive method for quantifying shape in gastropod shells,” <i>Journal of The Royal Society Interface</i>, vol. 17, no. 163. The Royal Society, 2020.","short":"J. Larsson, A.M. Westram, S. Bengmark, T. Lundh, R.K. Butlin, Journal of The Royal Society Interface 17 (2020).","ama":"Larsson J, Westram AM, Bengmark S, Lundh T, Butlin RK. A developmentally descriptive method for quantifying shape in gastropod shells. <i>Journal of The Royal Society Interface</i>. 2020;17(163). doi:<a href=\"https://doi.org/10.1098/rsif.2019.0721\">10.1098/rsif.2019.0721</a>","apa":"Larsson, J., Westram, A. M., Bengmark, S., Lundh, T., &#38; Butlin, R. K. (2020). A developmentally descriptive method for quantifying shape in gastropod shells. <i>Journal of The Royal Society Interface</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rsif.2019.0721\">https://doi.org/10.1098/rsif.2019.0721</a>","mla":"Larsson, J., et al. “A Developmentally Descriptive Method for Quantifying Shape in Gastropod Shells.” <i>Journal of The Royal Society Interface</i>, vol. 17, no. 163, 20190721, The Royal Society, 2020, doi:<a href=\"https://doi.org/10.1098/rsif.2019.0721\">10.1098/rsif.2019.0721</a>.","ista":"Larsson J, Westram AM, Bengmark S, Lundh T, Butlin RK. 2020. A developmentally descriptive method for quantifying shape in gastropod shells. Journal of The Royal Society Interface. 17(163), 20190721.","chicago":"Larsson, J., Anja M Westram, S. Bengmark, T. Lundh, and R. K. Butlin. “A Developmentally Descriptive Method for Quantifying Shape in Gastropod Shells.” <i>Journal of The Royal Society Interface</i>. The Royal Society, 2020. <a href=\"https://doi.org/10.1098/rsif.2019.0721\">https://doi.org/10.1098/rsif.2019.0721</a>."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"language":[{"iso":"eng"}],"volume":17,"article_type":"original","date_created":"2020-04-08T15:19:17Z","author":[{"full_name":"Larsson, J.","last_name":"Larsson","first_name":"J."},{"last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M","first_name":"Anja M","orcid":"0000-0003-1050-4969"},{"first_name":"S.","last_name":"Bengmark","full_name":"Bengmark, S."},{"first_name":"T.","full_name":"Lundh, T.","last_name":"Lundh"},{"full_name":"Butlin, R. K.","last_name":"Butlin","first_name":"R. K."}],"scopus_import":1,"day":"01","title":"A developmentally descriptive method for quantifying shape in gastropod shells","oa_version":"Published Version","publication_identifier":{"issn":["1742-5689"],"eissn":["1742-5662"]},"publication_status":"published","file_date_updated":"2020-07-14T12:48:01Z","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"text":"The growth of snail shells can be described by simple mathematical rules. Variation in a few parameters can explain much of the diversity of shell shapes seen in nature. However, empirical studies of gastropod shell shape variation typically use geometric morphometric approaches, which do not capture this growth pattern. We have developed a way to infer a set of developmentally descriptive shape parameters based on three-dimensional logarithmic helicospiral growth and using landmarks from two-dimensional shell images as input. We demonstrate the utility of this approach, and compare it to the geometric morphometric approach, using a large set of Littorina saxatilis shells in which locally adapted populations differ in shape. Our method can be modified easily to make it applicable to a wide range of shell forms, which would allow for investigations of the similarities and differences between and within many different species of gastropods.","lang":"eng"}],"intvolume":"        17","year":"2020","date_published":"2020-02-01T00:00:00Z","status":"public","publication":"Journal of The Royal Society Interface","date_updated":"2021-01-12T08:14:41Z","_id":"7651","type":"journal_article","doi":"10.1098/rsif.2019.0721","article_processing_charge":"No","publisher":"The Royal Society","quality_controlled":"1","ddc":["570"]},{"citation":{"ista":"Tomanek I, Grah R, Lagator M, Andersson AMC, Bollback JP, Tkačik G, Guet CC. 2020. Gene amplification as a form of population-level gene expression regulation. Nature Ecology &#38; Evolution. 4(4), 612–625.","chicago":"Tomanek, Isabella, Rok Grah, M. Lagator, A. M. C. Andersson, Jonathan P Bollback, Gašper Tkačik, and Calin C Guet. “Gene Amplification as a Form of Population-Level Gene Expression Regulation.” <i>Nature Ecology &#38; Evolution</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41559-020-1132-7\">https://doi.org/10.1038/s41559-020-1132-7</a>.","mla":"Tomanek, Isabella, et al. “Gene Amplification as a Form of Population-Level Gene Expression Regulation.” <i>Nature Ecology &#38; Evolution</i>, vol. 4, no. 4, Springer Nature, 2020, pp. 612–25, doi:<a href=\"https://doi.org/10.1038/s41559-020-1132-7\">10.1038/s41559-020-1132-7</a>.","apa":"Tomanek, I., Grah, R., Lagator, M., Andersson, A. M. C., Bollback, J. P., Tkačik, G., &#38; Guet, C. C. (2020). Gene amplification as a form of population-level gene expression regulation. <i>Nature Ecology &#38; Evolution</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41559-020-1132-7\">https://doi.org/10.1038/s41559-020-1132-7</a>","ama":"Tomanek I, Grah R, Lagator M, et al. Gene amplification as a form of population-level gene expression regulation. <i>Nature Ecology &#38; Evolution</i>. 2020;4(4):612-625. doi:<a href=\"https://doi.org/10.1038/s41559-020-1132-7\">10.1038/s41559-020-1132-7</a>","short":"I. Tomanek, R. Grah, M. Lagator, A.M.C. Andersson, J.P. Bollback, G. Tkačik, C.C. Guet, Nature Ecology &#38; Evolution 4 (2020) 612–625.","ieee":"I. Tomanek <i>et al.</i>, “Gene amplification as a form of population-level gene expression regulation,” <i>Nature Ecology &#38; Evolution</i>, vol. 4, no. 4. Springer Nature, pp. 612–625, 2020."},"issue":"4","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"language":[{"iso":"eng"}],"department":[{"_id":"GaTk"},{"_id":"CaGu"}],"file":[{"file_id":"8640","creator":"dernst","date_updated":"2020-10-09T09:56:01Z","date_created":"2020-10-09T09:56:01Z","file_size":745242,"checksum":"ef3bbf42023e30b2c24a6278025d2040","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_name":"2020_NatureEcolEvo_Tomanek.pdf","success":1}],"month":"04","file_date_updated":"2020-10-09T09:56:01Z","publication_identifier":{"issn":["2397-334X"]},"publication_status":"published","has_accepted_license":"1","abstract":[{"lang":"eng","text":"Organisms cope with change by taking advantage of transcriptional regulators. However, when faced with rare environments, the evolution of transcriptional regulators and their promoters may be too slow. Here, we investigate whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. Using real-time monitoring of gene-copy-number mutations in Escherichia coli, we show that gene duplications and amplifications enable adaptation to fluctuating environments by rapidly generating copy-number and, therefore, expression-level polymorphisms. This amplification-mediated gene expression tuning (AMGET) occurs on timescales that are similar to canonical gene regulation and can respond to rapid environmental changes. Mathematical modelling shows that amplifications also tune gene expression in stochastic environments in which transcription-factor-based schemes are hard to evolve or maintain. The fleeting nature of gene amplifications gives rise to a generic population-level mechanism that relies on genetic heterogeneity to rapidly tune the expression of any gene, without leaving any genomic signature."}],"intvolume":"         4","volume":4,"date_created":"2020-04-08T15:20:53Z","article_type":"original","day":"01","scopus_import":"1","author":[{"orcid":"0000-0001-6197-363X","first_name":"Isabella","last_name":"Tomanek","id":"3981F020-F248-11E8-B48F-1D18A9856A87","full_name":"Tomanek, Isabella"},{"orcid":"0000-0003-2539-3560","first_name":"Rok","last_name":"Grah","full_name":"Grah, Rok","id":"483E70DE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"M.","last_name":"Lagator","full_name":"Lagator, M."},{"full_name":"Andersson, A. M. C.","last_name":"Andersson","first_name":"A. M. C."},{"orcid":"0000-0002-4624-4612","first_name":"Jonathan P","full_name":"Bollback, Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","last_name":"Bollback"},{"orcid":"0000-0002-6699-1455","first_name":"Gašper","full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik"},{"first_name":"Calin C","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet"}],"oa_version":"Submitted Version","title":"Gene amplification as a form of population-level gene expression regulation","acknowledgement":"We thank L. Hurst, N. Barton, M. Pleska, M. Steinrück, B. Kavcic and A. Staron for input on the manuscript, and To. Bergmiller and R. Chait for help with microfluidics experiments. I.T. is a recipient the OMV fellowship. R.G. is a recipient of a DOC (Doctoral Fellowship Programme of the Austrian Academy of Sciences) Fellowship of the Austrian Academy of Sciences.","date_published":"2020-04-01T00:00:00Z","publication":"Nature Ecology & Evolution","status":"public","project":[{"_id":"267C84F4-B435-11E9-9278-68D0E5697425","name":"Biophysically realistic genotype-phenotype maps for regulatory networks"}],"isi":1,"year":"2020","related_material":{"link":[{"url":"https://ist.ac.at/en/news/how-to-thrive-without-gene-regulation/","description":"News on IST Homepage","relation":"press_release"}],"record":[{"relation":"dissertation_contains","status":"public","id":"8155"},{"id":"7383","status":"public","relation":"research_data"},{"id":"7016","relation":"research_data","status":"public"},{"id":"8653","relation":"used_in_publication","status":"public"}]},"external_id":{"isi":["000519008300005"]},"quality_controlled":"1","page":"612-625","ddc":["570"],"_id":"7652","date_updated":"2024-03-25T23:30:20Z","type":"journal_article","article_processing_charge":"No","doi":"10.1038/s41559-020-1132-7","publisher":"Springer Nature"},{"department":[{"_id":"GaTk"}],"article_number":"20","file":[{"date_created":"2020-04-14T12:20:39Z","file_size":4082937,"date_updated":"2020-07-14T12:48:01Z","creator":"dernst","file_id":"7659","file_name":"2020_Frontiers_Berry.pdf","access_level":"open_access","content_type":"application/pdf","relation":"main_file","checksum":"2b1da23823eae9cedbb42d701945b61e"}],"month":"03","citation":{"mla":"Berry, Michael J., and Gašper Tkačik. “Clustering of Neural Activity: A Design Principle for Population Codes.” <i>Frontiers in Computational Neuroscience</i>, vol. 14, 20, Frontiers, 2020, doi:<a href=\"https://doi.org/10.3389/fncom.2020.00020\">10.3389/fncom.2020.00020</a>.","apa":"Berry, M. J., &#38; Tkačik, G. (2020). Clustering of neural activity: A design principle for population codes. <i>Frontiers in Computational Neuroscience</i>. Frontiers. <a href=\"https://doi.org/10.3389/fncom.2020.00020\">https://doi.org/10.3389/fncom.2020.00020</a>","ista":"Berry MJ, Tkačik G. 2020. Clustering of neural activity: A design principle for population codes. Frontiers in Computational Neuroscience. 14, 20.","chicago":"Berry, Michael J., and Gašper Tkačik. “Clustering of Neural Activity: A Design Principle for Population Codes.” <i>Frontiers in Computational Neuroscience</i>. Frontiers, 2020. <a href=\"https://doi.org/10.3389/fncom.2020.00020\">https://doi.org/10.3389/fncom.2020.00020</a>.","short":"M.J. Berry, G. Tkačik, Frontiers in Computational Neuroscience 14 (2020).","ieee":"M. J. Berry and G. Tkačik, “Clustering of neural activity: A design principle for population codes,” <i>Frontiers in Computational Neuroscience</i>, vol. 14. Frontiers, 2020.","ama":"Berry MJ, Tkačik G. Clustering of neural activity: A design principle for population codes. <i>Frontiers in Computational Neuroscience</i>. 2020;14. doi:<a href=\"https://doi.org/10.3389/fncom.2020.00020\">10.3389/fncom.2020.00020</a>"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"language":[{"iso":"eng"}],"volume":14,"article_type":"original","date_created":"2020-04-12T22:00:40Z","author":[{"last_name":"Berry","full_name":"Berry, Michael J.","first_name":"Michael J."},{"orcid":"0000-0002-6699-1455","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper","last_name":"Tkačik"}],"scopus_import":"1","day":"13","oa_version":"Published Version","title":"Clustering of neural activity: A design principle for population codes","publication_identifier":{"eissn":["16625188"]},"publication_status":"published","file_date_updated":"2020-07-14T12:48:01Z","has_accepted_license":"1","intvolume":"        14","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"text":"We propose that correlations among neurons are generically strong enough to organize neural activity patterns into a discrete set of clusters, which can each be viewed as a population codeword. Our reasoning starts with the analysis of retinal ganglion cell data using maximum entropy models, showing that the population is robustly in a frustrated, marginally sub-critical, or glassy, state. This leads to an argument that neural populations in many other brain areas might share this structure. Next, we use latent variable models to show that this glassy state possesses well-defined clusters of neural activity. Clusters have three appealing properties: (i) clusters exhibit error correction, i.e., they are reproducibly elicited by the same stimulus despite variability at the level of constituent neurons; (ii) clusters encode qualitatively different visual features than their constituent neurons; and (iii) clusters can be learned by downstream neural circuits in an unsupervised fashion. We hypothesize that these properties give rise to a “learnable” neural code which the cortical hierarchy uses to extract increasingly complex features without supervision or reinforcement.","lang":"eng"}],"isi":1,"year":"2020","external_id":{"pmid":["32231528"],"isi":["000525543200001"]},"pmid":1,"date_published":"2020-03-13T00:00:00Z","publication":"Frontiers in Computational Neuroscience","status":"public","date_updated":"2023-08-18T10:30:11Z","_id":"7656","type":"journal_article","doi":"10.3389/fncom.2020.00020","article_processing_charge":"No","publisher":"Frontiers","quality_controlled":"1","ddc":["570"]},{"file":[{"date_updated":"2020-07-14T12:48:01Z","creator":"dernst","file_size":7108014,"date_created":"2020-04-20T10:43:36Z","file_id":"7667","access_level":"open_access","content_type":"application/pdf","file_name":"2020_NanoLetters_Felhofer.pdf","checksum":"fe46146a9c4c620592a1932a8599069e","relation":"main_file"}],"department":[{"_id":"MaLo"}],"month":"04","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"short":"M. Felhofer, P. Bock, A. Singh, B. Prats Mateu, R. Zirbs, N. Gierlinger, Nano Letters 20 (2020) 2647–2653.","ieee":"M. Felhofer, P. Bock, A. Singh, B. Prats Mateu, R. Zirbs, and N. Gierlinger, “Wood deformation leads to rearrangement of molecules at the nanoscale,” <i>Nano Letters</i>, vol. 20, no. 4. American Chemical Society, pp. 2647–2653, 2020.","ama":"Felhofer M, Bock P, Singh A, Prats Mateu B, Zirbs R, Gierlinger N. Wood deformation leads to rearrangement of molecules at the nanoscale. <i>Nano Letters</i>. 2020;20(4):2647-2653. doi:<a href=\"https://doi.org/10.1021/acs.nanolett.0c00205\">10.1021/acs.nanolett.0c00205</a>","mla":"Felhofer, Martin, et al. “Wood Deformation Leads to Rearrangement of Molecules at the Nanoscale.” <i>Nano Letters</i>, vol. 20, no. 4, American Chemical Society, 2020, pp. 2647–53, doi:<a href=\"https://doi.org/10.1021/acs.nanolett.0c00205\">10.1021/acs.nanolett.0c00205</a>.","apa":"Felhofer, M., Bock, P., Singh, A., Prats Mateu, B., Zirbs, R., &#38; Gierlinger, N. (2020). Wood deformation leads to rearrangement of molecules at the nanoscale. <i>Nano Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.nanolett.0c00205\">https://doi.org/10.1021/acs.nanolett.0c00205</a>","chicago":"Felhofer, Martin, Peter Bock, Adya Singh, Batirtze Prats Mateu, Ronald Zirbs, and Notburga Gierlinger. “Wood Deformation Leads to Rearrangement of Molecules at the Nanoscale.” <i>Nano Letters</i>. American Chemical Society, 2020. <a href=\"https://doi.org/10.1021/acs.nanolett.0c00205\">https://doi.org/10.1021/acs.nanolett.0c00205</a>.","ista":"Felhofer M, Bock P, Singh A, Prats Mateu B, Zirbs R, Gierlinger N. 2020. Wood deformation leads to rearrangement of molecules at the nanoscale. Nano Letters. 20(4), 2647–2653."},"issue":"4","language":[{"iso":"eng"}],"oa":1,"date_created":"2020-04-19T22:00:54Z","article_type":"original","volume":20,"oa_version":"Published Version","title":"Wood deformation leads to rearrangement of molecules at the nanoscale","day":"08","scopus_import":"1","author":[{"first_name":"Martin","full_name":"Felhofer, Martin","last_name":"Felhofer"},{"first_name":"Peter","last_name":"Bock","full_name":"Bock, Peter"},{"last_name":"Singh","full_name":"Singh, Adya","first_name":"Adya"},{"first_name":"Batirtze","id":"299FE892-F248-11E8-B48F-1D18A9856A87","full_name":"Prats Mateu, Batirtze","last_name":"Prats Mateu"},{"last_name":"Zirbs","full_name":"Zirbs, Ronald","first_name":"Ronald"},{"first_name":"Notburga","full_name":"Gierlinger, Notburga","last_name":"Gierlinger"}],"file_date_updated":"2020-07-14T12:48:01Z","publication_status":"published","publication_identifier":{"eissn":["15306992"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":"        20","abstract":[{"lang":"eng","text":"Wood, as the most abundant carbon dioxide storing bioresource, is currently driven beyond its traditional use through creative innovations and nanotechnology. For many properties the micro- and nanostructure plays a crucial role and one key challenge is control and detection of chemical and physical processes in the confined microstructure and nanopores of the wooden cell wall. In this study, correlative Raman and atomic force microscopy show high potential for tracking in situ molecular rearrangement of wood polymers during compression. More water molecules (interpreted as wider cellulose microfibril distances) and disentangling of hemicellulose chains are detected in the opened cell wall regions, whereas an increase of lignin is revealed in the compressed areas. These results support a new more “loose” cell wall model based on flexible lignin nanodomains and advance our knowledge of the molecular reorganization during deformation of wood for optimized processing and utilization."}],"has_accepted_license":"1","external_id":{"isi":["000526413400055"],"pmid":["32196350"]},"isi":1,"year":"2020","date_published":"2020-04-08T00:00:00Z","pmid":1,"publication":"Nano Letters","status":"public","type":"journal_article","_id":"7663","date_updated":"2023-08-21T06:12:09Z","publisher":"American Chemical Society","article_processing_charge":"No","doi":"10.1021/acs.nanolett.0c00205","quality_controlled":"1","ddc":["530"],"page":"2647-2653"},{"publication_identifier":{"eissn":["14220067"]},"publication_status":"published","file_date_updated":"2020-07-14T12:48:01Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"text":"Metabotropic γ-aminobutyric acid (GABAB) receptors contribute to the control of network activity and information processing in hippocampal circuits by regulating neuronal excitability and synaptic transmission. The dysfunction in the dentate gyrus (DG) has been implicated in Alzheimer´s disease (AD). Given the involvement of GABAB receptors in AD, to determine their subcellular localisation and possible alteration in granule cells of the DG in a mouse model of AD at 12 months of age, we used high-resolution immunoelectron microscopic analysis. Immunohistochemistry at the light microscopic level showed that the regional and cellular expression pattern of GABAB1 was similar in an AD model mouse expressing mutated human amyloid precursor protein and presenilin1 (APP/PS1) and in age-matched wild type mice. High-resolution immunoelectron microscopy revealed a distance-dependent gradient of immunolabelling for GABAB receptors, increasing from proximal to distal dendrites in both wild type and APP/PS1 mice. However, the overall density of GABAB receptors at the neuronal surface of these postsynaptic compartments of granule cells was significantly reduced in APP/PS1 mice. Parallel to this reduction in surface receptors, we found a significant increase in GABAB1 at cytoplasmic sites. GABAB receptors were also detected at presynaptic sites in the molecular layer of the DG. We also found a decrease in plasma membrane GABAB receptors in axon terminals contacting dendritic spines of granule cells, which was more pronounced in the outer than in the inner molecular layer. Altogether, our data showing post- and presynaptic reduction in surface GABAB receptors in the DG suggest the alteration of the GABAB-mediated modulation of excitability and synaptic transmission in granule cells, which may contribute to the cognitive dysfunctions in the APP/PS1 model of AD","lang":"eng"}],"intvolume":"        21","has_accepted_license":"1","article_type":"original","date_created":"2020-04-19T22:00:55Z","volume":21,"oa_version":"Published Version","title":"Density of GABAB receptors is reduced in granule cells of the hippocampus in a mouse model of Alzheimer's disease","author":[{"first_name":"Alejandro","last_name":"Martín-Belmonte","full_name":"Martín-Belmonte, Alejandro"},{"full_name":"Aguado, Carolina","last_name":"Aguado","first_name":"Carolina"},{"full_name":"Alfaro-Ruíz, Rocío","last_name":"Alfaro-Ruíz","first_name":"Rocío"},{"first_name":"Ana Esther","full_name":"Moreno-Martínez, Ana Esther","last_name":"Moreno-Martínez"},{"last_name":"De La Ossa","full_name":"De La Ossa, Luis","first_name":"Luis"},{"last_name":"Martínez-Hernández","full_name":"Martínez-Hernández, José","first_name":"José"},{"full_name":"Buisson, Alain","last_name":"Buisson","first_name":"Alain"},{"last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","first_name":"Ryuichi"},{"first_name":"Yugo","full_name":"Fukazawa, Yugo","last_name":"Fukazawa"},{"first_name":"Rafael","full_name":"Luján, Rafael","last_name":"Luján"}],"day":"02","scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"7","citation":{"ama":"Martín-Belmonte A, Aguado C, Alfaro-Ruíz R, et al. Density of GABAB receptors is reduced in granule cells of the hippocampus in a mouse model of Alzheimer’s disease. <i>International journal of molecular sciences</i>. 2020;21(7). doi:<a href=\"https://doi.org/10.3390/ijms21072459\">10.3390/ijms21072459</a>","short":"A. Martín-Belmonte, C. Aguado, R. Alfaro-Ruíz, A.E. Moreno-Martínez, L. De La Ossa, J. Martínez-Hernández, A. Buisson, R. Shigemoto, Y. Fukazawa, R. Luján, International Journal of Molecular Sciences 21 (2020).","ieee":"A. Martín-Belmonte <i>et al.</i>, “Density of GABAB receptors is reduced in granule cells of the hippocampus in a mouse model of Alzheimer’s disease,” <i>International journal of molecular sciences</i>, vol. 21, no. 7. MDPI, 2020.","chicago":"Martín-Belmonte, Alejandro, Carolina Aguado, Rocío Alfaro-Ruíz, Ana Esther Moreno-Martínez, Luis De La Ossa, José Martínez-Hernández, Alain Buisson, Ryuichi Shigemoto, Yugo Fukazawa, and Rafael Luján. “Density of GABAB Receptors Is Reduced in Granule Cells of the Hippocampus in a Mouse Model of Alzheimer’s Disease.” <i>International Journal of Molecular Sciences</i>. MDPI, 2020. <a href=\"https://doi.org/10.3390/ijms21072459\">https://doi.org/10.3390/ijms21072459</a>.","ista":"Martín-Belmonte A, Aguado C, Alfaro-Ruíz R, Moreno-Martínez AE, De La Ossa L, Martínez-Hernández J, Buisson A, Shigemoto R, Fukazawa Y, Luján R. 2020. Density of GABAB receptors is reduced in granule cells of the hippocampus in a mouse model of Alzheimer’s disease. International journal of molecular sciences. 21(7), 2459.","mla":"Martín-Belmonte, Alejandro, et al. “Density of GABAB Receptors Is Reduced in Granule Cells of the Hippocampus in a Mouse Model of Alzheimer’s Disease.” <i>International Journal of Molecular Sciences</i>, vol. 21, no. 7, 2459, MDPI, 2020, doi:<a href=\"https://doi.org/10.3390/ijms21072459\">10.3390/ijms21072459</a>.","apa":"Martín-Belmonte, A., Aguado, C., Alfaro-Ruíz, R., Moreno-Martínez, A. E., De La Ossa, L., Martínez-Hernández, J., … Luján, R. (2020). Density of GABAB receptors is reduced in granule cells of the hippocampus in a mouse model of Alzheimer’s disease. <i>International Journal of Molecular Sciences</i>. MDPI. <a href=\"https://doi.org/10.3390/ijms21072459\">https://doi.org/10.3390/ijms21072459</a>"},"language":[{"iso":"eng"}],"oa":1,"file":[{"checksum":"b9d2f1657d8c4a74b01a62b474d009b0","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2020_JournMolecSciences_Martin_Belmonte.pdf","file_id":"7669","date_updated":"2020-07-14T12:48:01Z","creator":"dernst","file_size":2941197,"date_created":"2020-04-20T11:43:18Z"}],"article_number":"2459","department":[{"_id":"RySh"}],"month":"04","quality_controlled":"1","ddc":["570"],"type":"journal_article","date_updated":"2023-08-21T06:13:19Z","_id":"7664","publisher":"MDPI","doi":"10.3390/ijms21072459","article_processing_charge":"No","date_published":"2020-04-02T00:00:00Z","pmid":1,"publication":"International journal of molecular sciences","status":"public","external_id":{"pmid":["32252271"],"isi":["000535574200201"]},"year":"2020","isi":1},{"date_published":"2020-03-19T00:00:00Z","ec_funded":1,"project":[{"call_identifier":"H2020","grant_number":"793482","name":"Ultrastructural analysis of phosphoinositides in nerve terminals: distribution, dynamics and physiological roles in synaptic transmission","_id":"2659CC84-B435-11E9-9278-68D0E5697425"},{"name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","grant_number":"694539","call_identifier":"H2020","_id":"25CA28EA-B435-11E9-9278-68D0E5697425"},{"_id":"265CB4D0-B435-11E9-9278-68D0E5697425","name":"Optical control of synaptic function via adhesion molecules","grant_number":"I03600","call_identifier":"FWF"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"publication":"Frontiers in Cellular Neuroscience","status":"public","external_id":{"isi":["000525582200001"]},"year":"2020","isi":1,"quality_controlled":"1","ddc":["570"],"type":"journal_article","date_updated":"2023-08-21T06:12:48Z","_id":"7665","publisher":"Frontiers Media","doi":"10.3389/fncel.2020.00063","article_processing_charge":"Yes (via OA deal)","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"apa":"Eguchi, K., Velicky, P., Saeckl, E., Itakura, M., Fukazawa, Y., Danzl, J. G., &#38; Shigemoto, R. (2020). Advantages of acute brain slices prepared at physiological temperature in the characterization of synaptic functions. <i>Frontiers in Cellular Neuroscience</i>. Frontiers Media. <a href=\"https://doi.org/10.3389/fncel.2020.00063\">https://doi.org/10.3389/fncel.2020.00063</a>","mla":"Eguchi, Kohgaku, et al. “Advantages of Acute Brain Slices Prepared at Physiological Temperature in the Characterization of Synaptic Functions.” <i>Frontiers in Cellular Neuroscience</i>, vol. 14, 63, Frontiers Media, 2020, doi:<a href=\"https://doi.org/10.3389/fncel.2020.00063\">10.3389/fncel.2020.00063</a>.","ista":"Eguchi K, Velicky P, Saeckl E, Itakura M, Fukazawa Y, Danzl JG, Shigemoto R. 2020. Advantages of acute brain slices prepared at physiological temperature in the characterization of synaptic functions. Frontiers in Cellular Neuroscience. 14, 63.","chicago":"Eguchi, Kohgaku, Philipp Velicky, Elena Saeckl, Makoto Itakura, Yugo Fukazawa, Johann G Danzl, and Ryuichi Shigemoto. “Advantages of Acute Brain Slices Prepared at Physiological Temperature in the Characterization of Synaptic Functions.” <i>Frontiers in Cellular Neuroscience</i>. Frontiers Media, 2020. <a href=\"https://doi.org/10.3389/fncel.2020.00063\">https://doi.org/10.3389/fncel.2020.00063</a>.","ieee":"K. Eguchi <i>et al.</i>, “Advantages of acute brain slices prepared at physiological temperature in the characterization of synaptic functions,” <i>Frontiers in Cellular Neuroscience</i>, vol. 14. Frontiers Media, 2020.","short":"K. Eguchi, P. Velicky, E. Saeckl, M. Itakura, Y. Fukazawa, J.G. Danzl, R. Shigemoto, Frontiers in Cellular Neuroscience 14 (2020).","ama":"Eguchi K, Velicky P, Saeckl E, et al. Advantages of acute brain slices prepared at physiological temperature in the characterization of synaptic functions. <i>Frontiers in Cellular Neuroscience</i>. 2020;14. doi:<a href=\"https://doi.org/10.3389/fncel.2020.00063\">10.3389/fncel.2020.00063</a>"},"language":[{"iso":"eng"}],"oa":1,"article_number":"63","file":[{"access_level":"open_access","content_type":"application/pdf","file_name":"2020_FrontiersCellularNeurosc_Eguchi.pdf","checksum":"1c145123c6f8dc3e2e4bd5a66a1ad60e","relation":"main_file","creator":"dernst","date_updated":"2020-07-14T12:48:01Z","date_created":"2020-04-20T10:59:49Z","file_size":9227283,"file_id":"7668"}],"department":[{"_id":"JoDa"},{"_id":"RySh"}],"month":"03","publication_identifier":{"issn":["16625102"]},"publication_status":"published","file_date_updated":"2020-07-14T12:48:01Z","abstract":[{"text":"Acute brain slice preparation is a powerful experimental model for investigating the characteristics of synaptic function in the brain. Although brain tissue is usually cut at ice-cold temperature (CT) to facilitate slicing and avoid neuronal damage, exposure to CT causes molecular and architectural changes of synapses. To address these issues, we investigated ultrastructural and electrophysiological features of synapses in mouse acute cerebellar slices prepared at ice-cold and physiological temperature (PT). In the slices prepared at CT, we found significant spine loss and reconstruction, synaptic vesicle rearrangement and decrease in synaptic proteins, all of which were not detected in slices prepared at PT. Consistent with these structural findings, slices prepared at PT showed higher release probability. Furthermore, preparation at PT allows electrophysiological recording immediately after slicing resulting in higher detectability of long-term depression (LTD) after motor learning compared with that at CT. These results indicate substantial advantages of the slice preparation at PT for investigating synaptic functions in different physiological conditions.","lang":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":"        14","has_accepted_license":"1","article_type":"original","date_created":"2020-04-19T22:00:55Z","volume":14,"title":"Advantages of acute brain slices prepared at physiological temperature in the characterization of synaptic functions","oa_version":"Published Version","author":[{"first_name":"Kohgaku","orcid":"0000-0002-6170-2546","last_name":"Eguchi","id":"2B7846DC-F248-11E8-B48F-1D18A9856A87","full_name":"Eguchi, Kohgaku"},{"orcid":"0000-0002-2340-7431","first_name":"Philipp","last_name":"Velicky","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","full_name":"Velicky, Philipp"},{"first_name":"Elena","last_name":"Hollergschwandtner","full_name":"Hollergschwandtner, Elena","id":"3C054040-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Makoto","full_name":"Itakura, Makoto","last_name":"Itakura"},{"full_name":"Fukazawa, Yugo","last_name":"Fukazawa","first_name":"Yugo"},{"orcid":"0000-0001-8559-3973","first_name":"Johann G","last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G"},{"orcid":"0000-0001-8761-9444","first_name":"Ryuichi","full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto"}],"scopus_import":"1","day":"19"},{"intvolume":"        64","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"text":"Generalizing the decomposition of a connected planar graph into a tree and a dual tree, we prove a combinatorial analog of the classic Helmholtz–Hodge decomposition of a smooth vector field. Specifically, we show that for every polyhedral complex, K, and every dimension, p, there is a partition of the set of p-cells into a maximal p-tree, a maximal p-cotree, and a collection of p-cells whose cardinality is the p-th reduced Betti number of K. Given an ordering of the p-cells, this tri-partition is unique, and it can be computed by a matrix reduction algorithm that also constructs canonical bases of cycle and boundary groups.","lang":"eng"}],"has_accepted_license":"1","publication_status":"published","publication_identifier":{"issn":["01795376"],"eissn":["14320444"]},"file_date_updated":"2020-11-20T13:22:21Z","oa_version":"Published Version","title":"Tri-partitions and bases of an ordered complex","author":[{"first_name":"Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner"},{"last_name":"Ölsböck","id":"4D4AA390-F248-11E8-B48F-1D18A9856A87","full_name":"Ölsböck, Katharina","first_name":"Katharina","orcid":"0000-0002-4672-8297"}],"day":"20","scopus_import":"1","article_type":"original","date_created":"2020-04-19T22:00:56Z","volume":64,"language":[{"iso":"eng"}],"oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ama":"Edelsbrunner H, Ölsböck K. Tri-partitions and bases of an ordered complex. <i>Discrete and Computational Geometry</i>. 2020;64:759-775. doi:<a href=\"https://doi.org/10.1007/s00454-020-00188-x\">10.1007/s00454-020-00188-x</a>","ieee":"H. Edelsbrunner and K. Ölsböck, “Tri-partitions and bases of an ordered complex,” <i>Discrete and Computational Geometry</i>, vol. 64. Springer Nature, pp. 759–775, 2020.","short":"H. Edelsbrunner, K. Ölsböck, Discrete and Computational Geometry 64 (2020) 759–775.","ista":"Edelsbrunner H, Ölsböck K. 2020. Tri-partitions and bases of an ordered complex. Discrete and Computational Geometry. 64, 759–775.","chicago":"Edelsbrunner, Herbert, and Katharina Ölsböck. “Tri-Partitions and Bases of an Ordered Complex.” <i>Discrete and Computational Geometry</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/s00454-020-00188-x\">https://doi.org/10.1007/s00454-020-00188-x</a>.","apa":"Edelsbrunner, H., &#38; Ölsböck, K. (2020). Tri-partitions and bases of an ordered complex. <i>Discrete and Computational Geometry</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00454-020-00188-x\">https://doi.org/10.1007/s00454-020-00188-x</a>","mla":"Edelsbrunner, Herbert, and Katharina Ölsböck. “Tri-Partitions and Bases of an Ordered Complex.” <i>Discrete and Computational Geometry</i>, vol. 64, Springer Nature, 2020, pp. 759–75, doi:<a href=\"https://doi.org/10.1007/s00454-020-00188-x\">10.1007/s00454-020-00188-x</a>."},"month":"03","file":[{"success":1,"file_name":"2020_DiscreteCompGeo_Edelsbrunner.pdf","access_level":"open_access","content_type":"application/pdf","relation":"main_file","checksum":"f8cc96e497f00c38340b5dafe0cb91d7","file_size":701673,"date_created":"2020-11-20T13:22:21Z","creator":"dernst","date_updated":"2020-11-20T13:22:21Z","file_id":"8786"}],"department":[{"_id":"HeEd"}],"ddc":["510"],"page":"759-775","quality_controlled":"1","publisher":"Springer Nature","doi":"10.1007/s00454-020-00188-x","article_processing_charge":"Yes (via OA deal)","type":"journal_article","date_updated":"2023-08-21T06:13:48Z","_id":"7666","project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"},{"_id":"266A2E9E-B435-11E9-9278-68D0E5697425","name":"Alpha Shape Theory Extended","grant_number":"788183","call_identifier":"H2020"},{"_id":"2561EBF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35"}],"status":"public","publication":"Discrete and Computational Geometry","date_published":"2020-03-20T00:00:00Z","acknowledgement":"This project has received funding from the European Research Council under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 78818 Alpha). It is also partially supported by the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, through Grant No. I02979-N35 of the Austrian Science Fund (FWF).","ec_funded":1,"external_id":{"isi":["000520918800001"]},"year":"2020","isi":1},{"article_processing_charge":"Yes (via OA deal)","doi":"10.1016/j.electacta.2020.137175","publisher":"Elsevier","_id":"7672","date_updated":"2023-08-21T06:14:21Z","type":"journal_article","ddc":["540"],"quality_controlled":"1","isi":1,"year":"2020","external_id":{"isi":["000582869700060"]},"status":"public","publication":"Electrochimica Acta","date_published":"2020-12-01T00:00:00Z","acknowledgement":"S.A.F. thanks the International Society of Electrochemistry for awarding the Tajima Prize 2019 “in recognition of outstanding re- searches on Li-Air batteries by the use of a range of in-situ elec- trochemical methods to achieve comprehensive understanding of the reactions taking place at the oxygen electrode”. This article is dedicated to the special issue of Electrochmica Acta associated with the awarding conference. S.A.F. is indebted to and the Austrian Federal Ministry of Science, Research and Economy and the Austrian Research Promotion Agency (grant No. 845364 ) and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 636069). The authors thank J. Schlegl for manufacturing instrumentation, M. Winkler of Acib GmbH and G. Strohmeier for help with HPLC measurements, S. Eder for cyclic voltammetry measurements, and C. Slugovc for discussions and continuous support. We thank S. Borisov for access and advice with fluorescence measurements. We thank EL-Cell GmbH, Hamburg, Germany for providing the PAT-Cell-Press electrochemical cell.","scopus_import":"1","day":"01","author":[{"first_name":"Aleksej","full_name":"Samojlov, Aleksej","last_name":"Samojlov"},{"last_name":"Schuster","full_name":"Schuster, David","first_name":"David"},{"full_name":"Kahr, Jürgen","last_name":"Kahr","first_name":"Jürgen"},{"first_name":"Stefan Alexander","orcid":"0000-0003-2902-5319","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","full_name":"Freunberger, Stefan Alexander","last_name":"Freunberger"}],"oa_version":"Published Version","title":"Surface and catalyst driven singlet oxygen formation in Li-O2 cells","volume":362,"date_created":"2020-04-20T19:29:31Z","article_type":"original","has_accepted_license":"1","intvolume":"       362","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"abstract":[{"text":"Large overpotentials upon discharge and charge of Li-O2 cells have motivated extensive research into heterogeneous solid electrocatalysts or non-carbon electrodes with the aim to improve rate capability, round-trip efficiency and cycle life. These features are equally governed by parasitic reactions, which are now recognized to be caused by the highly reactive singlet oxygen (1O2). However, the link between the presence of electrocatalysts and 1O2 formation in metal-O2 cells is unknown. Here, we show that, compared to pristine carbon black electrodes, a representative selection of electrocatalysts or non-carbon electrodes (noble metal, transition metal compounds) may both slightly reduce or severely increase the 1O2 formation. The individual reaction steps, where the surfaces impact the 1O2 yield are deciphered, showing that 1O2 yield from superoxide disproportionation as well as the decomposition of trace H2O2 are sensitive to catalysts. Transition metal compounds in general are prone to increase 1O2.","lang":"eng"}],"file_date_updated":"2020-10-01T13:20:45Z","publication_status":"published","month":"12","department":[{"_id":"StFr"}],"article_number":"137175","file":[{"success":1,"file_name":"2020_ElectrochimicaActa_Samojlov.pdf","access_level":"open_access","content_type":"application/pdf","relation":"main_file","checksum":"1ab1aa2024d431e2a089ea336bc08298","date_created":"2020-10-01T13:20:45Z","file_size":1404030,"creator":"dernst","date_updated":"2020-10-01T13:20:45Z","file_id":"8593"}],"oa":1,"language":[{"iso":"eng"}],"citation":{"ista":"Samojlov A, Schuster D, Kahr J, Freunberger SA. 2020. Surface and catalyst driven singlet oxygen formation in Li-O2 cells. Electrochimica Acta. 362(12), 137175.","chicago":"Samojlov, Aleksej, David Schuster, Jürgen Kahr, and Stefan Alexander Freunberger. “Surface and Catalyst Driven Singlet Oxygen Formation in Li-O2 Cells.” <i>Electrochimica Acta</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.electacta.2020.137175\">https://doi.org/10.1016/j.electacta.2020.137175</a>.","apa":"Samojlov, A., Schuster, D., Kahr, J., &#38; Freunberger, S. A. (2020). Surface and catalyst driven singlet oxygen formation in Li-O2 cells. <i>Electrochimica Acta</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.electacta.2020.137175\">https://doi.org/10.1016/j.electacta.2020.137175</a>","mla":"Samojlov, Aleksej, et al. “Surface and Catalyst Driven Singlet Oxygen Formation in Li-O2 Cells.” <i>Electrochimica Acta</i>, vol. 362, no. 12, 137175, Elsevier, 2020, doi:<a href=\"https://doi.org/10.1016/j.electacta.2020.137175\">10.1016/j.electacta.2020.137175</a>.","ama":"Samojlov A, Schuster D, Kahr J, Freunberger SA. Surface and catalyst driven singlet oxygen formation in Li-O2 cells. <i>Electrochimica Acta</i>. 2020;362(12). doi:<a href=\"https://doi.org/10.1016/j.electacta.2020.137175\">10.1016/j.electacta.2020.137175</a>","ieee":"A. Samojlov, D. Schuster, J. Kahr, and S. A. Freunberger, “Surface and catalyst driven singlet oxygen formation in Li-O2 cells,” <i>Electrochimica Acta</i>, vol. 362, no. 12. Elsevier, 2020.","short":"A. Samojlov, D. Schuster, J. Kahr, S.A. Freunberger, Electrochimica Acta 362 (2020)."},"issue":"12","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"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."}],"publication_status":"published","main_file_link":[{"url":"https://doi.org/10.1101/2020.04.18.047886 ","open_access":"1"}],"oa_version":"Preprint","title":"A minimal biophysical model of combined antibiotic action","publisher":"Cold Spring Harbor Laboratory","author":[{"first_name":"Bor","orcid":"0000-0001-6041-254X","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","full_name":"Kavcic, Bor","last_name":"Kavcic"},{"orcid":"0000-0002-6699-1455","first_name":"Gašper","full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik"},{"orcid":"0000-0003-4398-476X","first_name":"Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","full_name":"Bollenbach, Tobias","last_name":"Bollenbach"}],"doi":"10.1101/2020.04.18.047886","day":"18","article_processing_charge":"No","type":"preprint","date_created":"2020-04-22T08:27:56Z","date_updated":"2024-03-25T23:30:05Z","_id":"7673","project":[{"grant_number":"P27201-B22","name":"Revealing the mechanisms underlying drug interactions","call_identifier":"FWF","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425"},{"name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27","call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425"}],"publication":"bioRxiv","status":"public","language":[{"iso":"eng"}],"oa":1,"date_published":"2020-04-18T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Kavcic, Bor, Gašper Tkačik, and Mark Tobias Bollenbach. “A Minimal Biophysical Model of Combined Antibiotic Action.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, 2020. <a href=\"https://doi.org/10.1101/2020.04.18.047886\">https://doi.org/10.1101/2020.04.18.047886</a>.","ista":"Kavcic B, Tkačik G, Bollenbach MT. 2020. A minimal biophysical model of combined antibiotic action. bioRxiv, <a href=\"https://doi.org/10.1101/2020.04.18.047886\">10.1101/2020.04.18.047886</a>.","mla":"Kavcic, Bor, et al. “A Minimal Biophysical Model of Combined Antibiotic Action.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, 2020, doi:<a href=\"https://doi.org/10.1101/2020.04.18.047886\">10.1101/2020.04.18.047886</a>.","apa":"Kavcic, B., Tkačik, G., &#38; Bollenbach, M. T. (2020). A minimal biophysical model of combined antibiotic action. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/2020.04.18.047886\">https://doi.org/10.1101/2020.04.18.047886</a>","ama":"Kavcic B, Tkačik G, Bollenbach MT. A minimal biophysical model of combined antibiotic action. <i>bioRxiv</i>. 2020. doi:<a href=\"https://doi.org/10.1101/2020.04.18.047886\">10.1101/2020.04.18.047886</a>","short":"B. Kavcic, G. Tkačik, M.T. Bollenbach, BioRxiv (2020).","ieee":"B. Kavcic, G. Tkačik, and M. T. Bollenbach, “A minimal biophysical model of combined antibiotic action,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory, 2020."},"related_material":{"record":[{"id":"8997","relation":"later_version","status":"public"},{"status":"public","relation":"dissertation_contains","id":"8657"}]},"month":"04","year":"2020","department":[{"_id":"GaTk"}]},{"abstract":[{"text":"In prokaryotes, thermodynamic models of gene regulation provide a highly quantitative mapping from promoter sequences to gene expression levels that is compatible with in vivo and in vitro bio-physical measurements. Such concordance has not been achieved for models of enhancer function in eukaryotes. In equilibrium models, it is difficult to reconcile the reported short transcription factor (TF) residence times on the DNA with the high specificity of regulation. In non-equilibrium models, progress is difficult due to an explosion in the number of parameters. Here, we navigate this complexity by looking for minimal non-equilibrium enhancer models that yield desired regulatory phenotypes: low TF residence time, high specificity and tunable cooperativity. We find that a single extra parameter, interpretable as the “linking rate” by which bound TFs interact with Mediator components, enables our models to escape equilibrium bounds and access optimal regulatory phenotypes, while remaining consistent with the reported phenomenology and simple enough to be inferred from upcoming experiments. We further find that high specificity in non-equilibrium models is in a tradeoff with gene expression noise, predicting bursty dynamics — an experimentally-observed hallmark of eukaryotic transcription. By drastically reducing the vast parameter space to a much smaller subspace that optimally realizes biological function prior to inference from data, our normative approach holds promise for mathematical models in systems biology.","lang":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1101/2020.04.08.029405 ","open_access":"1"}],"publication_status":"published","author":[{"last_name":"Grah","full_name":"Grah, Rok","id":"483E70DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2539-3560","first_name":"Rok"},{"full_name":"Zoller, Benjamin","last_name":"Zoller","first_name":"Benjamin"},{"full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","first_name":"Gašper","orcid":"0000-0002-6699-1455"}],"doi":"10.1101/2020.04.08.029405","article_processing_charge":"No","day":"09","publisher":"Cold Spring Harbor Laboratory","oa_version":"Preprint","title":"Normative models of enhancer function","date_updated":"2023-09-07T13:13:26Z","_id":"7675","type":"preprint","date_created":"2020-04-23T10:12:51Z","oa":1,"project":[{"grant_number":"RGP0034/2018","name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?","_id":"2665AAFE-B435-11E9-9278-68D0E5697425"},{"_id":"267C84F4-B435-11E9-9278-68D0E5697425","name":"Biophysically realistic genotype-phenotype maps for regulatory networks"}],"language":[{"iso":"eng"}],"publication":"bioRxiv","status":"public","citation":{"short":"R. Grah, B. Zoller, G. Tkačik, BioRxiv (2020).","ieee":"R. Grah, B. Zoller, and G. Tkačik, “Normative models of enhancer function,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory, 2020.","ama":"Grah R, Zoller B, Tkačik G. Normative models of enhancer function. <i>bioRxiv</i>. 2020. doi:<a href=\"https://doi.org/10.1101/2020.04.08.029405\">10.1101/2020.04.08.029405</a>","mla":"Grah, Rok, et al. “Normative Models of Enhancer Function.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, 2020, doi:<a href=\"https://doi.org/10.1101/2020.04.08.029405\">10.1101/2020.04.08.029405</a>.","apa":"Grah, R., Zoller, B., &#38; Tkačik, G. (2020). Normative models of enhancer function. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/2020.04.08.029405\">https://doi.org/10.1101/2020.04.08.029405</a>","ista":"Grah R, Zoller B, Tkačik G. 2020. Normative models of enhancer function. bioRxiv, <a href=\"https://doi.org/10.1101/2020.04.08.029405\">10.1101/2020.04.08.029405</a>.","chicago":"Grah, Rok, Benjamin Zoller, and Gašper Tkačik. “Normative Models of Enhancer Function.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, 2020. <a href=\"https://doi.org/10.1101/2020.04.08.029405\">https://doi.org/10.1101/2020.04.08.029405</a>."},"date_published":"2020-04-09T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2020","related_material":{"record":[{"id":"8155","status":"public","relation":"dissertation_contains"}]},"month":"04","department":[{"_id":"CaGu"},{"_id":"GaTk"}]}]