[{"publication_identifier":{"eissn":["1936-086X"]},"doi":"10.1021/acsnano.9b08687","quality_controlled":"1","isi":1,"language":[{"iso":"eng"}],"issue":"3","author":[{"first_name":"Retno","last_name":"Miranti","full_name":"Miranti, Retno"},{"full_name":"Shin, Daiki","last_name":"Shin","first_name":"Daiki"},{"full_name":"Septianto, Ricky Dwi","first_name":"Ricky Dwi","last_name":"Septianto"},{"full_name":"Ibáñez, Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","first_name":"Maria","last_name":"Ibáñez"},{"first_name":"Maksym V.","last_name":"Kovalenko","full_name":"Kovalenko, Maksym V."},{"last_name":"Matsushita","first_name":"Nobuhiro","full_name":"Matsushita, Nobuhiro"},{"full_name":"Iwasa, Yoshihiro","first_name":"Yoshihiro","last_name":"Iwasa"},{"last_name":"Bisri","first_name":"Satria Zulkarnaen","full_name":"Bisri, Satria Zulkarnaen"}],"day":"24","title":"Exclusive electron transport in Core@Shell PbTe@PbS colloidal semiconductor nanocrystal assemblies","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"American Chemical Society","pmid":1,"department":[{"_id":"MaIb"}],"publication":"ACS Nano","article_processing_charge":"No","scopus_import":"1","article_type":"original","publication_status":"published","date_published":"2020-03-24T00:00:00Z","status":"public","external_id":{"pmid":["32073817"],"isi":["000526301400057"]},"intvolume":"        14","citation":{"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>","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.","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>.","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>","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.","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>.","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."},"page":"3242-3250","abstract":[{"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.","lang":"eng"}],"date_updated":"2023-08-18T10:25:40Z","oa_version":"None","month":"03","type":"journal_article","volume":14,"date_created":"2020-04-05T22:00:48Z","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.","year":"2020","_id":"7634"},{"publication_status":"published","publication_identifier":{"isbn":["9781450368186"]},"quality_controlled":"1","date_published":"2020-02-19T00:00:00Z","doi":"10.1145/3332466.3374503","status":"public","language":[{"iso":"eng"}],"citation":{"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>.","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>","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>","short":"N. Koval, M. Sokolova, A. Fedorov, D.-A. Alistarh, D. Tsitelov, in:, Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, PPOPP, Association for Computing Machinery, 2020, pp. 423–424.","ieee":"N. Koval, M. Sokolova, A. Fedorov, D.-A. Alistarh, and D. Tsitelov, “Testing concurrency on the JVM with Lincheck,” in <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.","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>."},"conference":{"start_date":"2020-02-22","location":"San Diego, CA, United States","name":"PPOPP: Principles and Practice of Parallel Programming","end_date":"2020-02-26"},"day":"19","date_updated":"2024-02-28T12:53:46Z","abstract":[{"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.","lang":"eng"}],"oa_version":"None","type":"conference","month":"02","page":"423-424","author":[{"last_name":"Koval","first_name":"Nikita","full_name":"Koval, Nikita","id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sokolova","first_name":"Mariia","full_name":"Sokolova, Mariia","id":"26217AE4-77FF-11EA-8101-AD24D49E41F4"},{"full_name":"Fedorov, Alexander","last_name":"Fedorov","first_name":"Alexander"},{"orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","last_name":"Alistarh"},{"last_name":"Tsitelov","first_name":"Dmitry","full_name":"Tsitelov, Dmitry"}],"date_created":"2020-04-05T22:00:48Z","title":"Testing concurrency on the JVM with Lincheck","year":"2020","department":[{"_id":"DaAl"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Association for Computing Machinery","article_processing_charge":"No","scopus_import":"1","publication":"Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, PPOPP","_id":"7635"},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1145/3332466.3374542"}],"date_published":"2020-02-19T00:00:00Z","oa":1,"publication_status":"published","citation":{"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>.","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.","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>","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>","short":"T.A. Brown, A. Prokopec, D.-A. Alistarh, in:, Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2020, pp. 276–291.","ieee":"T. A. Brown, A. Prokopec, and D.-A. Alistarh, “Non-blocking interpolation search trees with doubly-logarithmic running time,” in <i>Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i>, San Diego, CA, United States, 2020, pp. 276–291.","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>."},"status":"public","external_id":{"isi":["000564476500020"]},"date_created":"2020-04-05T22:00:49Z","date_updated":"2024-02-28T12:55:14Z","abstract":[{"lang":"eng","text":"Balanced search trees typically use key comparisons to guide their operations, and achieve logarithmic running time. By relying on numerical properties of the keys, interpolation search achieves lower search complexity and better performance. Although interpolation-based data structures were investigated in the past, their non-blocking concurrent variants have received very little attention so far.\r\nIn this paper, we propose the first non-blocking implementation of the classic interpolation search tree (IST) data structure. For arbitrary key distributions, the data structure ensures worst-case O(log n + p) amortized time for search, insertion and deletion traversals. When the input key distributions are smooth, lookups run in expected O(log log n + p) time, and insertion and deletion run in expected amortized O(log log n + p) time, where p is a bound on the number of threads. To improve the scalability of concurrent insertion and deletion, we propose a novel parallel rebuilding technique, which should be of independent interest.\r\nWe evaluate whether the theoretical improvements translate to practice by implementing the concurrent interpolation search tree, and benchmarking it on uniform and nonuniform key distributions, for dataset sizes in the millions to billions of keys. Relative to the state-of-the-art concurrent data structures, the concurrent interpolation search tree achieves performance improvements of up to 15% under high update rates, and of up to 50% under moderate update rates. Further, ISTs exhibit up to 2X less cache-misses, and consume 1.2 -- 2.6X less memory compared to the next best alternative on typical dataset sizes. We find that the results are surprisingly robust to distributional skew, which suggests that our data structure can be a promising alternative to classic concurrent search structures."}],"oa_version":"Published Version","month":"02","type":"conference","page":"276-291","_id":"7636","year":"2020","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). ","quality_controlled":"1","doi":"10.1145/3332466.3374542","publication_identifier":{"isbn":["9781450368186"]},"language":[{"iso":"eng"}],"isi":1,"conference":{"end_date":"2020-02-26","location":"San Diego, CA, United States","name":"PPOPP: Principles and Practice of Parallel Programming","start_date":"2020-02-22"},"project":[{"call_identifier":"H2020","_id":"268A44D6-B435-11E9-9278-68D0E5697425","name":"Elastic Coordination for Scalable Machine Learning","grant_number":"805223"}],"title":"Non-blocking interpolation search trees with doubly-logarithmic running time","day":"19","author":[{"id":"3569F0A0-F248-11E8-B48F-1D18A9856A87","full_name":"Brown, Trevor A","last_name":"Brown","first_name":"Trevor A"},{"last_name":"Prokopec","first_name":"Aleksandar","full_name":"Prokopec, Aleksandar"},{"first_name":"Dan-Adrian","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"}],"ec_funded":1,"scopus_import":"1","article_processing_charge":"No","publication":"Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming","department":[{"_id":"DaAl"}],"publisher":"Association for Computing Machinery","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"publication":"Nonlinearity","article_type":"original","article_processing_charge":"No","scopus_import":"1","publisher":"IOP Publishing","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"JuFi"}],"title":"From weakly interacting particles to a regularised Dean-Kawasaki model","arxiv":1,"author":[{"id":"2CEB641C-A400-11E9-A717-D712E6697425","orcid":"0000-0002-6269-5149","full_name":"Cornalba, Federico","first_name":"Federico","last_name":"Cornalba"},{"last_name":"Shardlow","first_name":"Tony","full_name":"Shardlow, Tony"},{"first_name":"Johannes","last_name":"Zimmer","full_name":"Zimmer, Johannes"}],"day":"10","isi":1,"issue":"2","language":[{"iso":"eng"}],"doi":"10.1088/1361-6544/ab5174","quality_controlled":"1","publication_identifier":{"issn":["09517715"],"eissn":["13616544"]},"_id":"7637","year":"2020","volume":33,"date_created":"2020-04-05T22:00:49Z","page":"864-891","type":"journal_article","month":"01","oa_version":"Preprint","date_updated":"2023-08-18T10:26:07Z","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","citation":{"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>","ista":"Cornalba F, Shardlow T, Zimmer J. 2020. From weakly interacting particles to a regularised Dean-Kawasaki model. Nonlinearity. 33(2), 864–891.","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>.","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.","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>.","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."},"status":"public","external_id":{"isi":["000508175400001"],"arxiv":["1811.06448"]},"date_published":"2020-01-10T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1811.06448"}],"oa":1,"publication_status":"published"},{"day":"22","file":[{"file_name":"2020_JournStatisticalMech_DeNicola.pdf","file_size":3159026,"relation":"main_file","content_type":"application/pdf","creator":"dernst","file_id":"7648","date_updated":"2020-07-14T12:48:01Z","checksum":"4030e683c15d30b7b4794ec7dc1b6537","date_created":"2020-04-06T13:15:49Z","access_level":"open_access"}],"author":[{"last_name":"De Nicola","first_name":"Stefano","id":"42832B76-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4842-6671","full_name":"De Nicola, Stefano"},{"first_name":"B.","last_name":"Doyon","full_name":"Doyon, B."},{"last_name":"Bhaseen","first_name":"M. J.","full_name":"Bhaseen, M. J."}],"title":"Non-equilibrium quantum spin dynamics from classical stochastic processes","arxiv":1,"article_number":"013106","department":[{"_id":"MaSe"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"IOP Publishing","article_processing_charge":"No","ec_funded":1,"scopus_import":"1","article_type":"original","publication":"Journal of Statistical Mechanics: Theory and Experiment","publication_identifier":{"eissn":["17425468"]},"quality_controlled":"1","doi":"10.1088/1742-5468/ab6093","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"language":[{"iso":"eng"}],"issue":"1","isi":1,"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"}],"date_updated":"2023-08-18T10:27:15Z","type":"journal_article","oa_version":"Published Version","month":"01","file_date_updated":"2020-07-14T12:48:01Z","date_created":"2020-04-05T22:00:50Z","volume":2020,"year":"2020","_id":"7638","has_accepted_license":"1","publication_status":"published","oa":1,"date_published":"2020-01-22T00:00:00Z","ddc":["530"],"status":"public","external_id":{"isi":["000520187500001"],"arxiv":["1909.13142"]},"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>","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.","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>","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.","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>.","short":"S. De Nicola, B. Doyon, M.J. Bhaseen, Journal of Statistical Mechanics: Theory and Experiment 2020 (2020)."},"intvolume":"      2020"},{"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). ","year":"2020","_id":"7643","page":"37-40","date_updated":"2023-09-07T13:13:04Z","type":"journal_article","month":"05","oa_version":"Published Version","volume":183,"date_created":"2020-04-06T10:06:40Z","status":"public","external_id":{"pmid":["32107280"],"isi":["000536641800018"]},"intvolume":"       183","related_material":{"record":[{"id":"8589","status":"public","relation":"dissertation_contains"}]},"citation":{"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>","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.","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>","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.","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>.","short":"H. Han, H. Rakusova, I. Verstraeten, Y. Zhang, J. Friml, Plant Physiology 183 (2020) 37–40."},"publication_status":"published","oa":1,"date_published":"2020-05-08T00:00:00Z","main_file_link":[{"url":"https://doi.org/10.1104/pp.20.00212","open_access":"1"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"American Society of Plant Biologists","pmid":1,"department":[{"_id":"JiFr"}],"publication":"Plant Physiology","scopus_import":"1","article_processing_charge":"No","ec_funded":1,"article_type":"letter_note","author":[{"last_name":"Han","first_name":"Huibin","full_name":"Han, Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Rakusova, Hana","id":"4CAAA450-78D2-11EA-8E57-B40A396E08BA","last_name":"Rakusova","first_name":"Hana"},{"full_name":"Verstraeten, Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7241-2328","first_name":"Inge","last_name":"Verstraeten"},{"full_name":"Zhang, Yuzhou","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2627-6956","last_name":"Zhang","first_name":"Yuzhou"},{"first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}],"day":"08","title":"SCF TIR1/AFB auxin signaling for bending termination during shoot gravitropism","project":[{"grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630"}],"isi":1,"language":[{"iso":"eng"}],"issue":"5","publication_identifier":{"issn":["0032-0889"],"eissn":["1532-2548"]},"doi":"10.1104/pp.20.00212","quality_controlled":"1"},{"year":"2020","_id":"7646","date_updated":"2023-08-18T10:27:52Z","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","type":"journal_article","month":"07","page":"3986–3998","date_created":"2020-04-06T10:57:08Z","file_date_updated":"2020-10-06T07:41:35Z","volume":71,"external_id":{"pmid":["32179893"],"isi":["000553125400007"]},"status":"public","citation":{"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>.","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.","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.","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>","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>","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>.","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."},"intvolume":"        71","has_accepted_license":"1","publication_status":"published","oa":1,"date_published":"2020-07-06T00:00:00Z","ddc":["580"],"pmid":1,"department":[{"_id":"JiFr"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Oxford University Press","article_processing_charge":"No","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","publication":"Journal of Experimental Botany","license":"https://creativecommons.org/licenses/by/4.0/","file":[{"creator":"dernst","content_type":"application/pdf","relation":"main_file","file_size":1916031,"success":1,"file_name":"2020_JourExperimBotany_Lee.pdf","access_level":"open_access","date_created":"2020-10-06T07:41:35Z","checksum":"b06aaaa93dc41896da805fe4b75cf3a1","date_updated":"2020-10-06T07:41:35Z","file_id":"8613"}],"day":"06","author":[{"full_name":"Lee, E","first_name":"E","last_name":"Lee"},{"full_name":"Vila Nova Santana, B","last_name":"Vila Nova Santana","first_name":"B"},{"full_name":"Samuels, E","first_name":"E","last_name":"Samuels"},{"full_name":"Benitez-Fuente, F","last_name":"Benitez-Fuente","first_name":"F"},{"last_name":"Corsi","first_name":"E","full_name":"Corsi, E"},{"full_name":"Botella, MA","first_name":"MA","last_name":"Botella"},{"first_name":"J","last_name":"Perez-Sancho","full_name":"Perez-Sancho, J"},{"full_name":"Vanneste, S","last_name":"Vanneste","first_name":"S"},{"last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"},{"last_name":"Macho","first_name":"A","full_name":"Macho, A"},{"last_name":"Alves Azevedo","first_name":"A","full_name":"Alves Azevedo, A"},{"full_name":"Rosado, A","last_name":"Rosado","first_name":"A"}],"title":"Rare earth elements induce cytoskeleton-dependent and PI4P-associated rearrangement of SYT1/SYT5 ER-PM contact site complexes in Arabidopsis","language":[{"iso":"eng"}],"issue":"14","isi":1,"publication_identifier":{"eissn":["1460-2431"],"issn":["0022-0957"]},"quality_controlled":"1","doi":"10.1093/jxb/eraa138"},{"publisher":"Springer Nature","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"RoSe"}],"publication":"Archive for Rational Mechanics and Analysis","ec_funded":1,"article_processing_charge":"Yes (via OA deal)","scopus_import":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","author":[{"first_name":"Andreas","last_name":"Deuchert","full_name":"Deuchert, Andreas","orcid":"0000-0003-3146-6746","id":"4DA65CD0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","first_name":"Robert","last_name":"Seiringer"}],"file":[{"file_name":"2020_ArchRatMechanicsAnalysis_Deuchert.pdf","success":1,"creator":"dernst","file_size":704633,"content_type":"application/pdf","relation":"main_file","checksum":"b645fb64bfe95bbc05b3eea374109a9c","file_id":"8785","date_updated":"2020-11-20T13:17:42Z","access_level":"open_access","date_created":"2020-11-20T13:17:42Z"}],"day":"09","arxiv":1,"title":"Gross-Pitaevskii limit of a homogeneous Bose gas at positive temperature","project":[{"name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"694227"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"isi":1,"language":[{"iso":"eng"}],"issue":"6","publication_identifier":{"issn":["0003-9527"],"eissn":["1432-0673"]},"doi":"10.1007/s00205-020-01489-4","quality_controlled":"1","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.","year":"2020","_id":"7650","page":"1217-1271","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."}],"date_updated":"2023-09-05T14:18:49Z","month":"03","type":"journal_article","oa_version":"Published Version","volume":236,"file_date_updated":"2020-11-20T13:17:42Z","date_created":"2020-04-08T15:18:03Z","status":"public","external_id":{"isi":["000519415000001"],"arxiv":["1901.11363"]},"intvolume":"       236","citation":{"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>.","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.","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.","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>."},"oa":1,"publication_status":"published","has_accepted_license":"1","date_published":"2020-03-09T00:00:00Z","ddc":["510"]},{"author":[{"last_name":"Larsson","first_name":"J.","full_name":"Larsson, J."},{"first_name":"Anja M","last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M"},{"last_name":"Bengmark","first_name":"S.","full_name":"Bengmark, S."},{"first_name":"T.","last_name":"Lundh","full_name":"Lundh, T."},{"full_name":"Butlin, R. K.","last_name":"Butlin","first_name":"R. K."}],"file":[{"access_level":"open_access","date_created":"2020-04-14T12:31:16Z","checksum":"4eb102304402f5c56432516b84df86d6","date_updated":"2020-07-14T12:48:01Z","file_id":"7660","creator":"dernst","content_type":"application/pdf","relation":"main_file","file_size":1556190,"file_name":"2020_JournRoyalSociety_Larsson.pdf"}],"day":"01","article_number":"20190721","title":"A developmentally descriptive method for quantifying shape in gastropod shells","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"The Royal Society","department":[{"_id":"NiBa"}],"publication":"Journal of The Royal Society Interface","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"scopus_import":1,"article_processing_charge":"No","publication_identifier":{"eissn":["1742-5662"],"issn":["1742-5689"]},"doi":"10.1098/rsif.2019.0721","quality_controlled":"1","issue":"163","language":[{"iso":"eng"}],"type":"journal_article","oa_version":"Published Version","month":"02","date_updated":"2021-01-12T08:14:41Z","abstract":[{"lang":"eng","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."}],"volume":17,"date_created":"2020-04-08T15:19:17Z","file_date_updated":"2020-07-14T12:48:01Z","year":"2020","_id":"7651","publication_status":"published","oa":1,"has_accepted_license":"1","ddc":["570"],"date_published":"2020-02-01T00:00:00Z","status":"public","intvolume":"        17","citation":{"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>.","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>","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.","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>."}},{"author":[{"orcid":"0000-0001-6197-363X","id":"3981F020-F248-11E8-B48F-1D18A9856A87","full_name":"Tomanek, Isabella","first_name":"Isabella","last_name":"Tomanek"},{"id":"483E70DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2539-3560","full_name":"Grah, Rok","first_name":"Rok","last_name":"Grah"},{"last_name":"Lagator","first_name":"M.","full_name":"Lagator, M."},{"last_name":"Andersson","first_name":"A. M. C.","full_name":"Andersson, A. M. C."},{"orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","full_name":"Bollback, Jonathan P","first_name":"Jonathan P","last_name":"Bollback"},{"last_name":"Tkačik","first_name":"Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper"},{"last_name":"Guet","first_name":"Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C"}],"file":[{"file_name":"2020_NatureEcolEvo_Tomanek.pdf","success":1,"file_size":745242,"relation":"main_file","content_type":"application/pdf","creator":"dernst","file_id":"8640","date_updated":"2020-10-09T09:56:01Z","checksum":"ef3bbf42023e30b2c24a6278025d2040","date_created":"2020-10-09T09:56:01Z","access_level":"open_access"}],"day":"01","title":"Gene amplification as a form of population-level gene expression regulation","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Springer Nature","department":[{"_id":"GaTk"},{"_id":"CaGu"}],"publication":"Nature Ecology & Evolution","article_processing_charge":"No","scopus_import":"1","article_type":"original","publication_identifier":{"issn":["2397-334X"]},"doi":"10.1038/s41559-020-1132-7","quality_controlled":"1","project":[{"name":"Biophysically realistic genotype-phenotype maps for regulatory networks","_id":"267C84F4-B435-11E9-9278-68D0E5697425"}],"isi":1,"language":[{"iso":"eng"}],"issue":"4","page":"612-625","abstract":[{"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.","lang":"eng"}],"date_updated":"2024-03-25T23:30:20Z","month":"04","oa_version":"Submitted Version","type":"journal_article","volume":4,"date_created":"2020-04-08T15:20:53Z","file_date_updated":"2020-10-09T09:56:01Z","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.","year":"2020","_id":"7652","oa":1,"publication_status":"published","has_accepted_license":"1","date_published":"2020-04-01T00:00:00Z","ddc":["570"],"status":"public","external_id":{"isi":["000519008300005"]},"related_material":{"record":[{"status":"public","id":"8155","relation":"dissertation_contains"},{"relation":"research_data","id":"7383","status":"public"},{"id":"7016","status":"public","relation":"research_data"},{"relation":"used_in_publication","status":"public","id":"8653"}],"link":[{"url":"https://ist.ac.at/en/news/how-to-thrive-without-gene-regulation/","description":"News on IST Homepage","relation":"press_release"}]},"intvolume":"         4","citation":{"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.","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>.","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.","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>","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.","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>.","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>"}},{"doi":"10.3389/fncom.2020.00020","quality_controlled":"1","publication_identifier":{"eissn":["16625188"]},"isi":1,"language":[{"iso":"eng"}],"article_number":"20","title":"Clustering of neural activity: A design principle for population codes","author":[{"full_name":"Berry, Michael J.","first_name":"Michael J.","last_name":"Berry"},{"full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","last_name":"Tkačik"}],"file":[{"creator":"dernst","file_size":4082937,"content_type":"application/pdf","relation":"main_file","file_name":"2020_Frontiers_Berry.pdf","access_level":"open_access","date_created":"2020-04-14T12:20:39Z","checksum":"2b1da23823eae9cedbb42d701945b61e","file_id":"7659","date_updated":"2020-07-14T12:48:01Z"}],"day":"13","publication":"Frontiers in Computational Neuroscience","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"scopus_import":"1","article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Frontiers","department":[{"_id":"GaTk"}],"pmid":1,"ddc":["570"],"date_published":"2020-03-13T00:00:00Z","oa":1,"publication_status":"published","has_accepted_license":"1","intvolume":"        14","citation":{"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.","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>.","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>.","ista":"Berry MJ, Tkačik G. 2020. Clustering of neural activity: A design principle for population codes. Frontiers in Computational Neuroscience. 14, 20.","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>","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>"},"status":"public","external_id":{"isi":["000525543200001"],"pmid":["32231528"]},"volume":14,"date_created":"2020-04-12T22:00:40Z","file_date_updated":"2020-07-14T12:48:01Z","oa_version":"Published Version","month":"03","type":"journal_article","date_updated":"2023-08-18T10:30:11Z","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"}],"_id":"7656","year":"2020"},{"title":"Wood deformation leads to rearrangement of molecules at the nanoscale","file":[{"file_name":"2020_NanoLetters_Felhofer.pdf","creator":"dernst","content_type":"application/pdf","relation":"main_file","file_size":7108014,"checksum":"fe46146a9c4c620592a1932a8599069e","date_updated":"2020-07-14T12:48:01Z","file_id":"7667","access_level":"open_access","date_created":"2020-04-20T10:43:36Z"}],"day":"08","author":[{"first_name":"Martin","last_name":"Felhofer","full_name":"Felhofer, Martin"},{"full_name":"Bock, Peter","last_name":"Bock","first_name":"Peter"},{"full_name":"Singh, Adya","last_name":"Singh","first_name":"Adya"},{"full_name":"Prats Mateu, Batirtze","id":"299FE892-F248-11E8-B48F-1D18A9856A87","last_name":"Prats Mateu","first_name":"Batirtze"},{"last_name":"Zirbs","first_name":"Ronald","full_name":"Zirbs, Ronald"},{"full_name":"Gierlinger, Notburga","first_name":"Notburga","last_name":"Gierlinger"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","article_processing_charge":"No","scopus_import":"1","publication":"Nano Letters","department":[{"_id":"MaLo"}],"pmid":1,"publisher":"American Chemical Society","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","quality_controlled":"1","doi":"10.1021/acs.nanolett.0c00205","publication_identifier":{"eissn":["15306992"]},"issue":"4","language":[{"iso":"eng"}],"isi":1,"date_created":"2020-04-19T22:00:54Z","file_date_updated":"2020-07-14T12:48:01Z","volume":20,"month":"04","oa_version":"Published Version","type":"journal_article","date_updated":"2023-08-21T06:12:09Z","abstract":[{"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.","lang":"eng"}],"page":"2647-2653","_id":"7663","year":"2020","date_published":"2020-04-08T00:00:00Z","ddc":["530"],"has_accepted_license":"1","oa":1,"publication_status":"published","citation":{"short":"M. Felhofer, P. Bock, A. Singh, B. Prats Mateu, R. Zirbs, N. Gierlinger, Nano Letters 20 (2020) 2647–2653.","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>.","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.","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>","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.","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>.","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>"},"intvolume":"        20","status":"public","external_id":{"pmid":["32196350"],"isi":["000526413400055"]}},{"date_published":"2020-04-02T00:00:00Z","ddc":["570"],"publication_status":"published","oa":1,"has_accepted_license":"1","intvolume":"        21","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>","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>","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>.","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)."},"external_id":{"isi":["000535574200201"],"pmid":["32252271"]},"status":"public","volume":21,"file_date_updated":"2020-07-14T12:48:01Z","date_created":"2020-04-19T22:00:55Z","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"}],"date_updated":"2023-08-21T06:13:19Z","oa_version":"Published Version","type":"journal_article","month":"04","_id":"7664","year":"2020","doi":"10.3390/ijms21072459","quality_controlled":"1","publication_identifier":{"eissn":["14220067"]},"isi":1,"language":[{"iso":"eng"}],"issue":"7","title":"Density of GABAB receptors is reduced in granule cells of the hippocampus in a mouse model of Alzheimer's disease","article_number":"2459","author":[{"full_name":"Martín-Belmonte, Alejandro","last_name":"Martín-Belmonte","first_name":"Alejandro"},{"first_name":"Carolina","last_name":"Aguado","full_name":"Aguado, Carolina"},{"full_name":"Alfaro-Ruíz, Rocío","first_name":"Rocío","last_name":"Alfaro-Ruíz"},{"last_name":"Moreno-Martínez","first_name":"Ana Esther","full_name":"Moreno-Martínez, Ana Esther"},{"full_name":"De La Ossa, Luis","last_name":"De La Ossa","first_name":"Luis"},{"first_name":"José","last_name":"Martínez-Hernández","full_name":"Martínez-Hernández, José"},{"last_name":"Buisson","first_name":"Alain","full_name":"Buisson, Alain"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","last_name":"Shigemoto"},{"last_name":"Fukazawa","first_name":"Yugo","full_name":"Fukazawa, Yugo"},{"last_name":"Luján","first_name":"Rafael","full_name":"Luján, Rafael"}],"day":"02","file":[{"checksum":"b9d2f1657d8c4a74b01a62b474d009b0","date_updated":"2020-07-14T12:48:01Z","file_id":"7669","access_level":"open_access","date_created":"2020-04-20T11:43:18Z","file_name":"2020_JournMolecSciences_Martin_Belmonte.pdf","creator":"dernst","relation":"main_file","content_type":"application/pdf","file_size":2941197}],"publication":"International journal of molecular sciences","scopus_import":"1","article_processing_charge":"No","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"MDPI","pmid":1,"department":[{"_id":"RySh"}]},{"title":"Advantages of acute brain slices prepared at physiological temperature in the characterization of synaptic functions","article_number":"63","day":"19","file":[{"access_level":"open_access","date_created":"2020-04-20T10:59:49Z","checksum":"1c145123c6f8dc3e2e4bd5a66a1ad60e","file_id":"7668","date_updated":"2020-07-14T12:48:01Z","creator":"dernst","file_size":9227283,"relation":"main_file","content_type":"application/pdf","file_name":"2020_FrontiersCellularNeurosc_Eguchi.pdf"}],"author":[{"orcid":"0000-0002-6170-2546","id":"2B7846DC-F248-11E8-B48F-1D18A9856A87","full_name":"Eguchi, Kohgaku","first_name":"Kohgaku","last_name":"Eguchi"},{"orcid":"0000-0002-2340-7431","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","full_name":"Velicky, Philipp","last_name":"Velicky","first_name":"Philipp"},{"last_name":"Hollergschwandtner","first_name":"Elena","full_name":"Hollergschwandtner, Elena","id":"3C054040-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Itakura","first_name":"Makoto","full_name":"Itakura, Makoto"},{"full_name":"Fukazawa, Yugo","last_name":"Fukazawa","first_name":"Yugo"},{"orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G","last_name":"Danzl","first_name":"Johann G"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","first_name":"Ryuichi"}],"scopus_import":"1","ec_funded":1,"article_processing_charge":"Yes (via OA deal)","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"publication":"Frontiers in Cellular Neuroscience","department":[{"_id":"JoDa"},{"_id":"RySh"}],"publisher":"Frontiers Media","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","quality_controlled":"1","doi":"10.3389/fncel.2020.00063","publication_identifier":{"issn":["16625102"]},"language":[{"iso":"eng"}],"isi":1,"project":[{"grant_number":"793482","_id":"2659CC84-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Ultrastructural analysis of phosphoinositides in nerve terminals: distribution, dynamics and physiological roles in synaptic transmission"},{"name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","call_identifier":"H2020","_id":"25CA28EA-B435-11E9-9278-68D0E5697425","grant_number":"694539"},{"name":"Optical control of synaptic function via adhesion molecules","_id":"265CB4D0-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I03600"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"file_date_updated":"2020-07-14T12:48:01Z","date_created":"2020-04-19T22:00:55Z","volume":14,"date_updated":"2023-08-21T06:12:48Z","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"}],"type":"journal_article","month":"03","oa_version":"Published Version","_id":"7665","year":"2020","date_published":"2020-03-19T00:00:00Z","ddc":["570"],"has_accepted_license":"1","oa":1,"publication_status":"published","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>","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.","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>.","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>","short":"K. Eguchi, P. Velicky, E. Saeckl, M. Itakura, Y. Fukazawa, J.G. Danzl, R. Shigemoto, Frontiers in Cellular Neuroscience 14 (2020).","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."},"intvolume":"        14","external_id":{"isi":["000525582200001"]},"status":"public"},{"ec_funded":1,"article_processing_charge":"Yes (via OA deal)","scopus_import":"1","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"publication":"Discrete and Computational Geometry","department":[{"_id":"HeEd"}],"publisher":"Springer Nature","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Tri-partitions and bases of an ordered complex","file":[{"checksum":"f8cc96e497f00c38340b5dafe0cb91d7","file_id":"8786","date_updated":"2020-11-20T13:22:21Z","access_level":"open_access","date_created":"2020-11-20T13:22:21Z","file_name":"2020_DiscreteCompGeo_Edelsbrunner.pdf","success":1,"creator":"dernst","file_size":701673,"content_type":"application/pdf","relation":"main_file"}],"day":"20","author":[{"last_name":"Edelsbrunner","first_name":"Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert"},{"orcid":"0000-0002-4672-8297","id":"4D4AA390-F248-11E8-B48F-1D18A9856A87","full_name":"Ölsböck, Katharina","first_name":"Katharina","last_name":"Ölsböck"}],"language":[{"iso":"eng"}],"isi":1,"project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"},{"call_identifier":"H2020","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","name":"Alpha Shape Theory Extended","grant_number":"788183"},{"call_identifier":"FWF","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35"}],"quality_controlled":"1","doi":"10.1007/s00454-020-00188-x","publication_identifier":{"eissn":["14320444"],"issn":["01795376"]},"_id":"7666","year":"2020","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).","date_created":"2020-04-19T22:00:56Z","file_date_updated":"2020-11-20T13:22:21Z","volume":64,"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"}],"date_updated":"2023-08-21T06:13:48Z","month":"03","oa_version":"Published Version","type":"journal_article","page":"759-775","citation":{"short":"H. Edelsbrunner, K. Ölsböck, Discrete and Computational Geometry 64 (2020) 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>.","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.","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>.","ista":"Edelsbrunner H, Ölsböck K. 2020. Tri-partitions and bases of an ordered complex. Discrete and Computational Geometry. 64, 759–775.","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>"},"intvolume":"        64","external_id":{"isi":["000520918800001"]},"status":"public","ddc":["510"],"date_published":"2020-03-20T00:00:00Z","has_accepted_license":"1","oa":1,"publication_status":"published"},{"publisher":"Elsevier","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"StFr"}],"publication":"Electrochimica Acta","article_type":"original","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"article_processing_charge":"Yes (via OA deal)","scopus_import":"1","author":[{"full_name":"Samojlov, Aleksej","first_name":"Aleksej","last_name":"Samojlov"},{"first_name":"David","last_name":"Schuster","full_name":"Schuster, David"},{"full_name":"Kahr, Jürgen","first_name":"Jürgen","last_name":"Kahr"},{"full_name":"Freunberger, Stefan Alexander","orcid":"0000-0003-2902-5319","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","first_name":"Stefan Alexander","last_name":"Freunberger"}],"file":[{"content_type":"application/pdf","relation":"main_file","file_size":1404030,"creator":"dernst","success":1,"file_name":"2020_ElectrochimicaActa_Samojlov.pdf","date_created":"2020-10-01T13:20:45Z","access_level":"open_access","date_updated":"2020-10-01T13:20:45Z","file_id":"8593","checksum":"1ab1aa2024d431e2a089ea336bc08298"}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","day":"01","article_number":"137175","title":"Surface and catalyst driven singlet oxygen formation in Li-O2 cells","isi":1,"issue":"12","language":[{"iso":"eng"}],"doi":"10.1016/j.electacta.2020.137175","quality_controlled":"1","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.","year":"2020","_id":"7672","type":"journal_article","oa_version":"Published Version","month":"12","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"}],"date_updated":"2023-08-21T06:14:21Z","volume":362,"date_created":"2020-04-20T19:29:31Z","file_date_updated":"2020-10-01T13:20:45Z","external_id":{"isi":["000582869700060"]},"status":"public","intvolume":"       362","citation":{"short":"A. Samojlov, D. Schuster, J. Kahr, S.A. Freunberger, Electrochimica Acta 362 (2020).","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>.","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.","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>","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.","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>"},"publication_status":"published","oa":1,"has_accepted_license":"1","date_published":"2020-12-01T00:00:00Z","ddc":["540"]},{"language":[{"iso":"eng"}],"citation":{"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>","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>.","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>.","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>","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.","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>.","short":"B. Kavcic, G. Tkačik, M.T. Bollenbach, BioRxiv (2020)."},"related_material":{"record":[{"id":"8997","status":"public","relation":"later_version"},{"status":"public","id":"8657","relation":"dissertation_contains"}]},"status":"public","project":[{"grant_number":"P27201-B22","call_identifier":"FWF","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","name":"Revealing the mechanisms underlying drug interactions"},{"name":"Biophysics of information processing in gene regulation","call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425","grant_number":"P28844-B27"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.04.18.047886 "}],"date_published":"2020-04-18T00:00:00Z","doi":"10.1101/2020.04.18.047886","publication_status":"published","oa":1,"article_processing_charge":"No","publication":"bioRxiv","_id":"7673","department":[{"_id":"GaTk"}],"year":"2020","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Cold Spring Harbor Laboratory","date_created":"2020-04-22T08:27:56Z","title":"A minimal biophysical model of combined antibiotic action","day":"18","date_updated":"2024-03-25T23:30:05Z","abstract":[{"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.","lang":"eng"}],"month":"04","oa_version":"Preprint","type":"preprint","author":[{"orcid":"0000-0001-6041-254X","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","full_name":"Kavcic, Bor","first_name":"Bor","last_name":"Kavcic"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","first_name":"Gašper","last_name":"Tkačik"},{"first_name":"Tobias","last_name":"Bollenbach","full_name":"Bollenbach, Tobias","orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"}]},{"author":[{"last_name":"Grah","first_name":"Rok","orcid":"0000-0003-2539-3560","id":"483E70DE-F248-11E8-B48F-1D18A9856A87","full_name":"Grah, Rok"},{"full_name":"Zoller, Benjamin","last_name":"Zoller","first_name":"Benjamin"},{"full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","last_name":"Tkačik","first_name":"Gašper"}],"oa_version":"Preprint","type":"preprint","month":"04","day":"09","date_updated":"2023-09-07T13:13:26Z","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"}],"title":"Normative models of enhancer function","date_created":"2020-04-23T10:12:51Z","publisher":"Cold Spring Harbor Laboratory","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"year":"2020","_id":"7675","publication":"bioRxiv","article_processing_charge":"No","publication_status":"published","oa":1,"doi":"10.1101/2020.04.08.029405","date_published":"2020-04-09T00:00:00Z","main_file_link":[{"url":"https://doi.org/10.1101/2020.04.08.029405 ","open_access":"1"}],"project":[{"grant_number":"RGP0034/2018","name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?","_id":"2665AAFE-B435-11E9-9278-68D0E5697425"},{"name":"Biophysically realistic genotype-phenotype maps for regulatory networks","_id":"267C84F4-B435-11E9-9278-68D0E5697425"}],"status":"public","related_material":{"record":[{"status":"public","id":"8155","relation":"dissertation_contains"}]},"citation":{"ieee":"R. Grah, B. Zoller, and G. Tkačik, “Normative models of enhancer function,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory, 2020.","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>.","short":"R. Grah, B. Zoller, G. Tkačik, BioRxiv (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>","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>.","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>"},"language":[{"iso":"eng"}]},{"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2663-337X"]},"doi":"10.15479/AT:ISTA:7680","department":[{"_id":"CaGu"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","day":"24","file":[{"checksum":"fb9a4468eb27be92690728e35c823796","date_updated":"2021-10-31T23:30:05Z","file_id":"7692","access_level":"open_access","date_created":"2020-04-28T11:19:21Z","file_name":"Thesis_without-signatures_PDFA.pdf","creator":"stgingl","embargo":"2021-10-30","relation":"main_file","content_type":"application/pdf","file_size":3268017},{"date_created":"2020-04-28T11:19:24Z","access_level":"closed","file_id":"7693","date_updated":"2021-10-31T23:30:05Z","checksum":"f6c80ca97104a631a328cb79a2c53493","file_size":5167703,"content_type":"application/octet-stream","relation":"source_file","embargo_to":"open_access","creator":"stgingl","file_name":"Thesis_without signatures.docx"}],"author":[{"last_name":"Kainrath","first_name":"Stephanie","full_name":"Kainrath, Stephanie","id":"32CFBA64-F248-11E8-B48F-1D18A9856A87"}],"degree_awarded":"PhD","title":"Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals","status":"public","alternative_title":["ISTA Thesis"],"citation":{"mla":"Kainrath, Stephanie. <i>Synthetic Tools for Optogenetic and Chemogenetic Inhibition of Cellular Signals</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7680\">10.15479/AT:ISTA:7680</a>.","ista":"Kainrath S. 2020. Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals. Institute of Science and Technology Austria.","apa":"Kainrath, S. (2020). <i>Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:7680\">https://doi.org/10.15479/AT:ISTA:7680</a>","ama":"Kainrath S. Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7680\">10.15479/AT:ISTA:7680</a>","short":"S. Kainrath, Synthetic Tools for Optogenetic and Chemogenetic Inhibition of Cellular Signals, Institute of Science and Technology Austria, 2020.","ieee":"S. Kainrath, “Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals,” Institute of Science and Technology Austria, 2020.","chicago":"Kainrath, Stephanie. “Synthetic Tools for Optogenetic and Chemogenetic Inhibition of Cellular Signals.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:7680\">https://doi.org/10.15479/AT:ISTA:7680</a>."},"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"1028"}]},"has_accepted_license":"1","oa":1,"publication_status":"published","date_published":"2020-04-24T00:00:00Z","ddc":["570"],"supervisor":[{"first_name":"Harald L","last_name":"Janovjak","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L"}],"year":"2020","_id":"7680","type":"dissertation","month":"04","oa_version":"None","date_updated":"2023-09-22T09:20:10Z","abstract":[{"lang":"eng","text":"Proteins and their complex dynamic interactions regulate cellular mechanisms from sensing and transducing extracellular signals, to mediating genetic responses, and sustaining or changing cell morphology. To manipulate these protein-protein interactions (PPIs) that govern the behavior and fate of cells, synthetically constructed, genetically encoded tools provide the means to precisely target proteins of interest (POIs), and control their subcellular localization and activity in vitro and in vivo. Ideal synthetic tools react to an orthogonal cue, i.e. a trigger that does not activate any other endogenous process, thereby allowing manipulation of the POI alone.\r\nIn optogenetics, naturally occurring photosensory domain from plants, algae and bacteria are re-purposed and genetically fused to POIs. Illumination with light of a specific wavelength triggers a conformational change that can mediate PPIs, such as dimerization or oligomerization. By using light as a trigger, these tools can be activated with high spatial and temporal precision, on subcellular and millisecond scales. Chemogenetic tools consist of protein domains that recognize and bind small molecules. By genetic fusion to POIs, these domains can mediate PPIs upon addition of their specific ligands, which are often synthetically designed to provide highly specific interactions and exhibit good bioavailability.\r\nMost optogenetic tools to mediate PPIs are based on well-studied photoreceptors responding to red, blue or near-UV light, leaving a striking gap in the green band of the visible light spectrum. Among both optogenetic and chemogenetic tools, there is an abundance of methods to induce PPIs, but tools to disrupt them require UV illumination, rely on covalent linkage and subsequent enzymatic cleavage or initially result in protein clustering of unknown stoichiometry.\r\nThis work describes how the recently structurally and photochemically characterized green-light responsive cobalamin-binding domains (CBDs) from bacterial transcription factors were re-purposed to function as a green-light responsive optogenetic tool. In contrast to previously engineered optogenetic tools, CBDs do not induce PPI, but rather confer a PPI already upon expression, which can be rapidly disrupted by illumination. This was employed to mimic inhibition of constitutive activity of a growth factor receptor, and successfully implement for cell signalling in mammalian cells and in vivo to rescue development in zebrafish. This work further describes the development and application of a chemically induced de-dimerizer (CDD) based on a recently identified and structurally described bacterial oxyreductase. CDD forms a dimer upon expression in absence of its cofactor, the flavin derivative F420. Safety and of domain expression and ligand exposure are demonstrated in vitro and in vivo in zebrafish. The system is further applied to inhibit cell signalling output from a chimeric receptor upon F420 treatment.\r\nCBDs and CDD expand the repertoire of synthetic tools by providing novel mechanisms of mediating PPIs, and by recognizing previously not utilized cues. In the future, they can readily be combined with existing synthetic tools to functionally manipulate PPIs in vitro and in vivo."}],"page":"98","date_created":"2020-04-24T16:00:51Z","file_date_updated":"2021-10-31T23:30:05Z"},{"isi":1,"language":[{"iso":"eng"}],"issue":"2","project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"doi":"10.1007/s00029-020-00553-x","quality_controlled":"1","publication_identifier":{"issn":["10221824"],"eissn":["14209020"]},"publication":"Selecta Mathematica, New Series","scopus_import":"1","article_processing_charge":"Yes (via OA deal)","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","publisher":"Springer Nature","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"TaHa"}],"title":"Cohomological Hall algebras for Higgs torsion sheaves, moduli of triples and sheaves on surfaces","arxiv":1,"article_number":"30","author":[{"full_name":"Minets, Sasha","id":"3E7C5304-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3883-1806","last_name":"Minets","first_name":"Sasha"}],"file":[{"checksum":"2368c4662629b4759295eb365323b2ad","date_updated":"2020-07-14T12:48:02Z","file_id":"7690","access_level":"open_access","date_created":"2020-04-28T10:57:58Z","file_name":"2020_SelectaMathematica_Minets.pdf","creator":"dernst","relation":"main_file","content_type":"application/pdf","file_size":792469}],"day":"15","intvolume":"        26","citation":{"ama":"Minets S. Cohomological Hall algebras for Higgs torsion sheaves, moduli of triples and sheaves on surfaces. <i>Selecta Mathematica, New Series</i>. 2020;26(2). doi:<a href=\"https://doi.org/10.1007/s00029-020-00553-x\">10.1007/s00029-020-00553-x</a>","apa":"Minets, S. (2020). Cohomological Hall algebras for Higgs torsion sheaves, moduli of triples and sheaves on surfaces. <i>Selecta Mathematica, New Series</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00029-020-00553-x\">https://doi.org/10.1007/s00029-020-00553-x</a>","ista":"Minets S. 2020. Cohomological Hall algebras for Higgs torsion sheaves, moduli of triples and sheaves on surfaces. Selecta Mathematica, New Series. 26(2), 30.","mla":"Minets, Sasha. “Cohomological Hall Algebras for Higgs Torsion Sheaves, Moduli of Triples and Sheaves on Surfaces.” <i>Selecta Mathematica, New Series</i>, vol. 26, no. 2, 30, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1007/s00029-020-00553-x\">10.1007/s00029-020-00553-x</a>.","chicago":"Minets, Sasha. “Cohomological Hall Algebras for Higgs Torsion Sheaves, Moduli of Triples and Sheaves on Surfaces.” <i>Selecta Mathematica, New Series</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/s00029-020-00553-x\">https://doi.org/10.1007/s00029-020-00553-x</a>.","ieee":"S. Minets, “Cohomological Hall algebras for Higgs torsion sheaves, moduli of triples and sheaves on surfaces,” <i>Selecta Mathematica, New Series</i>, vol. 26, no. 2. Springer Nature, 2020.","short":"S. Minets, Selecta Mathematica, New Series 26 (2020)."},"external_id":{"arxiv":["1801.01429"],"isi":["000526036400001"]},"status":"public","ddc":["510"],"date_published":"2020-04-15T00:00:00Z","oa":1,"publication_status":"published","has_accepted_license":"1","_id":"7683","year":"2020","volume":26,"date_created":"2020-04-26T22:00:44Z","file_date_updated":"2020-07-14T12:48:02Z","abstract":[{"text":"For any free oriented Borel–Moore homology theory A, we construct an associative product on the A-theory of the stack of Higgs torsion sheaves over a projective curve C. We show that the resulting algebra AHa0C admits a natural shuffle presentation, and prove it is faithful when A is replaced with usual Borel–Moore homology groups. We also introduce moduli spaces of stable triples, heavily inspired by Nakajima quiver varieties, whose A-theory admits an AHa0C-action. These triples can be interpreted as certain sheaves on PC(ωC⊕OC). In particular, we obtain an action of AHa0C on the cohomology of Hilbert schemes of points on T∗C.","lang":"eng"}],"date_updated":"2023-08-21T06:14:58Z","month":"04","type":"journal_article","oa_version":"Published Version"}]